bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sentiment Analysis of Web Sites Related to Vaginal Mesh Use in Pelvic Reconstructive Surgery
Authors: Hobson Deslyn T.G. , Meriwether Kate V. , Francis Sean L. , Kinman Casey L. , Stewart J. Ryan 
Published: April 2018

Objectives
The purpose of this study was to utilize sentiment analysis to describe online opinions toward vaginal mesh. We hypothesized that sentiment in legal Web sites would be more negative than that in medical and reference Web sites.

Methods
We generated a list of relevant key words related to vaginal mesh and searched Web sites using the Google search engine. Each unique uniform resource locator (URL) was sorted into 1 of 6 categories: “medical”, “legal”, “news/media”, “patient generated”, “reference”, or “unrelated”. Sentiment of relevant Web sites, the primary outcome, was scored on a scale of −1 to +1, and mean sentiment was compared across all categories using 1-way analysis of variance. Tukey test evaluated differences between category pairs.

Result
Google searches of 464 unique key words resulted in 11,405 URLs. Sentiment analysis was performed on 8029 relevant URLs (3472 legal, 1625 “medical”, 1774 “reference”, 666 “news media”, 492 “patient generated”). The mean sentiment for all relevant Web sites was +0.01 ± 0.16; analysis of variance revealed significant differences between categories (P < 0.001). Web sites categorized as “legal” and “news/media” had a slightly negative mean sentiment, whereas those categorized as “medical,” “reference,” and “patient generated” had slightly positive mean sentiments. Tukey test showed differences between all category pairs except the “medical” versus “reference” in comparison with the largest mean difference (−0.13) seen in the “legal” versus “reference” comparison.

Conclusions
Web sites related to vaginal mesh have an overall mean neutral sentiment, and Web sites categorized as “medical,” “reference,” and “patient generated” have significantly higher sentiment scores than related Web sites in “legal” and “news/media” categories.
Measured Glomerular Filtration Rate After Kidney Donation: No Evidence of Accelerated Decay
Authors: Berglund Danielle M. , Zhang Lei , Matas Arthur J. , Ibrahim Hassan N. 
Published: April 2018

Background
The rate of measured glomerular filtration rate (GFR) change in kidney donor years after donation has not been adequately addressed. Whether this change is accelerated in the setting of 1 kidney is also understudied.

Methods
Two hundred fourteen randomly selected donors underwent serial GFR measurements of nonradioactive iohexol. Estimated GFR at each visit was calculated using the Chronic Kidney Disease Epidemiology Collaboration and Modification of Diet in Renal Disease study equations.

Results
Glomerular filtration rate visits were 4.8 ± 1.3 years apart and the second occurring 16.9 ± 9.1 years after donation. Most (97.7%) were white, 60.8% female, and 78.5% were related to their recipient. Most, 84.6%, had a GFR of 60 mL/min per 1.73 m2 or higher, 14.0% had a GFR between 45 and 60 mL/min per 1.73 m2, and 1.4% had a GFR less than 45 mL/min per 1.73 m2. Between visits 1 and 2, 56.5% had a GFR decline, 36.0% increase, and in 7.5%, there was no change. Overall, GFR declined at a rate of −0.42 mL/min per 1.73 m2 per year. Of GFR estimating models, only Chronic Kidney Disease Epidemiology Collaboration-Creatinine equation produced a slope that was steeper than measured GFR.

Conclusions
Nearly 2 decades postdonation GFR declined at a rate similar to that seen in the general population, and in one third, GFR continues to increase.
How Should Social Media Be Used in Transplantation? A Survey of the American Society of Transplant Surgeons
Authors: Henderson Macey L. , Adler Joel T. , Van Pilsum Rasmussen Sarah E. , Thomas Alvin G. , Herron Patrick D. , Waldram Madeleine M. , Ruck Jessica M. , Purnell Tanjala S. , DiBrito Sandra R. , Holscher Courtenay M. , Haugen Christine E. , Alimi Yewande , Konel Jonathan M. , Eno Ann K. , Garonzik Wang Jacqueline M. , Gordon Elisa J. , Lentine Krista L. , Schaffer Randolph L. , Cameron Andrew M. , Segev Dorry L. 
Published: April 2018

Background.
Social media platforms are increasingly used in surgery and have shown promise as effective tools to promote deceased donation and expand living donor transplantation. There is a growing need to understand how social media-driven communication is perceived by providers in the field of transplantation.

Methods.
We surveyed 299 members of the American Society of Transplant Surgeons about their use of, attitudes toward, and perceptions of social media and analyzed relationships between responses and participant characteristics.

Results.
Respondents used social media to communicate with: family and friends (76%), surgeons (59%), transplant professionals (57%), transplant recipients (21%), living donors (16%), and waitlisted candidates (15%). Most respondents (83%) reported using social media for at least 1 purpose. Although most (61%) supported sharing information with transplant recipients via social media, 42% believed it should not be used to facilitate living donor-recipient matching. Younger age (P = 0.02) and fewer years of experience in the field of transplantation (P = 0.03) were associated with stronger belief that social media can be influential in living organ donation. Respondents at transplant centers with higher reported use of social media had more favorable views about sharing information with transplant recipients (P < 0.01), increasing awareness about deceased organ donation (P < 0.01), and advertising for transplant centers (P < 0.01). Individual characteristics influence opinions about the role and clinical usefulness of social media.

Conclusions.
Transplant center involvement and support for social media may influence clinician perceptions and practices. Increasing use of social media among transplant professionals may provide an opportunity to deliver high-quality information to patients.
Biomarkers to Assess Right Heart Pressures in Recipients of a Heart Transplant: A Proof-of-Concept Study
Authors: Huang Qi-Fang , Trenson Sander , Zhang Zhen-Yu , Van Keer Jan , Van Aelst Lucas N.L. , Yang Wen-Yi , Nkuipou-Kenfack Esther , Thijs Lutgarde , Wei Fang-Fei , Mujaj Blerim , Ciarka Agnieszka , Droogné Walter , Vanhaecke Johan , Janssens Stefan , Van Cleemput Johan , Mischak Harald , Staessen Jan A. 
Published: April 2018

Background
This proof-of-concept study investigated the feasibility of using biomarkers to monitor right heart pressures (RHP) in heart transplanted (HTx) patients.

Methods
In 298 patients, we measured 7.6 years post-HTx mean pressures in the right atrium (mRAP) and pulmonary artery (mPAP) and capillaries (mPCWP) along with plasma high-sensitivity troponin T (hsTnT), a marker of cardiomyocyte injury, and the multidimensional urinary classifiers HF1 and HF2, mainly consisting of dysregulated collagen fragments.

Results
In multivariable models, mRAP and mPAP increased with hsTnT (per 1-SD, +0.91 and +1.26 mm Hg; P < 0.0001) and with HF2 (+0.42 and +0.62 mm Hg; P ≤ 0.035), but not with HF1. mPCWP increased with hsTnT (+1.16 mm Hg; P < 0.0001), but not with HF1 or HF2. The adjusted odds ratios for having elevated RHP (mRAP, mPAP or mPCWP ≥10, ≥24, ≥17 mm Hg, respectively) were 1.99 for hsTnT and 1.56 for HF2 (P ≤ 0.005). In detecting elevated RHPs, areas under the curve were similar for hsTnT and HF2 (0.63 vs 0.65; P = 0.66). Adding hsTnT continuous or per threshold or HF2 continuous to a basic model including all covariables did not increase diagnostic accuracy (P ≥ 0.11), whereas adding HF2 per optimized threshold increased both the integrated discrimination (+1.92%; P = 0.023) and net reclassification (+30.3%; P = 0.010) improvement.

Conclusions
Correlating RHPs with noninvasive biomarkers in HTx patients is feasible. However, further refinement and validation of such biomarkers is required before their clinical application can be considered.
Interact: Automated analysis of protein-ligand interactions by 1D and 2D NMR
Authors: Millard Pierre , Lippens Guy 
Published: April 2018

AbstractNMR titration experiments contain rich information on the thermodynamic, kinetic and structural aspects of protein-ligand interactions. Automated tools are required to process the large number of signals typically acquired in these experiments and facilitate quantitative interpretations. We present Interact, a Python script accessible within the Bruker BioSpin TopSpin™ software, which allows automated analysis of both 1D and 2D NMR titration experiments. Interact performs peak picking and annotation of the successive spectra and supports quantitative interpretation of changes in chemical shifts and linewidths induced by the ligand (e.g. to estimate dissociation constants) through different fitting procedures. Interact can be applied to all types of 1D and 2D NMR experiments and all nuclei, hence facilitating routine analysis of existing and forthcoming NMR titration data. Interact was implemented in Python and can be used on Windows, Unix and MacOS platforms. The source code is distributed under OpenSource license at http://github.com/MetaSys-LISBP/Interact.
Cluster Tendency Assessment in Neuronal Spike Data
Authors: Mahallati Sara , Bezdek James C. , Popovic Milos R. , Valiante Taufik A. 
Published: April 2018

AbstractSorting spikes from extracellular recording into clusters associated with distinct single units (putative neurons) is a fundamental step in analyzing neuronal populations. Such spike sorting is intrinsically unsupervised, as the number of neurons are not known a priori. Therefor, any spike sorting is an unsupervised learning problem that requires either of the two approaches: specification of a fixed value c for the number of clusters to seek, or generation of candidate partitions for several possible values of c, followed by selection of a best candidate based on various post-clustering validation criteria. In this paper, we investigate the first approach and evaluate the utility of several methods for providing lower dimensional visualization of the cluster structure and on subsequent spike clustering. We also introduce a visualization technique called improved visual assessment of cluster tendency (iVAT) to estimate possible cluster structures in data without the need for dimensionality reduction. Experimental results are conducted on two datasets with ground truth labels. In data with a relatively small number of clusters, iVAT is beneficial in estimating the number of clusters to inform the initialization of clustering algorithms. With larger numbers of clusters, iVAT gives a useful estimate of the coarse cluster structure but sometimes fails to indicate the presumptive number of clusters. We show that noise associated with recording extracellular neuronal potentials can disrupt computational clustering schemes, highlighting the benefit of probabilistic clustering models. Our results show that t-Distributed Stochastic Neighbor Embedding (t-SNE) provides representations of the data that yield more accurate visualization of potential cluster structure to inform the clustering stage. Moreover, The clusters obtained using t-SNE features were more reliable than the clusters obtained using the other methods, which indicates that t-SNE can potentially be used for both visualization and to extract features to be used by any clustering algorithm.
Accurate Nonlinear Mapping between MNI Volumetric and FreeSurfer Surface Coordinate Systems
Authors: Wu Jianxiao , Ngo Gia H. , Greve Douglas , Li Jingwei , He Tong , Fischl Bruce , Eickhoff Simon B. , Yeo B.T. Thomas 
Published: April 2018

AbstractThe results of most neuroimaging studies are reported in volumetric (e.g., MNI152) or surface (e.g., fsaverage) coordinate systems. Accurate mappings between volumetric and surface coordinate systems can facilitate many applications, such as projecting fMRI group analyses from MNI152/Colin27 to fsaverage for visualization, or projecting resting-state fMRI parcellations from fsaverage to MNI152/Colin27 for volumetric analysis of new data. However, there has been surprisingly little research on this topic. Here, we evaluated three approaches for mapping data between MNI152/Colin27 and fsaverage coordinate systems by simulating the above applications: projection of group-average data from MNI152/Colin27 to fsaverage and projection of fsaverage parcellations to MNI152/Colin27. Two of the approaches are currently widely used. A third approach (registration fusion) was previously proposed, but not widely adopted. Two implementations of the registration fusion (RF) approach were considered, with one implementation utilizing the Advanced Normalization Tools (ANTs). We found that RF-ANTs performed the best for mapping between fsaverage and MNI152/Colin27, even for new subjects registered to MNI152/Colin27 using a different software tool (FSL FNIRT). This suggests that RF-ANTs would be useful even for researchers not using ANTs. Finally, it is worth emphasizing that the most optimal approach for mapping data to a coordinate system (e.g., fsaverage) is to register individual subjects directly to the coordinate system, rather than via another coordinate system. Only in scenarios where the optimal approach is not possible (e.g., mapping previously published results from MNI152 to fsaverage), should the approaches evaluated in this manuscript be considered. In these scenarios, we recommend RF-ANTs (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion).
ALS-linked SOD1 Mutants Enhance Outgrowth, Branching, and the Formation of Actin-Based Structures in Adult Motor Neurons
Authors: Osking Zachary , Ayers Jacob I. , Hildebrandt Ryan , Skruber Kristen , Brown Hilda , Ryu Daniel , Eukovich Amanda R. , Golde Todd E. , Borchelt David R. , Read Tracy-Ann , Vitriol Eric A. 
Published: April 2018

ABSTRACTAmyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disease characterized by motor neuron cell death. However, not all motor neurons are equally susceptible. Most of what we know about the surviving motor neurons comes from gene expression profiling, less is known about their functional traits. We found that resistant motor neurons cultured from SOD1 ALS mouse models have enhanced axonal outgrowth and dendritic branching. They also have an increase in the number and size of actin-based structures like growth cones and filopodia. These phenotypes occur in cells cultured from presymptomatic mice and mutant SOD1 models that do not develop ALS, but not in embryonic motor neurons. Enhanced outgrowth and upregulation of filopodia can be induced in wild-type adult cells by expressing mutant SOD1. These results demonstrate that mutant SOD1 can enhance the regenerative capability of ALS resistant motor neurons. Capitalizing on this mechanism could lead to new therapeutic strategies.
Natural ITD statistics predict human auditory spatial perception
Authors: Pavão Rodrigo , Sussman Elyse S. , Fischer Brian J. , Peña José L. 
Published: April 2018

A neural code adapted to the statistical structure of sensory cues may optimize perception. We investigated whether interaural time difference (ITD) statistics inherent in natural acoustic scenes are parameters determining spatial discriminability. The natural ITD rate of change across azimuth (ITDrc) and ITD variability over time (ITDv) were combined in a Fisher information statistic for assessing the amount of azimuthal information conveyed by this sensory cue. We hypothesized that natural ITD statistics drive the neural code for ITD and thus influence spatial perception. Human spatial discriminability and spatial novelty detection of sounds with invariant statistics correlated with natural ITD statistics. The lack of natural statistics in the stimuli suggests that this correlation results from natural statistics driving the neural code. Additionally, the density distribution of ITD tuning matching natural statistics is consistent with classic models of ITD coding and can explain the ITD tuning distribution observed in the mammalian brainstem.Impact statementHuman brain has incorporated natural statistics of spatial cues to the neural code supporting perception of sound location.Major subject areaNeuroscience;Research organismHuman;
Modelling the influence of the hippocampal memory system on the oculomotor system
Authors: Ryan Jennifer D. , Shen Kelly , Kacollja Arber , Tian Heather , Griffiths John , Bezgin Gleb , McIntosh Anthony R. 
Published: April 2018

AbstractVisual exploration is related to activity in the hippocampus (HC) and/or extended medial temporal lobe system (MTL), is influenced by stored memories, and is altered in amnesic cases. An extensive set of polysynaptic connections exists both within and between the HC and oculomotor systems such that investigating how HC responses ultimately influence neural activity in the oculomotor system, and the timing by which such neural modulation could occur is not trivial. We leveraged TheVirtualBrain, a software platform for large-scale network simulations, to model the functional dynamics that govern the interactions between the two systems in the macaque cortex. Evoked responses following the stimulation of the MTL and some, but not all, subfields of the HC resulted in observable responses in oculomotor regions, including the frontal eye fields (FEF), within the time of a gaze fixation. Modeled lesions to some MTL regions slowed the dissipation of HC signal to oculomotor regions, whereas HC lesions generally did not affect the rapid MTL activity propagation to oculomotor regions. These findings provide a framework for investigating how information represented by the HC/MTL may influence the oculomotor system during a fixation and predict how HC lesions may affect visual exploration.Author SummaryNo major account of oculomotor (eye movement) guidance considers the influence of the hippocampus (HC) and broader medial temporal lobe (MTL) system, yet it is clear that information is exchanged between the two systems. Prior experience influences current viewing, and cases of amnesia due to compromised HC/MTL function show specific alterations in viewing behaviour. By modeling large-scale network dynamics, we show that stimulation of subregions of the HC, and of the MTL, rapidly results in observable responses in oculomotor control regions, and that HC/MTL lesions alter signal propagation. These findings suggest that information from memory may readily guide visual exploration, and calls for a reconsideration of the neural circuitry involved in oculomotor guidance.
Targeting Human Retinoblastoma Binding Protein 4 (RBBP4) and 7 (RBBP7)
Authors: Abbey Megha , Trush Viacheslav , Gibson Elisa , Vedadi Masoud 
Published: April 2018

AbstractRBBP4 and RBBP7 (RBBP4/7) are highly homologous nuclear WD40 motif containing proteins widely implicated in various cancers and are valuable drug targets. They interact with multiple proteins within diverse complexes such as NuRD and PRC2, as well as histone H3 and H4 through two distinct binding sites. FOG-1, PHF6 and histone H3 bind to the top of the donut shape seven-bladed β-propeller fold, while SUZ12, MTA1 and histone H4 bind to a pocket on the side of the WD40 repeats. Here, we briefly review these six interactions and present binding assays optimized for medium to high throughput screening. These assays enable screening of RBBP4/7 toward the discovery of novel cancer therapeutics.
Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M
Authors: Sampath Srinath C. , Sampath Srihari C. , Ho Andrew T.V. , Corbel Stéphane Y. , Millstone Joshua D. , Lamb John , Walker John , Kinzel Bernd , Schmedt Christian , Blau Helen M. 
Published: April 2018

AbstractThe balance between stem cell quiescence and proliferation in skeletal muscle is tightly controlled, but perturbed in a variety of disease states. Despite progress in identifying activators of stem cell proliferation, the niche factor(s) responsible for quiescence induction remain unclear. Here we report an in vivo imaging-based screen which identifies Oncostatin M (OSM), a member of the interleukin-6 family of cytokines, as a potent inducer of muscle stem cell (MuSC, satellite cell) quiescence. OSM is produced by muscle fibers, induces reversible MuSC cell cycle exit, and maintains stem cell regenerative capacity as judged by serial transplantation. Conditional OSM receptor deletion in satellite cells leads to stem cell depletion and impaired regeneration following injury. These results identify Oncostatin M as a secreted niche factor responsible for quiescence induction, and for the first time establish a direct connection between induction of quiescence, stemness, and transplantation potential in solid organ stem cells.
Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli
Authors: Rajagopalan Krithika , Dworkin Jonathan 
Published: April 2018

AbstractIn bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such asE. coli,which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C phosphatases. These proteins, called eSTPs (eukaryotic-like Ser/Thr phosphatases), have been identified in a number of bacteria, but not inE. coli.Here, we describe a previously unknown eSTP encoded by anE. coliORF,yegK,and characterize its biochemical properties including its kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely relatedE. colistrains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon.ImportanceRegulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria including the model Gram-negative bacteriumE. colidemonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported inE. coli, no partner Ser/Thrphosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.