bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gating mass cytometry data by deep learning
Authors: Li Huamin , Shaham Uri , Stanton Kelly P , Yao Yi , Montgomery Ruth R , Kluger Yuval 
Published: July 2017

Abstract

Motivation
Mass cytometry or CyTOF is an emerging technology for high-dimensional multiparameter single cell analysis that overcomes many limitations of fluorescence-based flow cytometry. New methods for analyzing CyTOF data attempt to improve automation, scalability, performance and interpretation of data generated in large studies. Assigning individual cells into discrete groups of cell types (gating) involves time-consuming sequential manual steps, untenable for larger studies.

Results
We introduce DeepCyTOF, a standardization approach for gating, based on deep learning techniques. DeepCyTOF requires labeled cells from only a single sample. It is based on domain adaptation principles and is a generalization of previous work that allows us to calibrate between a target distribution and a source distribution in an unsupervised manner. We show that DeepCyTOF is highly concordant (98%) with cell classification obtained by individual manual gating of each sample when applied to a collection of 16 biological replicates of primary immune blood cells, even when measured across several instruments. Further, DeepCyTOF achieves very high accuracy on the semi-automated gating challenge of the FlowCAP-I competition as well as two CyTOF datasets generated from primary immune blood cells: (i) 14 subjects with a history of infection with West Nile virus (WNV), (ii) 34 healthy subjects of different ages. We conclude that deep learning in general, and DeepCyTOF specifically, offers a powerful computational approach for semi-automated gating of CyTOF and flow cytometry data.

Availability and implementation
Our codes and data are publicly available at https://github.com/KlugerLab/deepcytof.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effect of a New Matrix Therapy Agent in Persistent Epithelial Defects After Bacterial Keratitis Treated With Topical Fortified Antibiotics
Authors: Chappelet Marc-Antoine , Bernheim Diane , Chiquet Christophe , Aptel Florent 
Published: July 2017

Purpose:
To evaluate the effect of topical application of a matrix regenerating agent (RGTA) in subjects with a persistent epithelial defect after bacterial keratitis treated with topical fortified antibiotics.

Methods:
In this prospective case series of 14 subjects (14 eyes) with a persisting corneal ulcer after the cessation of fortified antibiotics, subjects were treated with an RGTA at a dose of 1 drop every other day. The main outcome measure was the proportion of subjects with complete corneal healing 1 month after initiation of treatment. The secondary outcome measures were the size and depth of corneal ulceration at 1 month, the duration from treatment initiation to complete healing, pain, and tolerability. The ulceration depth was measured with anterior segment optical coherence tomography.

Results:
Complete corneal healing was observed in 11 (78.6%) of the 14 patients after 1 month and in 14 of the 14 (100%) patients after 3 months. Mean logarithm of the minimum angle of resolution visual acuity improved from 1.22 ± 0.59 at inclusion to 0.57 ± 0.68 at 1 month and to 0.55 ± 0.68 at 3 months (P < 0.01). Pain according to a visual analog scale decreased from 0.34 ± 0.25 to 0.05 ± 0.09 at 1 month and to 0 at 3 months (P < 0.001). Amniotic membrane transplantation was not required for any patients. There were no RGTA-related side effects, and none of the patients reported pain or discomfort during instillation of the drops.

Conclusions:
The RGTA seems to be efficient for the treatment of a persistent epithelial defect after bacterial keratitis treated with topical fortified antibiotics.
Rose Bengal Photodynamic Antimicrobial Therapy: A Novel Treatment for Resistant Fusarium Keratitis
Authors: Amescua Guillermo , Arboleda Alejandro , Nikpoor Neda , Durkee Heather , Relhan Nidhi , Aguilar Mariela C. , Flynn Harry W. , Miller Darlene , Parel Jean-Marie 
Published: July 2017

Purpose:
To evaluate the efficacy of rose bengal PDAT for the management of a patient with multidrug-resistant Fusarium keratoplasticum keratitis unresponsive to standard clinical treatment.

Methods:
This case report presents a clinical case of F. keratoplasticum keratitis not responsive to standard medical care. In vitro studies from patients culture isolated responded to rose bengal PDAT. Patient received two treatments with rose bengal 0.1% and exposure to green light with a total energy of 2.7 J/cm2.

Results:
In vitro results demonstrated the efficacy of rose bengal PDAT a multidrug-resistant F. keratoplasticum species. There was complete fungal inhibition in our irradiation zone on the agar plates. In the clinical case, the patient was successfully treated with 2 sessions of rose bengal PDAT, and at 8-month follow-up, there was neither recurrence of infection nor adverse effects to report.

Conclusions:
Rose bengal PDAT is a novel treatment that may be considered in cases of aggressive infectious keratitis. Further studies are needed to understand the mechanisms of PDAT in vivo.
Brain signature and functional impact of centralized pain: a multidisciplinary approach to the study of chronic pelvic pain (MAPP) network study
Authors: Kutch Jason J. , Ichesco Eric , Hampson Johnson P. , Labus Jennifer S. , Farmer Melissa A. , Martucci Katherine T. , Ness Timothy J. , Deutsch Georg , Apkarian A. Vania , Mackey Sean C. , Klumpp David J. , Schaeffer Anthony J. , Rodriguez Larissa V. , Kreder Karl J. , Buchwald Dedra , Andriole Gerald L. , Lai H. Henry , Mullins Chris , Kusek John W. , Landis J. Richard , Mayer Emeran A. , Clemens J. Quentin , Clauw Daniel J. , Harris Richard E. ,   for the MAPP Research Network
Published: July 2017

Abstract
Chronic pain is often measured with a severity score that overlooks its spatial distribution across the body. This widespread pain is believed to be a marker of centralization, a central nervous system process that decouples pain perception from nociceptive input. Here, we investigated whether centralization is manifested at the level of the brain using data from 1079 participants in the Multidisciplinary Approach to the Study of Chronic Pelvic Pain Research Network (MAPP) study. Participants with a clinical diagnosis of urological chronic pelvic pain syndrome (UCPPS) were compared to pain-free controls and patients with fibromyalgia, the prototypical centralized pain disorder. Participants completed questionnaires capturing pain severity, function, and a body map of pain. A subset (UCPPS N = 110; fibromyalgia N = 23; healthy control N = 49) underwent functional and structural magnetic resonance imaging. Patients with UCPPS reported pain ranging from localized (pelvic) to widespread (throughout the body). Patients with widespread UCPPS displayed increased brain gray matter volume and functional connectivity involving sensorimotor and insular cortices (P < 0.05 corrected). These changes translated across disease diagnoses as identical outcomes were present in patients with fibromyalgia but not pain-free controls. Widespread pain was also associated with reduced physical and mental function independent of pain severity. Brain pathology in patients with centralized pain is related to pain distribution throughout the body. These patients may benefit from interventions targeting the central nervous system.
Chronic pancreatitis
Authors: Yang Dennis , Forsmark Chris E. 
Published: July 2017

Purpose of review
Summarize key clinical advances in chronic pancreatitis reported in 2016.

Recent findings
Early diagnosis of chronic pancreatitis remains elusive. Recent studies suggest that endoscopic ultrasound may be less accurate than previously thought and new MRI techniques may be helpful. Genetic predisposition may independently affect the clinical course of chronic pancreatitis and the risk for pancreatic cancer. Cigarette smoking may have a greater negative impact on chronic pancreatitis than previously thought and moderate alcohol consumption may be protective. A multidisciplinary approach is necessary for the treatment of type 3 diabetes and nutritional deficiencies in chronic pancreatitis. Although endoscopic therapy remains a reasonable first-line option in treating chronic pancreatitis and its complications, early surgical intervention may be indicated for pain in select patients.

Summary
Newer endoscopic ultrasound and MRI techniques are being evaluated to help with the early diagnosis of chronic pancreatitis. Both genetic predisposition and cigarette smoking are increasingly recognized as having a major impact in the course of the disease and the risk for pancreatic cancer. Endoscopic therapy is well tolerated and effective for the treatment of chronic pancreatitis and its complications although an early surgical approach for pain may be associated with improved clinical outcomes.
Survival and Neurodevelopmental Outcomes Among Periviable Infants
Authors: Younge Noelle , Goldstein Ricki F. , Bann Carla M. , Hintz Susan R. , Patel Ravi M. , Smith P. Brian , Bell Edward F. , Rysavy Matthew A. , Duncan Andrea F. , Vohr Betty R. , Das Abhik , Goldberg Ronald N. , Higgins Rosemary D. , Cotten C. Michael 
Published: July 2017

(Abstracted from N Engl J Med 2017;376:617–628)
The purpose of this study was to evaluate survival and neurodevelopmental outcomes among periviable infants (born at 22–24 weeks of gestation) assessed at 18 to 22 months of corrected age. In the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Neonatal Research Network (NRN) alone, this improvement has been documented for over 2 decades now with increasing survival of infants born after 2008 at 23 to 24 weeks of gestation.
Predictive Accuracy of Serial Transvaginal Cervical Lengths and Quantitative Vaginal Fetal Fibronectin Levels for Spontaneous Preterm Birth Among Nulliparous Women
Authors: Esplin M. Sean , Elovitz Michal A. , Iams Jay D. , Parker Corette B. , Wapner Ronald J. , Grobman William A. , Simhan Hyagriv N. , Wing Deborah A. , Haas David M. , Silver Robert M. , Hoffman Matthew K. , Peaceman Alan M. , Caritis Steve N. , Parry Samuel , Wadhwa Pathik , Foroud Tatiana , Mercer Brian M. , Hunter Shannon M. , Saade George R. , Reddy Uma M. 
Published: July 2017

(Abstracted from JAMA 2017;317(10):1047–1056)
Prediction of spontaneous preterm birth, a leading cause of infant mortality, depends in practice largely on a history of previous birth, and the risk for first time mothers and nulliparous women is more difficult to assess. The aim of this study was to assess the reliability of serial transvaginal cervical length (CL) and quantitative fetal fibronectin (fFN) measurements in predicting spontaneous preterm birth (before 37 weeks) in a large, prospective cohort of nulliparous women.
Readmission and Reoperation After Surgery for Pelvic Organ Prolapse
Authors: Hokenstad Erik D. , Glasgow Amy E. , Habermann Elizabeth B. , Occhino John A. 
Published: July 2017

(Abstracted from Female Pelvic Med Reconstr Surg 2017;23:131–135)
Unplanned hospital readmission and reoperation within 30 days of discharge in women who undergo pelvic organ prolapse (POP) surgery are associated with morbidity and mortality that are preventable in many cases. Reoperation subjects patients to postoperative complications.
The Clinical Significance of Posterior Insular Volume in Adolescent Anorexia Nervosa
Authors: Zucker Nancy L. , Kragel Philip A. , Wagner Henry Ryan , Keeling Lori , Mayer Emeran , Wang Joyce , Kang Min Su , Merwin Rhonda , Simmons W. Kyle , LaBar Kevin S. 
Published: July 2017

ABSTRACT

Objective
The diagnostic criterion disturbance in the experience of the body remains a poorly understood and persistent feature of anorexia nervosa (AN). Increased sophistication in understanding the structure of the insular cortex—a neural structure that receives and integrates visceral sensations with action and meaning—may elucidate the nature of this disturbance. We explored age, weight status, illness severity, and self-reported body dissatisfaction associations with insular cortex volume.

Methods
Structural magnetic resonance imaging data were collected from 21 adolescents with a history of AN and 20 age-, sex-, and body mass index–matched controls. Insular cortical volumes (bilateral anterior and posterior regions) were identified using manual tracing.

Results
Volumes of the right posterior insula demonstrated the following: (a) a significant age by clinical status interaction (β = −0.018 [0.008]; t = 2.32, p = .02) and (b) larger volumes were associated with longer duration of illness (r = 0.48, p < .04). In contrast, smaller volumes of the right anterior insula were associated with longer duration of illness (r = −0.50, p < .03). The associations of insular volume with body dissatisfaction were of moderate effect size and also of opposite direction, but a statistical trend in right posterior (r = 0.40, p < .10 in right posterior; r = −0.49, p < .04 in right anterior).

Conclusions
In this exploratory study, findings of atypical structure of the right posterior insular cortex point to the importance of future work investigating the role of visceral afferent signaling in understanding disturbance in body experience in AN.
An Unusual Bullet Trajectory: Entered Through the Face and Ended Up in the Neck
Authors: Bayram Ali , Kaya Altan , Kalkan Mehmet , Özcan Ibrahim , Mutlu Cemil 
Published: July 2017

Abstract
The authors describe a case of gunshot injury in a 26-year-old male patient with an unusual bullet trajectory. The bullet had an entry hole just near the right lateral alar cartilage of the nose, and the trajectory descended through the left side of the neck by route of the hard palate, soft palate, and posterior pharyngeal wall, respectively. Surgical removal of the bullet was achieved with neck exploration. Gunshot injuries of the head and neck necessitate a thorough clinical and radiological evaluation due to the possibility of an unusual bullet trajectory.
FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination
Authors: Fernandes Joiselle Blanche , Duhamel Marine , Séguéla-Arnaud Mathilde , Froger Nicole , Girard Chloé , Choinard Sandrine , De Winne Nancy , De Jaeger Geert , Gevaert Kris , Guerois Raphael , Kumar Rajeev , Mercier Raphael 
Published: July 2017

AbstractHomologous recombination is central to repair DNA double-strand breaks (DSB), either accidently arising in mitotic cells or in a programed manner at meiosis. Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny. However, mechanisms regulating CO formation remain elusive. Here, we identified through protein-protein interaction and genetic screens FIDGETIN-LIKE-1 INTERACTING PROTEIN (FLIP) as a new partner of the previously characterized anti-crossover factor FIDGETIN-LIKE-1 (FIGL1) inArabidopsis thaliana. We showed that FLIP limits meiotic crossover together with FIGL1. Further, FLIP and FIGL1 form a protein complex conserved from Arabidopsis to Human. FIGL1 interacts with the recombinases RAD51 and DMC1, the enzymes that catalyze the DNA stand exchange step of homologous recombination. Arabidopsisflipmutants recapitulates thefigl1phenotype, with enhanced meiotic recombination associated with change in DMC1 dynamics. Our data thus suggest that FLIP and FIGL1 form a conserved complex that regulates the crucial step of strand invasion in homologous recombination.
Using Structural Equation Modeling to Jointly Estimate Maternal and Foetal Effects on Birthweight in the UK Biobank
Authors: Warrington Nicole M , Freathy Rachel , Neale Michael C. , Evans David M 
Published: July 2017

AbstractBackgroundTo date, 60 genetic variants have been robustly associated with birthweight. It is unclear whether these associations represent the effect of an individual’s own genotype on their birthweight, their mother’s genotype, or both.MethodsWe demonstrate how structural equation modelling (SEM) can be used to estimate both maternal and foetal effects when phenotype information is present for individuals in two generations and genotype information is available on the older individual. We conduct an extensive simulation study to assess the bias, power and type 1 error rates of the SEM and also apply the SEM to birthweight data in the UK Biobank study.ResultsUnlike simple regression models, our approach is unbiased when there is both a maternal and foetal effect. The method can be used when either the individual’s own phenotype or the phenotype of their offspring is not available, and allows the inclusion of summary statistics from additional cohorts where raw data cannot be shared. We show that the type 1 error rate of the method is appropriate, there is substantial statistical power to detect a genetic variant that has a moderate effect on the phenotype, and reasonable power to detect whether it is a foetal and/or maternal effect. We also identify a subset of birth weight associated SNPs that have opposing maternal and foetal effects in the UK Biobank.ConclusionsOur results show that SEM can be used to estimate parameters that would be difficult to quantify using simple statistical methods alone.Key MessagesWe describe a structural equation model to estimate both maternal and foetal effects when phenotype information is present for individuals in two generations and genotype information is available on the older individual.Using simulation, we show that our approach is unbiased when there is both a maternal and foetal effect, unlike simple linear regression models. Additionally, we illustrate that the structural equation model is largely robust to measurement error and missing data for either the individual’s own phenotype or the phenotype of their offspring.We describe how the flexibility of the structural equation modelling framework will allow the inclusion of summary statistics from studies that are unable to share raw data.Using the structural equation model to estimate the maternal and foetal effects of known birthweight associated loci in the UK Biobank, we identify three loci that have primary effects through the maternal genome and six loci that have opposite effects in the maternal and foetal genomes.
Genotype, nitrogen and herbivory shape plant defense: the case of a vitamin-enriched maize
Authors: Ardanuy Agnès , Pastor Victoria , Glauser Gaëtan , Christou Paul , Turlings Ted C. J. , Albajes Ramon 
Published: July 2017

ABSTRACTThe cultivation of crops with novel traits could interfere with ecosystem services delivered by arthropods through bottom-up effects. Here we tested the hypothesis that a vitamin enriched maize (CarolightR) is similar in terms of plant-arthropod interactions to its wild type when compared in controlled environment and under field conditions. In order to assess the robustness of their equivalence we tested two nitrogen availability regimes. We used arthropod field abundance, the behavior and fitness of a keystone maize herbivore - the leafhopperZyginidia scutellaris- and above ground chemistry of maize plants (volatile, hormone and metabolite profiling) as indicators of potential changes in plant-insect interactions. Nitrogen availability was the key driver of herbivore abundance and behavior, and determined direct and indirect chemical defense in maize plants. Both genotypes presented similar constitutive and inducible phytohormone profiles independently of the nitrogen regime. However, feeding by the herbivore suppressed the levels of JA-Ile and JA, without impairing the release of induced plant volatiles. CarolightRand M37W differed to some degree in the concentrations of phenolics (hydroxycinnamic acids and lignans) and in the abundance of a volatile compound. Overall the effect of maize genotype on the herbivores was smaller than the effect of nitrogen fertilization.HIGHLIGHTWe show the separate and interactive effects of nitrogen availability and genotype on the performance and behavior of a herbivore, and related these changes to constitutive and inducible maize defenses.
Insertion force analysis of compliantly supported peg-in-hole assembly
Authors: Pitchandi Nagarajan , Subramanian Saravana Perumaal , Irulappan Muhilan 
Published: July 2017

Purpose
This paper aims to estimate the required insertion force and to analyze the influence of damping in a compliantly supported chamfered peg-in-hole assembly under dynamic conditions.

Design/methodology/approach
A mathematical model of the insertion process, including damping coefficient and stiffness of the compliance, insertion speed, mass, inertia and friction coefficient, has been developed. Computer aided design (CAD) model of the peg-in-hole assembly environment with passive compliance is created. The dynamic insertion force of the modeled environment is analyzed using multibody dynamics numerical solver.

Findings
The damping property of the viscoelastic materials used in the passive compliances suppresses the vibration caused due to the impulses in the transition of the peg in hole. It also increases the insertion force required for the peg insertion at the initial stage.

Research limitations/implications
As the search strategies are not considered in this work, it is assumed that the initial contact is ensured between the chamfer and the peg of the assembly. A constant insertion speed is maintained throughout the insertion. Otherwise, it could have been varied at different stages of the insertion for reducing the assembly time.

Practical implications
The developed assembly model can be used for predicting the insertion forces of a chamfered peg-in-hole assembly and for designing/selecting the compliance device for the required assembly environment.

Originality/value
The proposed insertion model has considered the damping and elastic property of the compliance material as a parallel arrangement of spring and dashpot. This approach aids in modeling an insertion process closer to real-time assembly process.
An integrative model for understanding team organizational citizenship behavior
Authors: Somech Anit , Khotaba Soha 
Published: July 2017

PurposeThe purpose of this paper is to use a model to broaden the understanding of the organizational citizenship behavior (OCB) phenomenon in educational teams and examines team OCB’s mediating role in the relation of the contextual variables of team justice climate (distributive justice, procedural justice, interpersonal justice) to team psychological capital (PsyCap) and team innovation.Design/methodology/approachData were collected through a survey consisting of validated scales. The sample covered 78 disciplinary teams, 78 coordinators and 13 school principals at 13 junior-high schools.FindingsThe PROCESS test confirmed the mediating role of team OCB, showing positive relations between team procedural justice and team PsyCap and team OCB, and also between team OCB and team innovation.Research limitations/implicationsBy taking a team perspective, the findings offer evidence that despite the usual approach treating OCB as an individual phenomenon; it may be regarded as shared norms of behaviors at the team level.Practical implicationsThe team-level approach may urge principals and other educational leaders to realize that teachers’ willingness to invest extra effort in school is mainly the result of an appropriate team context, which can be shaped and developed.Originality/valueThe present study explored team OCB by from a context perspective. This is important because to date most studies on OCB in schools have focused on teacher OCB as an individual phenomenon, disregarding its contextual nature.