bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creating reproducible pharmacogenomic analysis pipelines
Authors: Mammoliti Anthony , Smirnov Petr , Safikhani Zhaleh , Ba-Alawi Wail , Haibe-Kains Benjamin 
Published: September 2019

AbstractThe field of pharmacogenomics presents great challenges for researchers that are willing to make their studies reproducible and shareable. This is attributed to the generation of large volumes of high-throughput multimodal data, and the lack of standardized workflows that are robust, scalable, and flexible to perform large-scale analyses. To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. Our pipelines combine both pharmacological and molecular profiles into a portable data object that can be used for future analyses in cancer research. Our data objects and workflows are shared on Harvard Dataverse and Code Ocean where they have been assigned a unique Digital Object Identifier, providing a level of data provenance and a persistent location to access and share our data with the community.
Assessing the Protective Metabolome Using Machine Learning in World Trade Center Particulate Exposed Firefighters at Risk for Lung Injury
Authors: Crowley George , Kwon Sophia , Ostrofsky Dean F. , Clementi Emily A. , Haider Syed Hissam , Caraher Erin J. , Lam Rachel , St-Jules David E. , Liu Mengling , Prezant David J. , Nolan Anna 
Published: September 2019

AbstractThe metabolome of World Trade Center (WTC) particulate matter (PM) exposure has yet to be fully defined and may yield information that will further define bioactive pathways relevant to lung injury. A subset of Fire Department of New York firefighters demonstrated resistance to subsequent loss of lung function. We intend to characterize the metabolome of never smoking WTC-exposed firefighters, stratified by resistance to WTC-Lung Injury (WTC-LI) to determine metabolite pathways significant in subjects resistant to the loss of lung function. The global serum metabolome was determined in those resistant to WTC-LI and controls (n = 15 in each). Metabolites most important to class separation (top 5% by Random Forest (RF) of 594 qualified metabolites) included elevated amino acid and long-chain fatty acid metabolites, and reduced hexose monophosphate shunt metabolites in the resistant cohort. RF using the refined metabolic profile was able to classify cases and controls with an estimated success rate of 93.3%, and performed similarly upon cross-validation. Agglomerative hierarchical clustering identified potential influential pathways of resistance to the development of WTC-LI. These pathways represent potential therapeutic targets and warrant further research.
Phosphorylation-dependent modulation of CFTR macromolecular signalling complex activity by cigarette smoke condensate in airway epithelia
Authors: Schnúr Andrea , Premchandar Aiswarya , Bagdany Miklos , Lukacs Gergely L. 
Published: September 2019

AbstractGenetic and acquired loss-of-function defect of the cystic fibrosis transmembrane conductance regulator (CFTR) compromise airway surface liquid homeostasis and mucociliary clearance (MCC), culminating in recurrent lung inflammation/infection. While chronic cigarette smoke (CS), CS extract (CSE; water-soluble compounds) and CS condensate (CSC; particulate, organic fraction) exposure inhibit CFTR activity at transcriptional, biochemical, and functional levels, the acute impact of CSC remains incompletely understood. We report that CSC transiently activates CFTR chloride secretion in airway epithelia. The comparable CFTR phospho-occupancy after CSC- and forskolin-exposure, determined by affinity-enriched tandem mass spectrometry and pharmacology, suggest that localised cAMP-dependent protein kinase (PKA) stimulation by CSC causes the channel opening. Due to the inhibition of the MRP4/ABCC4, a cAMP-exporter confined to the CFTR macromolecular signalling-complex, PKA activation is accomplished by the subcompartmentalised elevation of cytosolic cAMP. In line, MRP4 inhibition results in CFTR activation and phospho-occupancy similar to that by forskolin. In contrast, acute CSC exposure reversibly inhibits the phosphorylated CFTR both in vivo and in phospholipid bilayers, without altering its cell surface density and phospho-occupancy. We propose that components of CSC elicit both a transient protective CFTR activation, as well as subsequent channel block in airway epithelia, contributing to the subacute MCC defect in acquired CF lung diseases.
Innate immune responses to paraquat exposure in a Drosophila model of Parkinson’s disease
Authors: Maitra Urmila , Scaglione Michael N. , Chtarbanova Stanislava , O’Donnell Janis M. 
Published: September 2019

AbstractParkinson’s disease (PD) is a progressive, neurodegenerative movement disorder characterized by the loss of dopaminergic (DA) neurons. Limited understanding of the early molecular pathways associated with the demise of DA neurons, including those of inflammatory exacerbation of neurodegeneration, is a major impediment to therapeutic development. Recent studies have implicated gene-environment interactions in PD susceptibility. We used transcriptomic profiling in a Drosophila PD model in response to paraquat (PQ)-induced oxidative stress to identify pre-symptomatic signatures of impending neuron dysfunction. Our RNAseq data analysis revealed extensive regulation of innate immune response genes following PQ ingestion. We found that PQ exposure leads to the activation of the NF-κB transcription factor, Relish, and the stress signaling factor JNK, encoded by the gene basket in Drosophila. Relish knockdown in the dopaminergic neurons confers PQ resistance and rescues mobility defects and DA neuron loss. Furthermore, PQ-induced toxicity is mediated through the immune deficiency signaling pathway. Surprisingly, the expression of Relish-dependent anti-microbial peptide (AMPs) genes is suppressed upon PQ exposure causing increased sensitivity to Gram-negative bacterial infection. This work provides a novel link between PQ exposure and innate immune system modulation underlying environmental toxin-induced neurodegeneration, thereby underscoring the role of the innate immune system in PD pathogenesis.
Delay effect and burden of weather-related tuberculosis cases in Rajshahi province, Bangladesh, 2007–2012
Authors: Kuddus Md Abdul , McBryde Emma S. , Adegboye Oyelola A. 
Published: September 2019

AbstractTuberculosis (TB) is a potentially fatal infectious disease that continues to be a public health problem in Bangladesh. Each year in Bangladesh an estimated 70,000 people die of TB and 300,000 new cases are projected. It is important to understand the association between TB incidence and weather factors in Bangladesh in order to develop proper intervention programs. In this study, we examine the delayed effect of weather variables on TB occurrence and estimate the burden of the disease that can be attributed to weather factors. We used generalized linear Poisson regression models to investigate the association between weather factors and TB cases reported to the Bangladesh National TB control program between 2007 and 2012 in three known endemic districts of North-East Bangladesh. The associated risk of TB in the three districts increases with prolonged exposure to temperature and rainfall, and persisted at lag periods beyond 6 quarters. The association between humidity and TB is strong and immediate at low humidity, but the risk decreases with increasing lag. Using the optimum weather values corresponding to the lowest risk of infection, the risk of TB is highest at low temperature, low humidity and low rainfall. Measures of the risk attributable to weather variables revealed that weather-TB cases attributed to humidity is higher than that of temperature and rainfall in each of the three districts. Our results highlight the high linearity of temporal lagged effects and magnitudes of the burden attributable to temperature, humidity, and rainfall on TB endemics. The results can hopefully advise the Bangladesh National TB control program and act as a practical reference for the early warning of TB cases.
Rapid and Highly Controlled Generation of Monodisperse Multiple Emulsions via a One-Step Hybrid Microfluidic Device
Authors: Azarmanesh Milad , Bawazeer Saleh , Mohamad Abdulmajeed A. , Sanati-Nezhad Amir 
Published: September 2019

AbstractMultiple Emulsions (MEs) contain a drop laden with many micro-droplets. A single-step microfluidic-based synthesis process of MEs is presented to provide a rapid and controlled generation of monodisperse MEs. The design relies on the interaction of three immiscible fluids with each other in subsequent droplet formation steps to generate monodisperse ME constructs. The design is within a microchannel consists of two compartments of cross-junction and T-junction. The high shear stress at the cross-junction creates a stagnation point that splits the first immiscible phase to four jet streams each of which are sprayed to micrometer droplets surrounded by the second phase. The resulted structure is then supported by the third phase at the T-junction to generate and transport MEs. The ME formation within microfluidics is numerically simulated and the effects of several key parameters on properties of MEs are investigated. The dimensionless modeling of ME formation enables to change only one parameter at the time and analyze the sensitivity of the system to each parameter. The results demonstrate the capability of highly controlled and high-throughput MEs formation in a one-step synthesis process. The consecutive MEs are monodisperse in size which open avenues for the generation of controlled MEs for different applications.
Immobilisation of α-amylase on activated amidrazone acrylic fabric: a new approach for the enhancement of enzyme stability and reusability
Authors: Al-Najada Ahmed R. , Almulaiky Yaaser Q. , Aldhahri Musab , El-Shishtawy Reda M. , Mohamed Saleh A. , Baeshen Mohammed , AL-Farga Ammar , Abdulaal Wesam H. , Al-Harbi Sami A. 
Published: September 2019

AbstractIn this study, amidrazone acrylic fabric was applied as an immobilising support for α-amylase. The immobilised α-amylase was characterised by Fourier transform infrared spectroscopy and scanning electron microscopy. Furthermore, the optimum conditions for immobilisation efficiency, immobilisation time, reusability, kinetic parameters and pH, for the immobilisation process were examined. The study demonstrated that with 4% cyanuric chloride, and a pH of 7.0, the highest immobilization efficiency of 81% was obtained. Around 65% of the initial activity was maintained after storage at 4 °C for 8 weeks. The immobilised enzyme retained 53% of its original activity after being reused 15 times and exhibited improved stability compared with the free enzyme in relation to heavy metal ions, pH, temperature and inhibitors. The immobilised enzyme presented kinetic parameters of 2.6 mg starch and 0.65 µmol maltose/mL for Km and Vmax respectively, compared with 3.7 mg starch and 0.83 µmol maltose/ mL for the free enzyme. The improvements in the enzyme’s catalytic properties, stability and reusability obtained from immobilisation make amidrazone acrylic fabric support a good promising candidate for bio-industrial applications.
Quantum confinement-induced semimetal-to-semiconductor evolution in large-area ultra-thin PtSe2 films grown at 400 °C
Authors: Ansari Lida , Monaghan Scott , McEvoy Niall , Coileáin Cormac Ó , Cullen Conor P. , Lin Jun , Siris Rita , Stimpel-Lindner Tanja , Burke Kevin F. , Mirabelli Gioele , Duffy Ray , Caruso Enrico , Nagle Roger E. , Duesberg Georg S. , Hurley Paul K. , Gity Farzan 
Published: September 2019

AbstractIn this work, we present a comprehensive theoretical and experimental study of quantum confinement in layered platinum diselenide (PtSe2) films as a function of film thickness. Our electrical measurements, in combination with density functional theory calculations, show distinct layer-dependent semimetal-to-semiconductor evolution in PtSe2 films, and highlight the importance of including van der Waals interactions, Green’s function calibration, and screened Coulomb interactions in the determination of the thickness-dependent PtSe2 energy gap. Large-area PtSe2 films of varying thickness (2.5–6.5 nm) were formed at 400 °C by thermally assisted conversion of ultra-thin platinum films on Si/SiO2 substrates. The PtSe2 films exhibit p-type semiconducting behavior with hole mobility values up to 13 cm2/V·s. Metal-oxide-semiconductor field-effect transistors have been fabricated using the grown PtSe2 films and a gate field-controlled switching performance with an ION/IOFF ratio of >230 has been measured at room temperature for a 2.5–3 nm PtSe2 film, while the ratio drops to <2 for 5–6.5 nm-thick PtSe2 films, consistent with a semiconducting-to-semimetallic transition with increasing PtSe2 film thickness. These experimental observations indicate that the low-temperature growth of semimetallic or semiconducting PtSe2 could be integrated into the back-end-of-line of a silicon complementary metal-oxide-semiconductor process.
Variation in appendages in early Cambrian bradoriids reveals a wide range of body plans in stem-euarthropods
Authors: Zhai Dayou , Williams Mark , Siveter David J. , Harvey Thomas H. P. , Sansom Robert S. , Gabbott Sarah E. , Siveter Derek J. , Ma Xiaoya , Zhou Runqing , Liu Yu , Hou Xianguang 
Published: September 2019

AbstractTraditionally, the origin and evolution of modern arthropod body plans has been revealed through increasing levels of appendage specialisation exhibited by Cambrian euarthropods. Here we show significant variation in limb morphologies and patterns of limb-tagmosis among three early Cambrian arthropod species conventionally assigned to the Bradoriida. These arthropods are recovered as a monophyletic stem-euarthropod group (and sister taxon to crown-group euarthropods, i.e. Chelicerata, Mandibulata and their extinct relatives), thus implying a radiation of stem-euarthropods where trends towards increasing appendage specialisation were explored convergently with other euarthropod groups. The alternative solution, where bradoriids are polyphyletic, representing several independent origins of a small, bivalved body plan in lineages from diverse regions of the euarthropod and mandibulate stems, is only marginally less parsimonious. The new data reveal a previously unknown disparity of body plans in stem-euarthropods and both solutions support remarkable evolutionary convergence, either of fundamental body plans or appendage specialization patterns.
Danggui buxue tang inhibited mesangial cell proliferation and extracellular matrix accumulation through GAS5/NF-κB pathway
Authors: Zhang Rui , Han Xiao , Huang Tao , Wang Xiuge 
Published: September 2019

Abstract
Diabetic nephropathy (DN) is the common complications of diabetes mellitus, but the efficacy of available treatments for the prevention of DN is still unsatisfactory. In the present study, we aimed to explore the effect of Danggui buxue tang (DGT) on the proliferation of high glucose (HG)-induced mesangial cells and accumulation of extracellular matrix in mesangial cells. We found DGT up-regulated the expression of growth arrest specific transcript 5 (GAS5) and IκB kinase (IKK) dose-dependently in mouse mesangial cells (SV40 MES-13). We found DGT regulated the expression IKK and the activity of nuclear transcription factor-κB (NF-κB) via GAS5, and proved that long non-coding RNA (lncRNA) GAS5 was positively related with IKK. And we proved GAS5 regulated the expression of IKK and the activity of NF-κB. In addition, DGT inhibited the viability of MES-13 cells and extracellular matrix-related proteins (laminin (LN), fibronectin (FN) and collagen IV (Col IV)) via GAS5. Moreover, we proved GAS5 regulated the viability of SV40 MES-13 cells and extracellular matrix-related proteins through NF-κB pathway. DGT inhibited the proliferation of mesangial cells and accumulation of extracellular matrix via GAS5/NF-κB, therefore, DGT could be an effective treatment for the prevention of DN.
Interleukin-17 receptor C gene polymorphism reduces treatment effect and promotes poor prognosis of ischemic stroke
Authors: Tian Jing , Bai Yongjie , You Aimin , Shen Ruile , Yan Junqiang , Deng Wenjing , Wen Lijun , Li Meng , Teng Junfang 
Published: September 2019

Abstract
Objective: To study the relationship between Interleukin-17 receptor C (IL-17RC) gene polymorphism and ischemic stroke (IS).
Methods: Three hundred cases of IS patients and 300 cases of the healthy controls were selected. Serum of IS patients and the controls was collected. The relative mRNA levels of IL-17, IL-17RC, IL-6, IL-8, G-CSF and granulocyte-macrophage colony stimulating factor (GM-CSF) by qRT-PCR. The protein expression of IL-17 and IL-17RC was determined by Western blotting. IL-17RC genotype was identified by PCR amplification. The proportion of IL-17RC, SNP and re37511 in IS and control group was determined. The treatment effect on IS and prognosis of patients with IL-17RC, SNP and re37511 was compared.
Results: The relative mRNA levels of IL-17, IL-17RC, IL-6, IL-8, G-CSF and GM-CSF in IS group were significantly higher than the control group. The protein expression of IL-17 and IL-17RC in IS group was also markedly higher than the control group. The proportion of IL-17RC re37511 in IS group was much larger than control group and proportion of IL-17RC much less. The percent of poor treatment effect in re37511 was much larger than IL-17RC. The percent of death and recrudescence in patients with IL-17RC re37511 was the highest.
Conclusion: IS up-regulates the expression of IL-17 and IL-17RC. IL-17RC re37511 indicates the patients have a poorer treatment effect and prognosis.
New insight on accretion shocks onto young stellar objects
Authors: de Sá L. , Chièze J.-P. , Stehlé C. , Hubeny I. , Lanz T. , Cayatte V. 
Published: September 2019

Context.Material accreted onto classical T Tauri stars is expected to form a hot quasi-periodic plasma structure that radiates in X-rays. Simulations of this phenomenon only partly match observations. They all rely on a static model for the chromosphere and on the assumption that radiation and matter are decoupled.Aims.We explore the effects of a shock-heated chromosphere and of the coupling between radiation and hydrodynamics on the structure and dynamics of the accretion flow.Methods.We simulated accretion columns that fall onto a stellar chromosphere using the 1D ALE code AstroLabE. This code solves the hydrodynamics equations along with the first two moment equations for radiation transfer, with the help of a dedicated opacity table for the coupling between matter and radiation. We derive the total electron and ion densities from collisional-radiative model.Results.The chromospheric acoustic heating affects the duration of the cycle and the structure of the heated slab. In addition, the coupling between radiation and hydrodynamics leads to a heating of the accretion flow and of the chromosphere: the whole column is pushed up by the inflating chromosphere over several times the steady chromosphere thickness. These last two conclusions are in agreement with the computed monochromatic intensity. Acoustic heating and radiation coupling affect the amplitude and temporal variations of the net X-ray luminosity, which varies between 30 and 94% of the incoming mechanical energy flux, depending on which model is considered.
Konservative Therapie der Arthrose unter Berücksichtigung der Physikalischen Therapie
Authors: Bork Hartmut , Gottfried Thomas 
Published: September 2019

ZusammenfassungDie konservative Therapie der Arthrose gliedert sich in nicht medikamentöse und medikamentöse Behandlungsmaßnahmen. Neben Information, Beratung sowie Edukation fallen unter die nichtmedikamentösen Therapieoptionen diverse physikalische Therapieverfahren wie Bewegungstherapie, Krankengymnastik, Medizinische Trainings- und Sporttherapie sowie Aquatisches Training. Klinisch relevante Effekte wie Schmerzreduktion und Funktionsverbesserung konnten bei günstigem Nutzen-Risiko-Profil und Kosteneffektivität in den vergangenen Jahren in mehreren Studien u. a. für die Behandlung der Hüft- und Kniearthrose nachgewiesen werden. Im nachfolgenden Beitrag werden die wichtigsten konservativen Behandlungsmöglichkeiten und ihre Wertigkeit aufgezeigt.
Trends Associated with Stillbirth in a Maternity Hospital School in the North Zone of São Paulo: A Cross-Sectional Study
Authors: Fonseca Raissa Magalhães de Mendonça , Garcia Carolina Laila , Angimahtz Talita Sampaio , Battaglia Cindy Fazio , Chalem Elisa , Sass Nelson 
Published: September 2019

Objective To evaluate conditions associated with stillbirth (SB), and possible trends related with it, in a maternity hospital school in the North zone of São Paulo.
Methods An observational, cross-sectional study conducted at the Hospital Maternidade-escola de Vila Nova Cachoeirinha with 1,139 SBs in the period of 2003 to 2017. Cases of intermediate SB (ISB) (weight between 500 and 999 g) and late SB (LSB) (weight ≥ 1,000 g) were compared. We evaluated clinical data, laboratory tests, and fetal and placental studies. Data were stored in Windows Excel (Microsoft Corp., Redmond, WA, USA) worksheets, according to which graphs and tables were constructed. We used the statistical software SPSS for Windows version 18.0 (SPSS In., Chicago, IL, USA), estimating the prevalence ratio (PR) and odds ratio (OR), considering the 95% confidence interval (95% CI).
Results The general SB rate was 11.9%, and the in-hospital SB rate was 2.8%. Pregnant women younger than 16 years of age were more likely to have ISB (OR 0.32, 0.15–0.76), while patients older than 40 years old had a higher chance of LSB (PR 0.85, 0.72–0.99). A total of 25.7% of the general population did not have prenatal care, and 77.1% of the cases presented fetal death at admission. The cases of ISB had a statistically significant association with home birth (OR 0.61, 0.46–0.80). Cesarean section was performed in 16.1% of the subjects, and misoprostol was the most used method for induction. Necropsy and placental study of the fetuses were performed, respectively, in 94.2% and 97.3% of the cases. Associated causes were not identified in 22.1% of the cases, and the main causes identified were amniotic sac infections (27.9%), fetal malformations (12.5%), placental abruption (11.2%), hypertensive syndromes (8.5%), and maternal syphilis (3.9%), the latter with an increasing trend.
Conclusion Among the factors associated to SB were: hypertensive syndromes, amniotic sac infections, fetal malformations, placental abruption and syphilis. There was a growing trend in the number of cases of syphilis, which translates an alert. Diagnostic limitations justify indeterminate causes.
Mixed Phenotype of Langer–Giedion's and Cornelia de Lange's Syndromes in an 8q23.3-q24.1 Microdeletion without TRPS1 Deletion
Authors: Herrero-García Ana , Marín-Reina Purificación , Cabezuelo-Huerta Gloria , Ferrer-Lorente M. Belén , Rosello Mónica , Orellana Carmen , Martínez Francisco , Pérez-Aytés Antonio 
Published: September 2019

AbstractLanger–Giedion's syndrome (LGS) or trichorhinophalangeal syndrome type II (TRPS II; MIM:150230) is a contiguous gene deletion syndrome caused by the haploinsufficiency of the TRPS1 and EXT1 genes. Cornelia de Lange's syndrome (CdLS) is a genetically heterogeneous dysmorphic syndrome where heterozygous mutations of RAD21 gene have been associated with a mild clinical presentation (CDLS type 4; MIM: 614701). We report a female patient with a 2.3-Mb interstitial deletion at 8q23.3-q24.1 encompassing EXT1 and RAD21 genes but not TRPS1. Clinical findings in this patient are correlated with a mixed phenotype of LGS and CdLS type 4.