bluuebunny/crossref_metadata_2025_split huggingface dataset:
Absence of Intragraft B Cells in Rejection Biopsies After Rituximab Induction Therapy: Consequences for Clinical Outcome
Authors: van den Hoogen Martijn W.F. , Steenbergen Eric J. , Baas Marije C. , Florquin Sandrine , Hilbrands Luuk B. 
Published: March 2017

Background
The pathophysiological role of intragraft B cells during renal allograft rejection is unclear.

Methods
We studied B-cell infiltration during acute rejection in 53 patients who participated in a clinical trial in which adult renal transplant patients were randomized between a single intraoperative dose of rituximab (375 mg/m2) or placebo as induction therapy. Two independent pathologists scored all biopsies in a blinded fashion according to the Banff classification and scored for the presence of B cells and plasma cells using CD79a and CD138 as markers.

Results
The majority of acute rejections were T cell–mediated. The proportion of acute rejections with an antibody-mediated component tended to be lower in rituximab-treated patients (4/23, 17.4%) than in placebo-treated patients (11/30, 36.7%; P = 0.14). Biopsies of rituximab-treated patients had significantly lower scores for B cells (0.00; range, 0.00-0.50 vs 1.70; range, 0.60-3.30; P < 0.0001) and plasma cells (0.10; range, 0.00-1.90 vs 0.40; range, 0.00-7.50; P = 0.006). During acute rejection, intragraft clusters of B cells were not observed after rituximab induction therapy. However, the depletion of intragraft B cells during acute rejection did not affect steroid resistance, proteinuria, graft function at 2 years follow-up, or patient and graft survival at a median follow-up of 4.1 years (range, 2.0-6.2 years).

Conclusions
These data do not support a harmful influence of intragraft B cells present during acute allograft rejection on the clinical course within the first few years after renal transplantation.
Decoys reveal the genetic and biochemical roles of redundant plant E3 ubiquitin ligases
Authors: Lee Chin-Mei , Feke Ann , Adamchek Christopher , Webb Kristofor , Pruneda-Paz José , Bennett Eric J. , Kay Steve A. , Gendron Joshua M. 
Published: March 2017

AbstractThe ubiquitin proteasome system (UPS) is the main cellular route for protein degradation in plants and is important for a wide range of biological processes including daily and seasonal timing. The UPS relies on the action of E3 ubiquitin ligases to specifically recognize substrate proteins and facilitate their ubiquitylation. In plants, there are three major challenges that inhibit studies of E3 ligase function: 1) rampant genetic redundancy, 2) labile interactions between an E3 ligase and its cognate substrates, and 3) a lack of tools for rapid validation of bona fide substrates. To overcome these 3 challenges, we have developed a decoy method that allows for rapid genetic analysis of E3 ligases,in vivoidentification of substrates using immunoprecipitation followed by mass spectrometry, and reconstitution of the ubiquitylation reaction in mammalian cells to rapidly validate potential substrates. We employ the strategy to study the plant F-box proteins, ZTL, LKP2, and FKF1 revealing differential genetic impacts on circadian clock period and seasonal flowering. We identify a group of circadian clock transcriptional regulators that interact with ZTL, LKP2, and FKF1in vivoproviding a host of potential substrates that have not been seen previously. We then validate one substrate of ZTL, the plant circadian clock transcription factor CHE, and show that ZTL mediates CHE ubiquitylation and that the levels of the CHE protein cycle in daily timecourses. This work further untangles the complicated genetic roles of this family of E3 ligases and suggests that ZTL is a master regulator of a diverse set of critical clock transcription factors. Furthermore, the method that is validated here can be tool employed widely to overcome traditional challenges in studying redundant plant E3 ubiquitin ligases.
Compensating for intersegmental dynamics across the shoulder, elbow and wrist joints during feedforward and feedback control
Authors: Maeda Rodrigo S. , Cluff Tyler , Gribble Paul L. , Pruszynski J. Andrew 
Published: March 2017

ABSTRACTMoving the arm is complicated by mechanical interactions that arise between limb segments. Such intersegmental dynamics cause torques applied at one joint to produce movement at multiple joints and, in turn, the only way to create single joint movement is by applying torques at multiple joints. Here, we investigated whether the nervous system accounts for intersegmental limb dynamics across the shoulder, elbow, and wrist joints during self-initiated reaching and when countering external mechanical perturbations. Our first experiment tested whether the timing and amplitude of shoulder muscle activity accounts for interaction torques produced during single-joint elbow movements from different elbow initial orientations and over a range of movement speeds. We found that shoulder muscle activity reliably preceded movement onset and elbow agonist activity, and was scaled to compensate for the magnitude of interaction torques arising because of forearm rotation. Our second experiment tested whether elbow muscles compensate for interaction torques introduced by single-joint wrist movements. We found that elbow muscle activity preceded movement onset and wrist agonist muscle activity, and thus the nervous system predicted interaction torques arising because of hand rotation. Our third and fourth experiments tested whether shoulder muscles compensate for interaction torques introduced by different hand orientations during self-initiated elbow movements and when countering mechanical perturbations that caused pure elbow motion. We found that the nervous system predicted the amplitude and direction of interaction torques, appropriately scaling the amplitude of shoulder muscle activity during self-initiated elbow movements and rapid feedback control. Taken together, our results demonstrate that the nervous system robustly accounts for intersegmental dynamics, and that the process is similar across the proximal to distal musculature of the arm as well as between feedforward (i.e., self-initiated) and feedback (i.e., reflexive) control.NEW & NOTEWORTHYIntersegmental dynamics complicate the mapping between applied joint torques and the resulting joint motions. Here, we provide evidence that the nervous system robustly predicts these intersegmental limb dynamics across the shoulder, elbow and wrist joints during reaching and when countering external perturbations.
High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Authors: Wang Wanxin , Penland Lolita , Gokce Ozgun , Croote Derek , Quake Stephen 
Published: March 2017

AbstractBackgroundHigh-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method will greatly expand the scope of feasible collaborations and maximize the utilization of technical expertise. When choosing a method, standardizability is as important a factor to consider as fidelity due to the susceptibility of single-cell RNAseq analysis to technical noises. Existing approaches such as cryopreservation and chemical fixation are less than ideal for failing to satisfy either or both of these standards.ResultsHere we propose a new strategy that leverages preservation schemes developed for organ transplantation. We evaluated the strategy by storing intact mouse kidneys in organ transplant preservative solution at hypothermic temperature for up to 4 days (6 hrs, 1, 2, 3, and 4 days), and comparing the quality of preserved and fresh samples using FACS and single cell RNAseq. We demonstrate that the strategy effectively maintained cell viability, transcriptome integrity, cell population heterogeneity, and transcriptome landscape stability for samples after up to 3 days of preservation. The strategy also facilitated the definition of the diverse spectrum of kidney resident immune cells, to our knowledge the first time at single cell resolution.ConclusionsHypothermic storage of intact primary tissues in organ transplant preservative maintains the quality and stability of the transcriptome of cells for single cell RNAseq analysis. The strategy is readily generalizable to primary specimens from other tissue types for single cell RNAseq analysis.
The Co-regulation Data Harvester forTetrahymena thermophila: automated high-throughput gene annotation and functional inference in a microbial eukaryote
Authors: Tsypin Lev M. , Turkewitz Aaron P. 
Published: March 2017

AbstractIdentifying co-regulated genes can provide a useful approach for defining pathway-specific machinery in an organism. To be efficient, this approach relies on thorough genome annotation, which is not available for most organisms with sequenced genomes. Studies inTetrahymena thermophila,the most experimentally accessible ciliate, have generated a rich transcriptomic database covering many well-defined physiological states. Genes that are involved in the same pathway show significant co-regulation, and screens based on gene co-regulation have identified novel factors in specific pathways, for example in membrane trafficking. However, a limitation has been the relatively sparse annotation of theTetrahymenagenome, making it impractical to approach genome-wide analyses. We have therefore developed an efficient approach to analyze both co-regulation and gene annotation, called the Co-regulation Data Harvester (CDH). The CDH automates identification of co-regulated genes by accessing theTetrahymenatranscriptome database, determines their orthologs in other organisms via reciprocal BLAST searches, and collates the annotations of those orthologs' functions. Inferences drawn from the CDH reproduce and expand upon experimental findings inTetrahymena.The CDH, which is freely available, represents a powerful new tool for analyzing cell biological pathways inTetrahymena.Moreover, to the extent that genes and pathways are conserved between organisms, the inferences obtained via the CDH should be relevant, and can be explored, in many other systems.
Temporal and Clonal Progression in a Pediatric Ependymoma Patient Through Multiple Treatments
Authors: Miller Christopher A. , Dahiya Sonika , Li Tiandao , Fulton Robert S. , Smyth Matthew D. , Dunn Gavin P. , Rubin Joshua B. , Mardis Elaine R. 
Published: March 2017

AbstractBackgroundMultiple recurrences after complete resection and irradiation of supratentorial ependymoma are common and frequently result in patient death. However, the molecular basis for treatment resistance, the impact that radiation and other adjuvant therapies have in promoting recurrence, and the use of this information to rationally design effective approaches to treat recurrent ependymoma are unknown. Due to the rarity of these tumors and the even less likely banking of multiple recurrent samples from the same patient, we initiated a study to characterize the evolution of a single patient’s ependymoma in response to therapy.Methods and FindingsA combination of high depth, whole genome and exome-based DNA sequencing of germline and tumor specimens, RNA sequencing of tumor specimens, and advanced computational analyses were employed to reconstruct the natural history of a supratentorial ependymoma case in which there were four local recurrences. The findings reveal the extent to which treatment with radiation and chemotherapies resulted in the diversification of the tumor subclonal architecture and shaped the neo-antigen landscape, and provide new insights into possible molecular mechanisms of oncogenesis, treatment response and recurrence.ConclusionsAlthough the recurrent tumors we studied were clearly shaped by therapy, the founding clone was never eradicated by any treatment. We conclude that DNA and RNA sequencing may provide critical prognostic indicators to identify ependymoma patients that should be observed, rather than irradiated, post gross total resection.
Evolution of age-specific decline in stress phenotypes is driven by both antagonistic pleiotropy and mutation accumulation
Authors: Everman Elizabeth R. , Morgan Theodore J. 
Published: March 2017

AbstractEfforts to more fully understand and test evolutionary theories of aging have produced distinct predictions for mutation accumulation (MA) and antagonistic pleiotropy (AP) mechanisms. We build on these predictions through the use of association mapping and investigation of the change in additive effects of polymorphisms across age and among traits for multiple stress response phenotypes. We found that cold stress survival with acclimation, cold stress survival without acclimation, and starvation resistance declined with age and that changes in the genetic architecture of each phenotype were consistent with MA predictions. We used a novel test for MA and AP by calculating the additive effect of polymorphisms across ages and found support for both MA and AP mechanisms in the age-related decline in stress tolerance. These patterns suggest both MA and AP contribute to age-related change in stress response and highlight the utility of association mapping to identify genetic shifts across age.
Combining theory, model and experiment to understand how theta rhythms are generated in the hippocampus
Authors: Ferguson Katie A. , Chatzikalymniou Alexandra P. , Skinner Frances K. 
Published: March 2017

AbstractScientists have observed theta rhythms (3–12 Hz) in the hippocampus for decades, but we do not have a clear understanding of how they are generated. This is largely due to the complex, multi-scale and nonlinear nature of the brain. To obtain insight into mechanisms underlying the generation of theta rhythms, we develop cellular-based network models of the hippocampus based on a whole hippocampusin vitropreparation that spontaneously generates theta rhythms. Building on theoretical and computational analyses, we find that spike frequency adaptation and post-inhibitory rebound constitute a basis for theta generation in large, minimally connected CA1 pyramidal (PYR) cell network models with fast-firing parvalbumin-positive (PV+) inhibitory cells. The particular theta frequency is more controlled by PYR to PV+ cell interactions rather than PV+ to PYR cell ones. We identify two scenarios by which theta rhythms can emerge and they can be differentiated by the ratio of excitatory to inhibitory currents to PV+ cells, but not to PYR cells. Only one of the scenarios is consistent with data from the whole hippocampus preparation, which leads to the prediction that the connection probability from PV+ to PYR cells needs to be larger than from PYR to PV+ cells. Our models can serve as a platform on which to build and develop an understanding ofin vivotheta generation, and of microcircuit dynamics in the hippocampus.SignificanceBrain rhythms have been linked to cognition and are disrupted in disease. This makes it essential to understand mechanisms underlying their generation. Theory and mathematical models help provide an understanding and generate hypotheses. Together with experiment they contribute a framework to dissect the cellular contributions to network activity. However, models are inherently biological approximations, and thus the specific experimental and theoretical context upon which they are built will shape their output. If the approximations and contexts are not taken into account, particularly when using previously constructed models, misinterpretations can arise. Here, we use both theory and microcircuit models derived from a specific experimental context to provide insight into cellular-based mechanisms involved in theta rhythm generation in the hippocampus.
Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan
Authors: Li Bin , Zhang Xiao-Qin , Liu Shu-Rong , Liu Shun , Sun Wen-Ju , Lin Qiao , Luo Yu-Xia , Zhou Ke-Ren , Zhang Chen-Min , Tan Ye-Ya , Yang Jian-Hua , Qu Liang-Hu 
Published: March 2017

AbstractAlthough tens of thousands of circular RNAs (circRNAs) have been identified in mammalian genomes, only few of them have been characterized with biological functions. Here, we report a new approach, circScan, to identify regulatory interactions between circRNAs and RNA-binding proteins (RBPs) by discovering back-splicing reads from Cross-Linking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq) data. By using our method, we have systematically scanned ~1500 CLIP-seq datasets, and identified ~12540 and ~1090 novel circRNA-RBP interactions in human and mouse genomes, respectively, which include all known interactions between circRNAs and Argonaute (AGO) proteins. More than twenty novel interactions were further experimentally confirmed by RNA Immunoprecipitation quantitative PCR (RIP-qPCR). Importantly, we uncovered that some natural circRNAs interacted with cap-independent translation factors eukaryotic initiation factor 3 (eIF3) and N6-Methyladenosine (m6A), indicating they can be translated into proteins. These findings demonstrate that circRNAs are regulated by various RBPs, suggesting they may play important roles in diverse biological processes.
Common Variant Associations with Fragile X Syndrome
Authors: Crowley James J , Szatkiewicz Jin , Kähler Anna K , Giusti-Rodriguez Paola , Ancalade NaEshia , Booker Jessica K , Carr Jennifer L , Crawford Greg E , Losh Molly , Stockmeier Craig A , Taylor Annette K , Piven Joseph , Sullivan Patrick F 
Published: March 2017

AbstractFragile X syndrome is a common cause of intellectual disability. It is usually caused by a de novo mutation which often occur on multiple haplotypes and should not be detectible using genome-wide association (GWA). We conducted GWA 89 male FXS cases and 266 male controls, and detected multiple genome-wide significant signals near FMR1 (odds ratio=8.10, P=2.5×10−10). These findings withstood robust attempts at falsification. Fine-mapping did not serve to narrow the interval (minimum P=1.13×l0−14), and functional genomic integration (including 5C data we generated for this region) did not provide a mechanistic hypothesis. Controls carrying a risk haplotype had significantly longer and more variable FMR1 CGG repeats than controls with the protective haplotype (P=4.75×10−5) which may predispose toward increases in CGG number to the pre-mutation range over many generations. This is a salutary reminder of the complexity of even “simple” monogenetic disorders.
Preponderance of Enterovirus Species C in RD-L20B cell culture negative stool samples from children diagnosed with Acute Flaccid Paralysis in Nigeria
Authors: Adeniji J.A. , Oragwa A.O. , George U.E. , Ibok U.I. , Faleye T.O.C. , Adewumi M.O. 
Published: March 2017

AbstractsRecently, a reverse transcriptase seminested polymerase chain reaction (RT-snPCR) assay was recommended by the WHO for direct detection of enteroviruses from clinical specimen. In this study, we use the assay and its modification to screen acute flaccid paralysis (AFP) samples previously confirmed negative for enteroviruses by the RD-L20B algorithm.Thirty paired stool suspensions collected in 2015 as part of the national AFP surveillance program in different states of Nigeria were analyzed in this study. The samples were previously confirmed negative for enteroviruses by the polio laboratory in accordance with the WHO recommended RD-L20B cell culture based algorithm. Two samples previously confirmed to contain enteroviruses were included as positive controls. All samples were subjected to RNA extraction, and the RT-snPCR assay and its modifications. All amplicons were sequenced and enteroviruses identified using the enterovirus genotyping tool.Overall, amplicons were recovered from the two controls and 50% (15/30) of samples screened. Fourteen were successfully typed of which, 7.1% (1/14), 21.4% (3/14), 64.3% (9/14) and 7.1% (1/14) were EV-A, EV-B, EV-C and a mixture of EV-B and C (EV-C99 and E25), respectively. The two controls were identified as EV-C99 and CV-A1, both EV-Cs. The PV-2 detected had VP1 ILE143. Hence, a vaccine strain.The results of this study showed that about 50% of enterovirus infections (including some Sabin PV2s) are being missed by the RD-L20B cell culture based algorithm. This highlights the value of the RT-snPCR assay and its modifications. The circulation and preponderance of EV-Cs in Nigeria was also confirmed.
Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P
Authors: Krafczyk Ralph , Macošek Jakub , Gast Daniel , Wunder Swetlana , Jagtap Pravin Kumar Ankush , Mitra Prithiba , Jha Amit Kumar , Rohr Jürgen , Hoffmann-Röeder Anja , Jung Kirsten , Hennig Janosch , Lassak Jürgen 
Published: March 2017

ABSTRACTGlycosylation is a universal strategy to post-translationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the glycosyltransferase EarP. However, the enzymatic mechanism remains elusive. In the present study, we solved the crystal structure of EarP fromPseudomonas putida.The enzyme is composed of two opposing domains with Rossmann-folds, thus constituting a GT-B glycosyltransferase. While TDP-rhamnose is located within a highly conserved pocket of the C-domain, EarP recognizes the EF-P via its KOW-like N-domain. Based on our structural data combined with anin vitro /in vivoenzyme characterization, we propose a mechanism of inverting arginine glycosylation. As EarP is essential for pathogenicity inP. aeruginosaour study provides the basis for targeted inhibitor design.
Classification of RNA-Seq Data via Gaussian Copulas
Authors: Zhang Qingyang 
Published: March 2017

AbstractRNA-sequencing (RNA-Seq) has become a preferred option to quantify gene expression, because it is more accurate and reliable than microarrays. In RNA-Seq experiments, the expression level of a gene is measured by the count of short reads that are mapped to the gene region. Although some normal-based statistical methods may also be applied to log-transformed read counts, they are not ideal for directly modeling RNA-Seq data. Two discrete distributions, Poisson distribution and negative binomial distribution, have been commonly used in the literature to model RNA-Seq data, where the latter is a natural extension of the former with allowance of overdispersion. Due to the technical difficulty in modeling correlated counts, most existing classifiers based on discrete distributions assume that genes are independent of each other. However, as we show in this paper, the independence assumption may cause non-ignorable bias in estimating the discriminant score, making the classification inaccurate. To this end, we drop the independence assumption and explicitly model the dependence between genes using Gaussian copula. We apply a Bayesian approach to estimate covariance matrix and the overdispersion parameter in negative binomial distribution. Both synthetic data and real data are used to demonstrate the advantages of our model.