bluuebunny/crossref_metadata_2025 huggingface dataset:
Radioactive Stent Insertion for Inoperable Malignant Common Biliary Obstruction
Authors: Yang Shan , Liu Yi , Teng Fei , Wu An-Le , Lin Jia , Xian Yu-Tao , Xu Yuan-Shun
Published: August 2020

Purpose:

The purpose of this study was to assess the clinical efficacy and long-term outcomes of radioactive stent insertion in patients with malignant common biliary obstruction (MCBO).

Materials and Methods:

This was a retrospective study conducted at a single-center. Consecutive patients with MCBO were treated by normal or radioactive stent insertion between January 2014 and December 2019. The baseline data, instant efficacy records, and the long-term outcome results of these 2 groups were compared.

Results:

During the experimental duration, at our center 71 patients with inoperable MCBO underwent normal (n=40) or radioactive (n=31) stent insertion. Rates of technical success of normal and radioactive stent insertions were both 100%. No patients exhibited procedure-related complications. All patients achieved improvements in their liver functions at 2 weeks after stent insertion. Stent dysfunction was recorded in 11 and 6 patients from the normal and radioactive stent groups, respectively (P=0.425). The median stent patency was 165 and 222 days with the normal and radioactive stents, respectively (P<0.001). All patients died due to tumor progression at the follow-up. Patients survived for a respective median of 182 and 242 days in the normal and radioactive stent groups (P<0.001). The complication rates were comparable between the 2 groups.

Conclusion:

Radioactive stent insertion may provide longer patency and overall survival in those exhibiting inoperable MCBO than normal stent insertion.
An Addition of U0126 Protecting Heart Grafts From Prolonged Cold Ischemia-Reperfusion Injury in Heart Transplantation: A New Preservation Strategy
Authors: Zheng Hao , Su Yale , Zhu Cuilin , Quan Douglas , Skaro Anton I. , McAlister Vivian , Lacefield James C. , Jiang Jifu , Xue Peng , Wang Yefu , Zheng Xiufen
Published: August 2020

Background.

Ischemia-reperfusion injury (IRI) is the major cause of primary graft dysfunction in organ transplantation. The mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) signaling pathway plays a crucial role in cell physiological and pathological processes including IRI. This study aims to investigate whether inhibition of ERK signaling with U0126 can prevent prolonged cold IRI in heart transplantation.

Methods.

Rat cardiac cell line H9c2 cells were treated with U0126 before exposure to hypothermic hypoxia/reoxygenation (H/R) conditions. The effect of U0126 on H9c2 cells in response to H/R stress was determined by measuring cell death, reactive oxygen species production, mitochondrial membrane potential, and ERK signaling activation. Mouse syngeneic heterotopic heart transplantation was conducted, where a donor heart was preserved in the University of Wisconsin (UW) solution supplemented with U0126 for 24 hours at 4°C before transplantation. Heart graft function, histopathologic changes, apoptosis, and fibrosis were measured to assess IRI.

Results.

Phosphorylated ERK was increased in both in vitro H/R-injured H9c2 cells and in vivo heart grafts with IRI. Pretreatment with U0126 inhibited ERK phosphorylation and prevented H9c2 cells from cell death, reactive oxygen species generation, and mitochondrial membrane potential loss in response to H/R. Preservation of donor hearts with U0126-supplemented solution improved graft function and reduced IRI by reductions in cell apoptosis/death, neutrophil infiltration, and fibrosis of the graft.

Conclusions.

Addition of U0126 to UW solution reduces ERK signal activation and attenuates prolonged cold IRI in a heart transplantation model. ERK inhibition with U0126 may be a useful strategy to minimize IRI in organ transplantation.
Outcomes of Renal Transplant Recipients With SARS-CoV-2 Infection in the Eye of the Storm: A Comparative Study With Waitlisted Patients
Authors: Mohamed Ismail H. , Chowdary Prashanth B. , Shetty Shraddha , Sammartino Cinzia , Sivaprakasam Rajesh , Lindsey Ben , Thuraisingham Raj , Yaqoob Muhammad M. , Khurram Muhammad A.
Published: August 2020

Background.

Patients with chronic kidney disease stage 5 and those on immunosuppression are particularly vulnerable and are shielded as per public health strategy. We present our experience of coronavirus disease 2019 (COVID-19) transplant patients in one of the most affected parts of the UK with direct comparison to waitlisted patients.

Methods.

A single-center prospective study of symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive waitlisted and transplant patients was undertaken to compare these groups and assess clinical outcomes.

Results.

A total of 60 consecutive symptomatic SARS-CoV-2 positive patients were identified with 32 active waitlisted patients and 28 functioning renal transplants. Demographics were similar. The incidence of symptomatic COVID-19 in the waitlisted group was 9.9% compared to 1.9% in renal transplant patients (P < 0.001). Immunosuppression did not influence initial symptomology. Fifteen percent of patients in the waitlisted and 32% in the transplant groups died (P = 0.726). Mortality as proportion of total waitlisted (321 patients) and transplant population (1434 patients) of our centre was 1.5% and 0.6% (P < 0.001), respectively. C-reactive protein (CRP) at 48 h and peak CRP were associated with mortality in both groups while quick sequential organ failure assessment score at 48 h (P = 0.036) was associated with mortality for transplant patients.

Conclusions.

Incidence of COVID-19 is higher in the waitlisted population but transplant patients have more severe disease, reflected by higher mortality. CRP at 48 h can be used as a predictive tool. In the absence of effective treatments, the current strategy of shielding is arguably the most important factor in protecting patients while resuming transplantation.
Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA
Authors: Lee Jean Y. H. , Best Nickala , McAuley Julie , Porter Jessica L. , Seemann Torsten , Schultz Mark B. , Sait Michelle , Orlando Nicole , Mercoulia Karolina , Ballard Susan A. , Druce Julian , Tran Thomas , Catton Mike G. , Pryor Melinda J. , Cui Huanhuan L. , Luttick Angela , McDonald Sean , Greenhalgh Arran , Kwong Jason C. , Sherry Norelle L. , Graham Maryza , Hoang Tuyet , Herisse Marion , Pidot Sacha J. , Williamson Deborah A. , Howden Benjamin P. , Monk Ian R. , Stinear Timothy P.
Published: August 2020

Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.

Aim. To establish and validate a reverse transcription loop-mediated isothermal amplification (RT- LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.

Methodology. We used a commercial RT-LAMP mastermix from OptiGene in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby 1 µl of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65 °C for 30 min and measure fluorescence in the FAM channel at 1 min intervals.

Results. Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87 and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 min (sd±7 min). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 ml−1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.

Conclusion. With a simplified workflow, The N1 gene Single Tube Optigene LAMP assay (N1-STOP-LAMP) is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.
Aprepitant as a combinant with Dexamethasone reduces the inflammation via Neurokinin 1 Receptor Antagonism in severe to critical Covid-19 patients and potentiates respiratory recovery: A novel therapeutic approach
Authors: Mehboob Riffat , Ahmad Fridoon Jawad , Qayyum Ahad , Rana Muhammad Asim , Gilani Syed Amir , Tariq Muhammad Akram , Akram Javed
Published: August 2020

Background

Corona virus infection is a respiratory infection, compromising the normal breathing in critical patients by damaging the lungs. Researches are ongoing to find an efficient treatment strategy for this disease by either inactivating the virus or boosting the immune system of patient or by managing the cytokine storm.

Aim

To evaluate the clinical outcomes of Substance P receptor Neurokinin 1 antagonist in Covid-19 patients against the usual treatments as controls.

Patients and Methods

It is a randomized clinical trial, open label, having two arms, one receiving normal management and care while other receiving Neurokinin-1 Receptor antagonist, Aprepitant, in addition. Dexamethasone, a corticosteroid is also administered orally to both the groups. PCR positive, hospitalized patients with more than 18 years of age, both genders, moderate to critical phase were included. 18 patients were randomly allocated in both arms, having 10 in group A and 8 in group B. Lab investigations were performed in both the groups before and after the intervention. We report preliminary results for the comparison of Aprepitant 80 mg given once daily for 3-5 days vs routine management. The primary outcome was total in hospital days and duration of disease.

Results

Mean age of patients in group A was 47.63 ±12.07years while 60.90± 9.75 years in group B. There were 3/8 males in group A and 8/10 in group B. There were 2 critical patients in group A and 5 in group B. Biochemical and hematological parameters in both groups didn’t show much difference except the C-reactive protein reduction in the intervention group, indicative of a reduced inflammation. Oxygen saturation also improved but more patients should be enrolled to get a statistically significant data. One patient was discharged from each group within 5 days and one patient expired in each.

Conclusions

It is a pilot study but the findings give a strong clue for the therapeutic potential of Aprepitant. Patients who received a combination therapy of Aprepitant and Dexamethasone were recovered earlier and showed improved clinical outcomes, laboratory findings and reduced C-reactive protein which is an inflammatory marker. We suggest here a study on larger sample size to get a deeper insight of its potential and efficacy. It may be more effective in severe to critical patients having respiratory difficulties.
Effects of Starter Feeds of Different Physical Forms on Rumen Fermentation and Microbial Composition for Pre-weaning and Post-weaning Lambs
Authors: Li Yong , Guo Yanli , Zhang Chengxin , Cai Xiaofang , Liu Peng , Li Cailian
Published: August 2020

This study aimed to evaluate the effects of starter feeds of different physical forms on rumen fermentation and microbial composition for lambs. Twenty-four eight-day-old male Hu lambs (5.04 ± 0.75 kg body weight) were fed either milk replacer (MR) and pelleted starter feed (PS), or MR and textured starter feed (TS) in pre-weaning (day 8 to 35) and post-weaning (day 36 to 42) lambs. And the MR was fed by bottles to lambs at 2% of body weight at day 8 divided as three equal amounts at 08:00, 14:00 and 20:00 in pre-weaning. And the lambs were readily availed starter feeds and clean fresh water in the whole experiment. Six lambs for each treatment were euthanized at day 21 or 42 for sampling. The results showed the total volatile fatty acids, propionate and butyrate of rumen liquid in TS groups were all higher than them in PS groups respectively for pre-weaning and post-weaning lambs (P< 0.05), and the pH of rumen liquid in TS group was lower than it in PS group for post-weaning lambs (P< 0.05). Moreover, the pH of rumen and OTUs in TS group had trends to lower than them in PS group for pre-weaned lambs (P= 0.061,P= 0.066). TS established the predominant Phylum,Bacteroidetes, earlier than PS, and increased significantly the relative abundances ofSharpeacompared to PS at level of genus (P< 0.05) for pre-weaning and post-weaning lambs. TS were more benefits to trigger rumen development for lambs.

IMPORTANCE

Early use of starter feed could trigger rumen fermentation and establishment of dominant flora, which were in favour of growth and development of rumen for ruminants. The physical form of starter feed is one of the important factors to promote rumen fermentation and establishment of dominant flora for ruminants of transition. However, limited study on effects of physical forms of starter feeds, especially the texturized starters containing steam-flaked grains, to rumen fermentative pattern and microbial composition for pre-weaning and post-weaning lambs to date. It was necessary to investigate the effects of physical form of starter feed on rumen fermentation and microbial composition for lambs. The significance of our research showed TS were better benefits to promote the rumen fermentation and establishment of dominant flora for lambs, which will greatly enhance our understanding of physical forms of starter feeds, leading to broader studies on rumen development for lambs.
An immobilization technique for long-term time-lapse imaging of explantedDrosophilatissues
Authors: Bostock Matthew P. , Prasad Anadika R. , Chaouni Rita , Yuen Alice C. , Sousa-Nunes Rita , Amoyel Marc , Fernandes Vilaiwan M.
Published: August 2020

Time-lapse imaging is an essential tool to study dynamic biological processes that cannot be discerned from fixed samples alone. However, imaging cell- and tissue-level processes in intact animals poses numerous challenges if the organism is opaque and/or motile. Explant cultures of intact tissues circumvent some of these challenges, but sample drift remains a considerable obstacle. We employed a simple yet effective technique to immobilize tissues in medium-bathed agarose. We applied this technique to study multipleDrosophilatissues from first-instar larvae to adult stages in various orientations and with no evidence of anisotropic pressure or stress damage. Using this method, we were able to image fine features for up to 18 hours and make novel observations. Specifically, we report that fibers characteristic of quiescent neuroblasts are inherited by their basal daughters during reactivation; that the lamina in the developing visual system is assembled roughly 2-3 columns at a time; that lamina glia positions are dynamic during development; and that the nuclear envelopes of adult testis cyst stem cells do not break down completely during mitosis. In all, we demonstrate that our protocol is well-suited for tissue immobilization and long-term live imaging, enabling new insights into tissue and cell dynamics inDrosophila.
Analysis of Structure and function by the LysR-Type Transcriptional Regulator CbbR of Nostoc sp. PCC 7120
Authors: Xu Hao-Xi , Han Shu-Jing , Jiang Yong-Liang , Zhou Cong-Zhao
Published: August 2020

The LysR-type Calvin–Benson–Bassham cycle transcriptional regulator CbbR plays an important role in CO2fixation in carbon metabolism in nature, which regulates the gene expression of the key enzyme RibisCO in the Calvin–Benson–Bassham (CBB) cycle. In this study, we optimized the conditions for the transformation, expression, and purification of CbbR in the model algae Nostoc sp. PCC 7120, obtained nick-DNA fragments that could tightly bind to CbbR_7120, and finally obtained CbbR protein crystals. These findings provide great assistance for the final crystallization of CbbR to solve the crystal structure of CbbR, and lay the foundation for understanding the mechanism of CO2fixation in the CBB cycle.
Paranode stability requires UNC5B expression by oligodendrocytes
Authors: de Faria Omar , Nakamura Diane S. , Clemot Samuel , Kim Doyeun , Mocanu Mihai Victor , Pilgram Roland , Bin Jenea M. , Wong Edwin W. , Shmuel Amir , Sadikot Abbas , Ackerman Susan L. , Kennedy Timothy E.
Published: August 2020

In the mature CNS, netrin-1 is expressed by neurons and oligodendrocytes and implicated in the stability of axo-oligodendroglial paranodal junctions. Here we report that the netrin receptor UNC5B is highly expressed by mature oligodendrocytes and enriched at paranodes. We demonstrate that paranodes become disorganized following conditional deletion of UNC5B in oligodendrocytes, with disruption of the interface between glial loops and detachment of loops from the axon. As a result, Caspr1 and Kv1.1 disperse along the axon, internodes fail to lengthen and compact myelin periodicity is reduced. Paranodal and axoglial domain disorganization progressively worsens and a delay in motor learning develops in aged mice lacking oligodendroglial UNC5B. Altered glial loop ultrastructure and reduced levels of claudin-11 and JAM-C tight junction proteins support the conclusion that disruption of autotypic junctions between paranodal loops underlies paranode disorganization. Our findings reveal an essential contribution of oligodendroglial UNC5B at paranodes that is required for the stability of mature myelin.
Random searchers cope with cognitive errors and uncertainty better than path planners
Authors: Campos Daniel , Méndez Vicenç , Palmer John , Cristín Javier , Bartumeus Frederic
Published: August 2020

There is a widespread belief in ecology that the capacity of animals to orchestrate systematic and planned paths should represent a significant benefit for efficient search and exploration. Within this view, stochasticity observed in real animal trajectories is mostly understood as undesirable noise caused by internal or external effects. Far less is known, however, about the case when cognitive errors and limitations inherent to living systems are explicitly put into play. Here we compare within this context the search efficiency of (i) walkers driven by Bayesian rules generating deterministic paths, (ii) standard random walkers, and (iii) human trajectories obtained from search experiments in a soccer field and on the computer screen. Our results clearly challenge the view that deterministic paths are generally better for exploration than random strategies, as the latter are more resilient to cognitive errors. Instead, we provide numerical and experimental evidence that stochasticity would provide living organisms with a sufficient and cognitively simple exploration solution to the problem of uncertainty.
Resistance to clothianidin reduces the efficacy of SumiShield® 50WG, a neonicotinoid formulation for indoor residual spraying, againstAnopheles gambiae
Authors: Fouet Caroline , Ashu Fred A. , Ambadiang Marilene M. , Tchapga Williams , Wondji Charles S. , Kamdem Colince
Published: August 2020

Chronic exposure of mosquito larvae to pesticide residues in agricultural areas is often associated with evolution of resistance to insecticides used for vector control. This presents a concern for the efficacy of clothianidin, an agricultural neonicotinoid qualified for Indoor Residual Spraying (IRS). Using standard bioassays, we tested if reduced susceptibility to clothianidin affects the efficacy of SumiShield® 50WG, one of the two newly approved formulations, which contains 50% clothianidin. We simultaneously monitored susceptibility to clothianidin and to SumiShield® 50WG, testing adults ofAnopheles gambiae,An. coluzziiandCulexsp collected from urban, suburban and agricultural areas of Yaoundé. We found that the level of susceptibility to the active ingredient predicted the efficacy of SumiShield® 50WG. This formulation was very potent against populations that achieved 100% mortality within 72 h of exposure to a discriminating dose of clothianidin. By contrast, mortality leveled off at 75.4 ± 3.5 % within 7 days of exposure to SumiShield® 50WG inAn. gambiaeadults collected from a farm where spraying of acetamiprid and imidacloprid is driving cross-resistance to clothianidin. These findings indicate that more potent formulations of clothianidin or different insecticides should be prioritized in areas where resistance is emerging.
Cellular barcoding of protozoan pathogens reveals the within-host population dynamics ofToxoplasma gondiihost colonization
Authors: Wincott Ceire J. , Sritharan Gayathri , Benns Henry J. , Liakath Farzana B. , Gilabert-Carbajo Carla , Bunyan Monique , Fairweather Aisling R. , Alves Eduardo , Andrew Ivan , Game Laurence , Frickel Eva M. , Tiengwe Calvin , Ewald Sarah E. , Child Matthew A.
Published: August 2020

Molecular barcoding techniques have emerged as powerful tools to understand microbial pathogenesis. However, barcoding strategies have not been extended to protozoan parasites, which have unique genomic structures and virulence strategies compared to viral and bacterial pathogens. Here, we present a versatile CRISPR-based method to barcode protozoa, which we successfully apply toToxoplasma gondiiandTrypanosoma brucei. The murine brain is an important transmission niche forT. gondii, and brain persistence is a clinically untreatable feature of infection. The blood-brain barrier is expected to physically restrict parasite colonization of this niche, resulting in a selection bottleneck. Using libraries of barcodedT. gondiiwe evaluate shifts in the population structure from acute to chronic infection of mice. Contrary to expectation, most barcodes were present in the brain one-month post-intraperitoneal infection in both inbred CBA/J and outbred Swiss mice. Although parasite cyst number and barcode diversity declined over time, barcodes that represented a minor fraction of the inoculum could become a dominant population in the brain by three months post-infection. Together, these data establish the first, robust molecular barcoding approach for protozoa and evidence that the blood-brain barrier does not represent a major bottleneck to colonization byT. gondii.
Expression of ACE2, TMPRSS2 and CTSL in human airway epithelial cells under physiological and pathological conditions: Implications for SARS-CoV-2 infection
Authors: Yin Junping , Kasper Brigitte , Petersen Frank , Yu Xinhua
Published: August 2020

SARS-CoV-2 enters into human airway epithelial cells via membrane fusion or endocytosis, and this process is dependent on ACE2, TMPRSS2, and cathepsin L. In this study, we examined the expression profiles of the three SARS-CoV-2 entry-related genes in primary human airway epithelial cells isolated from donors with different physiological and pathological backgrounds such as smoking, COPD, asthma, lung cancer, allergic rhinitis, cystic fibrosis, or viral infections. By reanalyzing 54 GEO datasets comprising transcriptomic data of 3428 samples, this study revealed that i) smoking is associated with an increased expression of ACE2 and TMPRSS2 and a decreased expression of cathepsin L; ii) infection of rhinovirus as well as poly(I:C) stimulation leads to high expression of all three SARS-CoV-2 entry-related genes; iii) expression of ACE2 and cathepsin L in nasal epithelial cells are decreased in patients with asthma and allergic rhinitis. In conclusion, this study implicates that infection of respiratory viruses, cigarette smoking and allergic respiratory diseases might affect the susceptibility to and the development of COVID-19.
Near-infrared Spectroscopy evaluations for rapid differentiation of carbapenem resistant Enterobacteriaceae from susceptible strains
Authors: Alharbi Bushra , Sikulu-Lord Maggy T. , Lord Anton , Zowawi Hosam M , Trembizki Ella
Published: August 2020

Antimicrobial resistance (AMR) caused by Carbapenem-Resistant Enterobacteriaceae (CRE) is a global threat. Accurate identification of these bacterial species with associated AMR is critical for their management. While highly accurate methods to detect CRE are available, they are costly, timely and require expert skills making their application infeasible in low-resource settings. Here, we investigated the potential of Near-infrared Spectroscopy (NIRS) for a range of applications; i) the detection and differentiation of isolates of two pathogenic Enterobacteriaceae species,Klebsiella pneumoniaeandEscherichia coliand, ii) the differentiation of carbapenem resistant and susceptibleK. pneumoniae. NIRS has successfully differentiated betweenK. pneumoniaeandE. coliisolates with a predictive accuracy of 89.04% (95% CI; 88.7-89.4%).K. pneumoniaeisolates harbouring carbapenem resistance determinants were differentiated from susceptibleK. pneumoniaestrains with an accuracy of 85% (95% CI; 84.2-86.1%). To our knowledge, this is the largest demonstration of a proof of concept for the utility and feasibility of NIRS for rapidly differentiating betweenK. pneumoniaefromE.colias well as from carbapenem resistantK. pneumoniaefrom susceptible strains.
Systematic comparison of developmental GRNs explains how novelty is incorporated in early development
Authors: Cary Gregory A. , McCauley Brenna S. , Zueva Olga , Pattinato Joseph , Longabaugh William , Hinman Veronica F.
Published: August 2020

The impressive array of morphological diversity among animal taxa represents the product of millions of years of evolution. Morphology is the output of development, therefore phenotypic evolution arises from changes to the topology of the gene regulatory networks (GRNs) that control the highly coordinated process of embryogenesis1. While genetic variation can arise anywhere in the genome and affect any part of an individual GRN, the need to form a viable embryo provides a constraint on the types of variation that pass the filter of selection. A particular challenge in understanding the origins of animal diversity lies in determining how GRNs incorporate novelty while preserving the overall stability of the network, and hence, embryonic viability. Here we assemble a comprehensive GRN, consisting of 42 genes (nodes) and 84 interactions (edges), for the model of endomesoderm specification in the sea star from zygote through gastrulation that corresponds to the GRN for sea urchin development of equivalent territories and stages2. Using these detailed models we make the first systems-level comparison of early development and examine how novelty is incorporated into GRNs. We show how the GRN is resilient to the introduction of a transcription factor,pmar1, the inclusion of which leads to a switch between two stable modes of Delta-Notch signaling. Signaling pathways can function in multiple modes and we propose that GRN changes that lead to switches between modes may be a common evolutionary mechanism for changes in embryogenesis. Our data additionally proposes a model in which evolutionarily conserved network motifs, or kernels, may function throughout development to stabilize these signaling transitions.
Nerve fibers in the Tumor Microenvironment are co-localized with Tertiary Lymphoid Structures
Authors: Heij Lara R. , Tan Xiuxiang , Kather Jakob N. , Niehues Jan M. , Sivakumar Shivan , Heussen Nicole , van der Kroft Gregory , Olde Damink Steven W.M. , Lang Sven , Bednarsch Jan , Aberle Merel R. , Luedde Tom , Gaisa Nadine T. , Liu Drolaiz H.W. , Cleutjens Jack P.M. , Modest Dominik P. , Wiltberger Georg J. , Neumann Ulf P.
Published: August 2020

Background

B cells and tertiary lymphoid structures (TLS) are reported to be important in the improvement of survival of cancer patients. These secondary lymphoid organs have been associated with the generation of an anti-tumor response. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancer types and the stromal architecture shapes the intratumoral heterogeneity. The stroma of PDAC is a complex system in which crosstalk takes place between cancer-associated fibroblasts, immune cells, endothelial cells and the cancer cells. Besides immune cells and fibroblasts, there is some limited data about the influence of nerve fibers on cancer progression.

Patients and methods

Nerve Fiber Density (NFD) was analysed in our cohort of 188 patients with Pancreatic Ductal Adenocarcinoma who underwent pancreatic surgery. We used immunohistochemistry and multiplex imaging to phenotype the immune cell infiltrate. The cell detection classifier measured distance from immune cell to cancer gland and with a heat map we could count TLS. By using Machine learning we were able to define the spatial distribution and counting Tertiary Lymphoid Structures.

Results

High NFD is significantly associated with prolonged overall survival (HR 1.676 (95%CI 1.126,2.495) for low vs. high NFD, p-value 0.0109). The immune cells surrounding the nerve fibers were phenotyped in B cells, T cells and dendritic follicular cells, matching a TLS. Here we show that small nerve fibers are located at the TLS in Pancreatic Cancer and a high Nerve Fiber Density combined with more than 5 TLS is associated with a better survival (HR 0.388 (95%CI 0.218, 0.689).

Conclusion

The co-localization of small nerve fibers with TLS is a new finding which has not been described before. However the precise roles of these TLS and nerve fibers remains unknown. These findings unravel future pathways and has the potential to reach new directions into already existing targeted therapy.
Reliability assessment of temporal discounting measures in virtual reality environments
Authors: Bruder Luca R. , Scharer Lisa , Peters Jan
Published: August 2020

In recent years the emergence of high-performance virtual reality (VR) technology has opened up new possibilities for the examination of context effects in psychological studies. The opportunity to create ecologically valid stimulation in a highly controlled lab environment is especially relevant for studies of psychiatric disorders, where it can be problematic to confront participants with certain stimuli in real life. However, before VR can be confidently applied widely it is important to establish that commonly used behavioral tasks generate reliable data within a VR surrounding. One field of research that could benefit greatly from VR-applications are studies assessing the reactivity to addiction related cues (cue-reactivity) in participants suffering from gambling disorder. Here we tested the reliability of a commonly used temporal discounting task in a novel VR set-up designed for the concurrent assessment of behavioral and psychophysiological cue-reactivity in gambling disorder. On two days, thirty-four healthy non-gambling participants explored two rich and navigable VR-environments (neutral: café vs. gambling-related: casino and sports-betting facility), while their electrodermal activity was measured using remote sensors. In addition, participants completed the temporal discounting task implemented in each VR environment. On a third day, participants performed the task in a standard lab testing context. We then used comprehensive computational modeling using both standard softmax and drift diffusion model (DDM) choice rules to assess the reliability of discounting model parameters assessed in VR. Test-retest reliability estimates were good to excellent for the discount rate log(k), whereas they were poor to moderate for additional DDM parameters. Differences in model parameters between standard lab testing and VR, reflecting reactivity to the different environments, were mostly numerically small and of inconclusive directionality. Finally, while exposure to VR generally increased tonic skin conductance, this effect was not modulated by the neutral vs. gambling-related VR-environment. Taken together this proof-of- concept study in non-gambling participants demonstrates that temporal discounting measures obtained in VR are reliable, suggesting that VR is a promising tool for applications in computational psychiatry, including studies on cue-reactivity in addiction.
Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine
Authors: Zeller Michael A. , Gauger Phillip C. , Arendsee Zebulun W. , Souza Carine K. , Vincent Amy L. , Anderson Tavis K.
Published: August 2020

The antigenic diversity of influenza A virus (IAV) circulating in swine challenges the development of effective vaccines, increasing zoonotic threat and pandemic potential. High throughput sequencing technologies are able to quantify IAV genetic diversity, but there are no accurate approaches to adequately describe antigenic phenotypes. This study evaluated an ensemble of non-linear regression models to estimate virus phenotype from genotype. Regression models were trained with a phenotypic dataset of pairwise hemagglutination inhibition (HI) assays, using genetic sequence identity and pairwise amino acid mutations as predictor features. The model identified amino acid identity, ranked the relative importance of mutations in the hemagglutinin (HA) protein, and demonstrated good prediction accuracy. Four previously untested IAV strains were selected to experimentally validate model predictions by HI assays. Error between predicted and measured distances of uncharacterized strains were 0.34, 0.70, 2.19, and 0.17 antigenic units. These empirically trained regression models can be used to estimate antigenic distances between different strains of IAV in swine using sequence data. By ranking the importance of mutations in the HA, we provide criteria for identifying antigenically advanced IAV strains that may not be controlled by existing vaccines and can inform strain updates to vaccines to better control this pathogen.
PELP1/SRC-3-dependent regulation of metabolic kinases drives therapy resistant ER+ breast cancer
Authors: Truong Thu H. , Benner Elizabeth A. , Hagen Kyla M. , Temiz Nuri A. , Kerkvliet Carlos Perez , Wang Ying , Cortes-Sanchez Emilio , Yang Chieh-Hsiang , Pengo Thomas , Guillen Katrin P. , Welm Bryan E. , Telang Sucheta , Lange Carol A. , Ostrander Julie H.
Published: August 2020

Recurrence of metastatic breast cancer stemming from acquired endocrine and chemotherapy resistance remains a health burden for women with luminal (ER+) breast cancer. Disseminated ER+ tumor cells can remain viable but quiescent for years to decades. Contributing factors to metastatic spread include the maintenance and expansion of breast cancer stem cells (CSCs). Breast CSCs frequently exist as a minority population in therapy resistant tumors. In this study, we show that cytoplasmic complexes composed of steroid receptor (SR) co-activators, PELP1 and SRC-3, modulate breast CSC expansion through upregulation of the HIF-activated metabolic target genesPFKFB3andPFKFB4. Seahorse metabolic assays demonstrated that cytoplasmic PELP1 influences cellular metabolism by increasing both glycolysis and mitochondrial respiration. PELP1 interacts with PFKFB3 and PFKFB4 proteins, and inhibition of PFKFB3 and PFKFB4 kinase activity blocks PELP1-induced tumorspheres and protein-protein interactions with SRC-3. PFKFB4 knockdown inhibitedin vivoemergence of circulating tumor cell (CTC) populations in mammary intraductal (MIND) models. Application of PFKFB inhibitors in combination with ER targeted therapies blocked tumorsphere formation in multiple models of advanced breast cancer, including tamoxifen (TamR) and paclitaxel (TaxR) resistant models and ER+ patient-derived organoids (PDxO). Together, our data suggest that PELP1, SRC-3, and PFKFBs cooperate to drive ER+ tumor cell populations that include CSCs and CTCs.

Significance

Identifying non-ER pharmacological targets offers a useful approach to blocking metastatic escape from standard of care ER/estrogen (E2)-targeted strategies to overcome endocrine and chemotherapy resistance.
Adipose tissue developmental growth constraints uncouple fat distribution from glucose metabolism in two mouse models of obesity
Authors: Sebo Zachary L. , Church Christopher , Berry Ryan , Rodeheffer Matthew S.
Published: August 2020

Subcutaneous obesity is associated with better metabolic health than visceral obesity. Here, we leverage two mouse models with differing quantities of visceral and subcutaneous fat to assess the role of fat distribution in glucose homeostasis. Interestingly, we found genetic ablation of inguinal subcutaneous fat does not exacerbate obesity-associated impairments in glucose metabolism. Consistent with this observation, mutant mice that preferentially accrue subcutaneous fat display a similar metabolic profile to controls with equal fat mass. Importantly, the increased subcutaneous adiposity in these mice occurs downstream of androgen receptor deficiency and is not driven by elevated adiponectin activity. Rather, it is caused by diminished adipocyte precursor seeding in nascent visceral fat and proportionally greater growth of subcutaneous fat. Thus, the pattern of obesogenic fat mass expansion can be determined early in development without impacting glucose metabolism. This suggests that different mechanisms underlying biased fat accumulation exert different effects on glucometabolic health.
Egg size variation in the context of polyandry: a case study using long-term field data from snowy plovers
Authors: Eberhart-Hertel Luke Joseph , Falcão Rodrigues Lourenço , Krietsch Johannes , Eberhart-Hertel Anne G. , Cruz-López Medardo , Vázquez-Rojas Karina Alejandra , González-Medina Erick , Schroeder Julia , Küpper Clemens
Published: August 2020

Gamete size variationbetweenthe sexes is central to the concept of sex roles, however, to what extent gamete size variationwithinthe sexes relates to sex role variation remains unclear. Comparative and theoretical studies suggest that, when clutch size is invariable, polyandry is linked to a reduction of egg size, while increased female-female competition for mates favors early breeding when females cannot monopolize multiple males. To understand whether and how breeding phenology, egg size, and mating behavior are related at the individual level, we studied the reproductive histories of 424 snowy plover females observed in the wild over a 15-year period. Egg size, but not polyandry, were highly repeatable for individual females. Consistent with theoretical predictions, we found that polyandrous females were the earliest breeders and that early clutches contained smaller eggs than clutches initiated later. Neither egg size nor mating behavior showed clear signs of an age-related deterioration, on the contrary, prior experience acquired either through age or local recruitment enabled females to nest early. Taken together, these results suggest that gamete size variation is not linked to mating behavior at the individual level, and, consequently, the adaptive potential of such variation appears to be limited.

Teaser Text

Comparative avian analyses have linked female polyandry and sex-role reversal to the production of smaller eggs: the notion being that smaller eggs allow polyandrous females to lay multiple sequential clutches quickly. Our research, however, has found that the notion is more complex at the individual level. We found that females who started breeding early in the season were more likely to be polyandrous and produce smaller eggs. Experience was also found to give older and locally-raised females a competitive advantage over younger and inexperienced females vying for early breeding opportunities. Despite this, we found limited evidence that egg size reduction gives a competitive advantage in the scramble for mates. Instead, seasonal variations in egg size can likely be attributed to other factors, such as the survival of early-hatching chicks, resource limitations during egg production, and individual differences. We found that senescence had little impact on egg size or mating behavior. Future research should also examine how seasonality, age, and mating behavior impact the reproductive fitness of males, who provide more parental care than females in many sex role reversed systems. By studying these effects in concert, we can gain a deeper understanding of sex roles in natural populations.
Probability-based methods for outlier detection in replicated high-throughput biological data
Authors: Smith Matthew S. , Devarajan Karthik
Published: August 2020

A problem that arises frequently in high-throughput biological studies is the assessment of technical reproducibility of data obtained under homogeneous experimental conditions. This is an important problem considering the significant growth in the number of high-throughput technologies that have become available to the researcher in the past decade. Although certain ad hoc and graphical methods for determining data quality have been in existence, these methods lack statistical rigor and are not broadly applicable across different technologies. There is an inherent need for the quantitative evaluation of the reproducibility of technical replicates from high-throughput compound and siRNA screening, next-generation sequencing and other modern “omics” studies. To this end, we have developed an approach that accounts for technical variability and potential asymmetry that arise naturally in the distribution of replicate data, and aids in the identification of outliers. Our methods for outlier detection rely on flexible statistical models, employ maximum likelihood methods for estimation and are broadly applicable to a variety of high-throughput biological studies. We discuss an adaptation of these methods when there are multiple replicates as well as current limitations to these techniques. We illustrate our methods using experimental data from high-throughput compound screening and protein expression studies as well as simulated data. Our methods are implemented in the R package replicateOutliers and are currently available at github.com/matthew-seth-smith/replicateOutliers.
Macrophages promote endothelial-to-mesenchymal transition via MT1-MMP/TGFβ1 after myocardial infarction
Authors: Alonso-Herranz Laura , Sahún-Español Álvaro , Gonzalo Pilar , Gkontra Polyxeni , Núñez Vanessa , Cedenilla Marta , Villalba-Orero María , Inserte Javier , Clemente Cristina , García-Dorado David , Arroyo Alicia G , Ricote Mercedes
Published: August 2020

Macrophages produce factors that participate in cardiac repair and remodeling after myocardial infarction (MI); however, how these factors crosstalk with other cell types mediating repair is not fully understood. In this study, we demonstrated that cardiac macrophages increased expression ofMmp14(MT1-MMP) 7 days post-MI. Specific macrophage-targeting of MT1-MMP (MT1-MMPΔLysMmice) attenuates post-MI cardiac dysfunction, reduces fibrosis, and preserves the cardiac capillary network. Mechanistically, we showed that MT1-MMP activates latent TGFβ1 in macrophages, leading to paracrine SMAD2-mediated signaling in endothelial cells and endothelial-to-mesenchymal transition (EndMT). Post-MI MT1-MMPΔLysMhearts contained fewer cells undergoing EndMT than their wild-type counterparts, and MT1-MMP-deficient macrophages showed a reduced ability to induce EndMT in co-cultures with endothelial cells. Our results demonstrate the contribution of EndMT to cardiac fibrosis and adverse remodeling post-MI and identify macrophage MT1-MMP as a key regulator of this process. The identified mechanism has potential as a therapeutic target in ischemic heart disease.
SETD1B controls cognitive function via cell type specific regulation of neuronal identity genes
Authors: Michurina Alexandra , Sakib Sadman , Kerimoglu Cemil , Krüger Dennis Manfred , Kaurani Lalit , Islam Rezaul , Centeno Tonatiuh Pena , Cha Julia , Xu Xingbo , Zeisberg Elisabeth M. , Kranz Andrea , Stewart Francis Adrian , Fischer Andre
Published: August 2020

Histone-3-lysine-4-methylation (H3K4me) is mediated by six different lysine methyltransferases (KMTs). Amongst these enzymes SET domain containing 1b (SETD1B) has been linked to intellectual disability but its role in the adult brain has not been studied yet. Here we show that mice lackingSetd1bfrom excitatory neurons of the adult forebrain exhibit severe memory impairment. By combining neuron-specific ChIP-seq, RNA-seq and single cell RNA-seq approaches we show thatSetd1bcontrols the expression of neuronal-identity genes with a broad H3K4me3 peak linked to learning and memory processes. Our data furthermore suggest that basal neuronal gene-expression is ensured by other H3K4 KMTs such asKmt2aandKmt2bwhile the additional presence ofSetd1bat the single cell level provides transcriptional consistency to the expression of genes important for learning & memory.
Individual human genomes frequently contain variants that have evolutionary couplings
Authors: Martell Henry J , Griffin Darren K , Wass Mark N
Published: August 2020

Coevolution has been widely studied between species and has an important role in our understanding of biological function. For proteins there has recently been interest in the identification of positions within proteins that have coevolved including their use for modelling protein structure. Such studies focus on the identification of coevolving positions (or evolutionary couplings) within multiple sequence alignments of proteins from many species. Here, we exploit large human genome resources to investigate if it is possible to use genetic variation data from a single species, human, to identify positions within proteins that have coevolved. We combine the 1000 genome project genetic variation data with protein structural data to identify variant-variant interactions within individual human genomes. We find >4,000 combinations of variants that are located close in 3D protein structure and >1,200 in protein-protein interfaces. Many variant combinations include compensatory amino acid changes (e.g. maintaining charge/functional groups), thus supporting that these are coevolutionary events. Our study highlights that it is possible to identify coevolution within a single species. Given the important role that genetic variation plays in causing disease it is important for variant interpretation and precision medicine to consider the gestalt effects of variants rather than individual variants in isolation.
Multi-omics approach highlights differences between functional RLP classes inArabidopsis thaliana
Authors: Steidele C. , Stam R.
Published: August 2020

The receptor-like protein (RLP) family is a complex gene family with 57 members inArabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others have found to be involved in defence responses. However, functional data is to date, only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function. Using publicly available datasets, we annotated those RLPs of unknown functions as either likely defence-related or likely fulfilling a more basal function in plants. Using these categories, we can identify important characteristics that differ between the RLP sub classes. We find the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic diversity of their individual members in accessible pan-genome data. Our work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions of which RLPs can be identified as potential immune receptors using genetics tools, which can be useful for disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.