bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fetal stomach and gallbladder in contact with the bladder wall is a common ultrasound sign of stomach‐down left congenital diaphragmatic hernia
Authors: Morgan Tara A. , Basta Amaya , Filly Roy A. 
Published: September 2016

ABSTRACTPurposeThe aim of this study was to identify sonographic (US) findings that can assist in prenatal diagnosis of stomach‐down left congenital diaphragmatic hernia (CDH), specifically related to positioning of the abdominal contents including the stomach, bladder, and gallbladder.MethodsAll US examinations with a postnatally confirmed diagnosis of stomach‐down left CDH over a 13‐year period were retrospectively reviewed for abnormal position of the abdominal contents, including whether the fetal stomach was in contact with the urinary bladder. Normal fetuses that underwent comprehensive US surveys were similarly evaluated for comparison in a 2:1 ratio.ResultsTwenty‐two fetuses with stomach‐down left CDH were identified in a cohort of 278 fetuses with left CDH. In 15/22 (68.2%) cases of stomach‐down left CDH, the bladder and stomach walls were in contact. Contact of the fetal gallbladder with the fetal bladder wall was also observed and was present even more commonly (17/22 cases [77.3%]). There was no case of either the stomach or gallbladder in contact with the bladder wall in the normal fetal cohort (n = 44).ConclusionsRecognition of the fetal stomach and/or gallbladder in contact with the bladder wall can help in the detection of stomach‐down left CDH. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:8–13, 2017
Comparative proteome analysis of egg yolk plasma proteins during storage
Authors: Gao Dan , Qiu Ning , Liu Yaping , Ma Meihu 
Published: September 2016

AbstractBACKGROUNDPhysical changes such as chicken egg white thinning and egg yolk flattening occur during storage, implying a decline in egg quality. To reveal the deteriorative process related to chicken egg internal quality, a comparative proteomic method was used in this study to analyze the alterations in egg yolk plasma proteins at different storage times (0, 20 and 40 days) under an ambient temperature of 22 ± 2 °C.RESULTSUsing two‐dimensional electrophoresis followed by matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry, 33 protein spots representing 12 proteins were identified with significant (P < 0.05) alterations in abundance at different storage times. The proteins that showed significant changes in abundance included serum albumin, vitellogenin fragments, IgY chains, ovalbumin, ovoinhibitor, α2‐macroglobulin‐like protein 1‐like, hemopexin, transthyretin, apolipoprotein A‐I and β2‐glycoprotein I precursor. Accelerating degradation for most egg yolk plasma proteins was observed after prolonged storage (from day 20 to day 40).CONCLUSIONIt is likely that the increased degradation of protease inhibitors such as ovoinhibitor and α2‐macroglobulin‐like protein 1‐like during prolonged storage lead to an imbalance of protease and antiprotease in egg yolk, which may play a key role in the degradation of egg yolk proteins. These findings will provide an insight into the effects of storage on egg yolk protein changes and give a deeper understanding of the deteriorative process of chicken egg yolk. © 2016 Society of Chemical Industry
Synthesis and characterization of poly(3,4‐ethylenedioxythiophene)/poly(lactic acid) nanofibres by electrospinning
Authors: Praharaj Bhatnagar Manoj , Kelkar Sunder , Mahanwar Prakash 
Published: September 2016

AbstractThe poly(3,4‐ethylenedioxythiophene) (PEDOT) family of polymers is a technologically important class of conducting polymers showing high stability, medium band gap, low redox potential and high optical transparency in the electrically conductive state. While PEDOT nanotubes and nanofibres have been synthesized electrochemically, significant opportunity exists for developing a convenient chemical synthetic route for the bulk synthesis of nanostructured PEDOT for potential use in the design of next‐generation nano‐electronic circuits and field emission devices. In this paper, chemical oxidative polymerization was used to synthesize PEDOT nanoparticles. These nanoparticles were co‐electrospun with poly(l‐lactic acid) from a solution in acetone and N,N‐dimethylformamide. The PEDOT particles were analysed using attenuated total reflectance–Fourier transform infrared spectroscopy and particle size distribution using dynamic light scattering. The synthesized nanofibre mats were studied using differential scanning calorimetry and scanning electron microscopy, and conductivity was measured using a two‐probe conductivity tester. © 2016 Society of Chemical Industry
Relationship of plant diversity with litter and soil available nitrogen in an alpine meadow under a 9‐year grazing exclusion
Authors: Zou Jingru , Luo Caiyun , Xu Xingliang , Zhao Na , Zhao Liang , Zhao Xinquan 
Published: September 2016

AbstractGrazing exclusion is widely used globally to restore degraded grasslands. Plant diversity has important impacts on grassland ecosystem functions, including grassland productivity and carbon storage. In this study, we selected a Kobresia meadow on the Qinghai–Tibetan Plateau to investigate how grazing exclusion affects plant diversity. Inorganic nitrogen (NH4+ and NO3−) was also measured because its availability impacts plant growth. We found that plant diversity in the meadow was significantly lower under grazing exclusion (fenced meadow) for 9 years compared with moderate grazing. Accumulated litter was significantly higher under grazing exclusion (386.41 g m−2) compared with grazing (58.77 g m−2). Soil inorganic nitrogen at 0–5 cm depth was significantly higher under grazing exclusion (13.60 × 10−2 g kg−1) than under grazing (9.40 × 10−2 g kg−1). The composition of the four functional groups (grasses, sedges, legumes, and forbs) might alter in response to significant changes in the amount of litter and soil available nitrogen content under grazing exclusion compared with grazing. However, the enhanced soil available nitrogen content showed weak feedbacks on plant diversity. In conclusion, light limitation induced by increased amounts of litter may be the main factor causing decreased plant diversity in grazing‐excluded meadows compared with moderately grazed meadows.
Association of the brain-derived neurotrophic factor Val66Met polymorphism with negative symptoms severity, but not cognitive function, in first-episode schizophrenia spectrum disorders
Authors: Mezquida G. , Penadés R. , Cabrera B. , Savulich G. , Lobo A. , González-Pinto A. , Penzol M.J. , Corripio I. , Fernandez-Egea E. , Gassó P. , Cuesta M.J. , Bernardo M. ,   PEPs group
Published: September 2016

AbstractObjectiveA functional polymorphism of the brain-derived neurotrophic factor gene (BDNF) Val66Met has been associated with cognitive function and symptom severity in patients with schizophrenia. It has been suggested that the Val66Met polymorphism has a role as a modulator in a range of clinical features of the illness, including symptoms severity, therapeutic responsiveness, age of onset, brain morphology and cognitive function. However, little work has been done in first-episode schizophrenia (FES) spectrum disorders. The objective of this study is to investigate the association of the BDNF Val66Met polymorphism on cognitive function and clinical symptomatology in FES patients.MethodsUsing a cross-sectional design in a cohort of 204 patients with FES or a schizophrenia spectrum disorder and 204 healthy matched controls, we performed BDNF Val66Met genotyping and tested its relationship with cognitive testing (attention, working memory, learning/verbal memory and reasoning/problem-solving) and assessment of clinical symptom severity.ResultsThere was no significant influence of the BDNF allele frequency on cognitive factor scores in either patients or controls. An augmented severity of negative symptoms was found in FES patients that carried the Met allele.ConclusionsThe results of this study suggest that in patients with a first-episode of schizophrenia or a schizophrenia spectrum disorder, the BDNF Val66Met polymorphism does not exert an influence on cognitive functioning, but is associated with negative symptoms severity. BDNF may serve as suitable marker of negative symptomatology severity in FES patients within the schizophrenia spectrum.
Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase
Authors: Li Dayong , Huang Zhiyuan , Song Shuhui , Xin Yeyun , Mao Donghai , Lv Qiming , Zhou Ming , Tian Dongmei , Tang Mingfeng , Wu Qi , Liu Xue , Chen Tingting , Song Xianwei , Fu Xiqin , Zhao Bingran , Liang Chengzhi , Li Aihong , Liu Guozhen , Li Shigui , Hu Songnian , Cao Xiaofeng , Yu Jun , Yuan Longping , Chen Caiyan , Zhu Lihuang 
Published: September 2016

SignificanceBecause of its practical importance and scientific significance, heterosis (hybrid vigor) is an interesting topic for both breeders and biologists. However, although heterosis has been applied successfully to increase crop yields, the molecular mechanisms involved remain obscure. In this study, using an integrative approach, we found that multiple quantitative trait loci (QTLs) cumulatively drive yield heterosis in hybrid rice by regulating two grain-yield component traits in which theRH8(rice heterosis 8) gene plays a major role. Our research highlights the importance of integrative methods to uncover the molecular mechanism of heterosis and thus pave a way toward revealing the molecular mechanisms in rice heterosis in detail.
Robust classification of single-cell transcriptome data by nonnegative matrix factorization
Authors: Shao Chunxuan , Höfer Thomas 
Published: September 2016

Abstract

Motivation
Single-cell transcriptome data provide unprecedented resolution to study heterogeneity in cell populations and present a challenge for unsupervised classification. Popular methods, like principal component analysis (PCA), often suffer from the high level of noise in the data.

Results
Here we adapt Nonnegative Matrix Factorization (NMF) to study the problem of identifying subpopulations in single-cell transcriptome data. In contrast to the conventional gene-centered view of NMF, identifying metagenes, we used NMF in a cell-centered direction, identifying cell subtypes (‘metacells’). Using three different datasets (based on RT-qPCR and single cell RNA-seq data, respectively), we show that NMF outperforms PCA in identifying subpopulations in an accurate and robust way, without the need for prior feature selection; moreover, NMF successfully recovered the broad classes on a large dataset (thousands of single-cell transcriptomes), as identified by a computationally sophisticated method. NMF allows to identify feature genes in a direct, unbiased manner. We propose novel approaches for determining a biologically meaningful number of subpopulations based on minimizing the ambiguity of classification. In conclusion, our study shows that NMF is a robust, informative and simple method for the unsupervised learning of cell subtypes from single-cell gene expression data.

Availability and Implementation
https://github.com/ccshao/nimfa

Supplementary information
Supplementary data are available at Bioinformatics online.
FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners
Authors: Rodriguez-Lujan Irene , Hasty Jeff , Huerta Ramón 
Published: September 2016

Abstract

Motivation
Despite RNA-seq reads provide quality scores that represent the probability of calling a correct base, these values are not probabilistically integrated in most alignment algorithms. Based on the quality scores of the reads, we propose to calculate a lower bound of the probability of alignment of any fast alignment algorithm that generates SAM files. This bound is called Fast Bayesian Bound (FBB) and serves as a canonical reference to compare alignment results across different algorithms. This Bayesian Bound intends to provide additional support to the current state-of-the-art aligners, not to replace them.

Results
We propose a feasible Bayesian bound that uses quality scores of the reads to align them to a genome of reference. Two theorems are provided to efficiently calculate the Bayesian bound that under some conditions becomes the equality. The algorithm reads the SAM files generated by the alignment algorithms using multiple command option values. The program options are mapped into the FBB reference values, and all the aligners can be compared respect to the same accuracy values provided by the FBB. Stranded paired read RNA-seq data was used for evaluation purposes. The errors of the alignments can be calculated based on the information contained in the distance between the pairs given by Theorem 2, and the alignments to the incorrect strand. Most of the algorithms (Bowtie, Bowtie 2, SHRiMP2, Soap 2, Novoalign) provide similar results with subtle variations.

Availability and Implementation
Current version of the FBB software is provided at https://bitbucket.org/irenerodriguez/fbb.

Supplementary information
Supplementary data are available at Bioinformatics online.
Patient Satisfaction and Quality of Life Following Surgery for Hidradenitis Suppurativa
Authors: Kohorst John J. , Baum Christian L. , Otley Clark C. , Roenigk Randall K. , Pemberton John H. , Dozois Eric J. , Tran Nho V. , Davis Mark D.P. 
Published: September 2016

BACKGROUND
Hidradenitis suppurativa (HS) is a progressive, recurrent inflammatory disorder.

OBJECTIVE
To assess long-term satisfaction and postoperative perceptions among patients who underwent surgical management of HS.

MATERIALS AND METHODS
A questionnaire was mailed to 499 HS surgical patients to assess surgical outcome, satisfaction, and quality of life.

RESULTS
Of the 499 questionnaires mailed, 113 were returned (22.6% response rate) and 2 were excluded for redundancy. Of the 111 respondents, 65 (58.6%) were female, 91 (82.0%) had Hurley Stage III disease, 88 (79.3%) were treated with excision and 23 (20.7%) with unroofing, 45 (40.5%) had perianal or perineal disease, and 41 (36.9%) had axillary disease. Most patients were satisfied or very satisfied with their surgical results (84.7%; 94 of 111), were glad they underwent surgery (96.3%; 105 of 109), and would recommend surgery to a friend or relative (82.6%; 90 of 109). Most patients were satisfied or very satisfied with the appearance of their healed wound (62.4%; 68 of 109). Retrospective mean quality of life increased significantly from 5 preoperatively to 8.4 postoperatively (p < .001).

CONCLUSION
Hidradenitis suppurativa surgical management was well regarded by patients and should be considered by future patients to limit the morbidity of HS.
The Northwestern Abdominoplasty Scar Model: A Novel Human Model for Scar Research and Therapeutics
Authors: Lanier Steven T. , Liu Jing , Chavez-Munoz Claudia , Mustoe Thomas A. , Galiano Robert D. 
Published: September 2016

Summary:
There is a growing interest in the development and evaluation of therapeutic agents that improve the cosmetic appearance of scars. Existing nonhuman animal models to study scarring, while valuable, have well-acknowledged limitations, as it is accepted that the biology of human scarring differs significantly from scarring in other species. Moreover, human clinical trials of scarring require large numbers of subjects to achieve statistical power and are plagued by inherent intersubject variability because of the complex nature of wound healing in human beings. As a better alternative, we have developed the Northwestern Abdominoplasty Scar Model—a novel human clinical model that permits analysis of up to 20 cutaneous scars in a single subject and allows for not only visual scar comparison, but also histologic and molecular analyses of factors involved in scarring and wound healing. We have utilized this model in 5 early phase clinical trials designed to test the safety and efficacy of a variety of scar therapeutics without any complications to date. The model not only is applicable to scar therapeutics, but also can be utilized for other applications, such as the testing of implantable biomaterials, injectable products, therapies such as lasers, or even for in vivo study of wound healing processes in humans.
Retroauricular Pleomorphic Adenoma Arising from Heterotopic Salivary Gland Tissue
Authors: Grome Luke , Bacaj Patrick , Borah Gregory 
Published: September 2016

Summary:
A 38-year-old woman is described who presented with a slowly growing mass on the posterior aspect of the left ear. Excision and histopathologic evaluation revealed a pleomorphic adenoma (PA) originating from heterotopic salivary gland tissue. Many authors have presented cases of PAs originating from ceruminous glands in the external auditory canal or of so-called chondroid syringoma originating from apocrine and eccrine sweat glands. This is the only case in the recent literature of a PA originating from a heterotopic rest of salivary gland tissue in the retroauricular region. The 3 main sources of PAs, their embryologic derivation, and treatment are described.
PARACENTRAL ACUTE MIDDLE MACULOPATHY AND DEEP RETINAL CAPILLARY PLEXUS INFARCTION SECONDARY TO REPERFUSED CENTRAL RETINAL ARTERY OCCLUSION
Authors: Iafe Nicholas A. , Onclinx Tania , Tsui Irena , Sarraf David 
Published: September 2016

Purpose:
To report a case of reperfused central retinal artery occlusion causing a globular pattern of paracentral acute middle maculopathy with en face optical coherence tomography (OCT).

Methods:
Retrospective case report. Widefield fluorescein angiography, en face OCT, and OCT-angiography were performed. Retinal capillary plexus vessel density (mm−1) was measured using OCT-angiography analysis and was defined as total vessel length (mm) per area (mm2).

Results:
A 76-year-old female presented with decreased vision in the left eye for 1 day. Widefield fluorescein angiography revealed delayed venous filling in the early phase and selective arterial staining in the late phase. Spectral domain OCT demonstrated paracentral acute middle maculopathy. Optical coherence tomography–angiography showed an ischemic deep retinal capillary plexus that colocalized with a globular shaped hyper-reflective pattern identified with structural en face OCT. Quantitative vessel density analysis comparing the fellow eye to the affected eye at presentation demonstrated 43% reduction in the superficial capillary plexus vessel density and 33% reduction of the deep capillary plexus in the affected eye. At 2 months follow-up, the reduction of superficial capillary plexus vessel density improved to 33%, whereas the deep capillary plexus vessel density reduced further to 35% compared with the fellow eye.

Conclusion:
The authors report a case of reperfused central retinal artery occlusion leading to a globular shaped paracentral acute middle maculopathy lesion with en face OCT. Quantitative OCT-angiography vessel density analysis in the chronic phase revealed disproportionate reduction of deep capillary plexus vessel density. The globular pattern of paracentral acute middle maculopathy with en face OCT can be an important clue to the diagnosis of central retinal artery occlusion.
Pulmonary Blastomycosis in a Hematopoietic Cell Transplant Recipient
Authors: Linder Kathleen A. , Kauffman Carol A. , Miceli Marisa H. 
Published: September 2016

Abstract
Infections with the endemic fungus Blastomyces dermatitidis are uncommonly reported in hematopoietic cell transplant recipients. We present a case of pulmonary blastomycosis in a patient who had an allogeneic hematopoietic cell transplant 10 months previously and who responded rapidly to treatment with voriconazole.
Outpatient Parenteral Antimicrobial Therapy and Antimicrobial Stewardship
Authors: Bauer Karri A. , Mangino Julie E. , Paolo-Hohman Debra , Goff Debra A. 
Published: September 2016

Objectives
Outpatient parenteral antimicrobial therapy (OPAT) is frequently used upon hospital discharge but often without infectious diseases (ID) or Antimicrobial Stewardship Programs (ASP) oversight. The purpose of this study was to evaluate the transition of care process for OPAT and identify the role of the ASP. Second, clinical and safety outcomes associated with the use of ertapenem for OPAT were evaluated.

Methods
This is a single-center, observational study of adult patients hospitalized from January 1, 2011, through December 31, 2011, who were discharged on ertapenem +/− additional antimicrobials. Population characteristics and clinical outcomes are outlined using descriptive statistics.

Results
There were 100 patients who met inclusion criteria. Clinical cure was achieved in 79% of patients. Median duration of ertapenem therapy was 21 (14–42) days. Among patients who had an ID consult, clinical cure was achieved in 59% compared with 41% of patients who did not have an ID consult (P = 1.000). The reasons for clinical failure included 15 (71%) lack of source control, 4 (19%) required an additional antibiotic, and 2 (10%) antibiotic-related adverse event. Sixteen patients could have potentially received an oral antibiotic instead of OPAT. Fourteen patients required readmission within 30 days.

Conclusions
The ASPs should assume a role in the management of OPAT patients and transition of care from inpatient to outpatient. We recommend a structured approach, including the implementation of a standard order set for patients discharged on OPAT.
Cytomegalovirus Polyradiculopathy in the Modern Age of Human Immunodeficiency Virus Therapies
Authors: Lee Timothy , Liu Sean , Kaplan-Lewis Emma , Lee Mikyung 
Published: September 2016

Abstract
Cytomegalovirus (CMV) polyradiculopathy in human immunodeficiency virus–infected patients is an increasingly rare disease given the widespread availability of effective antiretroviral therapy. Here, we describe a case of CMV polyradiculopathy in a man following the initiation of antiretrovirals. The patient presented with a 2-week history of rapidly progressing bilateral lower extremity weakness resulting in paraplegia; he was diagnosed with CMV polyradiculopathy based on cerebrospinal fluid and magnetic resonance imaging findings. Treatment with ganciclovir, foscarnet, and antiretroviral therapy resulted in rapid reduction of CMV viral load in cerebrospinal fluid and halting of disease progression. Six months after presentation, the patient continues to show improvement in lower extremity strength and has regained the ability to ambulate without assistance for short distances.
The Role of Metacognitive Self-Reflectivity in Emotional Awareness and Subjective Indices of Recovery in Schizophrenia
Authors: Bonfils Kelsey A. , Luther Lauren , George Sunita , Buck Kelly D. , Lysaker Paul H. 
Published: September 2016

Abstract
Emotional awareness deficits in people with schizophrenia have been linked to poorer objective outcomes, but no work has investigated the relationship between emotional awareness and subjective recovery indices or metacognitive self-reflectivity. The authors hypothesized that increased emotional awareness would be associated with greater self-esteem, hope, and self-reflectivity and that self-reflectivity would moderate links between emotional awareness and self-esteem and hope—such that significant relationships would only be observed at lower levels of self-reflectivity. Participants were 56 people with schizophrenia spectrum disorders. Correlations revealed that better emotional awareness was significantly associated with increased self-esteem and hope but not self-reflectivity. Self-reflectivity moderated the relationship between emotional awareness and self-esteem but not hope. Overall, findings suggest that emotional awareness may affect self-esteem for those low in self-reflectivity, but other factors may be important for those with greater self-reflectivity. Results emphasize the importance of interventions tailored to enhance self-reflective capacity in clients with schizophrenia.