bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective Evaluation of the Anatomy of the First Dorsal Compartment in Patients Requiring Surgery for De Quervain's Tenosynovitis
Authors: Matzon Jonas L. , Graham Jack G. , Lutsky Kevin F. , Takei T. Robert , Gallant Gregory G. , Beredjiklian Pedro K. 
Published: May 2019

Background We prospectively evaluated the surgical anatomy during first dorsal compartment release for De Quervain's tenosynovitis, with special attention to the superficial branch of the radial nerve (SBRN). Additionally, the incidence of tendon instability during surgery was assessed.
Methods This prospective cohort study consisted of 130 De Quervain's patients undergoing first dorsal compartment release. The treating surgeons recorded the type of incision used, the number of abductor pollicis longus (APL) and extensor pollicis brevis (EPB) tendon slips, the number of SBRN branches encountered, additional subcompartments created by any septations, and active/passive tendon stability.
Results A singular first dorsal compartment was found in 37% of cases, whereas 55% of patients had two subcompartments and 8% had three. Multiple APL tendon slips (range: 1–4) were identified in 78% of patients. In contrast, a single EPB tendon was found in 92% of patients (range: 0–2). At least one SBRN was encountered in 61% of cases. Following surgery, instability was evident in 9% of patients, who had tendons perch with passive wrist flexion. In one of these patients (<1%), the tendons dislocated volarly out of the first dorsal compartment during active flexion.
Conclusions The anatomical findings in our relatively large, prospective study of De Quervain's patients undergoing first dorsal compartment release are consistent with previous smaller and/or retrospective studies. Overall, we expect to encounter the SBRN during first dorsal compartment release in more than 50% of patients but are unconcerned if it is not visualized during a careful approach. Tendon instability has an incidence of 9%; however, dislocation is rare (<1%).
Plate Fixation for Unstable Displaced Distal Radius Fractures in Children
Authors: van Egmond Jeroen C. , Selles Caroline A. , Cleffken Berry I. , Roukema Gert R. , van der Vlies Kees H. , Schep Niels W.L. 
Published: May 2019

Background Distal radius fractures in children are normally treated by plaster immobilization. For displaced unstable distal radius fractures, closed reduction and Kirschner wire (k-wire) fixation can be performed. Disadvantages of k-wire fixation are the need for postoperative plaster treatment for several weeks, which may induce stiffness, and the risks of complications such as tendon irritation and pin-track infections. More invasive volar plate fixation is less popular, although this allows for direct mobilization and enhances anatomical reduction.
Purpose To present the functional outcomes of pediatric patients treated with volar plate fixation for unstable displaced distal radius fractures.
Patients and Methods A retrospective cohort study of all consecutive pediatric patients between September 2010 and July 2017 was performed. A total of 26 patients with a median age of 12.5 years were included. The primary objective was functional outcome determined by the Patient-Rated Wrist Evaluation (PRWE) questionnaire. Secondary objectives were range of motion, grip strength, radiological parameters, complications, and incidence of plate removal.
Results Median PRWE score was 3 after a median follow-up of 29 months. Range of motion and grip strength did not differ significantly between the injured and uninjured wrists. No wound infections were found. Plate removal was performed in 15 patients (58%).
Conclusion Volar plate fixation for unstable displaced distal radius fractures in children provides good functional and radiological outcomes with minor complications.
Level of evidence This is a Level IV cohort study.
Serotonin regulates mitochondrial biogenesis and function in rodent cortical neurons via the 5-HT2Areceptor and SIRT1–PGC-1α axis
Authors: Fanibunda Sashaina E. , Deb Sukrita , Maniyadath Babukrishna , Tiwari Praachi , Ghai Utkarsha , Gupta Samir , Figueiredo Dwight , Weisstaub Noelia , Gingrich Jay A. , Vaidya Ashok D. B. , Kolthur-Seetharam Ullas , Vaidya Vidita A. 
Published: May 2019

SignificanceNeuronal mitochondria are crucial organelles that regulate bioenergetics and also modulate survival and function under environmental challenges. Here, we show that the neurotransmitter serotonin (5-HT) plays an important role in the making of new mitochondria (mitochondrial biogenesis) in cortical neurons, through the 5-HT2Areceptor and via master regulators of mitochondrial biogenesis, SIRT1 and PGC-1α. Mitochondrial function is also enhanced by 5-HT, increasing cellular respiration and ATP, the energy currency of the cell. We found 5-HT reduces cellular reactive oxygen species and exerts potent neuroprotective action in neurons challenged with stress, an effect that requires SIRT1. These findings highlight a role for the mitochondrial effects of 5-HT in the facilitation of stress adaptation and identify drug targets to ameliorate mitochondrial dysfunction in neurons.
Photoluminescence properties of ultrathin CsPbCl3 nanowires on mica substrate
Authors: Gao Yan , Zhao Liyun , Shang Qiuyu , Li Chun , Liu Zhen , Li Qi , Wang Xina , Zhang Qing 
Published: May 2019

Abstract
Fabricating high-quality cesium lead chloride (CsPbCl3) perovskite nanowires (NWs) with dimension below 10 nm is not only of interests in fundamental physics, but also holds the great promise for optoelectronic applications. Herein, ultrathin CsPbCl3 NWs with height of ~7 nm, have been achieved via vapor phase deposition method. Power and temperature-dependent photoluminescence (PL) spectroscopy is performed to explore the emission properties of the CsPbCl3 NWs. Strong free exciton recombination is observed at ~3.02 eV as the temperature (T) is 78−294 K with binding energy of ~ 37.5 meV. With the decreasing of T, the PL peaks exhibit a first blueshift by 2 meV for T ~ 294−190 K and then a redshift by 4 meV for T ~ 190−78 K. The exciton–optical phonon interaction plays a major role in the linewidth broadening of the PL spectra with average optical phonon energy of ~48.0 meV and the interaction coefficient of 203.9 meV. These findings advance the fabrication of low dimensional CsPbCl3 perovskite and provide insights into the photophysics of the CsPbCl3 perovskite.
Assessing the cumulative adverse effects of offshore wind energy development on seabird foraging guilds along the East Coast of the United States
Authors: Goodale M Wing , Milman Anita , Griffin Curtice R 
Published: May 2019

Abstract
Offshore wind farms are rapidly being permitted along the East Coast of the US, and with subsequent development could cumulatively affect seabird populations. Yet, the seabird guilds most likely at risk of cumulative effects have not been identified. Assessments of cumulative effects must first calculate the cumulative exposure of seabirds to areas suitable for offshore wind farms and then estimate how exposure will affect populations. This paper addresses this first need, and quantifies how three different wind farm siting scenarios could cumulatively expose seven seabird foraging guilds. The coastal bottom gleaner guild (sea ducks) would be exposed at similar rates regardless of siting decision, while other coastal guilds would be exposed at a higher rate when projects are built in shallow areas and close to shore rather than in high-wind areas. The pelagic seabird guild would be exposed at high rates when projects are built in high-wind areas. There was no single offshore wind siting scenario that reduced the cumulative exposure for all guilds. Based upon these findings, we identify the foraging guilds most likely to be cumulatively exposed and propose an approach for siting and mitigation that may reduce cumulative exposure for all guilds.
Bayesian metabolic flux analysis reveals intracellular flux couplings
Authors: Heinonen Markus , Osmala Maria , Mannerström Henrik , Wallenius Janne , Kaski Samuel , Rousu Juho , Lähdesmäki Harri 
Published: May 2019

Abstract

Motivation
Metabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates.

Results
We introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis.

Availability and implementation
The COBRA compatible software is available at github.com/markusheinonen/bamfa.

Supplementary information
Supplementary data are available at Bioinformatics online.
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes
Authors: Zhang Song-Yao , Zhang Shao-Wu , Fan Xiao-Nan , Zhang Teng , Meng Jia , Huang Yufei 
Published: May 2019

Abstract

Motivation
As the most abundant mammalian mRNA methylation, N6-methyladenosine (m6A) exists in &gt;25% of human mRNAs and is involved in regulating many different aspects of mRNA metabolism, stem cell differentiation and diseases like cancer. However, our current knowledge about dynamic changes of m6A levels and how the change of m6A levels for a specific gene can play a role in certain biological processes like stem cell differentiation and diseases like cancer is largely elusive.

Results
To address this, we propose in this paper FunDMDeep-m6A a novel pipeline for identifying context-specific (e.g. disease versus normal, differentiated cells versus stem cells or gene knockdown cells versus wild-type cells) m6A-mediated functional genes. FunDMDeep-m6A includes, at the first step, DMDeep-m6A a novel method based on a deep learning model and a statistical test for identifying differential m6A methylation (DmM) sites from MeRIP-Seq data at a single-base resolution. FunDMDeep-m6A then identifies and prioritizes functional DmM genes (FDmMGenes) by combing the DmM genes (DmMGenes) with differential expression analysis using a network-based method. This proposed network method includes a novel m6A-signaling bridge (MSB) score to quantify the functional significance of DmMGenes by assessing functional interaction of DmMGenes with their signaling pathways using a heat diffusion process in protein-protein interaction (PPI) networks. The test results on 4 context-specific MeRIP-Seq datasets showed that FunDMDeep-m6A can identify more context-specific and functionally significant FDmMGenes than m6A-Driver. The functional enrichment analysis of these genes revealed that m6A targets key genes of many important context-related biological processes including embryonic development, stem cell differentiation, transcription, translation, cell death, cell proliferation and cancer-related pathways. These results demonstrate the power of FunDMDeep-m6A for elucidating m6A regulatory functions and its roles in biological processes and diseases.

Availability and implementation
The R-package for DMDeep-m6A is freely available from https://github.com/NWPU-903PR/DMDeepm6A1.0.

Supplementary information
Supplementary data are available at Bioinformatics online.
A statistical simulator scDesign for rational scRNA-seq experimental design
Authors: Li Wei Vivian , Li Jingyi Jessica 
Published: May 2019

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) has revolutionized biological sciences by revealing genome-wide gene expression levels within individual cells. However, a critical challenge faced by researchers is how to optimize the choices of sequencing platforms, sequencing depths and cell numbers in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information.

Results
Here we present a flexible and robust simulator, scDesign, the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. In an evaluation based on 17 cell types and 6 different protocols, scDesign outperformed four state-of-the-art scRNA-seq simulation methods and led to rational experimental design. In addition, scDesign demonstrates reproducibility across biological replicates and independent studies. We also discuss the performance of multiple differential expression and dimension reduction methods based on the protocol-dependent scRNA-seq data generated by scDesign. scDesign is expected to be an effective bioinformatic tool that assists rational scRNA-seq experimental design and comparison of scRNA–seq computational methods based on specific research goals.

Availability and implementation
We have implemented our method in the R package scDesign, which is freely available at https://github.com/Vivianstats/scDesign.

Supplementary information
Supplementary data are available at Bioinformatics online.
Representation transfer for differentially private drug sensitivity prediction
Authors: Niinimäki Teppo , Heikkilä Mikko A , Honkela Antti , Kaski Samuel 
Published: May 2019

Abstract

Motivation
Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymization strategies fail to provide sufficient level of protection for genomic data, because the data are inherently identifiable. Differentially private machine learning can help by guaranteeing that the published results do not leak too much information about any individual data point. Recent research has reached promising results on differentially private drug sensitivity prediction using gene expression data. Differentially private learning with genomic data is challenging because it is more difficult to guarantee privacy in high dimensions. Dimensionality reduction can help, but if the dimension reduction mapping is learned from the data, then it needs to be differentially private too, which can carry a significant privacy cost. Furthermore, the selection of any hyperparameters (such as the target dimensionality) needs to also avoid leaking private information.

Results
We study an approach that uses a large public dataset of similar type to learn a compact representation for differentially private learning. We compare three representation learning methods: variational autoencoders, principal component analysis and random projection. We solve two machine learning tasks on gene expression of cancer cell lines: cancer type classification, and drug sensitivity prediction. The experiments demonstrate significant benefit from all representation learning methods with variational autoencoders providing the most accurate predictions most often. Our results significantly improve over previous state-of-the-art in accuracy of differentially private drug sensitivity prediction.

Availability and implementation
Code used in the experiments is available at https://github.com/DPBayes/dp-representation-transfer.
Enabling Green and Blue Infrastructure to Improve Contributions to Human Well-Being and Equity in Urban Systems
Authors: Andersson Erik , Langemeyer Johannes , Borgström Sara , McPhearson Timon , Haase Dagmar , Kronenberg Jakub , Barton David N , Davis McKenna , Naumann Sandra , Röschel Lina , Baró Francesc 
Published: May 2019

AbstractThe circumstances under which different ecosystem service benefits can be realized differ. The benefits tend to be coproduced and to be enabled by multiple interacting social, ecological, and technological factors, which is particularly evident in cities. As many cities are undergoing rapid change, these factors need to be better understood and accounted for, especially for those most in need of benefits. We propose a framework of three systemic filters that affect the flow of ecosystem service benefits: the interactions among green, blue, and built infrastructures; the regulatory power and governance of institutions; and people's individual and shared perceptions and values. We argue that more fully connecting green and blue infrastructure to its urban systems context and highlighting dynamic interactions among the three filters are key to understanding how and why ecosystem services have variable distribution, continuing inequities in who benefits, and the long-term resilience of the flows of benefits.
Loss of Foxg1 Impairs the Development of Cortical SST-Interneurons Leading to Abnormal Emotional and Social Behaviors
Authors: Chen Dongsheng , Wang Chunlian , Li Meiyi , She Xinyu , Yuan Yonggui , Chen Huanxin , Zhang Weining , Zhao Chunjie 
Published: May 2019

AbstractFOXG1 syndrome is a severe encephalopathy that exhibit intellectual disability, emotional disorder, and limited social communication. To elucidate the contribution of somatostatin-expressing interneurons (SST-INs) to the cellular basis underlying FOXG1 syndrome, here, by crossing SST-cre with a Foxg1fl/fl line, we selectively ablated Foxg1. Loss of Foxg1 resulted in an obvious reduction in the number of SST-INs, accompanied by an altered ratio of subtypes. Foxg1-deficient SST-INs exhibited decreased membrane excitability and a changed ratio of electrophysiological firing patterns, which subsequently led to an excitatory/inhibitory imbalance. Moreover, cognitive defects, limited social interactions, and depression-like behaviors were detected in Foxg1 cKO mice. Treatment with low-dose of clonazepam effectively alleviated the defects. These results identify a link of SST-IN development to the aberrant emotion, cognition, and social capacities in patients. Our findings identify a novel role of Foxg1 in SST-IN development and put new insights into the cellular basis of FOXG1 syndrome.
Outcome of periodontal–orthodontic treatment in subjects with periodontal disease. Part II: a CBCT study of alveolar bone level changes
Authors: Zasčiurinskienė Eglė , Lund Henrik , Lindsten Rune , Jansson Henrik , Bjerklin Krister 
Published: May 2019

Abstract

Aim
To examine alveolar bone level (ABL) changes before (T1) and after (T2) orthodontic treatment (OT) in subjects with periodontal disease.

Methods
The study included 50 subjects with periodontal disease. All patients received subgingival debridement following baseline examination. Control group patients received final periodontal treatment before the start of OT. For the test group patients final periodontal treatment was performed simultaneous to OT. OT was performed with a straight-wire appliance. Micro-implants or temporary crowns on implants were used for posterior anchorage when needed. ABL measurements of 3821 tooth surfaces were performed on cone beam computed tomography images.

Results
No difference was observed between mean ABL at T1 and T2. ABL remained unchanged on 69 per cent of surfaces. A mean of 15.6 (SD 7.4) per cent of surfaces experienced ABL gain, and a mean of 15.1 (SD 7.5) per cent was found with ABL loss. Small significant median ABL difference was observed on mesial and distal surfaces (P < 0.001). A significant difference was found between median ABL changes on mesial/distal in comparison to buccal/lingual surfaces (P < 0.01). Significantly more buccal (17.9 %) and lingual (18.5 %) surfaces experienced ABL loss when compared with mesial (11.3 %) and distal (12.0 %) surfaces (P < 0.001). Significant difference was found in the median ABL change of intruded (0.5 (IQR 0.94) mm) and non-intruded (−0.4 (IQR 1.07) mm) maxillary incisors (P = 0.04). Significant median ABL gain was found on the lingual surface of maxillary incisors, which were retroclined more than 8.6 degree and intruded more than 1.6 mm.

Conclusions
ABL changes after periodontal–orthodontic treatment in patients with periodontal disease were small. ABL gain was more observed on mesial and distal surfaces and ABL loss on buccal and lingual surfaces. Larger orthodontic movements of maxillary incisors influenced ABL gain.
Growing condition variations and grain prices in Niger and Nigeria
Authors: Hatzenbuehler Patrick L , Abbott Philip C , Abdoulaye Tahirou 
Published: May 2019

AbstractIn this paper, we describe how both the existing degree of price correspondence and tradability are important factors explaining why and the extent to which grain price relationships adjust due to growing condition variations. For a set of maize and millet markets in Niger and Nigeria with different agro-ecological characteristics and strengths of price relationships, we use normalised difference vegetation index (NDVI) data to identify years with weather-related production shocks. We then measure the degree to which price transmission between the commercial hub and reference market in each country in the anomalous weather years varies from that in normal years.
Simulating the effects of wind and snow damage on the optimal management of Norwegian spruce forests
Authors: Díaz-Yáñez Olalla , Arias-Rodil Manuel , Mola-Yudego Blas , González-Olabarria José Ramón , Pukkala Timo 
Published: May 2019

AbstractOverlooking the risk of wind and snow damage in forest planning may lead to suboptimal management prescriptions. In this study, we analysed the optimal management of an even-aged, spruce-dominated stand in Norway under the risk of snow and wind damage. The management aim was to maximize discounted net revenues of timber production. We used a simulation-optimization system based on models for stand dynamics and damage, using either deterministic or stochastic approach to consider risk. The different approaches to simulating damage resulted in 41 optimization cases. The results show that considering risk leads to earlier cuttings, lower growing stock densities towards the end of the rotations and changes in the number and intensity of thinnings. The inclusion of stochastic damage provided a valid approach for considering the uncertainty associated with the risk of damage. Ignoring the effect of wind and snow damage in the calculations resulted in up to 25 per cent overestimation of the revenues. The results from this study will help to integrate the risk of natural disturbances into forestry decision-making, and provide a better understanding of the implications that snow and wind damage have on optimal forest management.