bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Investigation of Brain Functional Connectivity by Form of Craniosynostosis
Authors: Sun Alexander H. , Eilbott Jeffrey , Chuang Carolyn , Yang Jenny F. , Brooks Eric D. , Beckett Joel , Steinbacher Derek M. , Pelphrey Kevin , Persing John A. 
Published: April 2019

Purpose:
Long-term neurocognitive sequelae of nonsyndromic craniosynostosis (NSC) patients are just beginning to be clarified. This study uses functional MRI (fMRI) to determine if there is evidence of altered brain functional connectivity in NSC, and whether these aberrations vary by form of synostosis.

Methods:
Twenty adolescent participants with surgically treated NSC (10 sagittal synostosis, 5 right unilateral coronal synostosis [UCS], 5 metopic synostosis [MSO]) were individually matched to controls by age, gender, and handedness. A subgroup of MSO was classified as severe metopic synostosis (SMS) based on the endocranial bifrontal angle. Resting state fMRI was acquired in a 3T Siemens TIM Trio scanner (Erlangen, Germany), and data were motion corrected and then analyzed with BioImage Suite (Yale School of Medicine). Resulting group-level t-maps were cluster corrected with nonparametric permutation tests. A region of interest analysis was performed based on the left Brodmann's Areas 7, 39, and 40.

Results:
Sagittal synostosis had decreased whole-brain intrinsic connectivity compared to controls in the superior parietal lobules and the angular gyrus (P = 0.071). Unilateral coronal synostosis had decreased intrinsic connectivity throughout the prefrontal cortex (P = 0.031). The MSO cohort did not have significant findings on intrinsic connectivity, but the SMS subgroup had significantly decreased connectivity among multiple subcortical structures.

Conclusion:
Sagittal synostosis had decreased connectivity in regions associated with visuomotor integration and attention, while UCS had decreased connectivity in circuits crucial in executive function and cognition. Finally, severity of metopic synostosis may influence the degree of neurocognitive aberration. This study provides data suggestive of long-term sequelae of NSC that varies by suture type, which may underlie different phenotypes of neurocognitive impairment.
The Electrical Activity of Masseter and Anterior Temporal Muscles in Patients With Unilateral Cleft Lip and Palate
Authors: Jahanbin Arezoo , Ahrari Farzaneh , Saeidi Morteza , Moeinifar Azam , Sharifi Farid 
Published: April 2019

Abstract
This study aimed to determine the electrical activity of masseter and anterior temporal muscles in patients with unilateral cleft lip and palate (CLP) and compare it with healthy volunteers. The study involved 20 female patients (mean age 20 ± 4 years) with unilateral cleft lip and palate who had undergone lip and palate surgery in childhood and finished the first-phase orthodontic therapy with level and align teeth. Twenty age- and sex-matched volunteers with no cleft lip and palate were involved as controls. Electromyographic (EMG) signals of masseter and anterior temporal muscles were recorded at rest position, during swallowing and during maximum bite force (MBF). EMG signals at different test conditions were compared between the cleft and noncleft sides of CLP patients and between CLP patients and healthy individuals. The EMG potentials of masseter (rest, swallowing, MBF) and temporal (rest, MBF) muscles were significantly higher in the cleft than the noncleft side of CLP patients (P value <0.001). Generally, patients with unilateral cleft lip and palate experienced a significant increase in the electrical activity of the masseter and temporal muscles in both sides compared to the control group (P <0.05). In conclusion, patients with unilateral cleft lip and palate exhibit overall greater masticatory muscle activity compared to healthy individuals. The asymmetric masticatory function in subjects with unilateral cleft lip and palate may be associated with severe consequences such as asymmetric facial growth, implying the importance of early diagnosis and orthodontic treatment to achieve a favorable environment for balanced facial growth in CLP affected patients.
Correlation of Clinical Findings With Computed Tomography in Orbital Traumas
Authors: Aslan Fatih , Ozen Ozkan 
Published: April 2019

Background:
Although the eye is a well-protected organ, it is frequently affected by trauma. The timely detection of ocular injuries is extremely important. In this study, the authors evaluated the consistency between findings in computed tomography (CT) examination for orbital fractures and globe integrity and clinical findings in patients presenting to the emergency department due to orbital trauma.

Methods:
The authors retrospectively reviewed the files of patients presenting with orbital trauma between January 2015 and January 2018 from emergency department records. Ophthalmology consultation and follow-up notes, radiology reports, and the emergency physician's notes were reviewed.

Results:
During the study period, 286 patients presented to the emergency department with orbital trauma. A total of 119 eyes of 83 patients who underwent orbital CT were included in the study. Orbital bone fracture was detected in 54.6% (n = 65) of the eyes. Of these, 73.8% (n = 48) involved multiple fractures. Among all eyes, the distribution of fractures in the orbital walls was lateral wall in 41.2% (n = 49), floor in 32.8% (n = 39), medial wall in 31.1% (n = 37), and roof in 10.9% (n = 13). Multiple wall fractures were detected in 36.9% (n = 44) of the eyes. At least 1 clinical finding such as diplopia, laceration, abnormal pupillary response, hypoesthesia, and exophthalmos was observed in 47.1% (n = 56) of the eyes. This rate was 56.8% among eyes with orbital fractures and 35.2% in those without fracture. There was a statistically significant relationship between floor fractures and diplopia (P = 0.002). No significant correlations were found between the other radiological and clinical findings.

Conclusion:
Our study revealed a relationship between the presence of orbital fracture and eye damage. In particular, the authors found that the frequency of diplopia was significantly higher in eyes with maxillary bone fracture in the orbital floor. However, orbital CT findings other than bone fracture were not consistent with clinical findings.
Preoperative Evaluation of Iatrogenic Spinal Accessory Nerve Palsy: What Is the Place for Electrophysiological Testing?
Authors: Shen Jun , Ye Xuan , Qiu Yanqun , Xu Jing , Zhu Yi , Shen Yundong , Xu Wendong 
Published: April 2019

Purpose:Electrophysiological testing has been used for the early diagnosis of iatrogenic spinal accessory nerve palsy in clinical practice. However, the presence of low-amplitude compound action potential in 70% to 90% of the patients suffering from iatrogenic nerve transection was reported in several studies. We have encountered the same issue and made minor modifications to the methods of electrophysiological testing. The purpose of this study was to retrospectively evaluate the reliability of our modified electrophysiological testing as preoperative examination in patients receiving surgical revision.Methods:In this study, we compared preoperative electrophysiological testing results with intraoperative diagnosis in the 24 patients with iatrogenic spinal accessory nerve palsy who were referred to our hospital from 2009 to 2018.Results:During operation, 20 patients were diagnosed with neurotmesis and the remaining 4 patients were found axonotmesis depending on the results of surgical exploration and intraoperative electrophysiological examination. Six of the 20 patients with neurotmesis demonstrated a low-amplitude compound muscle action potential of the upper trapezius during preoperative electrophysiological testing. Needle electromyography revealed voluntary motor unit potentials in 8 of the 20 patients. Meanwhile, concomitant great auricular nerve or dorsal scapular nerve injuries were preoperatively revealed in 7 of 24 patients.Conclusions:The rate of low-amplitude compound muscle action potentials in these patients suffering from spinal accessory nerve neurotmesis was about 30% with our modified electrophysiological testing. We should be aware of this pitfall before surgical nerve repair. Furthermore, electrophysiological testing is an informative preoperative examination revealing the concomitant nerve injuries.
Real-time analysis of single influenza virus replication complexes reveals large promoter-dependent differences in initiation dynamics
Authors: Robb Nicole C. , te Velthuis Aartjan J.W. , Fodor Ervin , Kapanidis Achillefs N. 
Published: April 2019

ABSTRACTThe viral RNA (vRNA) genome of influenza viruses is replicated by the RNA-dependent RNA polymerase (RNAP) via a complementary RNA (cRNA) intermediate. The vRNA promoter can adopt multiple conformations when bound by the RNAP. However, the dynamics, determinants, and biological role of these conformations are unknown; further, little is known about cRNA promoter conformations. To probe the RNA conformations adopted during initial replication, we monitored single, surface-immobilised vRNA and cRNA initiation complexes in real-time. Our results show that, while the 3’ terminus of the vRNA promoter exists in dynamic equilibrium between pre-initiation and initiation conformations, the cRNA promoter exhibited very limited dynamics. Two residues in the proximal 3’ region of the cRNA promoter (residues absent in the vRNA promoter) allowed the cRNA template strand to reach further into the active site, limiting promoter dynamics. Our results highlight promoter-dependent differences in influenza initiation mechanisms, and advance our understanding of virus replication.
Inferring Protein Domain Semantic Roles Using word2vec
Authors: Buchan Daniel , Jones David 
Published: April 2019

AbstractIn this paper, using word2vec, we demonstrate that proteins domains may have semantic “meaning” in the context of multi-domain proteins. Word2vec is a group of models which can be used to produce semantically meaningful embeddings of words or tokens in a vector space. In this work we treat multi-domain proteins as “sentences” where domain identifiers are tokens which may be considered as “words”. Using all Interpro (Finn, Attwood et al. 2017) eukaryotic proteins as a corpus of “sentences” we demonstrate that Word2vec creates functionally meaningful embeddings of protein domains. We additionally show how this can be applied to identifying the putative functional roles for Pfam (Finn, Coggill et al. 2016) Domains of Unknown Function.
Structure-based validation can drastically under-estimate error rate in proteome-wide cross-linking mass spectrometry studies
Authors: Yugandhar Kumar , Wang Ting-Yi , Wierbowski Shayne D. , Shayhidin Elnur Elyar , Yu Haiyuan 
Published: April 2019

AbstractRecent, rapid advances in cross-linking mass spectrometry (XL-MS) has enabled detection of novel protein-protein interactions and their structural dynamics at the proteome scale. Given the importance and scale of the novel interactions identified in these proteome-wide XL-MS studies, thorough quality assessment is critical. Almost all current XL-MS studies validate cross-links against known 3D structures of representative protein complexes. However, current structure validation approach only includes cross-links where both peptides mapped to the 3D structures. Here we provide theoretical and experimental evidence demonstrating this approach can drastically underestimate error rates for proteome-wide XL-MS datasets. Addressing current shortcomings, we propose and demonstrate a comprehensive set of four metrics, including orthogonal experimental validation to thoroughly assess quality of proteome-wide XL-MS datasets.
Tracking the cells of tumor origin in breast organoids by light sheet microscopy
Authors: Alladin A , Chaible L , Reither S , Löschinger M , Wachsmuth M , Hériché JK , Tischer C , Jechlinger M 
Published: April 2019

AbstractHow tumors arise from individual transformed cells within an intact epithelium is a central, yet unanswered question. Here, we developed a new methodology that combines breast tissue organoids, where oncogenes can be switched on in single cells, with light-sheet imaging that allows us to track cell fates using a big-image-data analysis workflow. The power of this integrated approach is illustrated by our finding that small local groups of transformed cells form tumors while isolated transformed cells do not.
A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells
Authors: Jin Wen , Mulas Francesca , Gaertner Bjoern , Sui Yinghui , Wang Jinzhao , Zeng Chun , Vinckier Nicholas , Wang Allen , Nguyen-Ngoc Kim-Vy , Chiou Joshua , Kaestner Klaus H. , Frazer Kelly , Carrano Andrea C. , Shih Hung-Ping , Sander Maike 
Published: April 2019

SUMMARYPancreatic endocrine cell differentiation is orchestrated by transcription factors that operate in a gene regulatory network to activate endocrine lineage genes and repress lineage-inappropriate genes. MicroRNAs (miRNAs) are important modulators of gene expression, yet their role in endocrine cell differentiation has not been explored system-wide. Here we characterize miRNA-regulatory networks active in human endocrine cell differentiation by combining small RNA sequencing, miRNA overexpression experiments, and network modeling approaches. This analysis identifies Let-7g, Let-7a, miR-200a, and miR-375 as endocrine-enriched miRNAs with high impact on driving endocrine differentiation-associated gene expression changes. These miRNAs target different sets of transcription factors, which converge on a network of genes involved in cell cycle regulation. When expressed in human embryonic stem cell-derived pancreatic progenitors these miRNAs induce cell cycle exit and promote endocrine cell differentiation. Our study delineates the role of miRNAs in human endocrine cell differentiation and identifies miRNAs that could facilitate endocrine cell reprogramming.
Glutamine Synthetase-1 induces autophagy-lysosomal degradation of huntingtin aggregates and ameliorates animal motility in a Drosophila model for Huntington’s disease
Authors: Vernizzi Luisa , Paiardi Chiara , Licata Giusimaria , Vitali Teresa , Santarelli Stefania , Raneli Martino , Manelli Vera , Rizzetto Manuela , Gioria Mariarosa , Pasini Maria E. , Grifoni Daniela , Vanoni Maria A. , Gellera Cinzia , Taroni Franco , Bellosta Paola 
Published: April 2019

AbstractGlutamine Synthetase1 (GS1) is an enzyme that catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia as a key element of the glutamate glutamine cycle, a complex physiological process occurring between glia and neurons, necessary to control the homeostasis of glutamate. Using a Drosophila model for Huntington’s disease, we report that expression of GS1 in neurons ameliorates the motility defects of animals expressing the mutant Httex1-Q93 form of the huntingtin gene. At the cellular level, expression of GS1 increases the basal level of autophagy and significantly reduces the size of the toxic Htt-Q93 protein aggregates. In addition, we found that expression of GS1 prevents TOR localization at the lysosomal membrane and reduction in the phosphorylation of its effector S6K. This study reveals a novel function for GS1 in neurons linking its activity to the inhibition of TOR signaling and autophagy. The identification of novel pharmacological regulators of autophagy is of particular interest considering its beneficial role in controlling neuronal health and counteracting the detrimental effects of toxic aggregates of proteinopathies including Huntington’s disease.
Gene expression is associated with virulence in murine macrophages infected withLeptospiraspp
Authors: Corrêa de Araújo Junior Erivelto , Encarnação Garcia Leandro , Araújo Matheus Janeck , Oliveira-Junior Itamar Souza , Arnold Daniel Robert , Lopes Flavia Lombardi , Marinho Márcia 
Published: April 2019

AbstractLeptospiragenus contains species that affect human health with varying degrees of pathogenicity. In this context, we aimed to evaluate the differences in modulation of host gene expression by strains ofLeptospirawith varied virulence degrees. Our data showed a high number of differentilly expressed transcripts in murine macrophages following 6h of infection with both virulent and culture-attenuatedL. interrogansand to a lesser degree, with the saprophyte strainL. biflexa. That suggests that certain genes are modulated byLeptospirainfection independent of their degree of virulence, whether others are virulence and species associated. Pathway analysis indicated that Apoptosis, ATM Signaling and Cell Cycle: G2/M DNA Damage Checkpoint Regulation were exclusively regulated following infection with the virulent strain. Results demonstrated that species and virulence play a role during host response toLeptosppiraspp in murine macrophages.Author summaryLeptospirosis is an infectious disease that is transmitted from animals to humans. It is a re-emerging neglected zoonosis that is found in a range of environments worldwide, most notably tropical regions prone to flooding. This bacteria is found in soil and water and are eliminated in the urine by rats, their natural host reservoir. Through skin contacts with the bacteria people or animals can get infected however the infection process is still poorly understood, such as the fact that different strains can cause different severity of illness. In this study, we aimed to evaluate the differences in modulation of host gene expression by strains ofLeptospiravarying in virulence. After transcriptomic analysis, the results showed a high number of differentially expressed genes after 6h of infection by virulent and attenuatedL. interrogans, and to a lesser extent withL. biflexasaprophytic lineage. This suggests that RNAs are modulated after infection byLeptospirain macrophages, in a species and virulence related manner. It is hoped that the data produced will contribute to further our understanding on the pathogenesis of leptospirosis.
Trending topics and themes in offsite construction(OSC) research
Authors: Liu Guiwen , Nzige Juma Hamisi , Li Kaijian 
Published: April 2019

Purpose
The purpose of this study is to discover the distribution and trends of existing Offsite construction (OSC) literature with an intention to highlight research niches and propose the future outline.

Design/methodology/approach
The paper adopted literature reviews methodology involving 1,057 relevant documents published in 2008-2017 from 15 journals. The selected documents were empirically analyzed through a topic-modeling technique. A latent Dirichlet allocation model was applied to each document to infer 50 key topics. A machine learning for language toolkit was used to get topic posterior word distribution and word composition.

Findings
This is an exploratory study, which identifies the distribution of topics and themes; the trend of topics and themes; journal distribution trends; and comparative topic, themes and journal distribution trend. The distribution and trends show an increase in researcher’s interest and the journal’s priority on OSC research. Nevertheless, OSC existing literature is faced with; under-researched topics such as building information modeling, smart construction and marketing. The under-researched themes include organizational management, supply chain and context. The authors also found an overload of similar information in prefabrication and concrete topics. Furthermore, the innovative methods and constraints themes were found to be overloaded with similar information.

Research limitations/implications
The naming of the themes was based on our own interpretation; hence, the research results may lack generalizability. Therefore, a comparative study using different data processing is proposed. The study also provides future research outline as follows: studying OSC topics from dynamic evolution perspective and identifying the new emerging topics; searching for effective strategies to enhance OSC research; identifying the contribution of countries, affiliation and funding agency; and studying the impact of these themes to the adoption of OSC.

Practical implications
This study is of values to the scholars, as it could stimulate research to under-researched areas.

Originality/value
This paper justifies a need to have a broad understanding of the nature and structure of existing OSC literature.
Using grey relational analysis to analyze influential factor of hand, foot and mouth disease in Shenzhen
Authors: He Xiaoyi , Li Liping , Liu Xiaojian , Wu Yongsheng , Mei Shujiang , Zhang Zhen 
Published: April 2019

Purpose
Hand, foot and mouth disease (HFMD) is a common infectious disease in infants and children. HFMD has caused millions of cases and a large epidemic worldwide. A number of studies have shown that the incidence of HFMD is closely related to various factors such as meteorological factors, environmental air pollution factors and socio-economic factors. However, there are few studies that systematically consider the impact of various factors on the incidence of HFMD. The paper aims to discuss these issues.

Design/methodology/approach
This study used grey correlation analysis and principal component analysis (PCA) method to systematically analyse the impact of meteorological factors, health resource factors, socio-economic factors and environmental air pollution factors on the incidence of HFMD in Shenzhen.

Findings
The incidence of HFMD in Shenzhen was affected by multiple factors. Grey correlation analysis found eight influencing factors which are as follows: volume of industrial waste gas emission; the days of air quality equal to or above grade; the volume of industrial nitrogen oxide emission; precipitation; the mean air temperature; the gross domestic product; the expenditure for medical and health care; and the gross domestic product per capita. PCA found that the gross domestic product, the volume of industrial soot emission, the relative humidity, and the days of air quality equal to or above grade have a higher load value.

Originality/value
This study is the one of the first studies that apply the grey correlation analysis to analyse the influencing factors of HFMD in the English literature, which to some extent fills up the blank in this field.
Preferences of Iranian average risk population for colorectal cancer screening tests
Authors: Ramezani_Doroh Vajiheh , Delavari Alireza , Yaseri Mehdi , Emamgholipour Sefiddashti Sara , Akbarisari Ali 
Published: April 2019

Purpose
The purpose of this paper is to explore the preferences of the average risk Iranian population for colorectal cancer (CRC) screening tests.

Design/methodology/approach
A standard stated-preferences method with discrete choice models was used to identify the preferences. Data about socio-demographic status, health status and preferences for CRC screening tests were collected by a structured questionnaire that was completed by 500 people aged 50–75 years. Mixed logit model was used to analyze the preferences.

Findings
The regression model showed that the test process, pain, place, frequency, preparation, sensitivity, complication risk, mortality rate and cost were the final attributes; that had a statistically significant correlation with the preferences of the people in choosing CRC screening tests. The socio-demographic and health status of participants had no significant correlation with the individuals’ preferences.

Practical implications
This study provides insight into how different characteristics of a CRC screening test might influence the preferences of individuals about that test.

Originality/value
This was the first study of this type in Iran to elicit the preferences of the average risk population for CRC screening tests using a discrete choice model.