bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of computed tomography hepatic steatosis criteria for identification of abnormal liver function and clinical risk factors, in incidentally noted fatty liver
Authors: Jawahar Anugayathri , Gonzalez Beverly , Balasubramanian Neelam , Adams William , Goldberg Ari 
Published: October 2019

Objectives
Hounsfield Units (HU) to compare the various computed tomography (CT) criteria for diagnosing hepatic steatosis with laboratory liver function parameters, and clinical risk factors retrospectively, when hepatic steatosis was incidentally detected.

Methods
Institutional review board-approved, Health Insurance Portability and Accountability Act-compliant, retrospective study in 200 randomly selected patients who had either nonenhanced CT (NECT) or contrast-enhanced CT (CECT) studies with reported hepatic steatosis. The participants were matched to age, gender, and ethnicity with 200 patients without hepatic steatosis. For NECT, four different criteria have been proposed in the literature to diagnose fatty liver: (1) liver HU less than 48 HU; (2) ratio of liver to spleen HU less than 0.8; (3) HU difference between liver and spleen less than −10; and (4) hepatic vessel HU ≥ liver HU. For CECT, difference between liver and spleen HU, in portal venous phase, ≤ −20 to −25 HU. Serum glucose, aspartate aminotransferase (AST), amino alanine transferase (ALT), total bilirubin were documented. Clinical history and clinical risk factors were documented from the electronic health records. Matched analyses and Wilcoxon signed rank sum test analysis were performed for matched variables.

Results
Fatty liver by NECT criteria 1 and 3 has statistically significant correlation with elevated glucose levels (P = 0.02). Similarly, fatty liver by 1, 3, and 4 NECT criteria showed statistically significant associations with higher levels of ALT and AST. There were statistically significant higher prevalence of diabetes mellitus (P = 0.003) and alcohol consumption (P ≤ 0.0001) in cases when compared with the controls. There was marginal significance in CT Dose Index between cases and controls (95% confidence interval: 0.98, 1.00; odds ratio 0.99), reflecting that cases had slightly higher BMI compared to their matched controls, thereby requiring slightly higher mA/mAs for imaging.

Conclusion
Particular NECT criteria for fatty liver are best at identification of abnormal liver function and certain comorbidities, in the setting of incidental fatty liver detection, This creates the potential for benefits of early detection in clinical management.
Clinical Tests of the Shoulder
Authors: Chang Ke-Vin , Wu Wei-Ting , Hsu Po-Cheng , Lew Henry L. , Özçakar Levent 
Published: October 2019

Abstract
Shoulder pain is a common musculoskeletal disorder that has a significant impact on the patient’s quality of life and functional health. Because the shoulder joint is a complex structure, the relevant symptoms of shoulder pain may not directly reflect the underlying pathology. Hence, several shoulder tests have been developed to examine shoulder problems, and their diagnostic accuracy varies. Familiarization with the performance of those physical tests and their strength and limitation are of utmost importance for physicians dealing with shoulder disorders. Therefore, the present narrative review focuses on summarizing the most commonly used tests in physical examination and their diagnostic performance on several shoulder pathologies. This article also discusses how ultrasound imaging can serve as an extension of those tests.
Effects of Load Addition During Gait Training on Weight-Bearing and Temporal Asymmetry After Stroke
Authors: Ribeiro Tatiana Souza , Gomes de Souza e Silva Emília Márcia , Regalado Isabelly Cristina Rodrigues , Silva Stephano Tomaz da , Sousa Catarina de Oliveira , Ribeiro Karyna Myrelly Oliveira Bezerra de Figueiredo , Lindquist Ana Raquel Rodrigues 
Published: October 2019

Objective
The aim of the study was to evaluate the effects of adding load to restrain the nonparetic lower limb during gait training on weight-bearing and temporal asymmetry after stroke.

Design
Thirty-eight subjects were randomized into treadmill training with load (5% of body weight) on the nonparetic limb (experimental group) and treadmill training without load (control group). Interventions lasted 30 mins/d for 2 wks (9 sessions). Both groups performed home-based exercises and were instructed to increase the use of paretic limb in daily life situations. Ground reaction force was obtained by a force plate during standing position (static) and gait (dynamic). Temporal gait parameters were assessed by a motion system analysis. Outcome measures were evaluated at baseline, posttraining, and after a 40-day follow-up.

Results
The experimental group increased static ground reaction force of the paretic limb at posttraining (P = 0.037) and the control group increased dynamic ground reaction force of the paretic limb at posttraining (P = 0.021), both with maintenance at follow-up. Neither group showed a change in the swing time symmetry ratio after training (P = 0.190).

Conclusions
Treadmill training associated with behavioral strategies/home-based exercises seemed to be useful to minimize weight-bearing asymmetry, but not to improve temporal gait asymmetry. Load addition did not show additional benefits.
Recipient-Site Preconditioning with Deferoxamine Increases Fat Graft Survival by Inducing VEGF and Neovascularization in a Rat Model
Authors: Kim Junhyung , Park Minwoo , Jeong Woonhyeok , Lee Hyoun Wook , Lee Geumhong , Suk Lee Kyung , Park Sang Woo , Choi Jaehoon 
Published: October 2019

Background:
The authors hypothesize that ischemic preconditioning of the recipient site with deferoxamine will increase fat graft survival by enhancing angiogenesis in a rat model.

Methods:
Cell viability, tube formation, and mRNA expression were measured in human umbilical vein endothelial cells treated with deferoxamine. A total of 36 rats were then used for an in vivo study. A dose of 100 mg/kg of deferoxamine was injected subcutaneously into the rat scalp every other day for five treatments. On the day after the final injection, the scalp skin was harvested from half the animals to evaluate the effects of deferoxamine on the recipient site. In the remaining animals, inguinal fat tissue was transplanted to the scalp. Eight weeks after transplantation, the grafts were harvested to evaluate the effects of deferoxamine preconditioning on fat graft survival.

Results:
In human umbilical vein endothelial cells, treatment with a deferoxamine concentration higher than 400 μM decreased cell viability compared with the control (p = 0.002). Treatment with 100 and 200 μM deferoxamine increased endothelial tube formation (p = 0.001) and mRNA levels of angiogenesis-related factors (p = 0.02). Rat scalps treated with deferoxamine exhibited increased capillary neoformation (p = 0.001) and vascular endothelial growth factor protein expression (p = 0.024) compared with controls. Fat graft volume retention, capillary density (p < 0.001), and adipocyte viability (p < 0.001) in the grafted fat increased when the recipient site was preconditioned with deferoxamine.

Conclusion:
This study demonstrated that recipient site preconditioning with deferoxamine increases fat graft survival by inducing vascular endothelial growth factor and neovascularization.
Addressing Surgeon Fatigue: Current Understanding and Strategies for Mitigation
Authors: Janhofer David E. , Lakhiani Chrisovalantis , Song David H. 
Published: October 2019

Summary:
Fatigue is inevitable at all stages of a surgical career. The sustained high degree of concentration required for surgery is complicated by long surgeon working hours and sleep deprivation, which force surgeons to learn to manage and mitigate the effects of physical and mental fatigue on their performance. Extensive evidence exists detailing the potentially dangerous effects of surgeon fatigue on patient safety, but few reports exist offering a comprehensive strategy to mitigate the effects of fatigue on clinical performance. To promote improved detection and mitigation of fatigue among surgeons, the authors have highlighted several deliberate fatigue-management techniques that they have found to be particularly effective in their own experiences. These techniques include proper planning to maximize team efficiency, and the use of scheduled and unscheduled intraoperative breaks for mental and physical rest and regeneration. The decision to take a much-needed break is often neglected because of concerns about prolonging the duration of an operation; with proper self-awareness of fatigue and brief mental checks during natural intraoperative slowdowns, however, the surgeon can quickly assess the need for a much-needed moment of recovery. The authors hope surgeons will find the fatigue-mitigation strategies presented here to be helpful in promoting both their own wellness and the safety and wellness of their patients.
A Novel Application of [18F]Fluorothymidine-PET ([18F]FLT-PET) in Clinical Practice to Quantify Regional Bone Marrow Function in a Patient With Treatment-Induced Cytopenias and to Guide “Marrow-Sparing” Radiotherapy
Authors: Campbell Belinda A. , Hofman Michael S. , Prince H. Miles 
Published: October 2019

Abstract

18F-Fluorothymidine-positron emission tomography with CT fusion ([18F]FLT-PET/CT) offers a unique and non-invasive method for three-dimensional localization and quantification of functional bone marrow. [18F]FLT-PET/CT has potential application in radiotherapy planning when risk of marrow toxicity is a significant clinical concern. In this patient with chemo-refractory, transformed lymphoma and treatment-induced cytopenias, [18F]FLT-PET/CT was a novel and useful adjunct to (1) image the distribution of functional bone marrow reserve, (2) guide “marrow-sparing” radiotherapy planning, and (3) quantify the effects of radiotherapy-induced bone marrow suppression both in-field and out-of-field.
Lymphangioma in the Buccal Mucosa
Authors: Yalçin Mustafa , Laçin Nihat 
Published: October 2019

Abstract
Lymphangiomas are benign hamartomatous tumors which are characterized by abnormal proliferation of lymphatic vessels. They are lymphatic malformations which are commonly localized to head and neck region. They are rare located in the oral cavity and tongue, lips, buccal mucosa, soft palate, floor of the mouth are mostly affected.
APACHE IV Score is Useful For Assessment and Stratification of Elderly Patients Over 65 Years With Acute Cholecystitis
Authors: Jiang Hua , Yao Zhimin , Guo Guo , Wang Yuehua , Li Fei 
Published: October 2019

Purpose:
One of the main problems concerning the design of clinical trials in critically ill patients with acute cholecystitis (AC) is the lack of validated, well-established scoring systems to stratify the severity of patient disease states. The aim of this study was to evaluate the performance of the Acute Physiology and Chronic Health Evaluation IV (APACHE IV) scoring system in patients over 65 years with AC.

Methods:
All patients over 65 years of age admitted to our hospital for treatment of AC in the intensive care unit between January 2013 and January 2019 were retrospectively analyzed.

Results:
A total of 443 consecutive patients with AC were enrolled in this study. As for the patients over 65 years, the survivors had lower APACHE IV scores and lower risk of death than nonsurvivors (P<0.01). The discrimination of the APACHE IV score prediction was good, with an area under the curve of 0.850 (95% confidence interval, 0.780-0.932). The APACHE IV models were well-calibrated with the Hosmer-Lemeshow goodness-of-fit test (P=0.635). Similar results were obtained for patients over 85 years of age.

Conclusion:
The APACHE IV model was good at predicting hospital mortality in elderly patients with AC, which would be helpful to make clinical and therapeutic decisions in the future.
Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment
Authors: Liu Honghai , Zhang Cheng-Hai , Ammanamanchi Niyatie , Suresh Sangita , Lewarchik Christopher , Rao Krithika , Uys Gerrida M. , Han Lu , Abrial Maryline , Yimlamai Dean , Ganapathy Balakrishnan , Guillermier Christelle , Chen Nathalie , Khaladkar Mugdha , Spaethling Jennifer , Eberwine James H. , Kim Junhyong , Walsh Stuart , Choudhury Sangita , Little Kathryn , Francis Kimberly , Sharma Mahesh , Viegas Melita , Bais Abha , Kostka Dennis , Ding Jun , Bar-Joseph Ziv , Wu Yijen , Steinhauser Matthew L. , Kühn Bernhard 
Published: October 2019

ABSTRACT/SUMMARYOne million patients with congenital heart disease (CHD) live in the US. They have a lifelong risk of developing heart failure. Current concepts do not sufficiently address mechanisms of heart failure development specifically for these patients. We show that cardiomyocyte cytokinesis failure is increased in tetralogy of Fallot with pulmonary stenosis (ToF/PS), a common form of CHD. Labeling of a ToF/PS baby with isotope-tagged thymidine showed cytokinesis failure after birth. We used single-cell transcriptional profiling to discover that the underlying mechanism is repression of the cytokinesis gene ECT2, and show that this is downstream of β-adrenergic receptors (β-AR). Inactivation of the β-AR genes and administration of the β-blocker propranolol increased cardiomyocyte division in neonatal mice, which increased the endowment and conferred benefit after myocardial infarction in adults. Propranolol enabled the division of ToF/PS cardiomyocytes. These results suggest that β-blockers should be evaluated for increasing cardiomyocyte division in patients with ToF/PS and other types of CHD.
Diverse transcriptomic signatures across human tissues identify functional rare genetic variation
Authors: Ferraro Nicole M. , Strober Benjamin J. , Einson Jonah , Li Xin , Aguet Francois , Barbeira Alvaro N. , Castel Stephane E. , Davis Joe R. , Hilliard Austin T. , Kotis Bence , Park YoSon , Scott Alexandra J. , Smail Craig , Tsang Emily K. , Ardlie Kristin G. , Assimes Themistocles L. , Hall Ira , Im Hae Kyung ,   GTEx Consortium, Lappalainen Tuuli , Mohammadi Pejman , Montgomery Stephen B. , Battle Alexis 
Published: October 2019

AbstractRare genetic variation is abundant in the human genome, yet identifying functional rare variants and their impact on traits remains challenging. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants. Here, we expand detection of genetically driven transcriptome abnormalities by evaluating and integrating gene expression, allele-specific expression, and alternative splicing from multi-tissue RNA-sequencing data. We demonstrate that each signal informs unique classes of rare variants. We further develop Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function. Assessing rare variants prioritized by Watershed in the UK Biobank and Million Veterans Program, we identify large effects across 34 traits, and 33 rare variant-trait combinations with both high Watershed scores and large trait effect sizes. Together, we provide a comprehensive analysis of the transcriptomic impact of rare variation and a framework to prioritize functional rare variants and assess their trait relevance.One-sentence summaryIntegrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.
Differential antitumor activity of compounds targeting the ubiquitin-proteasome machinery in gastrointestinal stromal tumor (GIST) cells
Authors: Rausch Jessica L. , Ali Areej A. , Lee Donna M. , Gebreyohannes Yemarshet K. , Mehalek Keith R. , Agha Aya , Patil Sneha S. , Tolstov Yanis , Wellens Jasmien , Dhillon Harbir S. , Makielski Kathleen R. , Debiec-Rychter Maria , Schöffski Patrick , Wozniak Agnieszka , Duensing Anette 
Published: October 2019

ABSTRACTThe majority of gastrointestinal stromal tumors (GISTs) are driven by oncogenic KIT signaling and can therefore be effectively treated with the tyrosine kinase inhibitor (TKI) imatinib mesylate. However, most GISTs develop imatinib resistance through secondaryKITmutations. The type of resistance mutation determines sensitivity to approved second-/third-line TKIs but shows high inter- and intratumoral heterogeneity. Therefore, therapeutic strategies that target KIT independently of the mutational status are intriguing. Inhibiting the ubiquitin-proteasome machinery with bortezomib is effective in GIST cells through a dual mechanism ofKITtranscriptional downregulation and upregulation of the pro-apoptotic histone H2AX but clinically problematic due to the drug’s adverse effects. We therefore tested second-generation inhibitors of the 20S proteasome (delanzomib, carfilzomib and ixazomib) with better pharmacologic profiles as well as compounds targeting regulators of ubiquitination (b-AP15, MLN4924) for their effectiveness and mechanism of action in GIST. All three 20S proteasome inhibitors were highly effectivein vitroandin vivo, including in imatinib-resistant models. In contrast, b-AP15 and MLN4924 were only effective at high concentrations or had mostly cytostatic effects, respectively. Our results confirm 20S proteasome inhibitors as promising strategy to overcome TKI resistance in GIST, while highlighting the complexity of the ubiquitin-proteasome machinery as a therapeutic target.
Noncoding RNAs endogenously rule the cancerous regulatory realm while proteins govern the normal
Authors: Wang Anyou , Hai Rong 
Published: October 2019

AbstractAll cancers share a commonality in genome activation regulated by a systems endogenous network distinct from normal tissue, but such a network remains elusive. Here, we unearth a systems regulatory network endogenous for all types of cancers and normal human respectively from massive data, including all RNAseq data available from SRA and TCGA, and reveal distinctive systems realm for cancer and normal. In the cancerous realm, noncoding RNAs, especially pseudogenes, dominate endogenous network modules and centrality, and they work as the strongest systems inducers that cis-regulate their targets. However in the normal realm proteins dominate the entire endogenous network centrally controlled by ribosomal proteins and they trans-regulate their targets. Our finding establishes a systems picture of an endogenous mechanism overlooking the cancerous and normal realm, in which noncoding RNAs rule the overall cancer realm while proteins govern the normal one. This fundamentally refreshes the conventional concept of cancerous mechanism.
Repository-based plasmid design Cost-optimal Gibson Assembly with repository DNA selection and primer generation
Authors: Timmons Joshua J. , Densmore Doug 
Published: October 2019

ABSTRACTThere was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. The challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson Assembly. It finds existing DNA sequences in user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.
Maximizing the Reusability of Public Gene Expression Data by Predicting Missing Metadata
Authors: Lung Pei-Yau , Pang Xiaodong , Li Yan , Zhang Jinfeng 
Published: October 2019

AbstractReusability is part of the FAIR data principle, which aims to make data Findable, Accessible, Interoperable, and Reusable. One of the current efforts to increase the reusability of public genomics data has been to focus on the inclusion of quality metadata associated with the data. When necessary metadata are missing, most researchers will consider the data useless. In this study, we develop a framework to predict the missing metadata of gene expression datasets to maximize their reusability. We propose a new metric called Proportion of Cases Accurately Predicted (PCAP), which is optimized in our specifically-designed machine learning pipeline. The new approach performed better than pipelines using commonly used metrics such as F1-score in terms of maximizing the reusability of data with missing values. We also found that different variables might need to be predicted using different machine learning methods and/or different data processing protocols. Using differential gene expression analysis as an example, we show that when missing variables are accurately predicted, the corresponding gene expression data can be reliably used in downstream analyses.
Plasmodium falciparumimmunodominant IgG epitopes in subclinical malaria
Authors: Azcárate Isabel G. , Marín-García Patricia , Abad Paloma , Pérez-Benavente Susana , Paz-Artal Estela , Reche Pedro A. , Fobil Julius N. , Rubio José M. , Diez Amalia , Puyet Antonio , Bautista José M. 
Published: October 2019

AbstractIncomplete non-sterile immunity to malaria is attained in endemic regions after recurrent infections by a large percentage of the adult population, who carry the malaria parasite asymptomatically. Although blood-stagePlasmodium falciparumrapidly elicits IgG responses, the target antigens of partially protective and non-protective IgG antibodies as well as the basis for the acquisition of these antibodies remain largely unknown. We performed IgG-immunomics to screen forP. falciparumantigens and to identify epitopes associated with exposure and clinical disease. Sera from malaria cases identified five prevalent antigens recognized by all analyzed patients’ IgGs. For further epitope mapping, peptide microarrays designed to cover their sequences were probed with a set of 38 sera samples from adult individuals of an endemic malaria region in Ghana. Eight 20-mer peptides with the highest affinity and frequency of recognition among the population were subsequently validated with 16 sera from the same region, segregated into patients with positive or negative subclinical detection ofP. falciparum. Significant binding specificity for two immunodominant antigenic regions was uncovered within the START-related lipid transfer protein and the protein disulfide isomerase PDI8. These 20-mer peptides challenged with sera samples from children under 5 years old displayed specific IgG binding in those with detectable parasitemia, even at subclinical level. These results suggest that the humoral response against START and PDI8 antigens may be triggered even at submicroscopic parasitemia levels in children and may eventually be used to differentially diagnose subclinical malaria in children.SignificanceMalaria in Africa is a leading cause of morbidity and mortality. The reservoirs of the malaria parasite are asymptomatic patients who carry it subclinically. Identifying the parasite antigens and its fragments that trigger the most common immunity response by immunoglobulin G that partially protect people can have profound implications for both, development of a malaria vaccine and diagnosis of the subclinical parasite carriers. Antigen discovery and mapping, validated with sera from subclinical carriers, showed that immunoglobulin G responses in children against parasite’s START and PDI8 may eventually be used to differentially diagnose non-infected from subclinical cases. Furthermore, anti-START and anti-PDI8 endemic immunodominance provides association of these antigens with long-term acquired immunity and immune evasion to malaria.