bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence hearing loss of truck and bus drivers in a cross-sectional study of 65533 subjects
Authors: Pourabdian Siamak , Yazdanirad Saeid , Lotfi Saeid , Golshiri Parastoo , Mahaki Behzad 
Published: December 2019

Abstract
Background
Noise pollution is one of the most important occupational pollutants in heavy-vehicle drivers. Therefore, this epidemiological research was conducted with the aim of determining the prevalence of hearing loss in heavy-vehicle drivers in Iran.

Methods
This cross-sectional research was conducted on 65,533 heavy-vehicle drivers including truck and intercity bus drivers from February 2006 to March 2016. The air and bone threshold of pure tone was measured for each ear at 0.5, 1, 2, 3, 4, 6, and 8 kHz by a skillful radiology expert. The obtained data from this research was analyzed in SPSS software using statistical tests such as descriptive analysis and paired t test.

Results
Mean (standard deviation) of hearing loss in left and right ears of all people was 23.02 (8.25) and 22.48 (7.86), respectively. Paired t test showed that hearing loss difference in left and right ears was significant (P < 0.001). Mean and standard deviation of paired t test showed that hearing loss difference in left and right ears was significant in all frequencies except 1000 Hz (P < 0.001).

Conclusion
The findings of this research generally showed that 26.8% of the studied drivers have hearing loss. Hearing loss in the left ear was more than right ear.
Investigating skewness to understand gene expression heterogeneity in large patient cohorts
Authors: Church Benjamin V. , Williams Henry T. , Mar Jessica C. 
Published: December 2019

Abstract
Background
Skewness is an under-utilized statistical measure that captures the degree of asymmetry in the distribution of any dataset. This study applied a new metric based on skewness to identify regulators or genes that have outlier expression in large patient cohorts.

Results
We investigated whether specific patterns of skewed expression were related to the enrichment of biological pathways or genomic properties like DNA methylation status. Our study used publicly available datasets that were generated using both RNA-sequencing and microarray technology platforms. For comparison, the datasets selected for this study also included different samples derived from control donors and cancer patients. When comparing the shift in expression skewness between cancer and control datasets, we observed an enrichment of pathways related to the immune function that reflects an increase towards positive skewness in the cancer relative to control datasets. A significant correlation was also detected between expression skewness and the top 500 genes corresponding to the most significant differential DNA methylation occurring in the promotor regions for four Cancer Genome Atlas cancer cohorts.

Conclusions
Our results indicate that expression skewness can reveal new insights into transcription based on outlier and asymmetrical behaviour in large patient cohorts.
StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis
Authors: Kang Dongwon , Ahn Hongryul , Lee Sangseon , Lee Chai-Jin , Hur Jihye , Jung Woosuk , Kim Sun 
Published: December 2019

Abstract
Background
Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the stress response are available in databases. With the data, an integrated analysis of multiple stresses is possible, which identifies stress-responsive genes with higher specificity because considering multiple stress can capture the effect of interference between stresses. To analyze such data, a machine learning model needs to be built.

Results
In this study, we developed StressGenePred, a neural network-based machine learning method, to integrate time-series transcriptome data of multiple stress types. StressGenePred is designed to detect single stress-specific biomarker genes by using a simple feature embedding method, a twin neural network model, and Confident Multiple Choice Learning (CMCL) loss. The twin neural network model consists of a biomarker gene discovery and a stress type prediction model that share the same logical layer to reduce training complexity. The CMCL loss is used to make the twin model select biomarker genes that respond specifically to a single stress. In experiments using Arabidopsis gene expression data for four major environmental stresses, such as heat, cold, salt, and drought, StressGenePred classified the types of stress more accurately than the limma feature embedding method and the support vector machine and random forest classification methods. In addition, StressGenePred discovered known stress-related genes with higher specificity than the Fisher method.

Conclusions
StressGenePred is a machine learning method for identifying stress-related genes and predicting stress types for an integrated analysis of multiple stress time-series transcriptome data. This method can be used to other phenotype-gene associated studies.
LncRNA-miRNA interaction prediction through sequence-derived linear neighborhood propagation method with information combination
Authors: Zhang Wen , Tang Guifeng , Zhou Shuang , Niu Yanqing 
Published: December 2019

AbstractBackgroundResearchers discover lncRNAs can act as decoys or sponges to regulate the behavior of miRNAs. Identification of lncRNA-miRNA interactions helps to understand the functions of lncRNAs, especially their roles in complicated diseases. Computational methods can save time and reduce cost in identifying lncRNA-miRNA interactions, but there have been only a few computational methods.ResultsIn this paper, we propose a sequence-derived linear neighborhood propagation method (SLNPM) to predict lncRNA-miRNA interactions. First, we calculate the integrated lncRNA-lncRNA similarity and the integrated miRNA-miRNA similarity by combining known lncRNA-miRNA interactions, lncRNA sequences and miRNA sequences. We consider two similarity calculation strategies respectively, namely similarity-based information combination (SC) and interaction profile-based information combination (PC). Second, the integrated lncRNA similarity-based graph and the integrated miRNA similarity-based graph are respectively constructed, and the label propagation processes are implemented on two graphs to score lncRNA-miRNA pairs. Finally, the weighted averages of their outputs are adopted as final predictions. Therefore, we construct two editions of SLNPM: sequence-derived linear neighborhood propagation method based on similarity information combination (SLNPM-SC) and sequence-derived linear neighborhood propagation method based on interaction profile information combination (SLNPM-PC). The experimental results show that SLNPM-SC and SLNPM-PC predict lncRNA-miRNA interactions with higher accuracy compared with other state-of-the-art methods. The case studies demonstrate that SLNPM-SC and SLNPM-PC help to find novel lncRNA-miRNA interactions for given lncRNAs or miRNAs.ConclusionThe study reveals that known interactions bring the most important information for lncRNA-miRNA interaction prediction, and sequences of lncRNAs (miRNAs) also provide useful information. In conclusion, SLNPM-SC and SLNPM-PC are promising for lncRNA-miRNA interaction prediction.
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries
Authors: Zeng Shuai , Lyu Zhen , Narisetti Siva Ratna Kumari , Xu Dong , Joshi Trupti 
Published: December 2019

Abstract
Background
Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple organisms’ genomics and integrative omics data. KBCommons is designed and developed to integrate diverse multi-level omics data and to support biological discoveries for all species via a common platform.

Methods
KBCommons has four modules including data storage, data processing, data accessing, and web interface for data management and retrieval. It provides a comprehensive framework for new plant-specific, animal-specific, virus-specific, bacteria-specific or human disease-specific knowledge base (KB) creation, for adding new genome versions and additional multi-omics data to existing KBs, and for exploring existing datasets within current KBs.

Results
KBCommons has an array of tools for data visualization and data analytics such as multiple gene/metabolite search, gene family/Pfam/Panther function annotation search, miRNA/metabolite/trait/SNP search, differential gene expression analysis, and bulk data download capacity. It contains a highly reliable data privilege management system to make users’ data publicly available easily and to share private or pre-publication data with members in their collaborative groups safely and securely. It allows users to conduct data analysis using our in-house developed workflow functionalities that are linked to XSEDE high performance computing resources. Using KBCommons’ intuitive web interface, users can easily retrieve genomic data, multi-omics data and analysis results from workflow according to their requirements and interests.

Conclusions
KBCommons addresses the needs of many diverse research communities to have a comprehensive multi-level OMICS web resource for data retrieval, sharing, analysis and visualization. KBCommons can be publicly accessed through a dedicated link for all organisms at http://kbcommons.org/.
Endothelial glycocalyx in acute care surgery – what anaesthesiologists need to know for clinical practice
Authors: Astapenko David , Benes Jan , Pouska Jiri , Lehmann Christian , Islam Sufia , Cerny Vladimir 
Published: December 2019

AbstractThe endothelial glycocalyx (EG) is the thin sugar-based lining on the apical surface of endothelial cells. It has been linked to the physiological functioning of the microcirculation and has been found to be damaged in critical illness and after acute care surgery. This review aims to describe the role of EG in severely injured patients undergoing surgery, discuss specific situations (e.G.majortrauma, hemorrhagic shock, trauma induced coagulopathy) as well as specific interventions commonly applied in these patients (e.g. fluid therapy, transfusion) and specific drugs related to perioperative medicine with regard to their impact on EG.EG in acute care surgery is exposed to damage due to tissue trauma, inflammation, oxidative stress and inadequate fluid therapy. Even though some interventions (transfusion of plasma, human serum albumin, hydrocortisone, sevoflurane) are described as potentially EG protective there is still no specific treatment for EG protection and recovery in clinical medicine.The most important principle to be adopted in routine clinical practice at present is to acknowledge the fragile structure of the EG and avoid further damage which is potentially related to worsened clinical outcome.
Decreased Aerobic Exercise Capacity After Long-Term Remission From Cushing Syndrome: Exploration of Mechanisms
Authors: Roerink Sean H P P , Cocks Matthew S , Wagenmakers Margreet A E M , Rodighiero Raffaella P , Strauss Juliette A , Shepherd Sam O , Plantinga Theo S , Thijssen Dick H J , Hopman Maria T E , Pereira Alberto M , Smit Jan W , Wagenmakers Anton J M , Netea-Maier Romana T , Hermus Ad R M M 
Published: December 2019

AbstractBackgroundAlthough major improvements are achieved after cure of Cushing syndrome (CS), fatigue and decreased quality of life persist. This is the first study to measure aerobic exercise capacity in patients in remission of CS for more than 4 years in comparison with matched controls, and to investigate whether the reduction in exercise capacity is related to alterations in muscle tissue.MethodsSeventeen patients were included. A control individual, matched for sex, estrogen status, age, body mass index, smoking, ethnicity, and physical activity level was recruited for each patient. Maximal aerobic capacity (VO2peak) was assessed during incremental bicycle exercise to exhaustion. In 8 individually matched patients and controls, a percutaneous muscle biopsy was obtained and measures were made of cross-sectional areas, capillarization, and oxphos complex IV (COXIV) protein content as an indicator of mitochondrial content. Furthermore, protein content of endothelial nitric oxide synthase (eNOS) and eNOS phosphorylated on serine1177 and of the NAD(P)H-oxidase subunits NOX2, p47phox, and p67phox were measured in the microvascular endothelial layer.FindingsPatients showed a lower mean VO2peak (SD) (28.0 [7.0] vs 34.8 [7.9] ml O2/kg bw/min, P &lt; .01), maximal workload (SD) (176 [49] vs 212 [67] watt, P = .01), and oxygen pulse (SD) (12.0 [3.7] vs 14.8 [4.2] ml/beat, P &lt; .01) at VO2peak. No differences were seen in muscle fiber type–specific cross-sectional area, capillarization measures, mitochondrial content, and protein content of eNOS, eNOS-P-ser1177, NOX2, p47phox, and p67phox.InterpretationBecause differences in muscle fiber and microvascular outcome measures are not statistically significant, we hypothesize that cardiac dysfunction, seen in active CS, persists during remission and limits blood supply to muscles.
Testosterone Increases the Expression and Phosphorylation of AMP Kinase α in Men With Hypogonadism and Type 2 Diabetes
Authors: Ghanim Husam , Dhindsa Sandeep , Batra Manav , Green Kelly , Abuaysheh Sanaa , Kuhadiya Nitesh D , Makdissi Antoine , Chaudhuri Ajay , Sandhu Sartaj , Dandona Paresh 
Published: December 2019

Abstract

Context
Adenosine 5’-monophosphate-activated protein kinase-α (AMPKα) is a mediator of exercise-induced glucose uptake in skeletal muscle.

Objective
We evaluated whether AMPKα expression and phosphorylation are reduced in skeletal muscle and adipose tissue of patients with hypogonadotropic hypogonadism (HH), and whether testosterone replacement therapy results in restoration of the expression and phosphorylation of AMPKα.

Design
This is a secondary analysis of a previously completed trial that showed an insulin-sensitizing effect of testosterone therapy in men with type 2 diabetes and HH.

Setting
Clinical research center at university.

Patients
Thirty-two men with HH and 32 eugonadal men were compared at baseline.

Interventions
Men with HH were treated with intramuscular injections of testosterone or placebo every 2 weeks for 22 weeks. Quadriceps muscle biopsies and subcutaneous abdominal fat biopsies were obtained before and after 4-hour euglycemic hyperinsulinemic clamp, prior to and after testosterone or placebo therapy.

Outcome Measures and Results
mRNA expression of AMPKα in hypogonadal men was lower by 37% in adipose tissue and 29% in skeletal muscle, respectively, compared with levels in eugonadal men, while phosphorylated AMPKα was lower by 22% and 28%, respectively. Following testosterone replacement, the expression of AMPKα did not alter in the fasting state but increased markedly by 41% and 46% in adipose tissue and muscle, respectively, after the clamp. In contrast, phosphorylated AMPKα increased by 69% in muscle after testosterone therapy but did not change following the clamp.

Conclusions
Testosterone modulates the expression of AMPKα and phosphorylated AMPKα. These effects may contribute to the improved insulin sensitivity following testosterone therapy.
Deficient autophagy in epithelial stem cells drives aging in the freshwater cnidarian Hydra
Authors: Tomczyk Szymon , Suknovic Nenad , Schenkelaars Quentin , Wenger Yvan , Ekundayo Kazadi , Buzgariu Wanda , Bauer Christoph , Fischer Kathleen , Austad Steven , Galliot Brigitte 
Published: December 2019

ABSTRACT
Hydra possesses three distinct stem cell populations that continuously self-renew and prevent aging in Hydra vulgaris. However, sexual animals from the H. oligactis cold-sensitive strain Ho_CS develop an aging phenotype upon gametogenesis induction, initiated by the loss of interstitial stem cells. Animals stop regenerating, lose their active behaviors and die within 3 months. This phenotype is not observed in the cold-resistant strain Ho_CR. To dissect the mechanisms of Hydra aging, we compared the self-renewal of epithelial stem cells in these two strains and found it to be irreversibly reduced in aging Ho_CS but sustained in non-aging Ho_CR. We also identified a deficient autophagy in Ho_CS epithelial cells, with a constitutive deficiency in autophagosome formation as detected with the mCherry-eGFP-LC3A/B autophagy sensor, an inefficient response to starvation as evidenced by the accumulation of the autophagosome cargo protein p62/SQSTM1, and a poorly inducible autophagy flux upon proteasome inhibition. In the non-aging H. vulgaris animals, the blockade of autophagy by knocking down WIPI2 suffices to induce aging. This study highlights the essential role of a dynamic autophagy flux to maintain epithelial stem cell renewal and prevent aging.
Identification of a FGF18-expressing alveolar myofibroblast that is developmentally cleared during alveologenesis
Authors: Hagan Andrew S. , Zhang Bo , Ornitz David M. 
Published: December 2019

ABSTRACT
Alveologenesis is an essential developmental process that increases the surface area of the lung through the formation of septal ridges. In the mouse, septation occurs postnatally and is thought to require the alveolar myofibroblast (AMF). Though abundant during alveologenesis, markers for AMFs are minimally detected in the adult. After septation, the alveolar walls thin to allow efficient gas exchange. Both loss of AMFs or retention and differentiation into another cell type during septal thinning have been proposed. Using a novel Fgf18:CreERT2 allele to lineage trace AMFs, we demonstrate that most AMFs are developmentally cleared during alveologenesis. Lung mesenchyme also contains other poorly described cell types, including alveolar lipofibroblasts (ALF). We show that Gli1:CreERT2 marks both AMFs as well as ALFs, and lineage tracing shows that ALFs are retained in adult alveoli while AMFs are lost. We further show that multiple immune cell populations contain lineage-labeled particles, suggesting a phagocytic role in the clearance of AMFs. The demonstration that the AMF lineage is depleted during septal thinning through a phagocytic process provides a mechanism for the clearance of a transient developmental cell population.
Case Report: Peripartum cardiomyopathy in a young female complicated by cardioembolic stroke
Authors: Pradhan Ravi Ranjan , Yadav Ajay Kumar , Yadav Sant , Gupta Prashant Kumar 
Published: December 2019

Stroke in a young female is rare but, when it occurs, has a serious economic, and mental burden to the patient, and family members. Peripartum cardiomyopathy (PPCM) is one of the rare causes of stroke in young females. We report a case of a 20-year-old female with PPCM complicated by cardioembolic stroke. The patient was started on long-term anticoagulation, and her heart failure regimen was optimized upon discharge. Anticoagulation therapy in cardioembolic stroke prevents further complications.
Multi-plane, multi-band image projection via broadband diffractive
optics
Authors: Meem Monjurul , Majumder Apratim , Menon Rajesh 
Published: December 2019

We demonstrate visible and
near-IR image projection via non-absorbing, multi-level broadband
diffractive-optical elements (BDOEs) in one or more planes. By
appropriate design of the BDOE topography, we experimentally
demonstrate (1) different images in different spectral bands,
(2) different images in different image planes, (3) image
magnification by changing the distance between the illumination source
and the BDOE, (4) completely flat BDOE via an index-contrast top
coating, and (5) reflective BDOEs. All of these are accomplished with
broadband illumination. Furthermore, the BDOEs are highly efficient
and versatile and can be inexpensively mass manufactured using
imprint-based replication techniques.
Calibration-free laser-induced breakdown spectroscopic analysis of copper-rich mineral collected from the Gilgit-Baltistan region of Pakistan
Authors: Hafeez Muhammad , Abbasi Shahab Ahmed , Rafique Muhammad , Hayder Rizwan , Sajid Muhammad , Iqbal Javed , Ahmad Nasar , Shahida Shabnum 
Published: December 2019

In this paper, we present the results of compositional analysis of a copper-rich mineral known as malachite, collected from the Gilgit-Baltistan region of Pakistan. A calibration-free laser-induced breakdown spectroscopy (CF-LIBS) technique is employed for determination of elemental composition of the sample. The study aims at the investigation of the presence of precious elements, if any, in minerals of local origin. The laser beam of a 1064 nm wavelength from a nanosecond pulsed

Q

-switched Nd:YAG laser was focused on the surface of the sample, and an emission spectrum was obtained with the help of a LIBS2000 spectrometer covering the spectral range between 200 to 700 nm. Results obtained through analyzing the characteristic emission lines of different elements have confirmed the presence of sixteen (16) elements in the investigated sample, viz. Cu, Si, Al, K, Fe, Mn, Ag, Ti, Ba, Sr, Ca, Mg, Na, Li, C, and H. For quantification of the detected elements in the sample, a calibration-free method based on local thermodynamic equilibrium and optically thin plasma model was employed. Plasma parameters, such as electron number density and temperature, were calculated for the purpose of subsequent calculations. Seven elements, viz. Cu, Fe, Si, Ca, Mg, Mn, and Al, were quantified out of 16 initially detected elements, and their concentration in terms of weight percentage was 43.15%, 20.13%, 18.31%, 9.46%, 3.28%, 3.16%, and 2.51%, respectively. The presence of all seven elements quantified by CF-LIBS was confirmed by x-ray fluorescence analysis.
Simple and compact optical half-subtractor based on photonic crystal resonant cavities in silicon rods
Authors: Namdari Nima , Talebzadeh Reza 
Published: December 2019

We propose a very simple and compact structure to realize the
subtracting operation using resonant cavities in a photonic crystal
structure. The cross section of the structure is

103

µ

m

2

and is desirable for integration
based on popular planar technology. In the designed subtractor, the
cavity was responsible for selecting the wavelength. By changing the
boundary rods’ cavity condition, the mode could resonate at the
desired frequencies. To have resonant cavities, we introduce four
defect rods between the input and the output waveguides. The results
exhibit the true performance of the device. We used only silicon rods
in the proposed device, and hence it is very simple to be fabricated.
The finite-difference time-domain method was used for analyzing the
proposed structure. The simulation results show that the contrast
ratio of the device is 5 dB. The maximum rise and fall times are 1.5
and 0.5 ps, respectively.