bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies
Authors: Intosalmi Jukka , Scott Adrian C. , Hays Michelle , Flann Nicholas , Yli-Harja Olli , Lähdesmäki Harri , Dudley Aimée M. , Skupin Alexander 
Published: December 2019

Abstract
Background
Multicellular entities like mammalian tissues or microbial biofilms typically exhibit complex spatial arrangements that are adapted to their specific functions or environments. These structures result from intercellular signaling as well as from the interaction with the environment that allow cells of the same genotype to differentiate into well-organized communities of diversified cells. Despite its importance, our understanding how this cell–cell and metabolic coupling lead to functionally optimized structures is still limited.

Results
Here, we present a data-driven spatial framework to computationally investigate the development of yeast colonies as such a multicellular structure in dependence on metabolic capacity. For this purpose, we first developed and parameterized a dynamic cell state and growth model for yeast based on on experimental data from homogeneous liquid media conditions. The inferred model is subsequently used in a spatially coarse-grained model for colony development to investigate the effect of metabolic coupling by calibrating spatial parameters from experimental time-course data of colony growth using state-of-the-art statistical techniques for model uncertainty and parameter estimations. The model is finally validated by independent experimental data of an alternative yeast strain with distinct metabolic characteristics and illustrates the impact of metabolic coupling for structure formation.

Conclusions
We introduce a novel model for yeast colony formation, present a statistical methodology for model calibration in a data-driven manner, and demonstrate how the established model can be used to generate predictions across scales by validation against independent measurements of genetically distinct yeast strains.
Automated segmentation of cardiomyocyte Z-disks from high-throughput scanning electron microscopy data
Authors: Khadangi Afshin , Hanssen Eric , Rajagopal Vijay 
Published: December 2019

Abstract
Background
With the advent of new high-throughput electron microscopy techniques such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion-beam scanning electron microscopy (FIB-SEM) biomedical scientists can study sub-cellular structural mechanisms of heart disease at high resolution and high volume. Among several key components that determine healthy contractile function in cardiomyocytes are Z-disks or Z-lines, which are located at the lateral borders of the sarcomere, the fundamental unit of striated muscle. Z-disks play the important role of anchoring contractile proteins within the cell that make the heartbeat. Changes to their organization can affect the force with which the cardiomyocyte contracts and may also affect signaling pathways that regulate cardiomyocyte health and function. Compared to other components in the cell, such as mitochondria, Z-disks appear as very thin linear structures in microscopy data with limited difference in contrast to the remaining components of the cell.

Methods
In this paper, we propose to generate a 3D model of Z-disks within single adult cardiac cells from an automated segmentation of a large serial-block-face scanning electron microscopy (SBF-SEM) dataset. The proposed fully automated segmentation scheme is comprised of three main modules including “pre-processing”, “segmentation” and “refinement”. We represent a simple, yet effective model to perform segmentation and refinement steps. Contrast stretching, and Gaussian kernels are used to pre-process the dataset, and well-known “Sobel operators” are used in the segmentation module.

Results
We have validated our model by comparing segmentation results with ground-truth annotated Z-disks in terms of pixel-wise accuracy. The results show that our model correctly detects Z-disks with 90.56% accuracy. We also compare and contrast the accuracy of the proposed algorithm in segmenting a FIB-SEM dataset against the accuracy of segmentations from a machine learning program called Ilastik and discuss the advantages and disadvantages that these two approaches have.

Conclusions
Our validation results demonstrate the robustness and reliability of our algorithm and model both in terms of validation metrics and in terms of a comparison with a 3D visualisation of Z-disks obtained using immunofluorescence based confocal imaging.
Expression alteration of microRNAs in Nucleus Accumbens is associated with chronic stress and antidepressant treatment in rats
Authors: Song Weichen , Shen Yifeng , Zhang Yanhua , Peng Sufang , Zhang Ran , Ning Ailing , Li Huafang , Li Xia , Lin Guan Ning , Yu Shunying 
Published: December 2019

Abstract
Background
Nucleus Accumbens (NAc) is a vital brain region for the process of reward and stress, whereas microRNA plays a crucial role in depression pathology. However, the abnormality of NAc miRNA expression during the stress-induced depression and antidepressant treatment, as well as its biological significance, are still unknown.

Methods
We performed the small RNA-sequencing in NAc of rats from three groups: control, chronic unpredictable mild stress (CUMS), and CUMS with an antidepressant, Escitalopram. We applied an integrative pipeline for analyzing the miRNA expression alternation in different model groups, including differential expression analysis, co-expression analysis, as well as a subsequent pathway/network analysis to discover both miRNA alteration pattern and its biological significance.

Result
A total of 423 miRNAs were included in analysis.18/8 differential expressing (DE) miRNA (adjusted p < 0.05, |log2FC| > 1) were observed in controls Vs. depression/depression Vs. treatment, 2 of which are overlapping. 78% (14/18) of these miRNAs showed opposite trends of alteration in stress and treatment. Two micro RNA, miR-10b-5p and miR-214-3p, appeared to be hubs in the regulation networks and also among the top findings in both differential analyses. Using co-expression analysis, we found a functional module that strongly correlated with stress (R = 0.96, P = 0.003), and another functional module with a moderate correlation with anhedonia (R = 0.89, P = 0.02). We also found that predicted targets of these miRNAs were significantly enriched in the Ras signaling pathway, which is associated with both depression, anhedonia, and antidepressant treatment.

Conclusion
Escitalopram treatment can significantly reverse NAc miRNA abnormality induced by chronic stress. However, the novel miRNA alteration that is absent in stress pathology also emerges, which means that antidepressant treatment is unlikely to bring miRNA expression back to the same level as the controls. Also, the Ras-signaling pathway may be involved in explaining the depression disease etiology, the clinical symptom, and treatment response of stress-induced depression.
Genome-wide association study in Chinese cohort identifies one novel hypospadias risk associated locus at 12q13.13
Authors: Chen Zhongzhong , Lin Xiaoling , Lei Yunping , Chen Haitao , Finnell Richard H. , Wang Yaping , Xu Jianfeng , Lu Daru , Xie Hua , Chen Fang 
Published: December 2019

Abstract
Background
Hypospadias risk–associated gene variants have been reported in populations of European descent using genome-wide association studies (GWASs). There is little known at present about any possible hypospadias risk associations in Han Chinese populations.

Methods
To systematically investigate hypospadias risk–associated gene variants in Chinese patients, we performed the first GWAS in a Han Chinese cohort consisting of 197 moderate-severe hypospadias cases and 933 unaffected controls. Suggestive loci (p < 1 × 10− 4) were replicated in 118 cases and 383 controls, as well as in a second independent validation population of 137 cases and 190 controls. Regulatory and protein-protein interactions (PPIs) were then conducted for the functional analyses of candidate variants.

Results
We identified rs11170516 with the risk allele G within the SP1/SP7 region that was independently associated with moderate-severe hypospadias [SP1/SP7, rs11170516, Pcombine = 3.5 × 10− 9, odds ratio (OR) = 1.96 (1.59–2.44)]. Results also suggested that rs11170516 is associated with the expression of SP1 as a cis-expression quantitative trait locus (cis-eQTL). Protein SP1 could affect the risk of hypospadias via PPIs.

Conclusions
We performed the first GWAS of moderate-severe hypospadias in a Han Chinese cohort, and identified one novel susceptibility cis-acting regulatory locus at 12q13.13, which may regulate a variety of hypospadias-related pathways by affecting proximal SP1 gene expression and subsequent PPIs. This study complements known common hypospadias risk-associated variants and provides the possible role of cis-acting regulatory variant in causing hypospadias.
Combination of the gamma-glutamyltransferase-to-prealbumin ratio and other indicators may be a novel marker for predicting the prognosis of patients with hepatocellular carcinoma undergoing locoregional ablative therapies
Authors: Wang Q. , Zhao P. , He N. , Sun J. P. , Li K. , Zang C. R. , Zhao Y. N. , Zhao Y. , Zhang Y. H. 
Published: December 2019

Abstract
Objective
The aim of this study was to investigate the prognostic significance of the serum γ-glutamyltransferase (γ-GT)-to-prealbumin ratio (GPR) and whether combining this ratio with other parameters can lead to an improved prognostic value for patients with hepatocellular carcinoma (HCC) undergoing transcatheter arterial chemoembolization (TACE) combined with local ablation therapy.

Methods
A total of 235 HCC patients who were treated with combined therapies were retrospectively analyzed. The demographic data and clinicopathological data were collected. A fibrinogen (Fib)-GPR score of 2 was assigned to patients with elevated Fib and GPR values, and a score of 1 or 0 was assigned to patients with one or neither of these two markers, respectively. In addition, an N-score of 2 was assigned to patients with low neutrophil and high GPR values, and a score of 1 or 0 was assigned to patients with one or neither of these two markers, respectively. The optimal cutoff values and prognostic roles of GPR and other markers were identified according to the time-dependent receiver operating characteristic (ROC) curves and Youden’s index.

Results
Multiple tumors, high levels of α-fetoprotein (AFP) and Fib, as well as a high GPR, were found to be independent risk factors in recurrent patients, while multiple tumors, a low neutrophil count, and a high GPR were associated with reduced overall survival (OS) in patients with HCC who received combined therapies. Patients with a Fib-GPR score of 2 and N-GPR score of 2 had poor recurrence-free survival (RFS) and OS, respectively.

Conclusions
Fib-GPR and N-GPR scores may be helpful in predicting both recurrence and the prognosis of HCC patients, thereby assisting in the process to make a true clinical decision and optimize therapeutic options.
Influence of dyskalemia at admission and early dyskalemia correction on survival and cardiac events of critically ill patients
Authors:   on behalf of the OUTCOMEREA STUDY GROUP, Bouadma Lila , Mankikian Stefan , Darmon Michael , Argaud Laurent , Vinclair Camille , Siami Shidasp , Garrouste-Orgeas Maité , Papazian Laurent , Cohen Yves , Marcotte Guillaume , Styfalova Lenka , Reignier Jean , Lautrette Alexandre , Schwebel Carole , Timsit Jean-Francois 
Published: December 2019

Abstract
Objectives
Our objectives were (1) to characterize the distribution of serum potassium levels at ICU admission, (2) to examine the relationship between dyskalemia at ICU admission and occurrence of cardiac events, and (3) to study both the association between dyskalemia at ICU admission and dyskalemia correction by day 2 on 28-day mortality.

Design
Inception cohort study from the longitudinal prospective French multicenter OUTCOMEREA database (1999–2014)

Setting
22 French OUTCOMEREA network ICUs

Patients
Patients were classified into six groups according to their serum potassium level at admission: three groups of hypokalemia and three groups of hyperkalemia defined as serious hypokalemia [K+] < 2.5 and serious hyperkalemia [K+] > 7 mmol/L, moderate hypokalemia 2.5 ≤ [K+] < 3 mmol/L and moderate hyperkalemia 6 < [K+] ≤ 7 mmol/L, and mild hypokalemia 3 ≤ [K+] < 3.5 mmol/L and mild hyperkalemia 5 < [K+] ≤ 6 mmol/L. We sorted evolution at day 2 of dyskalemia into three categories: balanced, not-balanced, and overbalanced.

Intervention
None

Measurements and main results
Of 12,090 patients, 2108 (17.4%) had hypokalemia and 1445 (12%) had hyperkalemia.
Prognostic impact of dyskalemia and its correction was assessed using multivariate Cox models. After adjustment, hypokalemia and hyperkalemia were independently associated with a greater risk of 28-day mortality. Mild hyperkalemic patients had the highest mortality (hazard ratio (HR) 1.29, 95% confidence interval (CI) [1.13–1.47], p < 0.001). Adjusted 28-day mortality was higher if serum potassium level was not-balanced at day 2 (aHR = 1.51, 95% CI [1.30–1.76], p < 0.0001) and numerically higher but not significantly different if serum potassium level was overbalanced at day 2 (aHR = 1.157, 95% CI [0.84–1.60], p = 0.38). Occurrence of cardiac events was evaluated by logistic regression. Except for patients with serious hypokalemia at admission, the depth of dyskalemia was associated with increased risk of cardiac events.

Conclusions
Dyskalemia is common at ICU admission and associated with increased mortality. Occurrence of cardiac events increased with dyskalemia depth. A correction of serum potassium level by day 2 was associated with improved prognosis.
Efficacy of Behavioral Experiments in Cognitive Therapy for Social Anxiety Disorder: Study protocol for a randomized controlled trial
Authors: Clément Celina , Lin Jihong , Stangier Ulrich 
Published: December 2019

Abstract
Background
While the efficacy of cognitive therapy (CT) has been well established for social anxiety disorder (SAD) in several randomized controlled trials, there are still large differences between trials with respect to effect sizes. The present study investigates the question of whether enhanced training and the use of behavioral experiments (BEs) increases the efficacy of traditional CT, based on verbal methods of cognitive restructuring.

Methods/design
A mixed within/between conditions design will be applied, with therapists and patients being randomly allocated to one of two conditions: (1) training of CT plus BEs, (2) training of CT “as usual”.
Sixty patients with the primary diagnosis of SAD will be recruited and treated in the outpatient clinic of the Department of Psychology, University of Frankfurt. To ensure adherence to therapist protocols, all therapists will be trained and supervised by the project coordinators. In addition, videotaped treatment sessions will be independently evaluated to guarantee both adherence to protocols and the quality of the intervention. Treatment effects will be assessed by independent SAD symptom ratings using the Liebowitz Social Anxiety Scale as the primary outcome measure and self-report measures as secondary outcome measures.

Discussion
The present cognitive behavioral therapy (CBT) trial will be the first to clarify the contribution of BEs to the efficacy of CT in a randomized controlled design. Study results are relevant to clinical training and implementation of evidence-based treatments.

Trial registration
German Clinical Trials Register International Clinical Trials Registry Platform (ICTRP) identifier: DRKS00014349. Trial status: recruiting.
Regorafenib plus FOLFIRI with irinotecan dose escalated according to uridine diphosphate glucuronosyltransferase 1A1genotyping in previous treated metastatic colorectal cancer patients:study protocol for a randomized controlled trial
Authors: Ma Cheng-Jen , Chang Tsung-Kun , Tsai Hsiang-Lin , Su Wei-Chih , Huang Ching-Wen , Yeh Yung-Sung , Chang Yu-Tang , Wang Jaw-Yuan 
Published: December 2019

Abstract
Background
Regorafenib is an oral multikinase inhibitor for metastatic colorectal cancer (mCRC) previously treated with fluoropyrimidines, irinotecan, oxaliplatin, monoclonal antibodies targeting vascular endothelial growth factor, and monoclonal antibodies targeting epidermal growth factor receptor. A dose reduction from 160 mg to 120 mg regorafenib reduces regorafenib-associated adverse events (AEs). Dose adjustment of irinotecan in a 5-fluorouracil/leucovorin/irinotecan (FOLFIRI) regimen on the basis of an individual uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) genotype provides optimal oncological outcomes with acceptable AEs. The aim of this study is to address the efficacy and safety of a dose-adjusted combination of regorafenib and FOLFIRI for patients with mCRC.

Methods
A prospective, multicenter, randomized in a 2:1 ratio, controlled, clinical trial with two parallel arms will be conducted to compare irinotecan dose-escalated FOLFIRI according to UGT1A1 genotyping plus 120 mg regorafenib with 120 mg regorafenib alone in previously treated patients with mCRC. The primary endpoint is progression-free survival, and the secondary endpoints are overall survival, disease control rate, time to progression, and duration of treatment. Safety assessments will also be recorded.

Discussion
Dose adjustment for regorafenib and irinotecan makes treatment-related AEs tolerable and makes the concomitant treatment practicable. This study will provide initial evidence regarding the efficacy and safety of a new combination of chemotherapy and a targeted agent for mCRC.

Trial registration
ClinicalTrials.gov, NCT03880877. Prospectively registered on 19 March 2019.
Assessment of differences between DNA content of cell-cultured and freely suspended oocysts of Cryptosporidium parvum and their suitability as DNA standards in qPCR
Authors: Woolsey Ian D. , Blomstrand Berit , Øines Øivind , Enemark Heidi L. 
Published: December 2019

Abstract
Background
Although more modern methods are available, quantitative PCR (qPCR) is reproducible, sensitive and specific with instruments and expertise readily available in many laboratories. As such, the use of qPCR in Cryptosporidium research is well established and still widely used by researchers globally. This method depends upon the generation of standards at different concentrations to generate standard curves subsequently used for the quantification of DNA.

Methods
We assessed four types of DNA template used to generate standard curves in drug screening studies involving Cryptosporidium spp.: (i) serially diluted Cryptosporidium parvum oocysts (106–1); (ii) diluted template DNA from pure oocysts (×10–×106 dilution of 106 oocyst DNA template); (iii) oocysts incubated in human ileocecal adenocarcinoma (HCT-8) cells (105–1 and 5 × 104–50); and (iv) diluted DNA template (5 × 104) from cell culture incubated parasites (×10–×1000).

Results
Serial dilutions of both cell culture and pure oocyst suspension DNA template yielded better linearity than cell culture derived standards, with dilutions of 106 oocysts exhibiting similar quantification cycle (Cq) values to those obtained from DNA template dilutions of 106 oocysts. In contrast, cell culture incubated oocysts demonstrated significantly higher DNA content than equivalent freely suspended oocysts and diluted DNA template from both cell culture derived and freely suspended oocysts across numerous concentrations.

Conclusions
For many studies involving Cryptosporidium, only relative DNA content is required and as such, the superior linearity afforded by freely suspended oocysts and diluted DNA template (from either cell culture derived standards or freely suspended oocysts) will allow for more accurate relative quantification in each assay. Parasite division in the cell culture standards likely explains the higher DNA content found. These standards, therefore, have the potential to more accurately reflect DNA content in cell culture assays, and despite more modern methods available for absolute quantification, i.e. droplet digital PCR (ddPCR), the ubiquity of qPCR for the foreseeable future encourages further investigation into the reduced linearity observed in these standards such as varying oocyst seeding density, non-linear growth rates and assay efficiency.
Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Authors: Nakato Ryuichiro , Wada Youichiro , Nakaki Ryo , Nagae Genta , Katou Yuki , Tsutsumi Shuichi , Nakajima Natsu , Fukuhara Hiroshi , Iguchi Atsushi , Kohro Takahide , Kanki Yasuharu , Saito Yutaka , Kobayashi Mika , Izumi-Taguchi Akashi , Osato Naoki , Tatsuno Kenji , Kamio Asuka , Hayashi-Takanaka Yoko , Wada Hiromi , Ohta Shinzo , Aikawa Masanori , Nakajima Hiroyuki , Nakamura Masaki , McGee Rebecca C. , Heppner Kyle W. , Kawakatsu Tatsuo , Genno Michiru , Yanase Hiroshi , Kume Haruki , Senbonmatsu Takaaki , Homma Yukio , Nishimura Shigeyuki , Mitsuyama Toutai , Aburatani Hiroyuki , Kimura Hiroshi , Shirahige Katsuhiko 
Published: December 2019

AbstractBackgroundEndothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phenotypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from different organs are not well understood.ResultsTo characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome-wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identified 3765 EC-specific enhancers, some of which were associated with disease-associated genetic variations. We also identified various candidate marker genes for each EC type. We found that the nine EC types can be divided into two subgroups, corresponding to those with upper-body origins and lower-body origins, based on their epigenomic landscape. Epigenomic variations were highly correlated with gene expression patterns, but also provided unique information. Most of the deferentially expressed genes and enhancers were cooperatively enriched in more than one EC type, suggesting that the distinct combinations of multiple genes play key roles in the diverse phenotypes across EC types. Notably, many homeobox genes were differentially expressed across EC types, and their expression was correlated with the relative position of each organ in the body. This reflects the developmental origins of ECs and their roles in angiogenesis, vasculogenesis and wound healing.ConclusionsThis comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.