bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling management response and online reviews for improved financial performance of hospitals
Authors: Saha Mayukh , Jha Jitendra K. , Maiti Jhareswar
Published: November 2019

Hospitals are increasingly changing their online review strategy from active listening to proactive engagement to ensure proper responses to patients. Reviews of and responses from hospitals vary in different regions of the world, thereby the process of ranking of hospitals is bounded to a specific region. On the other hand, working conditions in public hospitals have been of great concern worldwide for healthcare personnel. Due to the poor review of a hospital, financial performance is gradually deteriorating, which leads to the migration of healthcare personnel from one hospital to another. This study investigates the combined effect of management responses and online reviews on the financial performance of hospitals by concentrating on three areas of concern. First, how variation in management responses, both within a hospital and on peer review sites, affects the motivation of healthcare personnel towards service and number of patients seeking services. Second, a cyclic link depicting interrelationships among four major domains, namely rating, management response, financial performance, and recommendation, has been presented. Third, a generic model is proposed to improve the performance of hospitals in each of the above domains, and analysis has been done to make the model region-specific. A case study on Indian hospitals is performed to depict the sufficiency of models. It is found that management intervention on social media should be strategic, and a higher average rating tends to mitigate the effect of negative responses.
Melanism protects alpine zooplankton from DNA damage caused by ultraviolet radiation
Authors: Ulbing Cynthia K. S. , Muuse Julia M. , Miner Brooks E.
Published: November 2019

Melanism is widely observed among animals, and is adaptive in various contexts for its thermoregulatory, camouflaging, mate-attraction or photoprotective properties. Many organisms exposed to ultraviolet radiation show increased fitness resulting from melanin pigmentation; this has been assumed to result in part from reduced UV-induced damage to DNA. However, to effectively test the hypothesis that melanin pigmentation reduces UV-induced DNA damage requires quantification of UV-specific DNA damage lesions following UV exposure under controlled conditions using individuals that vary in pigmentation intensity. We accomplished this using alpine genotypes of the freshwater microcrustaceanDaphnia melanica, for which we quantified cyclobutane pyrimide dimers in DNA, a damage structure that can only be generated by UV exposure. For genotypes with carapace melanin pigmentation, we found that individuals with greater melanin content sustained lower levels of UV-induced DNA damage. Individuals with more melanin were also more likely to survive exposure to ecologically relevant levels of UV-B radiation. Parallel experiments with conspecific genotypes that lack carapace melanin pigmentation provide additional support for our conclusion that melanism protects individuals from UV-induced DNA damage. Finally, within-genotype comparisons with asexually produced clonal siblings demonstrate that melanin content influences DNA damage even among genetically identical individuals raised in the same environment.
Influence of sexual risk behaviour and STI co-infection dynamics on the evolution of HIV set point viral load in MSM
Authors: Hendrickx Diana M , Delva Wim , Hens Niel
Published: November 2019

HIV viral load (VL) is an important predictor of HIV progression and transmission. Anti-retroviral therapy (ART) has been reported to reduce HIV transmission by lowering VL. However, apart from this beneficial effect, increased levels of population mean set-point viral load (SPVL), an estimator for HIV virulence, have been observed in men who have sex with men (MSM) in the decade following the introduction of ART in the Netherlands. Several studies have been devoted to explain these counter-intuitive trends in SPVL. However, to our knowledge, none of these studies has investigated an explanation in which it arises as the result of a sexually transmitted infection (STI) co-factor in detail.

In this study, we adapted an event-based, individual-based model to investigate how STI co-infection and sexual risk behaviour affect the evolution of HIV SPVL in MSM before and after the introduction of ART.

The results suggest that sexual risk behaviour has an effect on SPVL and indicate that more data are needed to test the effect of STI co-factors on SPVL. Furthermore, the observed trends in SPVL cannot be explained by sexual risk behaviour and STI co-factors only.

We recommend to develop mathematical models including also factors related to viral evolution as reported earlier in the literature. However, this requires more complex models, and the collection of more data for parameter estimation than what is currently available.
Heterogeneity in prognostic value of the neutrophil-to-lymphocyte ratio: a meta-analysis
Authors: Howard Rachel , Kanetsky Peter A. , Egan Kathleen M.
Published: November 2019

High pre-treatment values of the neutrophil-to-lymphocyte ratio (NLR) are strongly associated with poorer survival outcomes in cancer patients. Here, we assess heterogeneity in the magnitude of this association and the prognostic potential of the NLR between patient subgroups. We conducted a random effects meta-analysis of 228 published studies (N=75,555 patients) relating NLR with overall survival across 18 cancer types. Cochran’s Q test and Higgins I2 statistic were used to assess study heterogeneity. Pooled hazard ratios were compared between groups of studies classified by cancer type, geographic region, therapy type, and cut-off for high NLR to identify study-level characteristics associated with increased prognostic potential of the NLR. Pooled hazard ratios are highest in studies of melanoma and breast cancer and lowest in studies of brain cancer and lung cancer. Radiation as primary treatment also demonstrates a large pooled effect size as compared to other therapies. The NLR has greater prognostic value in certain cancer types and therapeutic regimens. Efforts are needed to comprehensively examine populations in which NLR has maximum prognostic power. Clinically meaningful thresholds for risk stratification should be identified within these patient subgroups to permit prospective validation of the prognostic potential of the NLR.
α-ketoglutaric acid stimulates muscle hypertrophy and fat loss through OXGR1-dependent adrenal activation
Authors: Yuan Yexian , Xu Pingwen , Jiang Qingyan , Cai Xingcai , Wang Tao , Peng Wentong , Sun Jiajie , Zhu Canjun , Zhang Cha , Yue Dong , He Zhihui , Yang Jinping , Zeng Yuxian , Du Man , Zhang Fenglin , Ibrahimi Lucas , Schaul Sarah , Jiang Yuwei , Wang Jiqiu , Sun Jia , Wang Qiaoping , Wang Songbo , Wang Lina , Zhu Xiaotong , Gao Ping , Xi Qianyun , Yin Cong , Li Fan , Xu Guli , Zhang Yongliang , Shu Gang
Published: November 2019

Beneficial effects of resistance exercise on metabolic health and particularly muscle hypertrophy and fat loss are well established, but the underlying chemical and physiological mechanisms are not fully understood. Here we identified a myometabolite-mediated metabolic pathway that is essential for the beneficial metabolic effects of resistance exercisein vivo. We showed that substantial accumulation of the tricarboxylic acid cycle intermediate α-ketoglutaric acid (AKG) is a metabolic signature of resistance exercise performance. Interestingly, human plasma AKG level is also negatively correlated with BMI. Pharmacological elevation of circulating AKG induces muscle hypertrophy, brown adipose tissue (BAT) thermogenesis, and white adipose tissue (WAT) lipolysisin vivo. We further found that AKG stimulates the adrenal release of adrenaline through 2-oxoglutarate receptor 1 (OXGR1) expressed in adrenal glands. Finally, by using both loss-of-function and gain-of-function mouse models, we showed that OXGR1 is essential for AKG-mediated exercise-induced beneficial metabolic effects. These findings reveal an unappreciated mechanism for the salutary effects of resistance exercise, using AKG as a systemically-derived molecule for adrenal stimulation of muscle hypertrophy and fat loss.
Charting extracellular transcriptomes in The Human Biofluid RNA Atlas
Authors: Hulstaert Eva , Morlion Annelien , Cobos Francisco Avila , Verniers Kimberly , Nuytens Justine , Eynde Eveline Vanden , Yigit Nurten , Anckaert Jasper , Geerts Anja , Hindryckx Pieter , Jacques Peggy , Brusselle Guy , Bracke Ken R. , Maes Tania , Malfait Thomas , Derveaux Thierry , Ninclaus Virginie , Van Cauwenbergh Caroline , Roelens Kristien , Roets Ellen , Hemelsoet Dimitri , Tilleman Kelly , Brochez Lieve , Kuersten Scott , Simon Lukas , Karg Sebastian , Kautzky-Willers Alexandra , Leutner Michael , Nöhammer Christa , Slaby Ondrej , Prins Roméo Willinge , Koster Jan , Lefever Steve , Schroth Gary P. , Vandesompele Jo , Mestdagh Pieter
Published: November 2019

Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease. Where most studies focus on plasma or serum, other biofluids may contain more informative RNA molecules, depending on the type of disease. Here, we present an unprecedented atlas of messenger, circular and small RNA transcriptomes of a comprehensive collection of 20 different human biofluids. By means of synthetic spike-in controls, we compared RNA content across biofluids, revealing a more than 10 000-fold difference in RNA concentration. The circular RNA fraction is increased in nearly all biofluids compared to tissues. Each biofluid transcriptome is enriched for RNA molecules derived from specific tissues and cell types. In addition, a subset of biofluids, including stool, sweat, saliva and sputum, contains high levels of bacterial RNAs. Our atlas enables a more informed selection of the most relevant biofluid to monitor particular diseases. To verify the biomarker potential in these biofluids, four validation cohorts representing a broad spectrum of diseases were profiled, revealing numerous differential RNAs between case and control subjects. Taken together, our results reveal novel insights in the RNA content of human biofluids and may serve as a valuable resource for future biomarker studies. All spike-normalized data is publicly available in the R2 web portal and serve as a basis to further explore the RNA content in biofluids.
ApoC-III overexpression and LDLr-/- protect mice from DSS-colitis: identifying a new role for lipoprotein metabolism in Tregs
Authors: Rodia Cayla N , Li Diana , Tambini Nicholas S , Johnson Zania K , Jellison Evan R , Vella Anthony T , Kohan Alison B
Published: November 2019

Objective

Cellular metabolism is a key regulator of CD4+Foxp3+regulatory T cell (Treg) homeostasis, but the foundational studies in this area use free fatty acid treatment as a proxy for plasma triglycerides. In vivo, plasma triglyceride is the main source of fatty acids for cells, not free fatty acids.

Design/Results

Using apolipoprotein C-III transgenic and LDLr-/-mice, we report that the loss of lipoprotein triglycerides transport in these models results in protection from DSS-colitis and accumulation of intestinal Tregs and plasma IL-10. Total loss of apoC-III increases colitis severity. Tregs exposed to apoC-III increase lipolysis and fatty acid oxidation and apoC-III inhibits Bodipy-triglyceride uptake. Therapeutic treatment of WT mice with apoC-III-containing lipoproteins protects mice from colitis.

Conclusion

Our data suggest that therapies that reduce apoC-III could have negative effects in patients who are at risk of IBD, and conversely, that apoC-III could be a new therapeutic target to stimulate intestinal Tregs and IL-10 for the management of IBD. These data identify apoC-III and lipoprotein metabolism as a novel regulator of tolerance in the intestine.

Summary Box

*What is already known about this subject:

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The relative capacity to use either glucose or FFA to generate acetyl CoA for mitochondrial fatty acid oxidation is a critical driver of Treg and T cell activity and proliferation.

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ApoC-III is a known regulator of triglyceride and fatty acid metabolism in cells via LPL and LDLr endocytosis pathways

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ApoC-III is reduced in Crohn’s and Colitis patients.

*What are the new findings:

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We show that Tregs express triglyceride transporters, and that LDLr expression is enriched in Tregs from the mesenteric lymph nodes.

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We show that T cells are capable of endocytosing triglyceride from lipoproteins, and this process is inhibited by apoC-III.

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Tregs fromapoC-IIITgare metabolically unique fromWTTregs and they upregulate the genes of lipolysis, and have an increase in basal respiration.

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The inhibition of TAG endocytosis, using 2 different models (LDLrKOand apoC-III-transgenic mice), protects mice from colitis and stimulates the accumulation of Tregs and IL-10 in the gut.

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Intraperitoneal delivery of apoC-III on chylomicrons protectsWTmice from DSS colitis.

* How might it impact on clinical practice in the foreseeable future?

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Due to the protective role apoC-III plays in these mouse models of colitis, IBD risk should be carefully considered before prescribing patient anti-apoC-III lipid-lowering therapies.
Meiosis and Kinetochore genes are used by cancer cells as genome destabilizers and transformation catalysts
Authors: Thapa Roshina , Vasudevan Swetha , Ashqar Mimi Abo-Ayoub , Reich Eli , Kravchenko-Balasha Nataly , Klutstein Michael
Published: November 2019

Cancer cells have an altered transcriptome which contributes to their altered behaviors compared to normal cells. Indeed, many tumors express high levels of genes participating in meiosis or kinetochore biology, but the role of this high expression has not been fully elucidated. In this study we explore the relationship between this overexpression and genome instability and transformation capabilities of cancer cells. For this, we obtained expression data from 5 different cancer types which were analyzed using computational information-theoretic analysis. We were able to show that highly expressed meiotic/kinetochore genes were enriched in the altered gene expression subnetworks characterizing unstable cancer types with high chromosome instability (CIN). However, altered subnetworks found in the cancers with low CIN did not include meiotic and kinetochore genes. Representative gene candidates, found by the analysis to be correlated with a CIN phenotype, were further explored by transfecting genomically-stable (HCT116) and unstable (MCF7) cancer cell lines with vectors overexpressing those genes. This overexpression resulted in an increase in the numbers of abnormal cell divisions and defective spindle formations and in increased transformation properties in stable cancer HCT116 cells. Interestingly, the same properties were less affected by the overexpressed genes in the unstable MCF7 cancer cells. Our results indicate that overexpression of both meiosis and kinetochore genes is capable of driving genomic instability and cancer progression.
Causes and consequences of mitochondrial proteome size-variation in animals
Authors: Muthye Viraj , Lavrov Dennis
Published: November 2019

Despite a conserved set of core mitochondrial functions, animal mitochondrial proteomes show a large variation in size. In this study, we analyzed the putative mechanisms behind and functional significance of this variation using experimentally-verified mt-proteomes of four bilaterian animals and two non-animal outgroups. We found that, of several factors affecting mitochondrial proteome size, evolution of novel mitochondrial proteins in mammals and loss of ancestral proteins in protostomes were the main contributors. Interestingly, gain and loss of conventional mitochondrial targeting signals was not a significant factor in the proteome size evolution.
RNA-binding protein altered expression and mislocalization in multiple sclerosis
Authors: Masaki Katsuhisa , Sonobe Yoshifumi , Ghadge Ghanashyam , Pytel Peter , Lépine Paula , Pernin Florian , Cui Qiao-Ling , Antel Jack P. , Zandee Stephanie , Prat Alexandre , Roos Raymond P.
Published: November 2019

Objective

Nuclear depletion and mislocalization of RNA-binding proteins (RBPs) trans-activation response DNA-binding protein of 43 kDa (TDP-43) and fused in sarcoma (FUS) are thought to contribute to the pathogenesis of a number of disorders, including amyotrophic lateral sclerosis (ALS). We recently found that TDP-43 as well as polypyrimidine tract binding protein (PTB) have decreased expression and mislocalization in oligodendrocytes in demyelinated lesions in an experimental mouse model of multiple sclerosis (MS) caused by Theiler’s murine encephalomyelitis virus infection.

Methods

The latter finding prompted us to investigate TDP-43, FUS, and PTB in the demyelinated lesions of MS and inin vitro culturedhuman brain-derived oligodendrocytes.

Results

We found: i) mislocalized TDP-43 in oligodendrocytes in active lesions in some MS patients; ii) decreased PTB1 expression in oligodendrocytes in mixed active/inactive demyelinating lesions; iii) decreased nuclear expression of PTB2 in neurons in cortical demyelinating lesions; iv) nuclear depletion of TDP-43 in oligodendrocytes under metabolic stress induced by low glucose/low nutrient conditions compared to optimal culture conditions.

Conclusion

TDP-43 has been found to have a key role in oligodendrocyte function and viability, while PTB is important in neuronal differentiation, suggesting that altered expression and mislocalization of these RBPs in MS lesions may contribute to the pathogenesis of demyelination and neurodegeneration. Our findings also identify nucleocytoplasmic transport as a target for treatment.
Towards Practical and Robust DNA-Based Data Archiving Using ‘Yin-Yang Codec’ System
Authors: Ping Zhi , Chen Shihong , Zhou Guangyu , Huang Xiaoluo , Zhu Sha Joe , Zhang Haoling , Lee Henry H. , Lan Zhaojun , Cui Jie , Chen Tai , Zhang Wenwei , Yang Huanming , Xu Xun , Church George M. , Shen Yue
Published: November 2019

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense however of introducing biocompatibility challenges or at the risk of decoding failure. Here, we propose a robust transcoding algorithm named the “Yin-Yang Codec” (YYC), using two rules to encode two binary bits into one nucleotide, to generate DNA sequences highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200-nt oligo pools and in vivo as an ~54-kb DNA fragment in yeast cells. Sequencing results show that YYC exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.94% at 104molecule copies and an achieved recovery rate of 87.53% at 100 copies. In addition, the in vivo storage demonstration achieved for the first time an experimentally measured physical information density of 198.8 EB per gram of DNA (44% of the theoretical maximum for DNA).
Turanose induced WOX5 restores symbiosis in the Medicago truncatula cytokinin perception mutant cre1
Authors: Kundu Anindya , Molla Firoz , DasGupta Maitrayee
Published: November 2019

Rhizobia-legume interaction recruits cytokinin-signaling that causes local auxin accumulation for the induction of nodule primordia in the cortex. Since sugar signaling can trigger auxin responses and regulate developmental processes, we explored whether sugar treatments could rescue cre1. Here we demonstrate that turanose, a non-metabolizable sucrose analogue can recover functional symbiosis in cytokinin perception mutant cre1. Additionally, turanose significantly upregulated the expression of WUSCHEL-related homeobox 5 (MtWOX5) which prompted us to check if ectopic expression of WOX5 could rescue cre1. Overexpression of WOX5 from Arachis hypogaea (AhWOX5), but not the intrinsic MtWOX5 could completely restore functional symbiosis in cre1 though both WOX5 (Mt and Ah) were functionally equivalent in inducing the expression of cytokinin inducible transcription factor Nodule Inception (NIN). Among the tested markers for cytokinin and auxin responses, significant differences were noted in the expression of IAA-Ala Resistant3 (MtIAR33), an auxin conjugate hydrolase. Turanose and AhWOX5 overexpression resulted in upregulation of MtIAR33 that further increased significantly in presence of rhizobia. On the other hand, MtIAR33 expression was unaffected in MtWOX5 overexpressed roots suggesting deconjugation driven auxin pool to be critical for rescuing symbiosis in cre1. We hypothesize a working model for sugar and WOX5 mediated rescue of symbiosis in cre1.

One sentence summary

Activation of sugar-WOX5 signaling axis restores root nodule symbiosis in cytokinin perception mutant cre1
PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms
Authors: Li Zhen , Yan Xu , Wei Qing , Gao Xin , Wang Sheng , Cui Shuguang
Published: November 2019

Accurate identifications of ligand binding sites (LBS) on protein structure is critical for understanding protein function and designing structure-based drug. As the previous pocket-centric methods are usually based on the investigation of pseudo surface points (PSPs) outside the protein structure, thus inherently cannot incorporate the local connectivity and global 3D geometrical information of the protein structure. In this paper, we propose a novel point clouds segmentation method, PointSite, for accurate identification of protein ligand binding atoms, which performs protein LBS identification at the atom-level in a protein-centric manner. Specifically, we first transfer the original 3D protein structure to point clouds and then conduct segmentation through Submanifold Sparse Convolution (SSC) based U-Net. With the fine-grained atom-level binding atoms representation and enhanced feature learning, PointSite can outperform previous methods in atom-IoU by a large margin. Furthermore, our segmented binding atoms can work as a filter on predictions achieved by previous pocket-centric approaches, which significantly decreases the false-positive of LBS candidates. Through cascaded filter and re-ranking aided by the segmented atoms, state-of-the-art performance can be achieved over various canonical benchmarks and CAMEO hard targets in terms of the commonly used DCA criteria. Our code is publicly available throughhttps://github.com/PointSite.
A novel experimental system reveals immunoregulatory responses as mediators of persistent orthohantavirus infections in a rodent reservoir host
Authors: Strandin Tomas , Smura Teemu , Ahola Paula , Aaltonen Kirsi , Sironen Tarja , Hepojoki Jussi , Eckerle Isabella , Ulrich Rainer G. , Vapalahti Olli , Kipar Anja , Forbes Kristian M.
Published: November 2019

Orthohantaviruses are globally emerging zoonotic pathogens. Human infections are characterized by an overt immune response that is efficient at counteracting virus replication but can also cause severe tissue damage. In contrast, orthohantavirus infections in rodent reservoir hosts are persistent and asymptomatic. The mechanisms facilitating asymptomatic virus persistence in reservoir hosts are not well understood but could help to guide therapeutic strategies for human infections. Here we report on a study usingin vivoandin vitroexperiments to investigate immune responses associated with persistent Puumala orthohantavirus (PUUV) infections in the bank vole (Myodes glareolus), its reservoir host. We examined adaptive cellular and humoral responses by quantifying changes in T-cell related gene expression in the spleen and immunoglobulin (Ig) responses in blood, respectively. Since existing Vero E6-cell adapted hantavirus isolates have been demonstrated to have lost their wild-type infection characteristics, infections were conducted with a novel PUUV strain isolated on a bank vole cell line. Whole virus genome sequencing revealed that only minor sequence changes occurred during the isolation process, and critically, experimental infections of bank voles with the new isolate resembled natural infections.In vitroinfection of bank vole splenocytes with the novel isolate demonstrated that PUUV promotes immunoregulatory responses by inducing interleukin-10, a cytokine strongly associated with chronic viral infections. A delayed virus-specific humoral response occurred in experimentally infected bank voles, which is likely to allow for initial virus replication and the establishment of persistent infections. These results suggest that host immunoregulation facilitates persistent orthohantavirus infections in reservoir hosts.

Importance

Orthohantaviruses are a group of global pathogens that regularly spillover from rodent reservoirs into humans and can cause severe disease. Conversely, infections in reservoir hosts do not cause obvious adverse effects. The mechanisms responsible for persistent asymptomatic reservoir infections are unknown, and progress has been hindered by the absence of an adequate experimental system. Knowledge on these mechanisms could help provide strategies to treat human infections. We developed and validated an experimental system based on an orthohantavirus isolated in cells of its vole reservoir host. Using animal and cell culture experiments in the reservoir host system, we demonstrated that infection suppresses immunity in the vole reservoir via specific mechanisms, likely allowing the virus to take hold and preventing immune responses that can cause self-damage.
Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus
Authors: Michieletto Davide , Colì Davide , Marenduzzo Davide , Orlandini Enzo
Published: November 2019

Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical – or epigenetic – marks that are deposited along the genome are thought to play an important, yet poorly understood, role in determining genome organisation and cell identity. The physical principles underlying the interplay between epigenetic dynamics and genome folding remain elusive. Here we propose and study a theory that assumes a coupling between epigenetic mark and genome densities, and which can be applied at the scale of the whole nucleus. We show that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for non-equilibrium processes which can stabilise microphase separated epigenomic domains. We finally discuss the potential biophysical origin of these terms.
Direct synthesis of self-organized blastocyst-like cysts derived from human pluripotent stem cells
Authors: Wen Xiaopeng , Terada Shiho , Yoshimoto Koki , Kamei Ken-ichiro
Published: November 2019

We introduce a simple, robust and scalable method to generate self-organized blastocyst-like cysts (soBLCs) from human pluripotent stem cells (hPSCs). We use a copolymer hydrogel of poly(N-isopropylacrylamide) and poly(ethylene glycol) (PNIPAAm-PEG). hPSC aggregates with a diameter of approximately 117.2 ± 5.1 µm are cultured in a medium supplemented with a hydrogel and a serum for three days. Molecular signatures in the medium revealed the generation of trophoblasts and inner cell mass at specific positions in the soBLCs.
Control and simulation impact on nonlinear Hepatitis-B model by using Padé-approximation based Differential Evolution
Authors: Farman Muhammad , Tabassum Muhammad Farhan , Saeed Muhammad , Chaudhry Nazir Ahmad
Published: November 2019

Hepatitis B is the main public health problem of the whole world. In epidemiology, mathematical models perform a key role in understanding the dynamics of infectious diseases. This paper proposes Padé approximation (Pa) with Differential Evolution (DE) for obtaining solution of Hepatitis-B model which is nonlinear numerically. The proposed strategy transforms the nonlinear model into optimization problem by using Padé approximation. Initial conditions are converted into problem constraints and constraint problem become unconstraint by using penalty function.DEis obtained numerical solution of Hepatitis-B model by solving the established problem of optimization. There is no need to choose step lengths in proposed Padé-approximation based Differential Evolution (PaDE) technique and alsoPaDEconverges to true steady state points. Finally, a convergence and error analysis evidence that the convergence speed ofPaDEis greater than Non-Standard Finite Difference (NSFD) method for different time steps.
Analysis of unusual and signature APOBEC-mutations in HIV-1polnext-generation sequences
Authors: Tzou Philip L. , Kosakovsky Pond Sergei L. , Avila-Rios Santiago , Holmes Susan P. , Kantor Rami , Shafer Robert W.
Published: November 2019

Introduction

At low mutation-detection thresholds, next generation sequencing (NGS) for HIV-1 genotypic resistance testing is susceptible to artifactual detection of mutations arising from PCR error and APOBEC-mediated G-to-A hypermutation.

Methods

We analyzed published HIV-1polIllumina NGS data to characterize the distribution of mutations at eight NGS thresholds: 20%, 10%, 5%, 2%, 1%, 0.5%, 0.2%, and 0.1%. At each threshold, we determined the proportion of amino acid mutations that were unusual (defined as having a prevalence <0.01% in HIV-1 group M sequences) or were signature APOBEC mutations.

Results

Eight studies, containing 855 samples, in the NCBI Sequence Read Archive were analyzed. As detection thresholds were lowered, there was a progressive increase in the proportion of positions with both usual and unusual mutations and in the proportion of all mutations that were unusual. The median proportion of positions with an unusual mutation increased gradually from 0% at the 20% threshold to 0.3% at the 1% threshold and then exponentially to 1.3% (0.5% threshold), 6.9% (0.2% threshold), and 23.2% (0.1% threshold). In two of three studies with available plasma HIV-1 RNA levels, the proportion of positions with unusual mutations was negatively associated with virus levels. Although the complete set of signature APOBEC mutations was much smaller than that of unusual mutations, the former outnumbered the latter in one-sixth of the samples at the 0.5%, 1%, and 2% thresholds.

Conclusions

The marked increase in the proportion of positions with unusual mutations at thresholds below 1% and in samples with lower virus loads suggests that, at low thresholds, many unusual mutations are artifactual, reflecting PCR error or G-to-A hypermutation. Profiling the numbers of unusual and signature APOBECpolmutations at different NGS thresholds may be useful to avoid selecting a threshold that is too low and poses an unacceptable risk of identifying artifactual mutations.
Decreased alertness reconfigures cognitive control networks
Authors: Canales-Johnson Andres , Beerendonk Lola , Blain Salome , Kitaoka Shin , Ezquerro-Nassar Alejandro , Nuiten Stijn , Fahrenfort Johannes , Gaal Simon van , Bekinschtein Tristan A.
Published: November 2019

Humans’ remarkable capacity to flexibly adapt their behaviour based on rapid situational changes is termed cognitive control. Intuitively, cognitive control is thought to be affected by the state of alertness, for example, when drowsy we feel less capable of adequately implementing effortful cognitive tasks. Although scientific investigations have focused on the effects of sleep deprivation and circadian time, little is known about how natural daily fluctuations in alertness in the regular awake state affect cognitive control. Here we combined a conflict task in the auditory domain with EEG neurodynamics to test how neural and behavioural markers of conflict processing are affected by fluctuations in alertness. Using a novel computational method, we segregated alert and drowsy trials from two testing sessions and observed that, although participants (both sexes) were generally sluggish, the typical Conflict Effect reflected in slower responses to conflicting information compared to non-conflicting information was still intact, as well as the moderating effect of previous conflict (Conflict Adaptation). However, the typical neural markers of cognitive control-local midfrontal-theta band power changes-that participants show during full alertness were no longer noticeable when alertness decreased. Instead, when drowsy, we found an increase in long-range information sharing (connectivity) between brain regions in the same frequency band. These results show the resilience of the human cognitive control system when affected by internal fluctuations of alertness, and suggest neural compensatory mechanisms at play in response to physiological pressure during diminished alertness.

Significance Statement

The normal variability in alertness we experience in daily tasks is rarely taking into account in cognitive neuroscience. Here we studied neurobehavioral dynamics of cognitive control with decreasing alertness. We used the classic Simon Task where participants hear the word “left” or “right” in the right or left ear, eliciting slower responses when the word and the side are incongruent - the conflict effect. Participants performed the task both while fully awake and while getting drowsy, allowing for the characterisation of alertness modulating cognitive control. The changes in the neural signatures of conflict from local theta oscillations to a long-distance distributed theta network suggests a reconfiguration of the underlying neural processes subserving cognitive control when affected by alertness fluctuations.
Loss of pseudouridine synthases in the RluA family causes hypersensitive nociception inDrosophila
Authors: Song Wan , Tracey W. Daniel
Published: November 2019

Nociceptive neurons ofDrosophila melanogasterlarvae are characterized by highly branched dendritic processes whose proper morphogenesis relies on a large number of RNA-binding proteins. Post-transcriptional regulation of RNA in these dendrites has been found to play an important role in their function. Here, we investigate the neuronal functions of two putative RNA modification genes,RluA-1andRluA-2, which are predicted to encode pseudouridine synthases.RluA-1is specifically expressed in larval sensory neurons whileRluA-2expression is ubiquitous. Nociceptor-specific RNAi knockdown ofRluA-1caused hypersensitive nociception phenotypes, which were recapitulated with genetic null alleles. These were rescued with genomic duplication and nociceptor-specific expression ofUAS-RluA-1-cDNA. As withRluA-1, RluA-2loss of function mutants also displayed hyperalgesia. Interestingly, nociceptor neuron dendrites showed a hyperbranched morphology in theRluA-1mutants. The latter may be a cause or a consequence of heightened sensitivity in mutant nociception behaviors.

Author Summary

Pseudouridine (Psi) is a C5-glycoside isomer of uridine and it is the most common posttranscriptional modification of RNAs, including noncoding tRNAs, rRNAs, snRNAs as well as mRNAs. Although first discovered in the 1950s, the biological functions of Psi in multicellular organisms are not well understood. Interestingly, a marker for sensory neurons inDrosophilaencodes for a putative pseudouridine synthase called RluA-1. Here, we report our characterization of nociception phenotypes for larvae with RluA-1 loss of function along with that of a related gene RluA-2. Disrupting either or both RluA-1 and RluA-2 resulted in hypersensitive nociception. In addition, RluA-1 mutants have more highly branched nociceptor neurites that innervate the epidermis. Our studies suggest an important role for the RluA family in nociception. This may be through its action on RNAs that regulate neuronal excitability and/or dendrite morphogenesis.
Towards a biotechnological platform for the production of human pro-angiogenic growth factors in the green alga Chlamydomonas reinhardtii
Authors: Jarquín-Cordero Montserrat , Chávez Myra Noemi , Centeno-Cerdas Carolina , Bohne Alexandra-Viola , Hopfner Ursula , Machens Hans-Günther , Tomás Egaña José , Nickelsen Jörg
Published: November 2019

The recent use of photosynthetic organisms such as Chlamydomonas reinhardtii in biomedical applications has demonstrated their potential for the treatment of acute and chronic tissue hypoxia. Moreover, transgenic microalgae have been suggested as an alternative in situ drug delivery system. In this study, we set out to identify the best available combination of strains and expression vectors to establish a robust platform for the expression of human pro-angiogenic growth factors, i.e. hVEGF-165, hPDGF-B, and hSDF-1, in biomedical settings. As a case study, combinations of two expression vectors (pOpt and pBC1) and two C. reinhardtii strains (UVM4 and UVM11) were compared with respect to hVEGF-165 transgene expression by determination of steady-state levels of transgenic transcripts as well as immunological detection of recombinant proteins produced and secreted by the generated strains. The results revealed the combination of the UVM11-strain with the pBC1-vector to be the most efficient one for high level hVEGF-165 production. To assess the robustness of this finding, the selected combination was used to create hPDGF-B and hSDF-1 transgenic strains for optimized recombinant protein expression. Furthermore, biological activity and functionality of algal-produced recombinant pro-angiogenic growth factors were assessed by receptor phosphorylation and in-vitro angiogenesis assays. The results obtained revealed a potentiating effect in the combinatorial application of transgenic strains expressing either of the three growth factors on endothelial cell tube formation ability, and thus support the idea of using transgenic algae expressing pro-angiogenic growth factors in wound healing approaches.
Equilin does not affect thyroid hormone signaling in the developing Xenopus laevis tadpole brain
Authors: Bass Robert G. , Husain Zahabiya , Dahora Lara , Thompson Christopher K.
Published: November 2019

Toxcast/Tox21 is a massive federally run research effort dedicated to better understanding the potential toxicity of thousands of compounds in a high throughput manner. Among this list of compounds is equilin, an estrogen-like compound that was flagged as a potential thyroid hormone agonist. Here we examine if equilin acts like a thyroid hormone agonist on cellular and molecular mechanisms of brain development in Xenopus laevis tadpoles. To examine the effect of equilin, tadpoles were divided into eight groups and received 4 days of exposure. The experimental groups were as follows: 1 μL, 10 μL, and 100 μL of equilin, 1 μL, 10μM, and 100 μM of 17-β estradiol as an estrogen control, 15 μg/mL thyroxine (T4) as a thyroid hormone control, and a no-exposure control. After 4 days of treatment, animals were treated with CldU to label dividing cells for 2hr and then euthanized in MS-222. After fixation, body length was measured and the brains dissected out. IHC was performed on brains for CldU to label proliferating neural progenitor cells. Brains were then whole-mounted and analyzed using confocal microscopy. We found that equilin did not increase the number of dividing progenitor cells in a T4-like manner. Instead, equilin decreased proliferation in a dose-dependent manner, as did estradiol. The same paradigm was performed separately staining for caspase-3 and h2ax, finding that equilin increased cell death in contrast to CNTL and T4. In another experiment, RNA was extracted from tadpole brains in each group and qPCR was performed to assess change in expression of thyroid hormone-sensitive genes, Equilin did not affect gene expression in a thyroid hormone-like manner. Our data indicate that equilin does not act as a thyroid hormone agonist in the Xenopus laevis nervous system but instead acts similarly to estradiol. Our data strongly suggest that equilin is not a TH disruptor, contrary to the findings of the ToxCast/Tox21 dataset.
Monitoring Dynamics of Large Membrane Proteins by 19F Paramagnetic Longitudinal Relaxation: Domain Movement in a Glutamate Transporter Homolog
Authors: Huang Yun , Wang Xiaoyu , Lv Guohua , Razavi Asghar M. , Huysmans Gerard H. M. , Weinstein Harel , Bracken Clay , Eliezer David , Boudker Olga
Published: November 2019

In proteins where conformational changes are functionally important, the number of accessible states and their dynamics are often difficult to establish. Here we describe a novel 19F-NMR spectroscopy approach to probe dynamics of large membrane proteins. We labeled a glutamate transporter homologue with a 19F probe via cysteine chemistry and with a Ni2+ ion via chelation by a di-histidine motif. We used distance-dependent enhancement of the longitudinal relaxation of 19F nuclei by the paramagnetic metal to assign the observed resonances. We identified two outward- and one inward-facing states of the transporter, in which the substrate-binding site is near the extracellular and intracellular solutions, respectively. We then resolved the structure of the unanticipated second outward-facing state by Cryo-EM. Finally, we showed that the rates of the conformational exchange are accessible from measurements of the metal-enhanced longitudinal relaxation of 19F nuclei.
Segment2P: Parameter-free automated segmentation of cellular fluorescent signals
Authors: Dolev Noah , Pinkus Lior , Rivlin-Etzion Michal
Published: November 2019

The availability of genetically modified calcium indicators has made calcium imaging of neural signaling accessible and widespread whereby recording hundreds or even thousands of cells simultaneously is commonplace. Immunocytochemistry also produces large images with a great number of antibody labeled cells. A major bottleneck towards fully harnessing these techniques is the delineation of the neural cell bodies. We designed an online robust cell segmentation algorithm based on deep learning which does not require installation or expertise. The robust segmentation is achieved by pre-processing images submitted to the site and running them through DeepLabv3 networks trained on human segmented micrographs. The algorithm does not entail any parameter tuning; can be further trained if necessary; is robust to cell types and microscopy techniques (from immunocytochemistry to single and multi-photon microscopy) and does not require image pre-processing.
The primary cilium dampens proliferative signaling and represses a G2/M transcriptional network in quiescent myoblasts
Authors: Venugopal Nisha , Ghosh Ananga , Gala Hardik , Aloysius Ajoy , Vyas Neha , Dhawan Jyotsna
Published: November 2019

Reversible cell cycle arrest (quiescence/G0) is characteristic of adult stem cells and is actively controlled at multiple levels. G0 cells extend a primary cilium, which functions as a signaling hub, but how it controls the quiescence program is not clear. Here, we report that primary cilia distinguish different states of cell cycle exit: quiescent myoblasts elaborate a primary ciliumin vivoandin vitro, but terminally differentiated myofibers do not. Myoblasts where ciliogenesis is ablated using RNAi against a key ciliary assembly protein (IFT88) can exit the cell cycle but display an altered quiescence program and impaired self-renewal. Specifically, the G0 transcriptome in IFT88 knockdown cells is aberrantly enriched for G2/M regulators, suggesting a focused repression of this network by the cilium. Cilium-ablated cells also exhibit features of activation including enhanced activity of Wnt and mitogen signaling, and elevated protein synthesis via inactivation of the translational repressor 4EBP1. Taken together, our results show that the primary cilium integrates and dampens proliferative signaling, represses translation and G2/M genes, and is integral to the establishment of the quiescence program.

Summary statement

The primary cilium contributes to reversible arrest (quiescence) in skeletal muscle myoblasts, by coordinating and dampening mitogenic signaling focused on a G2/M transcriptional program and protein synthesis.
Immune cell-specific Cre reporter mouse labels a subset of CNS neurons
Authors: Bouteau Aurélie , Igyártó Botond Z.
Published: November 2019

HuLangerin-Cre-YFPf/f mice were generated to specifically mark a subset of antigen presenting immune cells, called Langerhans cells (LCs). During histological characterization of these mice, we found that, in addition to LCs an uncharacterized cell population in the central nervous system (CNS) also expressed YFP. In this study, we found that the CNS YFP+ cells were negative for microglia and astrocyte markers, but they expressed mature neuronal marker NeuN and showed neuronal localization/morphology. Thus, these mice might be used to study the ontogeny, migration and the role of a subset of CNS neurons.
Expressing of Cytochrome-c, ADAM 17, Wnt-5a, and Hedgehog gene during the tissue regeneration of digit tip mice (Mus musculus) var Swiss Webster post amputation
Authors: Novianti Titta , Wahyuni Febriana Dwi , Jamilah It , Ilyas Syafruddin
Published: November 2019

The tissue regeneration of digit tip mice needs some proteins that play a role in overcoming the inflammatory state. The functional protein plays a role in the continuous growth of specific cells, continuous migration, functional differentiation, and tissue morphogenesis. All of the cells need energy related to cell respiration. Naturally expressing mRNA of ADAM 17, Wnt-5a, Hedgehog (HH), and Cytochrome-c (Cyt-c) reliably produced the accordance with their respective roles in each specific phase of tissue regeneration until the whole tissues formed again. The ADAM 17 gen expressed in the inflammatory phase, it positively related its essential role to the inflammatory process. Cyt-c gene expression naturally occurs throughout the tissue regeneration because of its key role in the cellular respiration. Expressed Wnt-5a gene mRNA in the granulation phase, the specific HH gene expressed after the blastema phase. Both expressed genes positively correlate with the continual growth of the digit tip mice by the specific Spearman test (p <0.05) because of their active role of cell proliferation, cell differentiation, extensive migration, and morphogenesis.
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
Authors: Oberbeckmann Elisa , Wolff Michael , Krietenstein Nils , Heron Mark , Ellins Jessica L. , Schmid Andrea , Krebs Stefan , Blum Helmut , Gerland Ulrich , Korber Philipp
Published: November 2019

Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.