bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of patients hospitalized with peptic ulcer disease diagnosed in acute upper endoscopy
Authors: Malmi Hanna , Kautiainen Hannu , Virta Lauri J. , Färkkilä Martti A. 
Published: August 2017

Objectives
The incidence and complications of peptic ulcer disease (PUD) have declined, but mortality from bleeding ulcers has remained unchanged. The aims of the current study were to evaluate the significance of PUD among patients admitted for acute upper endoscopy and to evaluate the survival of PUD patients.

Patients and methods
In this prospective, observational cohort study, data on 1580 acute upper endoscopy cases during 2012–2014 were collected. A total of 649 patients were included with written informed consent. Data on patients’ characteristics, living habits, comorbidities, drug use, endoscopy and short-term and long-term survival were collected.

Results
Of all patients admitted for endoscopy, 147/649 (23%) had PUD with the main symptom of melena. Of these PUD patients, 35% had major stigmata of bleeding (Forrest Ia–IIb) in endoscopy. Patients with major stigmata had significantly more often renal insufficiency, lower level of blood pressure with tachycardia and lower level of haemoglobin, platelets and ratio of thromboplastin time. No differences in drug use, Charlson comorbidity class, BMI, smoking or alcohol use were found. Of the PUD patients, 31% were Helicobacter pylori positive. The 30-day mortality was 0.7% (95% confidence interval: 0.01–4.7), 1-year mortality was 12.9% (8.4–19.5) and the 2-year mortality was 19.4% (13.8–26.8), with no difference according to major or minor stigmata of bleeding. Comorbidity (Charlson>1) was associated with decreased survival (P=0.029) and obesity (BMI≥30) was associated with better survival (P=0.023).

Conclusion
PUD is still the most common cause for acute upper endoscopy with very low short-term mortality. Comorbidity, but not the stigmata of bleeding, was associated with decreased long-term survival.
Human Immunodeficiency Virus, Chlamydia, and Gonorrhea Testing in New York Medicaid–Enrolled Adolescents
Authors: Wang Li Yan , Chang Man-Huei , Burstein Gale , Hocevar Adkins Susan 
Published: August 2017

Background
Although growing public health efforts have been expended on increasing adolescents' access to human immunodeficiency virus (HIV) and sexually transmitted infection (STI) testing, little is known about the current utilization of those services in clinical settings.

Methods
Using 2010 to 2012 New York State Center for Medicare and Medicaid Services Medicaid Analytic eXtract data, we estimated the annual percentage of 13- to 19-year-olds who were tested for HIV, chlamydia (CT), and gonorrhea (GC). A regression analysis was performed to identify factors independently associated with testing utilization. We further examined testing utilization in all adolescent females with 1 or more health care encounter, pregnant females, and adolescents at increased risk for HIV/STI.

Results
From 2010 to 2012, HIV, CT, and GC testing rates increased in the overall study population and in most demographic subgroups. Female adolescents, black and Hispanic adolescents, at-risk adolescents, and adolescents with 6 months or longer of enrollment were significantly more likely to be tested. Among adolescent females with 1 or more health care encounter, 19.2% were tested for CT and 16.9% tested for GC in 2012. Among pregnant females, 35.2%, 53.9%, and 46.1% were tested for HIV, CT, and GC, respectively. Among at-risk adolescents, 39.9%, 63.7%, and 54.4% were tested for HIV, CT, and GC, respectively.

Conclusions
Although progress had been made by New York State providers to adhere to recommended testing for adolescents, there was a clear gap between the recommended level of testing and the actual level of utilization among sexually active females, pregnant females, and at-risk adolescents. Opportunities exist for community provider and public health collaboration to increase adolescent HIV and STI testing.
2015 Charles F. Prentice Medal Award Lecture: Neural Organization of Binocular Vision
Authors: Freeman Ralph D. 
Published: August 2017

ABSTRACT
During a Research Career Development Award from the National Eye Institute, I spent a year at the University of Cambridge doing research with John Robson. The goal was to use a visual stimulation approach that had not been previously attempted, with the intention of exploring fundamental organization principles of the neural basis of binocular vision. The idea was to use sinusoidal gratings that drifted before both eyes such that the relative phase for one eye was fixed while that of the other was varied. This provided binocular stimuli of variable relative phase, i.e. retinal disparity, to enable testing of binocular response characteristics. We were able to obtain different types of disparity tuning functions for neurons in the primary visual cortex. This work, followed by extended investigations in Berkeley, provided basic information regarding response characteristics of simple and complex cells. We have also shown for monocular deprivation, an approximate model for human amblyopia, that many neurons remain connected to the deprived eye, as demonstrated with dichoptic activation. A selected portion of this work is described here.
Motion-Corrected Real-Time Cine Magnetic Resonance Imaging of the Heart
Authors: Rahsepar Amir Ali , Saybasili Haris , Ghasemiesfe Ahmadreza , Dolan Ryan S. , Shehata Monda L. , Botelho Marcos P. , Markl Michael , Spottiswoode Bruce , Collins Jeremy D. , Carr James C. 
Published: August 2017

Objectives
Free-breathing real-time (RT) imaging can be used in patients with difficulty in breath-holding; however, RT cine imaging typically experiences poor image quality compared with segmented cine imaging because of low resolution. Here, we validate a novel unsupervised motion-corrected (MOCO) reconstruction technique for free-breathing RT cardiac images, called MOCO-RT. Motion-corrected RT uses elastic image registration to generate a single heartbeat of high-quality data from a free-breathing RT acquisition.

Materials and Methods
Segmented balanced steady-state free precession (bSSFP) cine images and free-breathing RT images (Cartesian, TGRAPPA factor 4) were acquired with the same spatial/temporal resolution in 40 patients using clinical 1.5 T magnetic resonance scanners. The respiratory cycle was estimated using the reconstructed RT images, and nonrigid unsupervised motion correction was applied to eliminate breathing motion. Conventional segmented RT and MOCO-RT single-heartbeat cine images were analyzed to evaluate left ventricular (LV) function and volume measurements. Two radiologists scored images for overall image quality, artifact, noise, and wall motion abnormalities. Intraclass correlation coefficient was used to assess the reliability of MOCO-RT measurement.

Results
Intraclass correlation coefficient showed excellent reliability (intraclass correlation coefficient ≥ 0.95) of MOCO-RT with segmented cine in measuring LV function, mass, and volume. Comparison of the qualitative ratings indicated comparable image quality for MOCO-RT (4.80 ± 0.35) with segmented cine (4.45 ± 0.88, P = 0.215) and significantly higher than conventional RT techniques (3.51 ± 0.41, P < 0.001). Artifact and noise ratings for MOCO-RT (1.11 ± 0.26 and 1.08 ± 0.19) and segmented cine (1.51 ± 0.90, P = 0.088 and 1.23 ± 0.45, P = 0.182) were not different. Wall motion abnormality ratings were comparable among different techniques (P = 0.96).

Conclusions
The MOCO-RT technique can be used to process conventional free-breathing RT cine images and provides comparable quantitative assessment of LV function and volume measurements to conventional segmented cine imaging while providing improved image quality and less artifact and noise. The free-breathing MOCO-RT reconstruction method may have considerable clinical utility in cardiac magnetic resonance imaging for patients with difficulty breath-holding.
Albuminuria in Pediatric Patients With Adenotonsillar Hypertrophy
Authors: Unsal Ozlem , Bozkurt Gulpembe , Esen Akpinar Meltem , Salepci Egehan , Aktas Oguz Gokce , Uslu Coskun Berna 
Published: August 2017

Abstract
The relationship between intermittent nocturnal hypoxia and albuminuria in pediatric patients with adenotonsillar hypertrophy was evaluated in this prospective study. Fifty children with grade 3 to 4 adenotonsillar hypertrophy scheduled for adenoidectomy and/or adenotonsillectomy were selected for study group. Fifteen patients with adenotonsillar grade 1 to 2 or adenotonsillectomized subjects in a similar range of sex, age, and body mass index scheduled for other surgeries were selected for control group. All children were monitored using finger pulse oximeter during the night before surgery. At the day of surgery, first morning urine samples were sent to the laboratory for analysis of albuminuria.
Albuminuria was determined in 8 (16%) patients in study group and 1 (6.7%) patient in control group. This difference between groups was determined not to be statistically significant (P > 0.05). None of the pulse oximetry parameters was also found to be associated with albuminuria statistically (P > 0.05). However, the adenoid grade was observed to be associated with albuminuria (P = 0.011).
This study revealed no relationship between albuminuria and intermittent hypoxia in children, although previous studies have reported that intermittent hypoxia causes albuminuria in adults. On the contrary, the adenoid grade was found to be in association with albuminuria. The reason seems to be unclear because of the lack of studies investigating albuminuria in children with adenotonsillar hypertrophy. However, inflammatory mediators arising from adenoid tissue may cause increase in renal capillary permeability and urine albumin excretion.
Can Clinical Findings Predict Orbital Fractures and Treatment Decisions in Patients With Orbital Trauma? Derivation of a Simple Clinical Model
Authors: Scolozzi Paolo , Jacquier Paul , Courvoisier Delphine S. 
Published: August 2017

Abstract
The aim of this study was to determine the predictive value of 4 clinical signs (periorbital ecchymosis, periorbital emphysema, diplopia, and inferior orbital nerve hypoesthesia) for the diagnosis of orbital fractures (OFs) and the need for surgical treatment in patients with orbital trauma. The investigators designed and implemented a retrospective cohort study composed of patients with orbital trauma. The primary and secondary outcomes were respectively the diagnosis of OFs and the need for surgical treatment. Multivariable logistic regressions including the clinical signs, age, and causes of injury were used to determine the independent contribution of each clinical sign to the prediction of the outcomes and to obtain weights to compute OF and surgery scores. The outcomes were assessed by receiver-operating characteristic (ROC) curves, sensitivity, specificity, and positive and negative predictive values. A total of 912 patients were included. All clinical signs except periorbital ecchymosis were significantly associated with OFs and the need for surgical treatment (P < 0.001). The predictive power of each clinical sign taken separately was moderate for the 2 outcomes (area under ROC curve [AUC] <0.7). A better predictive value was found when all clinical signs were used together (AUC >0.7). Patients with an OF score >3 were likely to have an OF and patients with a surgery score ≤2 were unlikely to have surgery.
The present study demonstrated that our OF and surgery scores resulted in an effective model that allowed the stratification of patients with orbital trauma based on their risk of having OFs and risk of needing a surgical treatment.
The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks
Authors: Torrecilla Ignacio , Oehler Judith , Ramadan Kristijan 
Published: August 2017

DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.
This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.
Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA inArabidopsis thaliana
Authors: Krahmer Johanna , Goralogia Greg , Kubota Akane , Johnson Richard S. , Song Young Hun , MacCoss Michael J. , LeBihan Thierry , Halliday Karen J , Imaizumi Takato , Millar Andrew J. 
Published: August 2017

SummaryThe large, plant-specific protein GIGANTEA (GI) is involved in many physiological processes, mediating rhythmic, post-translational regulation in part through circadian and light regulation ofGIRNA expression. GI binds several proteins implicated in the circadian clock, the control of photoperiodic flowering, and abiotic stress responses, and has co-chaperone activity. By extension, further interaction partners might mediate the less well-understood roles of GI but the number and rhythmicity of these interactors is unknown. Here, we seek potential interactors in a time-specific manner, using quantitative proteomics from a time series study of transgenicArabidopsis thalianaplants constitutively expressing an epitope-tagged GI protein. Previously-identified, direct and indirect interactors of GI were detected but no further F-box proteins related to known GI partners ZTL/FKF1/LKP2. The predominantly non-rhythmic, interacting proteins were implicated in protein folding or degradation, metabolism and chromatin modification, including a small set of partners shared with other clock-related proteins. A transcription factor homologue that we nameCYCLING DOF FACTOR 6(CDF6) was shown to interact both with GI and the ZTL/FKF1/LKP2 proteins and to control photoperiodic flowering. Our results indicate the biochemical pathways, beyond circadian and flowering regulation, that might be affected by GIGANTEA’s rhythmic, post-translational control.Significance StatementSignificance statement of up to two sentences of no more than 75 words total;The GIGANTEA protein of Arabidopsis was known for circadian and flowering functions, mediated by the FKF1/LKP2/ZTL family of GI-interacting, F-box proteins, then for a co-chaperone activity of unknown scope. We performed time-resolved, interaction proteomics, identifying CDF6 (At1g26790) as a morning-specific GI interactor that controls flowering time. Unlike FKF1 and CDF proteins, most of the 240 candidate partners were not rhythmically enriched. They link GI to proteostasis and metabolic functions that might mediate GI’s physiological functions.
CRISPR-based herd immunity limits phage epidemics in bacterial populations
Authors: Payne Pavel , Geyrhofer Lukas , Barton Nicholas H. , Bollback Jonathan P. 
Published: August 2017

AbstractPathogens are a driving force in evolution, giving rise to a diversity of host immune defenses. In order for a pathogen to spread in a population a sufficient number of its members must be susceptible to infection, as resistant individuals can prevent the spread of a pathogen among susceptible hosts in a process known as herd immunity. While herd immunity has been extensively studied in vertebrate populations, little is known about its role, if any, in the dynamics between bacteria and their phage pathogens. Here we explore the dynamics of T7 phage epidemics in structured and unstructuredEscherichia colipopulations consisting of differing mixtures of susceptible and resistant individuals harboring CRISPR immunity to the phage. Using both experiments and mathematical modelling we describe the conditions under which herd immunity arises in bacterial populations. Notably, the effects of herd immunity depend strongly on the presence of spatial structure in the population, the bacterial growth rate, and phage replication rate. The results of our model can apply to other host-pathogen systems to determine the herd immunity threshold from the relative speed of an epidemic wave in partially resistant populations. In addition, our findings suggest that herd immunity plays an important role in bacterial communities, as seen in other host-pathogen systems, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.
Fast and Simple Tool for the Quantification of Biofilm-Embedded Cells Sub-Populations from Fluorescent Microscopic Images
Authors: Bogachev Mikhail I , Volkov Vladimir Yu , Markelov Oleg A , Trizna Elena Yu , Baydamshina Diana R , Melnikov Vladislav , Murtazina Regina R , Zelenikhin Pavel V , Sharafutdinov Irshad S , Kayumov Airat R 
Published: August 2017

AbstractFluorescent staining is a common tool for both quantitative and qualitative assessment of pro- and eukaryotic cells sub-population fractions by using microscopy and flow cytometry. However, direct cell counting by flow cytometry is often limited, for example when working with cells rigidly adhered either to each other or to external surfaces like bacterial biofilms or adherent cell lines and tissue samples. An alternative approach is provided by using fluorescent microscopy and confocal laser scanning microscopy (CLSM), which enables the evaluation of fractions of cells subpopulations in a given sample. For the quantitative assessment of cell fractions in microphotographs, we suggest a simple two-step algorithm that combines single cells selection and the statistical analysis. To facilitate the first step, we suggest a simple procedure that supports finding the balance between the detection threshold and the typical size of single cells based on objective cell size distribution analysis. Based on a series of experimental measurements performed on bacterial and eukaryotic cells under various conditions, we show explicitly that the suggested approach effectively accounts for the fractions of different cell sub-populations (like the live/dead staining in our samples) in all studied cases that are in good agreement with manual cell counting on microphotographs and flow cytometry data. This algorithm is implemented as a simple software tool that includes an intuitive and user-friendly graphical interface for the initial adjustment of algorithm parameters to the microphotographs analysis as well as for the sequential analysis of homogeneous series of similar microscopic images without further user intervention. The software tool entitled BioFilmAnalyzer is freely available online at https://bitbucket.org/rogex/biofilmanalyzer/downloads/.
Optical Coherence Tomography Reveals Self-Organizing Di-Fork Architecture of Mice Cutaneous Scars
Authors: Ghosh Biswajoy , Mandal Mousumi , Mitra Pabitra , Chatterjee Jyotirmoy 
Published: August 2017

AbstractScientific studies report crucial impacts of biomechanical effectors to modulate wound healing either by scarring or regeneration. Further, the biological decision to predominantly favor the former is still cryptic. Real-time visualization of biomechanical manifestationsin situin scarring is hence necessary. Endorsed by nanostructural testing, synthetic phantom analysis, and computational simulations, we found strong mechanobiological correlates for Swept Source Optical Coherence Tomography (SS-OCT) speckles in mice cutaneous repair (full-thickness) up to 10 months. The theoretical basis of the optomechanics to provide insights into scar form-factor and evolution is proposed. Optomechanical changes have been considered as the resultant of intrinsic (e.g. fiber elastic modulus) and gross tissue mechanics (extracellular matrix (ECM)) in maturing scars. Non-invasive optomechanics supported with microscopic findings reveal scar’s cross-sectional self-organizing di-fork architecture. Dual-compartment heterogeneity of di-fork exhibits stress-evading features with a dichotomy in inhabitant cellular stress-fiber distributions. This differential interactivity of scar with adjoining tissues reflects its architectural intelligence to compensate tissue loss (hypodermis/muscle) by assembling into a di-fork. Gradual establishment of baseline shifted lasting mechanobiological steady-state, later in scarring, expose scar as an alternate stable state within the skin.Significance StatementWound repair in mammals, predominantly culminates into function compromising scar that is occasionally fatal in vital organs. How the biological system often adopts scarring over a restorative regeneration is yet a conundrum. Wound and ambient mechanics play a pivotal role in deciding the healing fate. SS-OCT is hence demonstrated here as a non-invasive window to such mechanical manifestations during skin wound healing. This exposed gradual emergence of temporally maintained and stress-resilient di-fork architecture of the scar with differential neighborhood interfaces. Accommodation of such an alternate self-organizing steady-state of scar sheds light on its sustenance and paradoxical selection.
A Rho-GTPase based model explains spontaneous collective migration of neural crest cell clusters
Authors: Merchant Brian , Edelstein-Keshet Leah , Feng James J. 
Published: August 2017

AbstractWe propose a model to explain the spontaneous collective migration of neural crest cells in the absence of an external gradient of chemoattractants. The model is based on the dynamical interaction between Rac1 and RhoA that is known to regulate the polarization, contact inhibition and co-attraction of neural crest cells. Coupling the reaction-diffusion equations for active and inactive Rac1 and RhoA on the cell membrane with a mechanical model for the overdamped motion of membrane vertices, we show that co-attraction and contact inhibition cooperate to produce persistence of polarity in a cluster of neural crest cells by suppressing the random onset of Rac1 hotspots that may mature into new protrusion fronts. This produces persistent directional migration of cell clusters in corridors. Our model confirms a prior hypothesis that co-attraction and contact inhibition are key to spontaneous collective migration, and provides an explanation of their cooperative working mechanism in terms of Rho GTPase signaling. The model shows that the spontaneous migration is more robust for larger clusters, and is most efficient in a corridor of optimal confinement.