bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining disparate data sources for improved poverty prediction and mapping
Authors: Pokhriyal Neeti , Jacques Damien Christophe 
Published: October 2017

SignificanceSpatially finest poverty maps are essential for improved diagnosis and policy planning, especially keeping in view the Sustainable Development Goals. “Big Data” sources like call data records and satellite imagery have shown promise in providing intercensal statistics. This study outlines a computational framework to efficiently combine disparate data sources, like environmental data, and mobile data, to provide more accurate predictions of poverty and its individual dimensions for finest spatial microregions in Senegal. These are validated using the concurrent census data.
Continuum limit of the vibrational properties of amorphous solids
Authors: Mizuno Hideyuki , Shiba Hayato , Ikeda Atsushi 
Published: October 2017

Significance
The thermal properties of crystalline solids follow universal laws that are explained by theories based on phonons. Amorphous solids are also characterized by universal laws that are, however, anomalous with respect to their crystalline counterparts. These anomalies begin to emerge at very low temperatures, suggesting that the vibrational properties of amorphous solids differ from phonons, even in the continuum limit. In this work, we reveal that phonons coexist with soft localized modes in the continuum limit of amorphous solids. Importantly, we discover that the phonons follow the Debye law, whereas the soft localized modes follow another universal non-Debye law. Our findings provide a firm theoretical basis for explaining the thermal anomalies of amorphous solids.
Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq
Authors: Chen Lihe , Lee Jae Wook , Chou Chung-Lin , Nair Anil V. , Battistone Maria A. , Păunescu Teodor G. , Merkulova Maria , Breton Sylvie , Verlander Jill W. , Wall Susan M. , Brown Dennis , Burg Maurice B. , Knepper Mark A. 
Published: October 2017

Significance
A long-term goal in mammalian biology is to identify the genes expressed in every cell type of the body. In the kidney, the expressed genes (i.e., transcriptome) of all epithelial cell types have already been identified with the exception of the cells that make up the renal collecting duct, which is responsible for regulation of blood pressure and body fluid composition. Here, single-cell RNA-sequencing was used in mouse to identify transcriptomes for the major collecting duct cell types: type A intercalated cells, type B intercalated cells, and principal cells. The information was used to create a publicly accessible online resource. The data allowed identification of genes that are selectively expressed in each cell type, which is informative for cell-level understanding of physiology and pathophysiology.
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations
Authors: Cario Clinton L , Witte John S 
Published: October 2017

Abstract

Motivation
As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments and machine learning algorithms, there is also a need for the integration of functionality across frameworks.

Results
We present orchid, a python based software package for the management, annotation and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier.

Availability and implementation
Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid. Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution.

Supplementary information
Supplementary data are available at Bioinformatics online.
Vancomycin Plus Piperacillin-Tazobactam and Acute Kidney Injury in Adults: A Systematic Review and Meta-Analysis
Authors: Luther Megan K. , Timbrook Tristan T. , Caffrey Aisling R. , Dosa David , Lodise Thomas P. , LaPlante Kerry L. 
Published: October 2017

Objectives:
The objective of this systematic review and meta-analysis was to assess acute kidney injury with combination therapy of vancomycin plus piperacillin-tazobactam, in general, adult patients and in critically ill adults. Rates of acute kidney injury, time to acute kidney injury, and odds of acute kidney injury were compared with vancomycin monotherapy, vancomycin plus cefepime or carbapenem, or piperacillin-tazobactam monotherapy.

Data Sources:
Studies were identified by searching Pubmed, Embase, Web of Science, and Cochrane from inception to April 2017. Abstracts from selected conference proceedings were manually searched.

Study Selection:
Articles not in English, pediatric studies, and case reports were excluded.

Data Extraction:
Two authors independently extracted data on study methods, rates of acute kidney injury, and time to acute kidney injury. Effect estimates and 95% CIs were calculated using the random effects model in RevMan 5.3.

Data Synthesis:
Literature search identified 15 published studies and 17 conference abstracts with at least 24,799 patients. The overall occurrence rate of acute kidney injury was 16.7%, with 22.2% for vancomycin plus piperacillin-tazobactam and 12.9% for comparators. This yielded an overall number needed to harm of 11. Time to acute kidney injury was faster for vancomycin plus piperacillin-tazobactam than vancomycin plus cefepime or carbapenem, but not significantly (mean difference, –1.30; 95% CI, –3.00 to 0.41 d). The odds of acute kidney injury with vancomycin plus piperacillin-tazobactam were increased versus vancomycin monotherapy (odds ratio, 3.40; 95% CI, 2.57–4.50), versus vancomycin plus cefepime or carbapenem (odds ratio, 2.68; 95% CI, 1.83–3.91), and versus piperacillin-tazobactam monotherapy (odds ratio, 2.70; 95% CI, 1.97–3.69). In a small subanalysis of 968 critically ill patients, the odds of acute kidney injury were increased versus vancomycin monotherapy (odds ratio, 9.62; 95% CI, 4.48–20.68), but not significantly different for vancomycin plus cefepime or carbapenem (odds ratio, 1.43; 95% CI, 0.83–2.47) or piperacillin-tazobactam monotherapy (odds ratio, 1.35; 95% CI, 0.86–2.11).

Conclusions:
The combination of vancomycin plus piperacillin-tazobactam increased the odds of acute kidney injury over vancomycin monotherapy, vancomycin plus cefepime or carbapenem, and piperacillin-tazobactam monotherapy. Limited data in critically ill patients suggest the odds of acute kidney injury are increased versus vancomycin monotherapy, and mitigated versus the other comparators. Further research in the critically ill population is needed.
Pilot Study Assessing the Use of High-density Polyethylene (Su-Por) for Tube Shunt Patch Grafts
Authors: Abramowitz Benjamin , Moster Marlene R. , Pro Michael , Schmidt Courtland , Dale Elizabeth , Yung Edward , Williams Alice 
Published: October 2017

Purpose:
To assess the viability of a manufactured high-density polyethylene patch graft material (Su-Por) for prevention of tube shunt exposure.

Materials and Methods:
Retrospective review of the first 11 patients from the Wills Eye Hospital Glaucoma Service to receive the high-density polyethylene patch graft during tube shunt surgery.

Results:
Four patients (36.3%) experienced an extrusion of the Su-Por patch without a leak within 2.5 months of postoperative follow-up. All 4 patients developed either symptomatic or progressive extrusion. Operative repair was completed with Su-Por removal and replacement with a new human donor patch graft. No patient developed any sign of infection despite the extrusions. The remaining 7 patients had an uneventful postoperative course and continue to have no complications from the Su-Por patch with 9 months of follow-up.

Conclusions:
Given the high rate of extrusion of the Su-Por graft, this material seems to be an inadequate alternative for covering tube shunts. Harvested human tissue or other more flexible, manufactured grafts remain the standard of care for covering tube shunts.
Roles of High-resolution Manometry in Predicting Incomplete Bolus Transit in Patients With Dysphagia
Authors: Shi Zhaohong , Guo Jie , Clarke John , Jin Haifeng , Wang Xinjun , Zhang Nina , Stein Ellen , Dhalla Sameer , Pasricha Pankaj J. , Chen Jiande D.Z. 
Published: October 2017

Background:
High-resolution manometry (HRM) is used to assess esophageal motility diseases. Abnormalities in a number of HRM parameters have been reported in patients with dysphagia. However, it is unclear whether some of abnormal HRM parameters are predictive of dysphagia. The aim of this retrospective study was to investigate the roles of HRM parameters in predicting incomplete bolus clearance (IBC) in patients with dysphagia using high-resolution impedance manometry.

Methods:
A total of 644 wet swallows were reviewed and analyzed in 63 patients with symptoms of dysphagia or reflux who underwent a clinical high-resolution impedance manometry test. IBC was defined based on impedance measurement. The relationship of each of abnormal HRM parameters with IBC was analyzed and their roles in predicting IBC were determined.

Results:
Patients with symptoms of both dysphagia and reflux showed the highest IBC rate, and patients with symptoms of reflux had the lowest IBC rate. The IBC was more prevalent in the distal esophagus. Premature contractions and peristalsis with large breaks were associated with a higher IBC rate in the proximal esophagus (P<0.05); large breaks, ineffective peristalsis, and abnormalities of the esophageal gastric junction functions were associate with higher IBC rates in the distal esophagus (P<0.05). Abnormalities in a number of motility parameters were able to predict IBC with high specificities and/or high sensitivity, such as pan esophageal pressurization, ineffective peristalsis, and large breaks. Abnormal integrative relaxation pressure of the lower esophageal sphincter with concurrent pan esophageal pressurization, ineffective peristalsis, or large breaks is predictive of IBC with nearly 100% of specificity.

Conclusions:
Abnormalities in a number of HRM parameters are not only useful in diagnosing esophageal motility diseases, but also valuable in predicting IBC during swallowing.
Rates of Duodenal Biopsy During Upper Endoscopy Differ Widely Between Providers
Authors: Pitman Max , Sanders David S. , Green Peter H.R. , Lebwohl Benjamin 
Published: October 2017

Goal:
The goal of this study is to determine factors associated with performance of duodenal biopsy during upper endoscopy.

Background:
Celiac disease (CD) prevalence approaches 1% in the United States and Europe, yet CD remains underdiagnosed, in part because of low rates of duodenal biopsy during upper endoscopy. We aimed to identify patient and provider factors associated with performance of duodenal biopsy during upper endoscopy.

Study:
In our hospital-based endoscopy suite, we identified all patients not previously diagnosed with CD who underwent upper endoscopy during a 5-year period for one of the following indications: abdominal pain/dyspepsia, gastroesophageal reflux (GERD), anemia/iron deficiency, diarrhea, and weight loss. We employed univariate and multivariate analysis to determine the association between clinical factors and the performance of duodenal biopsy.

Results:
Of 8572 patients included in the study, 4863 (57%) underwent duodenal biopsy. Of those who underwent duodenal biopsy, 24 (0.49%) were found to have CD. On multivariate analysis, age, gender, indication, gross endoscopic appearance, physician affiliation with a celiac disease center, and absence of a participating trainee were all significantly associated with the performance of duodenal biopsy. There was wide variability among providers, with duodenal biopsy rates ranging from 27% to 91% during these procedures.

Conclusions:
A duodenal biopsy is more likely to be performed in younger patients, females, and for key indications such as weight loss, diarrhea, and anemia. Providers varied widely in the performance of duodenal biopsy. Further study is warranted to better understand the decision to perform duodenal biopsy and to determine the optimal scenarios for its performance.
C9ORF72 Intermediate Repeat Expansion in a Patient With Psychiatric Disorders and Progressive Cerebellar Ataxia
Authors: Meloni Mario , Farris Rita , Solla Paolo , Mascia Marcello M. , Marrosu Francesco , Cannas Antonino 
Published: October 2017

Introduction:
Large expansions of the noncoding GGGGCC repeat (more than 30) in the first intron of the C9ORF72 gene have been demonstrated to cause amyotrophic lateral sclerosis and frontotemporal dementia. Recent papers have investigated the possible pathogenic role and associated clinical phenotypes of hexanucleotide expansions with intermediate repeat lengths ranging between 20 and 29 repeats.

Case Report:
We report a case of a 71-year-old Sardinian female patient with a long history of psychiatric disorders such as mixed anxiety-depressive disorder associated with somatization disorder and histrionic personality who developed a slowly progressive cerebellar syndrome, mild cognitive impairment, pyramidal signs, and rapid eye movement sleep behavior disorder with imaging abnormalities on the DaTSCAN single-photon emission computed tomography indicating an alteration in the presynaptic dopaminergic system. The patient was found to have intermediate C9ORF72 repeat expansions.

Conclusions:
Early psychiatric presentations are a recurrent phenotypic manifestation of C9ORF72 expansions. In our patient, the intermediate C9ORF72 repeat expansion may have a pathogenic role in the cooccurrence of psychiatric and sleep disorders, cognitive dysfunctions, pyramidal system involvement, and late-onset cerebellar ataxia. This observation widens the spectrum of neurodegenerative conditions linked to C9ORF72 mutations.
Novel GFAP Variant in Adult-onset Alexander Disease With Progressive Ataxia and Palatal Tremor
Authors: Gass Jennifer M. , Cheema Anvir , Jackson Jessica , Blackburn Patrick R. , Van Gerpen Jay , Atwal Paldeep S. 
Published: October 2017

Introduction:
Alexander disease is a rare neurodegenerative disease caused by variants in the glial fibrillary acidic protein gene (GFAP). This disorder can develop as an infantile, juvenile or adult-onset form and is characterized by several clinical features, including macrocephaly, seizures, ataxia, and bulbar/pseudobulbar signs. While the majority of these patients have the more progressive infantile form which causes severe leukodystrophy and early death; the less common adult form is more variable (ie, onset age, symptoms), with bulbar dysfunction as the primary feature.

Case Report:
In our investigation, we describe a patient with progressive neuromuscular issues including dyspnea, dysphagia, dysarthria and progressive ataxia with palatal tremor.

Conclusions:
Through genetic testing, we determined that our patient has a novel variant in GFAP typical of Alexander disease.
ALKALs arein vivoligands for ALK family Receptor Tyrosine Kinases in the neural crest and derived cells
Authors: Fadeev Andrey , Garcia Patricia Mendoza , Irion Uwe , Guan Jikui , Pfeifer Kathrin , Wiessner Stephanie , Serluca Fabrizio , Singh Ajeet Pratap , Nüsslein-Volhard Christiane , Palmer Ruth H. 
Published: October 2017

AbstractMutations in Anaplastic Lymphoma Kinase (ALK) are implicated in somatic and familial neuroblastoma, a paediatric tumour of neural crest-derived tissues. Recently, biochemical analyses have identified secreted small ALKAL proteins (FAM150, AUG) as potential ligands for human ALK and the related Leukocyte Tyrosine Kinase (LTK). In the zebrafishDanio rerio, DrLtk, which is similar to human ALK in sequence and domain structure, controls the development of iridophores, neural crest-derived pigment cells. Hence, the zebrafish system allows studying Alk/Ltk and Alkals involvement in neural crest regulationin vivo. Using zebrafish pigment pattern formation,Drosophilaeye patterning, and cell culture-based assays, we show that zebrafish Alkals potently activate zebrafish Ltk and human ALK driving downstream signalling events. Overexpression of the three Dr Alkals cause ectopic iridophore development whereas loss of function alleles lead to spatially distinct patterns of iridophore loss in zebrafish larvae and adults.alkalloss of function triple mutants completely lack iridophores and are larval lethal as is the case forltknull mutants. Our results provide the firstin vivoevidence of (i) activation of ALK/LTK family receptors by ALKALs and (ii) an involvement of these ligand-receptor complexes in neural crest development.
Analysis of the Genomic Basis of Functional Diversity in Dinoflagellates using a Transcriptome-Based Sequence Similarity Network
Authors: Meng Arnaud , Corre Erwan , Probert Ian , Gutierrez-Rodriguez Andres , Siano Raffaele , Annamale Anita , Alberti Adriana , Da Silva Corinne , Wincker Patrick , Le Crom Stéphane , Not Fabrice , Bittner Lucie 
Published: October 2017

ABSTRACTDinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
Targeting the Untargetable: Predicting Pramlintide Resistance Using a Neural Network Based Cellular Automata
Authors: Kim Eunjung , Schenck Ryan , West Jeffrey , Cross William , Harris Valerie , McKenna Joseph , Cho Heyrim , Coker Elizabeth , Tsai Steven Lee-Kramer Kenneth Y. , Flores Elsa R. , Gatenbee Chandler 
Published: October 2017

AbstractDe novo resistance is a major issue for the use of targeted anticancer drugs in the clinic. By integrating experimental data we have created a hybrid neural network/agent-based model to simulate the evolution and spread of resistance to the drug Pramlintide in cutaneous squamous cell carcinoma. Our model can eventually be used to predict patient responses to the drug and thus enable clinicians to make decisions regarding personalized, precision treatment regimes for patients.
Extracting active modules from multilayer PPI network: a continuous optimization approach
Authors: Li Dong , Zhu Zexuan , Pan Zhisong , Hu Guyu , He Shan 
Published: October 2017

AbstractActive modules identification has received much attention due to its ability to reveal regulatory and signaling mechanisms of a given cellular response. Most existing algorithms identify active modules by extracting connected nodes with high activity scores from a graph. These algorithms do not consider other topological properties such as community structure, which may correspond to functional units. In this paper, we propose an active module identification algorithm based on a novel objective function, which considers both and network topology and nodes activity. This objective is formulated as a constrained quadratic programming problem, which is convex and can be solved by iterative methods. Furthermore, the framework is extended to the multilayer dynamic PPI networks. Empirical results on the single layer and multilayer PPI networks show the effectiveness of proposed algorithms.Availability: The package and code for reproducing all results and figures are available at https://github.com/fairmiracle/ModuleExtraction.
Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making
Authors: Dezfouli Amir , Balleine Bernard W. 
Published: October 2017

AbstractState-space and action representations form the building blocks of decision-making processes in the brain; states map external cues to the current situation of the agent whereas actions provide the set of motor commands from which the agent can choose to achieve specific goals. Although these factors differ across environments, it is not currently known whether or how accurately state and action representations are acquired by the agent because previous experiments have typically provided this information a priori through instruction or pre-training. Here we show that, in the absence of such a priori knowledge, state and action representations adapt to reflect the structure of the world. We used a sequential decision-making task in rats in which they were required to pass through multiple states before reaching the goal, and for which the number of states and how they map onto external cues were not known a priori. We found that, early in training, animals selected actions as if the task was not sequential and outcomes were the immediate consequence of the most proximal action. During the course of training, however, rats recovered the true structure of the environment and made decisions based on the expanded state-space, reflecting the multiple stages of the task. We found a similar pattern with actions; early in training animals only considered the execution of single actions whereas, after training, they created useful action sequences that expanded the set of available actions. We conclude that the profile of choices shows a gradual shift from simple representations of actions and states to more complex structures compatible with the structure of the world.