bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sonographic Spectrum of Pelvic Endometriosis
Authors: Jones Lisa P. , Morgan Matthew A. , Chauhan Anil 
Published: April 2019

Abstract
Endometriosis is a common disease of reproductive-age women that is often first encountered with ultrasound. Therefore, familiarity with the variety of manifestations of endometriosis is important for appropriate diagnosis and management. The aim of this article is to review the spectrum of appearance of pelvic endometriosis and to discuss potential mimics on ultrasound. Given that magnetic resonance imaging is an important problem-solving tool in female pelvic imaging, magnetic resonance imaging correlation is also provided.
Spectral Doppler Ultrasound Can Help Diagnose Children With Hepatic Sinusoidal Obstructive Syndrome After Hematopoietic Stem Cell Transplantation
Authors: Thumar Vishal D. , Vallurupalli Vivek M. , Robinson Amie L. , Staggs Vincent S. , Shah Vidhi , Dalal Jignesh , Chan Sherwin S. 
Published: April 2019

Background
Hepatic sinusoidal obstruction syndrome (SOS) is a potentially fatal complication after hematopoietic stem cell transplantation (HSCT). Current clinical guidelines state that spectral Doppler changes occur late in the disease, and imaging is only useful for confirming SOS diagnosis.

Objective
Our primary objective was to examine abdominal ultrasound variables as predictors of development of SOS in pediatric HSCT patients.

Materials and Methods
A single-center cohort retrospective study was conducted on patients aged 0 to 21 years who underwent HSCT between September 2001 and May 2017 at our institution. Patients were excluded if they did not have abdominal ultrasounds after HSCT. Clinical, demographic, grayscale, and spectral Doppler liver ultrasound findings were evaluated. We modeled the odds of SOS diagnosis within 100 days after HSCT as a function of each of the 15 ultrasound variables.

Results
A total of 333 patients received an HSCT. One hundred forty subjects had ultrasound data available. Thirty-two patients developed SOS, and 9 of these patients died. Sinusoidal obstruction syndrome odds more than double per 1-SD increase in peak systolic velocity in common hepatic artery or left hepatic artery and more than triple per 1-SD decrease in main portal vein velocity or change in ascites severity. Several ultrasound variables were statistically significant predictors in the Cox models for time to SOS diagnosis.

Conclusion
Several ultrasound variables can be used as predictors for a patient's risk of developing SOS. The strongest predictors are ascites severity, main portal vein velocity, common hepatic artery peak systolic velocity, and left hepatic artery peak systolic velocity.
Diaphragmatic Ultrasonography, a Novel Approach in Critical Care
Authors: Garrido-Aguirre Eduardo , Ñamendys-Silva Silvio A. , del Moral Oscar Rojo , Cortés-Soto Carlos A. , Romero-González Juan P. 
Published: April 2019

Abstract
The evaluation of the diaphragm in critically ill patients is simple and noninvasive and has shown good repeatability. The aim of the study was to generate a predictive index for successful weaning (ULDIMex) from invasive mechanical ventilation (IMV) based on an ultrasonographic diaphragmatic assessment before performing a spontaneous breathing test. We recruited patients who required IMV and who were candidates for weaning from ventilation. The measurement of diaphragmatic excursion and time during inspiration and expiration was obtained with a 3- to 5-MHz probe in the M mode. Using the formula (a + b)c/2, the value for the ULDIMex was obtained to evaluate its impact on predicting the successful weaning of IMV, where a is the time during the inspiratory phase, b is the time during expiration, and c is the diaphragmatic excursion during the inspiratory phase, which corresponds to the highest point of the curve from the baseline. We recruited 114 patients, of whom 86 (76%) were successfully weaned from IMV. The patients who were successfully weaned from the IMV had a cutoff value greater than 4.06 cm/s for the ULDIMex index, with a sensitivity of 92.8% (95% confidence interval, 76.5–99.1), specificity of 63.9% (95% confidence interval, 52.9–74.0), positive predictive value of 45.6%, and negative predictive value of 96.5%. The ULDIMex index demonstrated a good level of discrimination for successful weaning prediction. Considering the excellent negative likelihood ratio of the ULDIMex index of greater than 4.06, this index may be considered before performing an spontaneous breathing test to identify critically ill adult patients who will extubate successfully.
The Normal Fetal Cephalic Index in the Second and Third Trimesters of Pregnancy
Authors: Constantine Sarah , Kiermeier Andreas , Anderson Peter 
Published: April 2019

Abstract
The cephalic index (CI) is used in the evaluation of individuals with craniosynostosis. There is little agreement as to the normal range and stability of the CI during the fetal period, partly due to limited literature. We sought to determine the range, distribution and stability of the fetal CI in the second half of pregnancy. We also aimed to identify any relationship to delivery complications such as obstructed labor and malpresentation.
The fetal head circumference, biparietal diameter (BPD) and occipitofrontal diameter (OFD) measurements were obtained from standard ultrasound images. Each of 4304 fetuses had measurements taken at morphology scan performed between 17 and 22 weeks' gestation, and at growth scanning at 28 to 33 weeks' gestation. The cephalic index was calculated using the formula: CI = BPD/OFD × 100. The distribution of the CI at both scans is very close to a normal distribution. The mean CI at 17 to 22 weeks was 75.9 (SD, 3.7); the mean CI at 28 to 33 weeks was 77.8 (SD, 3.5). The mean change in CI was 1.9 (SD, 4.28), which is not statistically significantly different from zero (t = 0.656, P = 0.512, 95% confidence interval). No relationship was found between the CI in normal fetuses and delivery complications. There is a wide variation in the change in CI in the third trimester. A value below the normal range in the third trimester or a progressive reduction in CI during the latter half of pregnancy should provoke detailed scanning of the fetal cranial sutures to check for craniosynostosis.
Deceased Donor–initiated Chains: First Report of a Successful Deliberate Case and Its Ethical Implications
Authors: Furian Lucrezia , Cornelio Cristina , Silvestre Cristina , Neri Flavia , Rossi Francesca , Rigotti Paolo , Cozzi Emanuele , Nicolò Antonio 
Published: April 2019

Background.
It has been suggested that deceased donor kidneys could be used to initiate chains of living donor kidney paired donation, but the potential gains of this practice need to be quantified and the ethical implications must be addressed before it can be implemented.

Methods.
The gain of implementing deceased donor–initiated chains was measured with an algorithm, using retrospective data on the pool of incompatible donor/recipient pairs, at a single center. The allocation rules for chain-ending kidneys and the characteristics and quality of the chain-initiating kidney are described.

Results.
The benefit quantification process showed that, with a pool of 69 kidneys from deceased donors and 16 pairs enrolled in the kidney paired donation program, it was possible to transplant 8 of 16 recipients (50%) over a period of 3 years. After obtaining the approval of the Veneto Regional Authority’s Bioethical Committee and the revision of the Italian National Transplant Center’s allocation policies, the first successful case was completed. For the recipient (male, aged 53 y), who entered the program for a chain-initiating kidney with a Kidney Donor Risk Index of 0.61 and a Kidney Donor Profile Index of 3%, the waiting time was 4 days. His willing donor (female, aged 53 y) with a Living Kidney Donor Profile Index of 2, donated 2 days later to a chain-ending recipient (male, aged 47 y) who had been on dialysis for 5 years.

Conclusions.
This is the first report of a successfully completed, deliberate deceased donor–initiated chain, which was made possible after a thorough assessment of the ethical issues and the impact of allocation policies. This article includes a preliminary efficacy assessment and describes the development of a dedicated algorithm.
Metrics for Graph Comparison: A Practitioner’s Guide
Authors: Wills Peter , Meyer François G. 
Published: April 2019

AbstractComparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience [1], cyber security [2], social network analysis [3], and bioinformatics [4], among others. Discovery and comparison of structures such as modular communities, rich clubs, hubs, and trees in data in these fields yields insight into the generative mechanisms and functional properties of the graph.Often, two graphs are compared via a pairwise distance measure, with a small distance indicating structural similarity and vice versa. Common choices include spectral distances (also known asλdistances) and distances based on node affinities (such asDeltaCon[5]). However, there has of yet been no comparative study of the efficacy of these distance measures in discerning between common graph topologies and different structural scales.In this work, we compare commonly used graph metrics and distance measures, and demonstrate their ability to discern between common topological features found in both random graph models and empirical datasets. We put forward a multi-scale picture of graph structure, in which the effect of global and local structure upon the distance measures is considered. We make recommendations on the applicability of different distance measures to empirical graph data problem based on this multi-scale view. Finally, we introduce the Python libraryNetCompwhich implements the graph distances used in this work.
Loss of microbial diversity and body site heterogeneity in individuals with Hidradenitis Suppurativa
Authors: Schneider Andrea M. , Cook Lauren C. , Zhan Xiang , Banerjee Kalins , Cong Zhaoyuan , Imamura-Kawasawa Yuka , Gettle Samantha L. , Longenecker Amy L. , Kirby Joslyn S. , Nelson Amanda M. 
Published: April 2019

ABSTRACTHidradenitis Suppurativa (HS) is a chronic, scarring, inflammatory skin disease affecting hair follicles in axillae, inguinal, and anogenital regions. Dysbiosis in HS patients compared to healthy subjects is documented. However, whether dysbiosis is specific to particular body sites or skin niches is unknown. We investigated the follicular and skin surface microbiome of the axilla and groin of HS patients (n=11) and healthy individuals (n=10) using 16S rRNA gene sequencing (V3-V4). We sampled non-lesional (HSN) and lesional skin (HSL) of HS patients. β-diversity was significantly decreased (p<0.05) in HSN and HSL skin compared to normal skin with loss of body site and skin niche heterogeneity in HS samples. The relative bacterial abundance of specific microbes was also significantly different between normal and HSN (15 genera) or HSL (21 genera) skin. Smoking and alcohol use influenced the β-diversity (p<0.08) in HS skin. We investigated metabolic profiles of bacterial communities in HS and normal skin using a computational approach.Metabolism, Genetic Information Processing, andEnvironmental Information Processingwere significantly different between normal and HS samples. Altered metabolic pathways associated with dysbiosis of HS skin suggest mechanisms underlying the disease pathology and information about treatment with drugs targeting those pathways.
A novel reporter gene assay for pyrogen detection
Authors: He Qing , Yu Chuan-fei , Wang Lang , Ni Yong-bo , Zhang Heng , Du Ying , Gao Hua , Wang Jun-zhi 
Published: April 2019

AbstractFever is a systemic inflammatory response of the body to pyrogens. Nuclear factor κB (NF-κB) is a central signalling molecule that causes the excessive secretion of various proinflammatory factors induced by pyrogens. This study explored the feasibility of a novel reporter gene assay (RGA) for pyrogen detection using RAW 264.7 cells stably transfected with the NF-κB reporter gene as a pyrogenic marker. Pyrogen was incubated with the transgenic cells, and the intensity of the fluorescence signal generated by luciferase secreted by the reporter gene was used to reflect the degree of activation of NF-κB, so as to quantitatively detect the pyrogens. The RGA could detect different types of pyrogens, including the lipopolysaccharide (LPS) of gram-negative bacteria, the lipoteichoic acid (LTA) of gram-positive bacteria, and the zymosan of fungi, and a good dose-effect relationship was observed in terms of NF-κB activity. The limits of detection of the RGA to those pyrogens were 0.03 EU/ml, 0.001 μg/ml, and 1 μg/ml, respectively. The method had good precision and accuracy and could be applied to many biological products (e.g., nivolumab, rituximab, bevacizumab, etanercept, basiliximab, haemophilus influenzae type b conjugate vaccine, 23-valent pneumococcal polysaccharide vaccine, and group A and group C meningococcal conjugate vaccine). The results of this study suggest that the novel RGA has a wide pyrogen detection spectrum and is sufficiently sensitive, stable, and accurate for various applications.ImportancePyrogen testing is mandatory and a critical method to ensure the safety of parenteral products including vaccines.Currently, only two pharmacological tests, including the rabbit pyrogen test and the bacterial endotoxins test (BET), are applied to evaluate pyrogenic contamination in parenteral pharmaceuticals by most of state pharmacopoeias. Although generally reliable, both of these assays have shortcomings. The rabbit test is not quantitative but is expensive and involves the use of animals. It can also produce varying responses depending on the strain, age and housing conditions of the rabbits. The BET, however, does not detect pyrogens other than gram-negative bacterial endotoxins and is often problematic when used to test solutions with a high protein content.To overcome these shortcomings and satisfy the growing need for new methods prompted by the constantly increasing production of biological compounds, it is necessary to develop the novel assay for pyrogen detection.HighlightsThis novel reporter gene assay can detect different types of pyrogens, including the lipopolysaccharide of gram-negative bacteria, the lipoteichoic acid of gram-positive bacteria, and the zymosan of fungi.The novel reporter gene assay is sufficiently sensitive, stable, and accurate for various applications.
The molecular mechanism of Hsp90-induced oligomerization of Tau
Authors: Weickert Sabrina , Wawrzyniuk Magdalena , John Laura , Rüdiger Stefan G. D. , Drescher Malte 
Published: April 2019

AbstractAggregation of the microtubule-associated protein Tau is a hallmark of Alzheimer’s disease with Tau oligomers suspected as the most toxic agent. Tau is a client of Hsp90, though it is unclear whether and how the chaperone massages the structure of intrinsically disordered Tau. Using electron paramagnetic resonance, we extract structural information from the very broad conformational ensemble of Tau: Tau in solution is highly dynamic and polymorphic, though ‘paper-clip’-shaped by long-range contacts. Interaction with Hsp90 promotes an open Tau conformation, which we identify as the molecular basis for the formation of small Tau oligomers by exposure of the aggregation-prone repeat domain to other Tau molecules. At the same time, formation of Tau fibrils is inhibited. We therefore provide the nanometer-scale zoom into chaperoning an amyloid client, highlighting formation of oligomers as the consequence of this biologically relevant interaction.
Macrophage plasticity is Rac signalling and MMP9 dependant
Authors: Travnickova Jana , Nhim Sandra , Abdellaoui Naoill , Djouad Farida , Nguyen-Chi Maï , Parmeggiani Andrea , Kissa Karima 
Published: April 2019

AbstractIn vitro, depending on extracellular matrix (ECM) architecture, macrophages migrate either in amoeboid or mesenchymal mode; while the first is a general trait of leukocytes, the latter is associated with tissue remodelling via Matrix Metalloproteinases (MMPs). To assess whether these stereotyped migrations could be also observed in a physiological context, we used the zebrafish embryo and monitored macrophage morphology, behaviour and capacity to mobilisation haematopoietic stem/progenitor cells (HSPCs), as a final functional readout. Morphometric analysis identified 4 different cell shapes. Live imaging revealed that macrophages successively adopt all four shapes as they migrate through ECM. Treatment with inhibitors of MMPs or Rac GTPase to abolish mesenchymal migration, suppresses both ECM degradation and HSPC mobilisation while differently affecting macrophage behaviour. This study depicts real time macrophage behaviour in a physiological context and reveals extreme reactivity of these cells constantly adapting and switching migratory shapes to achieve HSPCs proper mobilisation.
Threat-Induced Anxiety During Goal Pursuit Disrupts Amygdala-Prefrontal Cortex Connectivity in Posttraumatic Stress Disorder
Authors: Sun Delin , Gold Andrea L. , Swanson Chelsea A. , Haswell Courtney C. , Brown Vanessa M. , Stjepanovic Daniel ,   VA Mid-Atlantic MIRECC Workgroup, LaBar Kevin S. , Morey Rajendra A. 
Published: April 2019

AbstractTo investigate how unpredictable threat during goal pursuit impacts fronto-limbic activity and functional connectivity in posttraumatic stress disorder (PTSD), we compared military veterans with PTSD (n=25) versus trauma-exposed Control (n=25). Participants underwent functional magnetic resonance imaging (fMRI) while engaged in a computerized chase-and-capture game task that involved optimizing monetary rewards obtained from capturing virtual prey while simultaneously avoiding capture by virtual predators. The game was played under two alternating contexts – one involving exposure to unpredictable, task-irrelevant threat by randomly occurring electrical shocks, and a nonthreat control condition. Activation in and functional connectivity between the amygdala and ventromedial prefrontal cortex (vmPFC) was tested across threat and nonthreat task contexts with generalized psychophysiological interaction (gPPI) analyses. PTSD patients reported higher anxiety than controls across contexts. Better task performance represented by successfully avoiding capture by predators under threat than nonthreat contexts was associated with stronger left amygdala-vmPFC functional connectivity in controls and greater vmPFC activation in PTSD patients. PTSD symptom severity was negatively correlated with vmPFC activation in trauma-exposed controls and with right amygdala-vmPFC functional connectivity across all participants in the threat relative to nonthreat contexts. The findings showed that veterans with PTSD have disrupted amygdala-vmPFC functional connectivity and greater localized vmPFC processing under threat-modulation of goal-directed behavior, specifically related to successful task performance while avoiding loss of monetary rewards. In contrast, trauma survivors without PTSD rely on stronger threat-modulated left amygdala-vmPFC functional connectivity during goal-directed behavior, which may represent a resilience-related functional adaptation.
Creating reproducible pharmacogenomic analysis pipelines
Authors: Mammoliti Anthony , Smirnov Petr , Safikhani Zhaleh , Ba-Alawi Wail , Haibe-Kains Benjamin 
Published: April 2019

ABSTRACTThe field of Pharmacogenomics presents great challenges for researchers that are willing to make their studies reproducible and shareable. This is attributed to the generation of large volumes of high-throughput multimodal data, and the lack of standardized workflows that are robust, scalable, and flexible to perform large-scale analyses. To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. Our pipelines combine both pharmacological and molecular profiles into a portable data object that can be used for future analyses in cancer research. Our data objects and workflows are shared on Harvard Dataverse and Code Ocean where they have been assigned a unique Digital Object Identifier, providing a level of data provenance and a persistent location to access and share our data with the community.
Small molecule inhibitors of a human recombination-associated ATPase, RAD54
Authors: Ehmsen Kirk T. , Ang Kenny K.H. , Wright William D. , Davies Julia L. , Younis Yassir , Birman Yuliya , Bryant Clifford , Gallardo-Godoy Alejandra , Renslo Adam R. , Neitz R. Jeffrey , Arkin Michelle R. , Heyer Wolf-Dietrich 
Published: April 2019

ABSTRACTHomologous recombination (HR) is a principal support pathway for DNA replication and for recovery from DNA breaks and interstrand crosslinks, making it a rational target for inhibition in cancer therapy. The ATPase RAD54 functions in molecular events that promote DNA sequence-preservation during HR-mediated damage repair, including homology search, DNA strand exchange, and transition to DNA repair synthesis within a displacement loop intermediate. We developed a high-throughput biochemical screen to identify small-molecule inhibitors of human RAD54, using a phosphate detection assay to monitor RAD54 ATPase activity in the presence of double-stranded DNA (dsDNA). After filtering potential DNA intercalators and ‘frequent hitters,’ we identified two chemotypes that reproducibly inhibited RAD54 ATPase in vitro. We evaluated these chemotypes for inhibition of RAD54-dsDNA binding and cancer cell survival. A halogenated carbazole/dihydroacridine scaffold inhibited a panel of SWI2/SNF2-related ATPases but not VCP/p97, an unrelated ATPase. Small molecules that interfere with key steps in HR— such as inhibitors of RAD54—may expose DNA repair-dependent vulnerabilities in cancer cells.
Radiator: a cloud-based framework for deploying re-usable bioinformatics tools
Authors: Lo Emily K.W. , Schwab Remy M. , Burke Zak , Cahan Patrick 
Published: April 2019

AbstractSummaryAccessibility and usability of compute-intensive bioinformatics tools can be increased with simplified web-based graphic user interfaces. However, deploying such tools as web applications presents additional barriers, including the complexity of developing a usable interface, network latency in transferring large datasets, and cost, which we encountered in developing a web-based version of our command-line tool CellNet. Learning and generalizing from this experience, we have devised a lightweight framework, Radiator, to facilitate deploying bioinformatics tools as web applications. To achieve reproducibility, usability, consistent accessibility, throughput, and cost-efficiency, Radiator is designed to be deployed on the cloud. Here, we describe the internals of Radiator and how to use it.Availability and ImplementationCode for Radiator and the CellNet Web Application are freely available at https://github.com/pcahan1 under the MIT license. The CellNet WebApp, Radiator, and Radiator-derived applications can be launched through public Amazon Machine Images from the cloud provider Amazon Web Services (AWS) (https://aws.amazon.com/).