bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intestinal Microbiota in Hirschsprung Disease
Authors: Neuvonen Malla I. , Korpela Katri , Kyrklund Kristiina , Salonen Anne , de Vos Willem , Rintala Risto J. , Pakarinen Mikko P. 
Published: April 2018

ABSTRACTObjectives:The aim of the study was to characterize the microbiota profiles of patients with Hirschsprung disease (HD) and to evaluate this in relation to postoperative bowel function and the incidence of Hirschsprung‐associated enterocolitis (HAEC).Methods:All patients operated on for HD at our center between 1987 and 2011 were invited to answer questionnaires on bowel function and to participate in a clinical follow‐up for laboratory investigations, including fecal DNA extraction, fecal calprotectin (FC), and brush border lactase (LCT)genotyping. The microbiota compositions of patients with HD were compared with those of healthy controls aged between 2 and 7 years.Results:The microbiota composition of eligible patients with HD (n = 34; median age 12 [range, 3–25] years) differed from the healthy controls (n = 141), showing decreased overall microbial richness (P< 0.005). Seventy‐seven percent had experienced HAEC. Normal maturation of the intestinal flora was not observed, but patients had a significantly increased abundance of Proteobacteria among other taxa (P< 0.005) resulting in a reduced carbohydrate degradation potential, as predicted by the taxonomic composition. Genetic lactase deficiency was present in 17% and did not correlate with bowel symptoms. No patients reported active HAEC at the time of sampling and FC was within the normal range in all samples.Conclusions:Patients with HD and HAEC had a significantly altered intestinal microbiome compared to healthy individuals, characterized by a lack of richness and pathologic expansions of taxa, particularly Enterobacteria and Bacilli. Further evaluation is needed to identify whether these observations are intrinsic to HD or secondary to the recurrent use of antibiotics during early childhood.
Investigating Changes in Weight and Body Composition Among Women in Adjuvant Treatment for Breast Cancer
Authors: Pedersen Birgith , Delmar Charlotte , Lörincz Tamás , Falkmer Ursula , Grønkjær Mette 
Published: April 2018

Background
Despite several investigations, findings on weight changes during and after adjuvant treatment for breast cancer are diverse and point in several directions.

Objective
The aims of this study were to investigate changes in weight and body composition associated with contemporary anticancer medication and to examine factors that might influence the assessment and diversity of the findings.

Methods
This article used the method of a scoping review to map the body of literature. From searching the databases PubMed, CINAHL, and EMBASE using MeSH terms, CINAHL terms, and Emtree, as well as free text, 19 articles were selected for further investigation.

Results
The scoping review illustrates how findings in weight and body composition changes fluctuate over time as illustrated in 4 measure points: short term, 1 year, 18 months/2 years, and long term. The studies displayed differences regarding study designs, sample sizes, treatment regimens, measure points and techniques, and cutoff values for assessing weight changes, which make it difficult to synthesize findings and provide strong evidence for use in clinical practice.

Conclusion
Synthesizing findings over time illustrates the need for attention on younger premenopausal women given chemotherapy. Weight need to be monitored for at least 2 years as short-term changes may be caused by increased body water, whereas long-term changes seem to be related with increased fat mass essential for risking recurrence and early death.

Implications for Practice
The diversity in methods discloses the need for the research community to reach consensus regarding study designs for future research in this area.
Psychometric Testing of the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire–Chemotherapy-Induced Peripheral Neuropathy 20-Item Scale Using Pooled Chemotherapy-Induced Peripheral Neuropathy Outcome Measures Standardization and Alliance for Clinical Trials in Oncology A151408 Study Data
Authors: Smith Ellen M. Lavoie , Banerjee Tanima , Yang James J. , Bridges Celia M. , Alberti Paola , Sloan Jeff A. , Loprinzi Charles 
Published: April 2018

Background
No criterion-standard patient-reported outcome measure of chemotherapy-induced peripheral neuropathy (CIPN) exists.

Objectives
The aims of this study were to reevaluate the sensitivity, reliability, and validity of the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire–CIPN (QLQ-CIPN20) measure and suggest possible revisions that could strengthen it.

Methods
Cross-sectional QLQ-CIPN20 data from 8 European countries (n = 271) were pooled with data from 4 North American multisite CIPN intervention trials (n = 884). The combined sample (N = 1155) included patients with varied cancer diagnoses who had received neurotoxic chemotherapy. Item score ranges, Cronbach's α, and exploratory factor analysis were used to evaluate sensitivity, internal consistency, and structural validity.

Results
Individual item mean scores ranged from 1.21 to 2.34 (SD range, 0.55–1.17). All item scores encompassed the entire 1 to 4 range. We recommend that 4 items be removed because of low item-item score correlations (r < 0.30). On the basis of the remaining 16 items, 88% of the variance was explained by 2 factors whose Cronbach's α coefficients were .90 and .85. However, items lacked conceptual alignment with previously published factor structures.

Conclusion
Using a large, diverse sample of European and North American participants, the reduced 16-item QLQ-CIPN20 is sensitive and internally consistent. However, factor analysis results revealed an unstable factor structure.

Implications for Practice
The use of a reliable, valid, and sensitive criterion-standard QLQ-CIPN20 variant in clinical practice settings could improve function, quality of life, and CIPN symptom control by facilitating patient reporting and thereby clinician awareness of this underrecognized consequence of cancer therapy.
Using Hourly Time-Outs and a Standardized Tool to Promote Team Communication, Medical Record Documentation, and Patient Satisfaction During Second-Stage Labor
Authors: Wood Jessica , Stevenson Eleanor 
Published: April 2018

Abstract

Background:
During labor, effective communication and collaboration among the healthcare team is critical for patient safety; however, there is currently no standard for communication and documentation of the plan of care as agreed upon by healthcare team members and the woman in labor.

Objectives:
The goal of this project was to increase consistency in communication and collaboration between clinicians and laboring women during second-stage labor.

Methods:
An hourly “time-out” meeting of all healthcare team members was initiated for all women during second-stage labor. A documentation tool was implemented to ensure regular and clear communication between the clinical team and laboring women. Data were collected via medical review of cases of second-stage labor lasting more than 2 hours (n = 21 in the pre-implementation group; n = 39 for 3 months postimplementation; and n = 468 patients for 2 years post-implementation). Surveys were conducted of the clinical team (n = 40) and patients (n = 28).

Results:
Following implementation, documented agreement of the plan of care increased from 14.3% before the project to 82.1% 3 months after implementation and remained at 81.6% 2 years after implementation. All nurses who participated in the survey reported a clear understanding of how and when to complete necessary medical record documentation during second-stage labor. The providers viewed the project favorably. Most women (92.9%) reported satisfaction with their experience. This project enhanced collaborative communication between members of the clinical team and laboring women and improved patient satisfaction. The improvements were sustainable over a 2-year period.
Eliminating Geographic Bias Improves Match Results: An Analysis of Program Preferences and Their Impact on Rank Lists and Results
Authors: Nagarkar Purushottam A. , Janis Jeffrey E. 
Published: April 2018

Background:
Previous studies have demonstrated that programs emphasize United States Medical Licensing Examination scores, publications, and geography in creating rank lists. The authors aimed to quantify the importance of geography and to determine how eliminating geographic preferences would affect Match outcomes.

Methods:
The Match algorithm was implemented and validated on 6 years of deidentified data from the San Francisco Match (2009 to 2014). A “consensus” ranking was generated for each year—all applicants were ordered into a single list using Markov chain rank aggregation. Each program’s rank list was reordered using the consensus list, and a new Match result was simulated. Statistical analysis was carried out with Microsoft Excel.

Results:
Variation of program rank lists from the consensus rank list was driven by geography (training in the same medical center or state as the ranking program), “pedigree” (top 25 ranking of applicants’ prior training), and foreign medical graduation status. Step 1 scores, publications, and medical school or residency region were not factors. The simulated Match resulted in a slight increase in the match rate. The median normalized number needed to match decreased from 6.7 to 6.5, and 80 percent of applicants had an unchanged or better result compared to the actual Match.

Conclusions:
Geography is the primary driver of variation between program rank lists. Removing this variation would result in fewer unfilled positions, no significant change in the average number needed to match, and improved Match outcomes for most applicants. Programs should critically evaluate whether their geographic biases reflect underlying information about applicant quality.
Chronic Recurrent Multifocal Osteomyelitis of the Mandible: A Diagnostic Challenge
Authors: Camison Liliana , Mai Rick S. , Goldstein Jesse A. , Costello Bernard J. , Torok Kathryn S. , Losee Joseph E. 
Published: April 2018

Summary:
Chronic recurrent multifocal osteomyelitis is a rare autoinflammatory bone disorder of children and adolescents characterized by monofocal or multifocal inflammatory bone lesions that are culture-negative on biopsy, associated with periods of exacerbation and resolution that can last over several months to years. Although it is predominantly a disease of long bones and the spine, craniofacial involvement is not uncommon, affecting the mandible in up to one-fifth of cases. Similarities with other causes of osteitis in clinical presentation and imaging, and the lack of specific symptoms or laboratory tests, make chronic recurrent multifocal osteomyelitis mainly a diagnosis of exclusion. An accurate diagnosis is required for appropriate treatment to induce remission. This article highlights the challenges faced by plastic and oral surgeons in diagnosing mandibular chronic recurrent multifocal osteomyelitis, and describes two pediatric patients affected with the disease. Both cases were initially confused with other entities, leading to unnecessary initial treatments and a delayed diagnosis. A review aimed at surgeons summarizes the major aspects of this condition so that it is considered as a differential diagnosis in young patients presenting with a facial bony mass.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, V.
Enhancement of Progenitor Cells by Two-Step Centrifugation of Emulsified Lipoaspirates
Authors: Pallua Norbert , Grasys Justinas , Kim Bong-Sung 
Published: April 2018

Background:
Adipose-derived stem cells, endothelial progenitor cells, and soluble factors jointly contribute to the regenerative effect of fat grafts. Nanofat grafting emulsifies the lipoaspirate and increases the progenitor cell yield. In the present study, the authors evaluated their extended nanofat grafting method that includes two additional centrifugation steps and results in a lipoaspirate of low volume that they termed “lipoconcentrate.” Furthermore, the authors investigated the oily fractions after centrifugation for their regenerative potential.

Methods:
Lipoaspirates of 20 healthy patients were processed by emulsification and/or centrifugation. Six groups were created: native (not emulsified) fat, 1× centrifuged native fat, 2× centrifuged native fat, nanofat (emulsified), 1× centrifuged nanofat, and lipoconcentrate (i.e., 2× centrifuged nanofat). The oily phases after the centrifugation steps were collected. Progenitor cells and basic fibroblast growth factor, insulin-like growth factor 1, matrix metalloproteinase-9, platelet-derived growth factor-BB, and vascular endothelial growth factor-A levels were measured by flow cytometry and immunoassays.

Results:
Lipoconcentrate contained significantly higher numbers of adipose-derived stem cells and endothelial progenitor cells per gram compared with all other fractions. No difference of all five soluble factors between groups was found. The oily phases after centrifugation showed no or very few adipose-derived stem cells and endothelial progenitor cells, and no or very low levels of soluble factors.

Conclusions:
Centrifugation of emulsified lipoaspirates increases the progenitor cell count in the lipoaspirate. The oily phase after centrifugation of lipoaspirates may be disposable because of the minuscule content of progenitor cells and soluble factors.
Ezrin enrichment on curved membranes requires a specific conformation or interaction with a curvature-sensitive partner
Authors: Tsai Feng-Ching , Bertin Aurélie , Bousquet Hugo , Manzi John , Senju Yosuke , Tsai Meng-Chen , Picas Laura , Miserey-Lenkei Stéphanie , Lappalainen Pekka , Lemichez Emmanuel , Coudrier Evelyne , Bassereau Patricia 
Published: April 2018

AbstractOne challenge in current cell biology is to decipher the biophysical mechanisms governing protein enrichment on curved membranes and the resulting membrane deformation. The ERM protein ezrin is abundant and associated with cellular membranes that are flat or with positive or negative curvatures. Using in vitro and cell biology approaches, we assess mechanisms of ezrin’s enrichment on curved membranes. We evidence that ezrin (ezrinWT) and its phosphomimetic mutant T567D (ezrinTD) do not deform membranes but self-assemble anti-parallelly, zipping adjacent membranes. EzrinTD’s specific conformation reduces intermolecular ezrin interactions, allows binding to actin filaments, and promotes ezrin binding to positively curved membranes. While neither ezrinTD nor ezrinWT senses negative membrane curvature alone, we demonstrate that interacting with curvature sensors I-BAR-domain proteins facilitates ezrin enrichment in negatively curved membrane protrusions. Overall, our work reveals new mechanisms, specific conformation or binding to a curvature sensor partner, for targeting curvature insensitive proteins to curved membranes.
Voltage gated N-type Ca-channels in Neurogliaform interneurons in the rat Prefrontal Cortex
Authors: Dalby Nils Ole , Grunnet Morten 
Published: April 2018

AbstractThe fastspiking parvalbumin expressing basketcells (FS BC) and the neurogliaform interneurons (NGF IN) innervate somatic and dendritic compartments of postsynaptic pyramidal neurons, respectively. Here we have used paired recordings of each type of interneuron with a postsynaptic pyramidal neuron in layer II-IV of the adult rat prefrontal cortex (PFC) to characterize the interneuron action potentials (AP), evoked IPSC characteristics and response to the GAT-1 inhibitor NNC 711 and the N-type Ca-channel inhibitor ω-conotoxin GVIA. GABA released from FS BCs were insensitive to ω-conotoxin GVIA (0.5 μM), the postsynaptic response did not desensitize and the IPSC was unchanged in NNC 711 (2 μM). Conversely, IPSCs generated by APs from NGF INs were 80 % inhibited by ω-conotoxin GVIA, displayed a strong degree of desensitization and the decay-time of the IPSCs doubled in NNC 711. We used these pharmacological differences to identify the source of GABA in paradigms of synaptic overspill induced by extracellular stimulation. The decaytime of the electrically evoked event doubled in NNC 711 and this increase was reversed by subsequent application of ω-conotoxin GVIA, suggesting that the source of GABA responding to NNC 711 originate from axons that terminate on pyramidal neuron dendrites and employ N-type Ca-channels for release.
One prophage WO gene rescues cytoplasmic incompatibility inDrosophila melanogaster
Authors: Shropshire J. Dylan , On Jungmin , Layton Emily M. , Zhou Helen , Bordenstein Seth R. 
Published: April 2018

AbstractWolbachiaare maternally-inherited, intracellular bacteria at the forefront of vector control efforts to curb arbovirus transmission. In international field trials, the cytoplasmic incompatibility (CI) drive system ofwMelWolbachiais deployed to replace target vector populations, whereby aWolbachia– induced modification of the sperm genome kills embryos. However,Wolbachiain the embryo rescue the sperm genome impairment, and therefore CI results in a strong fitness advantage for infected females that transmit the bacteria to offspring. The two genes responsible for thewMel-induced sperm modification of CI,cifAandcifB, were recently identified in the eukaryotic association module of prophage WO, but the genetic basis of rescue is unresolved. Here we use transgenic and cytological approaches to demonstrate thatcifAindependently rescues CI and nullifies embryonic death caused bywMelWolbachiainDrosophila melanogaster. Discovery ofcifAas the rescue gene and previously one of two CI induction genes establishes a new ‘Two-by-One’ model that underpins the genetic basis of CI. Results highlight the central role of prophage WO in shapingWolbachiaphenotypes that are significant to arthropod evolution and vector control.Significance StatementThe World Health Organization recommended pilot deployment ofWolbachia-infected mosquitoes to curb viral transmission to humans. Releases of mosquitoes are underway worldwide becauseWolbachiacan block replication of these pathogenic viruses and deterministically spread by a drive system termed cytoplasmic incompatibility (CI). Despite extensive research, the underlying genetic basis of CI remains only half-solved. We recently reported that two prophage WO genes recapitulate the modification component of CI in a released strain for vector control. Here we show that one of these genes underpins rescue of CI. Together, our results reveal the complete genetic basis of this selfish trait and pave the way for future studies exploring WO prophage genes as adjuncts or alternatives to current control efforts.
Circular RNA expression in human hematopoietic cells is widespread and cell-type specific
Authors: Nicolet Benoit P , Engels Sander , Aglialoro Francesca , van den Akker Emile , von Lindern Marieke , Wolkers Monika C 
Published: April 2018

ABSTRACTHematopoietic stem cells differentiate into a broad range of specialized blood cells. This process is tightly regulated and depends on transcription factors, micro-RNAs, and long non-coding RNAs. Recently, also circular RNA (circRNA) were found to regulate cellular processes. Their expression pattern and their identity is however less well defined. Here, we provide the first comprehensive analysis of circRNA expression in human hematopoietic progenitors, and in differentiated lymphoid and myeloid cells. We here show that the expression of circRNA is cell-type specific, and increases upon maturation. circRNA splicing variants can also be cell-type specific. Furthermore, nucleated hematopoietic cells contain circRNA that have higher expression levels than the corresponding linear RNA. Enucleated blood cells, i.e. platelets and erythrocytes, were suggested to use RNA to maintain their function, respond to environmental factors or to transmit signals to other cells via microvesicles. Here we show that platelets and erythrocytes contain the highest number of circRNA of all hematopoietic cells, and that the type and numbers of circRNA changes during maturation. This cell-type specific expression pattern of circRNA in hematopoietic cells suggests a hithero unappreciated role in differentiation and cellular function.
Pervasive chromatin remodeling at X-inactivation escape genes in schizophrenic males
Authors: Hassan Hezha , Hegyi Hedi 
Published: April 2018

AbstractReanalyzing a large methylome dataset of 225 schizophrenic and 450 control samples derived from the prefrontal cortex revealed that 6 male patients have predominantly hypomethylated probes mostly on chromosome X, affecting the same genes in all six. Network analysis of the differentially methylated genes revealed a dense network of transcription factors, histone and chromatin remodeling proteins, with 15 of the X-located genes expressed at the synapse, including NLGN4X, SYN1 and MECP2. Mapping a recent experimental dataset of G-quadruplexes (G4s) onto the differentially methylated probes revealed that the probes in the group of six overlapping with G4s on chromosome X are significantly more hypomethylated than non-overlapping and non-X probes whereas in the rest of the patients G4-overlapping probes are more methylated than non-overlapping ones, revealing a distinct pathology, involving chromatin remodeling for the six patients. Unexpectedly, the hypomethylated genes in them significantly overlapped with gene locations where X-inactivation escapism was observed in women.
Single cell RNA-seq denoising using a deep count autoencoder
Authors: Eraslan Gökcen , Simon Lukas M. , Mircea Maria , Mueller Nikola S. , Theis Fabian J. 
Published: April 2018

AbstractSingle-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene expression at a cellular resolution. However, noise due to amplification and dropout may obstruct analyses, so scalable denoising methods for increasingly large but sparse scRNAseq data are needed. We propose a deep count autoencoder network (DCA) to denoise scRNA-seq datasets. DCA takes the count distribution, overdispersion and sparsity of the data into account using a zero-inflated negative binomial noise model, and nonlinear gene-gene or gene-dispersion interactions are captured. Our method scales linearly with the number of cells and can therefore be applied to datasets of millions of cells. We demonstrate that DCA denoising improves a diverse set of typical scRNA-seq data analyses using simulated and real datasets. DCA outperforms existing methods for data imputation in quality and speed, enhancing biological discovery.
GNE: A deep learning framework for gene network inference by aggregating biological information
Authors: Kishan K C , Li Rui , Cui Feng , Yu Qi , Haake Anne R. 
Published: April 2018

AbstractThe topological landscape of gene interaction networks provides a rich source of information for inferring functional patterns of genes or proteins. However, it is still a challenging task to aggregate heterogeneous biological information such as gene expression and gene interactions to achieve more accurate inference for prediction and discovery of new gene interactions. In particular, how to generate a unified vector representation to integrate diverse input data is a key challenge addressed here. We propose a scalable and robust deep learning framework to learn embedded representations to unify known gene interactions and gene expression for gene interaction predictions. These low-dimensional embeddings derive deeper insights into the structure of rapidly accumulating and diverse gene interaction networks and greatly simplify downstream modeling. We compare the predictive power of our deep embeddings to the strong baselines. The results suggest that our deep embeddings achieve significantly more accurate predictions. Moreover, a set of novel gene interaction predictions are validated by up-to-date literature-based database entries. GNE is freely available under the GNU General Public License and can be downloaded from Github (https://github.com/kckishan/GNE)