bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimum Coupling of an Active Middle Ear Actuator: Effect of Loading Forces on Actuator Output and Conductive Losses
Authors: Gamm Ute A. , Grossöhmichen Martin , Salcher Rolf B. , Prenzler Nils K. , Lenarz Thomas , Maier Hannes
Published: April 2019

Introduction:

The desired outcome of the implantation of active middle ear implants is maximum coupling efficiency and a minimum of conductive loss. It has not been investigated yet, which loading forces are applied during the process of coupling, which forces lead to an optimum actuator performance and which forces occur when manufacturer guidelines for coupling are followed.

Methods:

Actuator output was measured by laser Doppler vibrometry of stapes motion while the actuator was advanced in 20 μm steps against the incus body while monitoring static contact force. The occurrence of conductive losses was investigated by measuring changes in stapes motion in response to acoustic stimulation for each step of actuator displacement. Additionally, the electrical impedance of the actuator was measured over the whole frequency range at each actuator position.

Results:

Highest coupling efficiency was achieved at forces above 10 mN. Below 1 mN no efficient coupling could be achieved. At 30 mN loading force, which is typical when coupling according to manufacturer guidelines, conductive losses of more than 5 dB were observed in one out of nine TBs. The electrical impedance of the actuator showed a prominent resonance peak which vanished after coupling.

Conclusion:

A minimum coupling force of 10 mN is required for efficient coupling of the actuator to the incus. In most cases, coupling forces up to 100 mN will not result in clinically relevant conductive losses. The electrical impedance is a simple and reliable metric to indicate contact.
Effects of different strategies on high thrombus burden in patients with ST-segment elevation myocardial infarction undergoing primary percutaneous coronary catheterization
Authors: Xiao Yuyang , Fu Xianghua , Wang Yanbo , Fan Yanming , Wu Yanqiang , Wang Wenlu , Zhang Qian
Published: April 2019

Objective

This study aimed at evaluating efficacy and safety of thrombus aspiration and intracoronary-targeted thrombolysis on coronary thrombus burden in ST-elevation myocardial infarction (STEMI) patients undergoing primary percutaneous catheterization, comparing their effects on myocardial perfusion through index of microcirculatory resistance (IMR) and single-photon emission computed tomography (SPECT).

Participants and methods

From January 2017 to January 2018, STEMI patients with high thrombus burden undergoing primary catheterization were enrolled and randomly assigned to receiving thrombus aspiration (TA group) or intracoronary thrombolysis (IT group). IMR, SPECT, and other conventional measurements were adopted to assess myocardial perfusion. Major adverse cardiovascular events (MACEs) and complications were recorded over a 90-day follow-up and a 12-month follow-up after the procedure.

Results

The study consisted of 38 patients in the IT group and 33 in the TA group. After recanalization, thrombus burden score, corrected thrombolysis in myocardial infarction (TIMI) frame count, the proportion of TIMI myocardial perfusion 3 grade, and IMR in the IT group were significantly better than those of the TA group (P<0.05). During the 90-day follow-up, no difference was observed in cardiac function and MACEs. During the 12-month follow-up, there were significant differences in infarct size of SPECT (18.56±8.56 vs. 22.67±7.66, P=0.046), left ventricular ejection fraction of echocardiography (58.13±5.92 vs. 55.17±5.68, P=0.043), and the composite MACEs between the two groups (P=0.034).

Conclusion

Thrombus aspiration and intracoronary-targeted thrombolysis are effective and safe strategies in managing high coronary thrombus burden in STEMI patients. Compared with aspiration, intracoronary-targeted thrombolysis is more beneficial in improving myocardial microcirculation perfusion.
Trochanteric Fractures in Young Children
Authors: Harding Richard John , Moideen Abdul Nazeer , Carpenter Eleanor Clare , Thomas Daniel Phillip , Hemmadi Sandeep
Published: April 2019

Background

Isolated avulsion fractures of the greater and lesser trochanter are usually seen in adolescents prior to the fusion of the apophysis. Greater trochanter fractures in adults have a high incidence of intertrochanteric extension1, 2 and lesser trochanter fractures are regarded as a pathognomonic sign of metastatic disease. These fractures are very rare among children.

Methods

We report five cases of trochanteric fractures in children of less than two years of age three of which were unrecognized initially in the accident and emergency department.

Results

Early and complete recovery ensued following immobilization and symptomatic treatment. Surgical intervention was not required.

Conclusions

There needs to be a high index of suspicion to diagnose these fractures in children and plain radiographs need to be carefully examined when assessing a limping child. Our experience shows when correctly diagnosed these injuries can be treated successfully with supportive treatment and no need for surgical intervention.

Level of Evidence

IV Case series.
Resting blood pressure modulates chest pain intensity in patients with acute myocardial infarction
Authors: Granot Michal , Dagul Pnina , Aronson Doron
Published: April 2019

Introduction and Objectives:

Animal models and human studies show that resting blood pressure (BP) is inversely associated with pain sensitivity. The phenomenon of “hypertension-associated hypoalgesia” was proposed as a possible explanation for the intervariability in pain perception. Given that a portion of patients with acute myocardial infarction (AMI) do not experience significant pain, we used the model of severe cardiac ischemia to explore whether BP affects the intensity of chest pain.

Methods:

Patients with AMI admitted to the cardiac intensive care unit with coronary catheterization-proven completely occluded coronary artery were included (n = 67). Resting BP at admission and 5 days after AMI was obtained. Participants reported chest pain intensity and underwent psychophysical evaluation including pain ratings for pressure, heat, and pinprick stimuli as well as temporal summation and conditioned pain modulation paradigms.

Results:

Patients with lower systolic BP (≤120 mm Hg) vs higher (≥140 mm Hg) reported higher chest pain scores at symptom onset (82.3 vs 61.7, P = 0.048) and during peak AMI (82.8 vs 57.5, P = 0.019). Higher pain ratings in response to pinprick stimulus were associated with lower BP at admission (analysis of variance P = 0.036). Patients with hypertension demonstrated lower pain sensitivity in response to pressure stimulation (531.7 ± 158.9 kPa/s vs 429.1 ± 197.4). No significant associations were observed between BP and the other assessed psychophysical measures.

Conclusion:

Study findings reinforce the phenomenon of hypertension-associated hypoalgesia through characterization of the association between BP and clinical pain experiences at onset and during AMI in a model of acute clinical pain.
A New Face Subunit Transplant Model in Mice, Containing Skin, Mandible, and Oral Mucosa for Future Face Vascularized Composite Allotransplantation Studies
Authors: Cardona Esteban , Wang Aline Yen Ling , Loh Charles Yuen Yung , Chuang Sheng-Hao , Lee Chin-Ming , ALDeek Nidal , Lin Cheng-Hung , Wei Fu-Chan
Published: April 2019

Background:

In immunologic research, mice have advantages over other animals, such as low costs, easy handling, suitable life cycle, and adequate laboratory resources. However, vascularized composite allotransplantation surgery using mice is not popular, partly because of technical difficulties and high mortality rates. The authors’ goal was to demonstrate a face transplantation model in mice that includes skin, mandible, and oral mucosa.

Methods:

The authors developed a new syngeneic face transplantation model composed of skin, mandible, teeth, and oral mucosa in C57BL/6 mice. The following assessment included measuring the length of the right incisor on the transplanted mandibles, computed tomographic scan in one mouse for mandibular structure evaluation, and histologic examination of different tissue samples in another mouse for viability evaluation.

Results:

The authors performed five consecutive transplantations. The donor vessels were the common carotid artery (approximately equal to 0.4 mm) and the anterior facial vein (approximately equal to 0.2 mm), and the recipients were the common carotid artery and the posterior facial vein (approximately equal to 0.4 mm). The mean operative time was 80 minutes for the donor and 123 minutes for the recipient. There were neither flap failures nor animal deaths. The follow-up was 6 months. The right incisor of the transplant grew at different rates in all cases. Histologic samples showed viability in all tissues, including mandibular bone marrow. Computed tomography demonstrated normal structure of the transplanted bone.

Conclusion:

The authors’ syngeneic partial face transplantation model in mice, which included skin, oral mucosa, and mandible with teeth, should be useful for future face allotransplantation research, as the myriad of tissues it provides, of different immunomodulatory functions, is similar to that in the clinical scenario.
Lysosomal cystine mobilization shapes the response of mTORC1 and tissue growth to fasting
Authors: Jouandin Patrick , Marelja Zvonimir , Parkhitko Andrey A , Dambowsky Miriam , Asara John M , Nemazanyy Ivan , Dibble Christian C. , Simons Matias , Perrimon Norbert
Published: April 2019

Adaptation to nutrient scarcity involves an orchestrated response of metabolic and signaling pathways to maintain homeostasis. We provide evidence that lysosomal export of cystine coordinates remobilization of internal nutrient stores with reactivation of the growth regulator TORC1 signaling upon fasting in theDrosophilafat body. Mechanistically, cystine is reduced to cysteine and metabolized to acetyl-CoA by consuming lipids. In turn, acetyl-CoA retains carbons from alternative amino acids in the form of TCA cycle intermediates, thereby restricting amino acids availability, notably aspartate. This process limits TORC1 reactivation to maintain autophagy and allows animals to cope with starvation periods. We propose that cysteine metabolism mediates a communication between lysosomes and mitochondria to maintain the balance between nutrient supply and consumption under starvation, highlighting how changes in diet divert the fate of an amino acid into a growth suppressive program.

One Sentence Summary

Lysosomal cysteine recycling is a metabolic break that maintains autophagy upon starvation through coenzyme A synthesis.
Random burst sensing of neurotransmitters
Authors: Montague P. Read , Lohrenz Terry , White Jason , Moran Rosalyn J , Kishida Kenneth T.
Published: April 2019

We introduce a random sensing approach to neurotransmitter detection that provides concurrent, co-localized detection of dopamine, serotonin, norepinephrine and pH. The approach generates high quality out-of-sample predictions at 10 milliseconds per estimate. Similar high-quality estimates result when the data are down-sampled suggesting that even more dramatic speedups are possible. The method also works using electrophysiological probes in routine use in clinical preparations thus transforming these and similar electrodes into ultra-fast sources of multi-transmitter information.
The disease progression and molecular defense response in Chenopodium quinoa infected with Peronospora variabilis, the causal agent of quinoa downy mildew
Authors: Rollano-Peñaloza Oscar M. , Palma-Encinas Valeria , Widell Susanne , Rasmusson Allan G. , Mollinedo Patricia
Published: April 2019

The downy mildew disease, caused by the biotrophic oomycete Peronospora variabilis, is the largest environmental threat to quinoa (Chenopodium quinoa Willd.) cultivation in the Andean highlands. However, so far no molecular information on the quinoa-Peronospora interaction has been reported. Here, we have developed tools to study the downy mildew disease in quinoa at gene expression level. Living P. variabilis could be isolated and maintained in the presence of a fungicide, allowing the characterization of downy mildew disease progression in two differently susceptible quinoa cultivars under controlled conditions. Quinoa gene expression changes induced by P. variabilis were analysed by qRT-PCR for quinoa homologues of Arabidopsis thaliana pathogen-associated genes. Overall, we observed a slower disease progression and higher tolerance in the quinoa cultivar Kurmi than in the cultivar Maniquena Real. We also observed that quinoa orthologs of A. thaliana genes involved in the salicylic acid defense response pathway (AtCAT2 and AtEP3) did not have changes in its gene expression. In contrast, quinoa orthologs of A. thaliana gene markers of the induction of the jasmonic acid response pathway (AtWRKY33 and AtHSP90) were significantly induced in plants infected with P. variabilis. These genes could be used as defense response markers to select quinoa cultivars that are more tolerant to P. variabilis infection.
The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response
Authors: Finkel Omri M. , Salas-González Isai , Castrillo Gabriel , Spaepen Stijn , Law Theresa F. , Lima Teixeira Paulo José Pereira , Jones Corbin D. , Dangl Jeffery L.
Published: April 2019

Phosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms – the plant microbiota – are exposed to direct influence by the soil’s phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrationsper sethan bacteria, and less depended on the soil community composition.

Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genusBurkholderiais specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence ofBurkholderiafrom the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant’s P starvation.
The meaning of the Michaelis-Menten constant: Kmdescribes a steady-state
Authors: Canela Enric I. , Navarro Gemma , Beltrán José Luis , Franco Rafael
Published: April 2019

Often, in vitro or in vivo enzyme-mediated catalytic events occur far from equilibrium and, therefore, substrate affinity measured as the inverse of ES ⇄ E+S dissociation equilibrium constant (Kd) has a doubtful physiological meaning; in practice it is almost impossible to determineKd(except using stopped-flow or other sophisticated methodologies). The Michaelis-Menten constant (Km), the concentration of substrate ([S]) providing half of enzyme maximal activity, is not the (Kd). In the simple E+S ⇄ ES → E+P or in more complex models describing S conversion into P,Kmmust be considered the constant defining the steady state at any substrate concentration. Enzyme kinetics is based on initial rate determination, i.e. in the linear part of the S to P conversion when the concentration of [ES] remains constant while steady state occurs. We also show that Systems Biology issues such as the time required to respond to a system perturbation, is more dependent onk1, the kinetic constant defining substrateenzyme association, than onKm. WhereasKmis instrumental for biochemical basic and applied approaches, in any physiological condition, an important parameter to be considered is the substrate association rate (k1).
Loss-of-function tolerance of enhancers in the human genome
Authors: Xu Duo , Gokcumen Omer , Khurana Ekta
Published: April 2019

Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that each individual human genome possesses at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers are more tissue-specific and regulate fewer and more dispensable genes. They are enriched in immune-related cells while LoF-intolerant enhancers are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoF-tolerance of enhancers, which achieved an AUROC of 96%. We predict 5,677 more enhancers would be likely tolerant to LoF and 75 enhancers that would be highly LoF-intolerant. Our predictions are supported by known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies.
Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER) Workflow for Research and Clinical Brain PET Applications
Authors: Raman Fabio , Grandhi Sameera , Murchison Charles F. , Kennedy Richard E. , Landau Susan , Roberson Erik D. , McConathy Jonathan ,   Alzheimer’s Disease Neuroimaging Initiative
Published: April 2019

Objective

There is a need for tools enabling efficient evaluation of amyloid- and tau-PET images suited for both clinical and research settings. The purpose of this study was to assess and validate a semi-automated imaging workflow, called Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER). We tested BLAzER using two different segmentation platforms, FreeSurfer (FS) and Neuroreader (NR), for regional brain PET quantification in images from participants in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset.

Methods

127 amyloid-PET and 55 tau-PET studies along with corresponding volumetric MRI were obtained from ADNI. The BLAzER workflow utilizes segmentation of MR images by FS or NR, then visualizes and quantifies regional brain PET data using FDA-cleared software (MIM), enabling quality control to ensure optimal registration and detect segmentation errors.

Results

BLAzER analysis required only ∼5 min plus segmentation time. BLAzER using FS segmentation showed strong agreement with ADNI for global amyloid-PET standardized uptake value ratios (SUVRs) (r = 0.9922, p < 0.001) and regional tau-PET SUVRs across all Braak staging regions (r > 0.97, p < 0.001) with high inter-operator reproducibility for both (ICC > 0.97) and nearly identical dichotomization as amyloid-positive or -negative (2 discrepant cases out of 127). Comparing FS vs. NR segmentation with BLAzER, the global SUVRs were strongly correlated for global amyloid-PET (r = 0.9841, p < 0.001), but were systematically higher (4% on average) with NR, likely due to more inclusion of white matter, which has high florbetapir binding.

Conclusions

BLAzER provides an efficient workflow for regional brain PET quantification. FDA-cleared components and the ability to visualize registration reduce barriers between research and clinical applications.
Host sex and genotype modify the gut microbiome response to helminth infection
Authors: Ling Fei , Steinel Natalie , Weber Jesse , Ma Lei , Smith Chris , Correa Decio , Zhu Bin , Bolnick Daniel , Wang Gaoxue
Published: April 2019

The microbial community can be altered by direct/indirect interactions with parasites infecting host. Direct interactions can arise from physical/chemical contact with the parasite. Indirect interactions can involve parasite-induced changes in host immunity. If so, this would represent a case of genetic polymorphism in one species controlling an ecological interaction between other species. Here, we report a test of this expectation: we experimentally exposed Gasterosteus aculeatus to their naturally co-evolved parasite, Schistocephalus solidus. The host microbiome differed in response to parasite exposure, and between infected and uninfected fish. The microbial response to infection differed between host sexes, and also varied between variants at autosomal quantitative trait loci (QTL). These results indicate that host genotype regulates the indirect effect of infection on a vertebrate gut microbiome. Our results also raise the possibility that this sex-bias may be related to sex-specific microbial responses to the presence (or, absence) of helminthes. Therefore, helminth-based therapeutics as possible treatments for inflammatory bowel diseases might need to take account of these interactions, potentially requiring therapies tailored to host sex or genotype.
Network science inspires novel tree shape statistics
Authors: Chindelevitch Leonid , Hayati Maryam , Poon Art F. Y. , Colijn Caroline
Published: April 2019

1

The shape of phylogenetic trees can be used to gain evolutionary insights. A tree’s shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package athttp://github.com/Leonardini/treeCentrality.
VARUS: Sampling Complementary RNA Reads from the Sequence Read Archive
Authors: Stanke Mario , Bruhn Willy , Becker Felix , Hoff Katharina
Published: April 2019

Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However, selecting a subset of available experiments, sequencing runs and reads for this purpose is a nontrivial task and complicated by the inhomogeneity of the data.

This article presents the software VARUS that selects, downloads and aligns reads from NCBI’s Sequence Read Archive, given only the species’ binomial name and genome. VARUS automatically chooses runs from among all archived runs to randomly select subsets of reads. The objective of its online algorithm is to cover a large number of transcripts adequately when network bandwidth and computing resources are limited. For most tested species VARUS achieved both a higher sensitivity and specificity with a lower number of downloaded reads than when runs were manually selected. At the example of twelve eukaryotic genomes, we show that RNA-Seq that was sampled with VARUS is well-suited for fully-automatic genome annotation with BRAKER.

With VARUS, genome annotation can be automatized to the extent that not even the selection and quality control of RNA-Seq has to be done manually. This introduces the possibility to have fully automatized genome annotation loops over potentially many species without incurring a loss of accuracy over a manually supervised annotation process.
Interleukin-12 elicits a non-canonical response in B16 melanoma cells to enhance survival
Authors: Byrne-Hoffman C. N. , Deng W. , McGrath O. , Wang P. , Rojanasakul Y. , Klinke D. J.
Published: April 2019

Oncogenesis rewires signaling networks to confer a fitness advantage to malignant cells. For instance, the B16F0 melanoma cell model creates a cytokine sink for Interleukin-12 (IL-12) to deprive neighboring cells of this important anti-tumor immune signal. While a cytokine sink provides an indirect fitness advantage, does IL-12 provide an intrinsic advantage to B16F0 cells? Functionally, stimulation with IL-12 enhanced B16F0 cell survival but not normal Melan-A melanocytes that were challenged with a cytotoxic agent. To identify a mechanism, we assayed the phosphorylation of proteins involved in canonical IL-12 signaling, STAT4, and cell survival, Akt. In contrast to T cells that exhibited a canonical response to IL-12 by phosphorylating STAT4, IL-12 stimulation of B16F0 cells predominantly phosphorylated Akt. Mechanistically, the differential response in B16F0 cells is explained by both ligand-dependent and ligand-independent aspects to initiate PI3K-AKT signaling upon IL12RB2 homodimerization. Namely, IL-12 promotes IL12RB2 homodimerization with low affinity and IL12RB2 overexpression promotes homodimerization via molecular crowding on the plasma membrane. Collectively, the data suggest that B16F0 cells shifted the intra-cellular response to IL-12 from engaging immune surveillance to favoring cell survival. Identifying how signaling networks are rewired in model systems of spontaneous origin can inspire therapeutic strategies in humans.

Statement of Significance

While Interleukin-12 is a key cytokine that promotes anti-tumor immunity, thinking of cancer as an evolutionary process implies that an immunosuppressive tumor microenvironment could arise during oncogenesis by interfering with endogenous anti-tumor immune signals, like IL-12. Previously, we found that B16F0 cells, a cell line derived from a spontaneous melanoma, interrupts this heterocellular signal by sequestering IL-12, which provides an indirect fitness advantage. Here, we report that B16F0 cells gain an intrinsic advantage by rewiring the canonical response to IL-12 to instead initiate PI3K-AKT signaling, which promotes cell survival. The data suggest a model where overexpressing one component of the IL-12 receptor, IL12RB2, enables melanoma cells to shift the functional response via both IL-12-mediated and molecular crowding-based IL12RB2 homodimerization.
Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Authors: Venkatasubramanian Meenakshi , Chetal Kashish , Atluri Gowtham , Salomonis Nathan
Published: April 2019

The rapid proliferation of single-cell RNA-Sequencing (scRNA-Seq) technologies has spurred the development of diverse computational approaches to detect transcriptionally coherent populations. While the complexity of the algorithms for detecting heterogeneity have increased, most existing algorithms require significant user-tuning, are heavily reliant on dimensionality reduction techniques and are not scalable to ultra-large datasets. We previously described a multi-step algorithm, Iterative Clustering and Guide-gene selection (ICGS), which applies intra-gene correlation and hybrid clustering to uniquely resolve novel transcriptionally coherent cell populations from an intuitive graphical user interface. Here, we describe a new iteration of ICGS that outperforms state-of-the-art scRNA-Seq detection workflows when applied to well-established benchmarks. This approach combines multiple complementary subtype detection methods (HOPACH, sparse-NMF, cluster “fitness”, SVM) to resolve rare and common cell-states, while minimizing differences due to donor or batch effects. Using data from the Human Cell Atlas, we show that the PageRank algorithm effectively down samples ultra-large scRNA-Seq datasets, without losing extremely rare or transcriptionally similar distinct cell-types and while recovering novel transcriptionally unique cell populations. We believe this new approach holds tremendous promise in reproducibly resolving hidden cell populations in complex datasets.

Highlights

ICGS2 outperforms alternative approaches in small and ultra-large benchmark datasets

Integrates multiple solutions for cell-type detection with supervised refinement

Scales effectively to resolve rare cell-states from ultra-large datasets using PageRank sampling with a low memory footprint

Integrated into AltAnalyze to enable sophisticated and automated downstream analysis
Identification of novel key biomarkers in Simpson-Golabi-Behmel Syndrome: Evidence from bioinformatics analysis
Authors: Mustafa Mujahed I. , Abdelmoneim Abdelrahman H. , Elfadol Nafisa M. , Murshed Naseem S. , Mohammed Zainab O. , Hassan Mohamed A.
Published: April 2019

Background

The Simpson-Golabi-Behmel Syndrome (SGBS) or overgrowth Syndrome is a rare inherited X-linked condition characterized by pre- and postnatal overgrowth. The aim of the present study is to identify functional non-synonymous SNPs of GPC3 gene using various in silico approaches. These SNPs are supposed to have a direct effect on protein stability through conformation changes.

Material and methods

The SNPs were retrieved from the Single Nucleotide Polymorphism database (dbSNP) and further used to investigate a damaging effect using SIFT, PolyPhen, PROVEAN, SNAP2, SNPs&GO, PHD-SNP and P-mut, While we used I-mutant and MUPro to study the effect of SNPs on GPC3 protein structure. The 3D structure of human GPC3 protein is not available in the Protein Data Bank, so we used RaptorX to generate a 3D structural model for wild-type GPC3 to visualize the amino acids changes by UCSF Chimera. For biophysical validation we used project HOPE. Lastly we run conservational analysis by BioEdit and Consurf web server respectively.

Results

our results revealed three novel missense mutations (rs1460413167, rs1295603457 and rs757475450) that are found to be the most deleterious which effect on the GPC3 structure and function.

Conclusion

This present study could provide a novel insight into the molecular basis of overgrowth Syndrome.
Studying early embryogenesis in the flatwormMaritigrella crozieriindicates a unique modification of the spiral cleavage program in polyclad flatworms
Authors: Girstmair Johannes , Telford Maximilian J.
Published: April 2019

Background

Spiral cleavage is a conserved early developmental mode found in several phyla of Lophotrochozoans with highly diverse adult body plans. While the cleavage pattern has clearly been broadly conserved, it has also undergone many modifications in various taxa. The precise mechanisms of how different adaptations have altered the ancestral spiral cleavage pattern is an important ongoing evolutionary question and adequately answering this question requires obtaining a broad developmental knowledge of different spirally cleaving taxa.

In flatworms (Platyhelminthes), the spiral cleavage program has been lost or severely modified in most taxa. Polyclad flatworms, however, have retained the pattern up to the 32-cell stage. Here we study early embryogenesis of the cotylean polyclad flatwormMaritigrella crozierito investigate how closely this species follows the canonical spiral cleavage pattern and to discover any potential deviations from it.

Results

Using live imaging recordings and 3D reconstructions of embryos, we give a detailed picture of the events that occur during spiral cleavage inM. crozieri. We suggest, contrary to previous observations, that the 4-cell stage is a product of unequal cleavages. We show that that the formation of third and fourth micromere quartets are accompanied by strong blebbing events; blebbing also accompanies the formation of micromere 4d. We find an important deviation from the canonical pattern of cleavages with clear evidence that micromere 4d follows an atypical cleavage pattern, so far exclusively found in polyclad flatworms.

Conclusions

Our findings highlight that early development inM. crozierideviates in several important aspects from the canonical spiral cleavage pattern. We suggest that some of our observations extend to polyclad flatworms in general as they have been described in both suborders of the Polycladida, the Cotylea and Acotylea.
Activation of a Protein Kinase Via Asymmetric Allosteric Coupling of Structurally Conserved Signaling Modules
Authors: Hao Yuxin , England Jeneffer , Belluci Luca , Paci Emanuele , Hodges H. Courtney , Taylor Susan S. , Maillard Rodrigo A.
Published: April 2019

Abstract

Cyclic nucleotide binding (CNB) domains are universally conserved signaling modules that regulate the activities of diverse protein functions. Yet, the structural and dynamic features that enable the cyclic nucleotide binding signal to allosterically regulate other functional domains remain unknown. We use force spectroscopy and molecular dynamics to monitor in real time the pathways of signals transduced by cAMP binding in protein kinase A (PKA). Despite being structurally conserved, we find that the response of the folding energy landscape to cAMP is domain-specific, resulting in unique but mutually coordinated regulatory tasks: one CNB domain initiates cAMP binding and cooperativity, while the other triggers inter-domain interactions that lock the active conformation. Moreover, we identify a new cAMP-responsive switch, whose stability and conformation depends on cAMP occupancy. Through mutagenesis and nucleotide analogs we show that this dynamic switch serves as a signaling hub, a previously unidentified role that amplifies the cAMP binding signal during the allosteric activation of PKA.
Centromere clustering stabilizes meiotic homolog pairing
Authors: Hatkevich Talia , Boudreau Vincent , Rubin Thomas , Maddox Paul S. , Huynh Jean-René , Sekelsky Jeff
Published: April 2019

During meiosis, each chromosome must selectively pair and synapse with its own unique homolog to enable crossover formation and subsequent segregation. How homolog pairing is maintained in early meiosis to ensure synapsis occurs exclusively between homologs is unknown. We aimed to further understand this process by utilizing a uniqueDrosophilameiotic mutant,Mcm5A7. We found thatMcm5A7mutants are proficient in homolog pairing at meiotic onset yet fail to maintain pairing as meiotic synapsis ensues, causing seemingly-normal synapsis between non-homologous loci. This pairing defect corresponds with a reduction of SMC1-dependent centromere clustering at meiotic onset. Overexpressing SMC1 in this mutant significantly restores centromere clustering, homolog pairing, and crossover formation. These data indicate that the initial meiotic pairing of homologs is not sufficient to yield synapsis between exclusively between homologs and provide a model in which meiotic homolog pairing must be stabilized by SMC1-dependent centromere clustering to ensure proper synapsis.
The coordinate actions of calcineurin and Hog1 mediate the response to cellular stress through multiple nodes of the cell cycle network
Authors: Leech Cassandra M. , Flynn Mackenzie J. , Arsenault Heather E. , Ou Jianhong , Liu Haibo , Zhu Lihua Julie , Benanti Jennifer A.
Published: April 2019

Upon exposure to environmental stressors, cells transiently arrest the cell cycle while they adapt and restore homeostasis. A challenge for all cells is to distinguish between diverse stress signals and coordinate the appropriate adaptive response with cell cycle arrest. Here we investigate the role of the stress-activated phosphatase calcineurin (CN) in this process and show that CN utilizes multiple pathways to control the cell cycle. Upon activation, CN inhibits transcription factors (TFs) that regulate the G1/S transition through activation of the stress-activated MAPK Hog1. In contrast, CN inactivates G2/M TFs through a combination of Hog1-dependent and -independent mechanisms. These findings demonstrate that CN and Hog1 act in a coordinated manner at multiple nodes of the cell cycle-regulatory network to rewire gene expression and arrest cells in response to stress. Our results suggest that crosstalk between CN and stress-activated MAPKs helps cells tailor their adaptive responses to specific stressors.
Regardless of the deposition pathway, aminoacid 31 in histone variant H3 is essential at gastrulation in Xenopus
Authors: Sitbon David , Boyarchuk Ekaterina , Almouzni Geneviève
Published: April 2019

The closely related replicative H3 and non-replicative H3.3 variants show specific requirement during development in vertebrates. Whether it involves distinct mode of deposition or unique roles once incorporated into chromatin remains unclear. To disentangle the two aspects, we took advantage of the Xenopus early development combined with chromatin assays. Our previous work showed that in Xenopus, depletion of the non-replicative variant H3.3 impairs development at gastrulation, without compensation through provision of the replicative variant H3.2. We systematically mutated H3.3 at each four residues that differ from H3.2 and tested their ability to rescue developmental defects. Surprisingly, all H3.3 mutated variants functionally complemented endogenous H3.3, regardless of their incorporation pathways, except for one residue. This particular residue, the serine at position 31 in H3.3, gets phosphorylated onto chromatin in a cell cycle dependent manner. While the alanine substitution failed to rescue H3.3 depletion, a phosphomimic residue sufficed. We conclude that the time of gastrulation reveals a critical importance of the H3.3S31 residue independently of the variant incorporation pathway. We discuss how this single evolutionary conserved residue conveys a unique property for this variant in vertebrates during cell cycle and cell fate commitment.
Phosphatase PP2C6 negatively regulates phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato
Authors: Giska Fabian , Martin Gregory B.
Published: April 2019

Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRR) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level, and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a protein phosphatase, PP2C6. An in vitro pull-down assay and in vivo split luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233 and this phosphorylation was abolished in the presence of PP2C6. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to PP2C6 phosphatase activity, although it still interacted with PP2C6. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. Expression of PP2C6, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that PP2C6 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.
A study of psychological pain in substance use disorder and its relationship to treatment outcome
Authors: Mee Steven , Bunney Blynn G , Fujimoto Ken , Penner John , Seward Garrett , Bunney William E , Reist Christopher
Published: April 2019

Substance Use Disorder (SUD) is a major public health concern affecting an estimated 22.5 million individuals in the United States. The primary aim of this study was to characterize psychological pain in a cohort of patients participating in outpatient substance abuse treatment. A secondary aim was to determine the relationships between pre-treatment assessments of psychological pain, depression, anxiety and hopelessness with treatment retention time and completion rates. Data was analyzed from 289 patients enrolled in an outpatient community drug treatment clinic that provides mental healthcare to the underserved. A previously determined threshold score on the Mee-Bunney Psychological Pain Assessment Scale (MBP) was utilized to group patients into high and low-moderate scoring subgroups. The higher pain group reported increased levels of anxiety, hopelessness and depression compared to those in the low-moderate pain group. Additionally, patients scoring in the higher psychological pain group exhibited reduced retention times in treatment and more than two-fold increased odds of dropout relative to patients with lower pre-treatment levels of psychological pain. Among all assessments, the correlation between psychological pain and treatment retention time was strongest. To our knowledge, this is the first study to demonstrate that psychological pain is an important construct that correlates with relevant clinical outcomes in substance abuse treatment. Further, pre-treatment screening for psychological pain may be of benefit in identifying higher-risk patients in need of targeted additional clinical resources to improve treatment retention and completion rates.
Identification of flowering-time genes in mast flowering plants usingde novotranscriptomic analysis
Authors: Samarth  , Lee Robyn , Song Jason , Macknight Richard , Jameson Paula E.
Published: April 2019

Mast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. In this study, a high-throughput large-scale RNA-sequencing was performed on two masting plant species,Celmisia lyallii(Asteraceae), andChionochloa pallens(Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively forCelmisiaandChionochloa. The two datasets generated were blasted against the publicly available databases, TAIR, Swiss-Prot, non-redundant protein (nr), KEGG and COG for unigene annotations. On average, 56% of the unigenes were finally annotated with gene descriptions mapped to known protein sequences for both the species. Gene ontology analysis was then performed on the assembled reference transcriptomes, categorising the transcripts on the basis of putative biological processes, molecular function, and cellular localisation. A total of 543 transcripts fromCelmisiaand 470 transcripts fromChionochloawere also mapped to unique flowering-time proteins identified in Arabidopsis, suggesting the conservation of the flowering network in these wild alpine plants, growing in natural field conditions. These genes can further be analysed to understand the molecular regulation of the reproductive phase transition in the masting plants.
Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA
Authors: Wepprich Tyson , Adrion Jeffrey R. , Ries Leslie , Wiedmann Jerome , Haddad Nick M.
Published: April 2019

Severe insect declines make headlines, but they are rarely based on systematic monitoring outside of Europe. We estimate the rate of change in total butterfly abundance and the population trends for 81 species using 21 years of systematic monitoring in Ohio, USA. Total abundance is declining at 2% per year, resulting in a cumulative 33% reduction in butterfly abundance. Three times as many species have negative population trends compared to positive trends. The rate of total decline and the proportion of species in decline mirror those documented in three comparable long-term European monitoring programs. Multiple environmental changes such as climate change, habitat degradation, and agricultural practices may contribute to these declines in Ohio and shift the makeup of the butterfly community by benefiting some species over others. Our analysis of life-history traits associated with population trends shows an impact of climate change, as species with northern distributions and fewer annual generations declined more rapidly. However, even common and invasive species associated with human-dominated landscapes are declining, suggesting widespread environmental causes for these trends. Declines in common species, although they may not be close to extinction, will have an outsized impact on the ecosystem services provided by insects. These results from the most extensive, systematic insect monitoring program in North America demonstrate an ongoing defaunation in butterflies that on an annual scale might be imperceptible, but cumulatively has reduced butterfly numbers by a third over 20 years.