bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major changes in chromosomal somy, gene expression and gene dosage driven by SbIII in Leishmania braziliensis and Leishmania panamensis
Authors: Patino Luz H. , Imamura Hideo , Cruz-Saavedra Lissa , Pavia Paula , Muskus Carlos , Méndez Claudia , Dujardin Jean Claude , Ramírez Juan David 
Published: July 2019

AbstractLeishmania braziliensis and Leishmania panamensis are two species clinically and epidemiologically important, among others because of their relative resistance to first-line drugs (antimonials). The precise mechanism underlying the ability of these species to survive antimony treatment remains unknown. Therefore, elucidating the pathways mediating drug resistance is essential. We herein experimentally selected resistance to trivalent antimony (SbIII) in the reference strains of L. braziliensis (MHOM/BR75/M2904) and L. panamensis (MHOM/COL/81L13) and compared whole genome and transcriptome alterations in the culture promastigote stage. The results allowed us to identify differences in somy, copy number variations in some genes related to antimony resistance and large-scale copy number variations (deletions and duplications) in chromosomes with no somy changes. We found mainly in L. braziliensis, a direct relation between the chromosomal/local copy number variation and the gene expression. We identified differentially expressed genes in the resistant lines that are involved in antimony resistance, virulence, and vital biological processes in parasites. The results of this study may be useful for characterizing the genetic mechanisms of these Leishmania species under antimonial pressure, and for clarifying why the parasites are resistant to first-line drug treatments.
Deciphering the genetic basis for vitamin E accumulation in leaves and grains of different barley accessions
Authors: Schuy Christian , Groth Jennifer , Ammon Alexandra , Eydam Julia , Baier Steffen , Schweizer Günther , Hanemann Anja , Herz Markus , Voll Lars M. , Sonnewald Uwe 
Published: July 2019

AbstractTocopherols and tocotrienols, commonly referred to as vitamin E, are essential compounds in food and feed. Due to their lipophilic nature they protect biomembranes by preventing the propagation of lipid-peroxidation especially during oxidative stress. Since their synthesis is restricted to photosynthetic organisms, plant-derived products are the major source of natural vitamin E. In the present study the genetic basis for high vitamin E accumulation in leaves and grains of different barley (Hordeum vulgare L.) accessions was uncovered. A genome wide association study (GWAS) allowed the identification of two genes located on chromosome 7H, homogentisate phytyltransferase (HPT-7H) and homogentisate geranylgeranyltransferase (HGGT) that code for key enzymes controlling the accumulation of tocopherols in leaves and tocotrienols in grains, respectively. Transcript profiling showed a correlation between HPT-7H expression and vitamin E content in leaves. Allele sequencing allowed to decipher the allelic variation of HPT-7H and HGGT genes corresponding to high and low vitamin E contents in the respective tissues. Using the obtained sequence information molecular markers have been developed which can be used to assist smart breeding of high vitamin E barley varieties. This will facilitate the selection of genotypes more tolerant to oxidative stress and producing high-quality grains.
HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells
Authors: Klinge Carolyn M. , Piell Kellianne M. , Tooley Christine Schaner , Rouchka Eric C. 
Published: July 2019

AbstractMicroRNAs are dysregulated in breast cancer. Heterogeneous Nuclear Ribonucleoprotein A2/B1 (HNRNPA2/B1) is a reader of the N(6)-methyladenosine (m6A) mark in primary-miRNAs (pri-miRNAs) and promotes DROSHA processing to precursor-miRNAs (pre-miRNAs). We examined the expression of writers, readers, and erasers of m6A and report that HNRNPA2/B1 expression is higher in tamoxifen-resistant LCC9 breast cancer cells as compared to parental, tamoxifen-sensitive MCF-7 cells. To examine how increased expression of HNRNPA2/B1 affects miRNA expression, HNRNPA2/B1 was transiently overexpressed (~5.4-fold) in MCF-7 cells for whole genome miRNA profiling (miRNA-seq). 148 and 88 miRNAs were up- and down-regulated, respectively, 48 h after transfection and 177 and 172 up- and down-regulated, respectively, 72 h after transfection. MetaCore Enrichment analysis identified progesterone receptor action and transforming growth factor β (TGFβ) signaling via miRNA in breast cancer as pathways downstream of the upregulated miRNAs and TGFβ signaling via SMADs and Notch signaling as pathways of the downregulated miRNAs. GO biological processes for mRNA targets of HNRNPA2/B1-regulated miRNAs included response to estradiol and cell-substrate adhesion. qPCR confirmed HNRNPA2B1 downregulation of miR-29a-3p, miR-29b-3p, and miR-222 and upregulation of miR-1266-5p, miR-1268a, miR-671-3p. Transient overexpression of HNRNPA2/B1 reduced MCF-7 sensitivity to 4-hydroxytamoxifen and fulvestrant, suggesting a role for HNRNPA2/B1 in endocrine-resistance.
Smoking is associated with ulnar nerve entrapment: a birth cohort study
Authors: Hulkkonen Sina , Auvinen Juha , Miettunen Jouko , Karppinen Jaro , Ryhänen Jorma 
Published: July 2019

AbstractUlnar nerve entrapment is the second most common compression neuropathy of the upper extremity. It has been associated with smoking in cross-sectional studies. Our aim was to study whether smoking is associated with ulnar nerve entrapment. The study population consisted of the Northern Finland Birth Cohort 1966 participants, who attended the 31-year follow-up in 1997 (N = 8,716). Information on smoking, body mass index (BMI), long-term illnesses, and socio-economic status were recorded at baseline in 1997. Data on hospitalizations due to ulnar nerve entrapment neuropathies was obtained from the Care Register for Health Care, 1997–2016. Hazard ratios (HR) with 95% confidence intervals (CI) and population attributable risk (PAR) were calculated adjusted for gender, BMI and socio-economic status. 66 patients were diagnosed with ulnar nerve entrapment in the follow-up 1997–2016. Before the age of 31 years, smoking ≤10 pack years associated with more than doubled (HR = 2.57, 95% CI = 1.29–5.15) and smoking >10 pack years with more than five-folded (HR = 5.61, 95% CI = 2.80–11.23) risk for ulnar nerve entrapment compared to non-smokers in the adjusted analyses. Adjusted PAR for smoking (reference of no smoking) was 53.6%. In our study, smoking associated with increased risk for ulnar nerve entrapment, accounting for considerable proportion of increased risk.
Reaching measures and feedback effects in auditory peripersonal space
Authors: Hüg Mercedes X. , Vergara Ramiro O. , Tommasini Fabián C. , Etchemendy Pablo E. , Bermejo Fernando , Fernandez Laura G. 
Published: July 2019

AbstractWe analyse the effects of exploration feedback on reaching measures of perceived auditory peripersonal space (APS) boundary and the auditory distance perception (ADP) of sound sources located within it. We conducted an experiment in which the participants had to estimate if a sound source was (or not) reachable and to estimate its distance (40 to 150 cm in 5-cm steps) by reaching to a small loudspeaker. The stimulus consisted of a train of three bursts of Gaussian broadband noise. Participants were randomly assigned to two groups: Experimental (EG) and Control (CG). There were three phases in the following order: Pretest–Test–Posttest. For all phases, the listeners performed the same task except for the EG-Test phase where the participants reach in order to touch the sound source. We applied models to characterise the participants’ responses and provide evidence that feedback significantly reduces the response bias of both the perceived boundary of the APS and the ADP of sound sources located within reach. In the CG, the repetition of the task did not affect APS and ADP accuracy, but it improved the performance consistency: the reachable uncertainty zone in APS was reduced and there was a tendency to decrease variability in ADP.
High Power UV-Light Irradiation as a New Method for Defect Passivation in Degraded Perovskite Solar Cells to Recover and Enhance the Performance
Authors: Arabpour Roghabadi Farzaneh , Mansour Rezaei Fumani Nasibeh , Alidaei Maryam , Ahmadi Vahid , Sadrameli Seyed Mojtaba 
Published: July 2019

AbstractAlthough the power conversion efficiency (PCE) of perovskite solar cells (PSCs) reached up to 23%, their short lifetime and fast degradation still remain as the main challenges. In this work, a new facile optical method based on the high power UV-irradiation is presented for the recovery of the degraded PSCs. Addition to the full recovery of the performance, about 20% PCE enhancement and hystersis reduction are also achieved by UV-irradiation. UV-treatment causes modifications in both the bulk properties of the perovskite layer and the energy equilibrium at the interfaces. It is shown that UV-treatment effectively passivates the surface and grain boundaries defects in different types of the devices comprising normal and inverted configurations that is confirmed by the reduction of the density of defect states (DOS). It is proposed that UV-light passivates the shallow and deep defects by dissociation of adsorbed hydroxyl groups and water molecules during the device storage.
Repeatability of Multiparametric Prostate MRI Radiomics Features
Authors: Schwier Michael , van Griethuysen Joost , Vangel Mark G. , Pieper Steve , Peled Sharon , Tempany Clare , Aerts Hugo J. W. L. , Kikinis Ron , Fennessy Fiona M. , Fedorov Andriy 
Published: July 2019

AbstractIn this study we assessed the repeatability of radiomics features on small prostate tumors using test-retest Multiparametric Magnetic Resonance Imaging (mpMRI). The premise of radiomics is that quantitative image-based features can serve as biomarkers for detecting and characterizing disease. For such biomarkers to be useful, repeatability is a basic requirement, meaning its value must remain stable between two scans, if the conditions remain stable. We investigated repeatability of radiomics features under various preprocessing and extraction configurations including various image normalization schemes, different image pre-filtering, and different bin widths for image discretization. Although we found many radiomics features and preprocessing combinations with high repeatability (Intraclass Correlation Coefficient > 0.85), our results indicate that overall the repeatability is highly sensitive to the processing parameters. Neither image normalization, using a variety of approaches, nor the use of pre-filtering options resulted in consistent improvements in repeatability. We urge caution when interpreting radiomics features and advise paying close attention to the processing configuration details of reported results. Furthermore, we advocate reporting all processing details in radiomics studies and strongly recommend the use of open source implementations.
Functional characterization of SMN evolution in mouse models of SMA
Authors: Osman Erkan Y. , Bolding Madeline R. , Villalón Eric , Kaifer Kevin A. , Lorson Zachary C. , Tisdale Sarah , Hao Yue , Conant Gavin C. , Pires J. Chris , Pellizzoni Livio , Lorson Christian L. 
Published: July 2019

AbstractSpinal Muscular Atrophy (SMA) is a monogenic neurodegenerative disorder and the leading genetic cause of infantile mortality. While several functions have been ascribed to the SMN (survival motor neuron) protein, their specific contribution to the disease has yet to be fully elucidated. We hypothesized that some, but not all, SMN homologues would rescue the SMA phenotype in mouse models, thereby identifying disease-relevant domains. Using AAV9 to deliver Smn homologs to SMA mice, we identified a conservation threshold that marks the boundary at which homologs can rescue the SMA phenotype. Smn from Danio rerio and Xenopus laevis significantly prevent disease, whereas Smn from Drosophila melanogaster, Caenorhabditis elegans, and Schizosaccharomyces pombe was significantly less efficacious. This phenotypic rescue correlated with correction of RNA processing defects induced by SMN deficiency and neuromuscular junction pathology. Based upon the sequence conservation in the rescuing homologs, a minimal SMN construct was designed consisting of exons 2, 3, and 6, which showed a partial rescue of the SMA phenotype. While a significant extension in survival was observed, the absence of a complete rescue suggests that while the core conserved region is essential, additional sequences contribute to the overall ability of the SMN protein to rescue disease pathology.
Arsenic accumulation in lentil (Lens culinaris) genotypes and risk associated with the consumption of grains
Authors: Alam Mohammad Zahangeer , Hoque Md. Anamul , Ahammed Golam Jalal , McGee Rebecca , Carpenter-Boggs Lynne 
Published: July 2019

AbstractArsenic (As) is a toxic metalloid. As phyto-toxicity is manifested by its accumulation in different tissue types and subsequent growth inhibition in plants. Despite the vital role of leguminous crops in providing proteins to human diets, a little is known about the As accumulation in lentil. In this study, the rate of As uptake and transport from soil to root, shoot and grain of lentil as well as associated risks with the consumption of As contaminated food were examined. Biomass accumulation of lentil genotypes pardina, red chief and precoz drastically decreased when treated with As at 6 mg kg−1 concentration in comparison to 0 and 3 mg kg−1 As. Quantification of As concentrations following different treatment periods showed that As accumulation in roots and shoots of 0, 3 and 6 mg kg−1 As-treated lentil genotypes was statistically different. Arsenic content in grains of red chief genotype was found significantly lower than pardina and precoz. Moreover, As transport significantly increased in roots and shoots compared to the grains. Due to the high concentrations of As in biomass of lentil genotypes, animal as well as human health risk might be associated with the consumption of the As contaminated legume crops.
Neighborhood environments influence emotion and physiological reactivity
Authors: Hackman Daniel A. , Robert Stephanie A. , Grübel Jascha , Weibel Raphael P. , Anagnostou Eirini , Hölscher Christoph , Schinazi Victor R. 
Published: July 2019

AbstractLiving in a disadvantaged neighborhood is associated with worse health and early mortality. Although many mechanisms may partially account for this effect, disadvantaged neighborhood environments are hypothesized to elicit stress and emotional responses that accumulate over time and influence physical and mental health. However, evidence for neighborhood effects on stress and emotion is limited due to methodological challenges. In order to address this question, we developed a virtual reality experimental model of neighborhood disadvantage and affluence and examined the effects of simulated neighborhoods on immediate stress and emotion. Exposure to neighborhood disadvantage resulted in greater negative emotion, less positive emotion, and more compassion, compared to exposure to affluence. However, the effect of virtual neighborhood environments on blood pressure and electrodermal reactivity depended on parental education. Participants from families with lower education exhibited greater reactivity to the disadvantaged neighborhood, while those from families with higher education exhibited greater reactivity to the affluent neighborhood. These results demonstrate that simulated neighborhood environments can elicit immediate stress reactivity and emotion, but the nature of physiological effects depends on sensitization to prior experience.
Short-period scattering-assisted terahertz quantum cascade lasers operating at high temperatures
Authors: Wang Li , Lin Tsung-Tse , Wang Ke , Grange Thomas , Birner Stefan , Hirayama Hideki 
Published: July 2019

AbstractOperating at high temperatures in the range of thermoelectric coolers is essential for terahertz quantum cascade lasers to real applications. The use of scattering-assisted injection scheme enables an increase in operating temperature. This concept, however, has not been implemented in a short-period structure consisting of two quantum wells. In this work, based on non-equilibrium Green’s function calculations, it emphasizes on the current leakage and parasitic absorption via high-energy states as fundamental limitations in this scheme with short-period. A new design concept employing asymmetric wells composition is proposed to suppress these limitations. A peak gain of 40 cm−1 at 230 K is predicted in the GaAs/AlGaAs semiconductor material system with an emission frequency of 3.5 THz.
Retinoic acid and arsenic trioxide induce lasting differentiation and demethylation of target genes in APL cells
Authors: Huynh Thomas T. , Sultan Mohammad , Vidovic Dejan , Dean Cheryl A. , Cruickshank Brianne M. , Lee Kristen , Loung Chao-Yu , Holloway Ryan W. , Hoskin David W. , Waisman David M. , Weaver Ian C. G. , Marcato Paola 
Published: July 2019

AbstractAcute promyelocytic leukemia (APL) is characterized by arrested differentiation of promyelocytes. Patients treated with all-trans retinoic acid (ATRA) alone experience relapse, while patients treated with ATRA and arsenic trioxide (ATO) are often relapse-free. This suggests sustained changes have been elicited by the combination therapy. To understand the lasting effects of the combination therapy, we compared the effects of ATRA and ATO on NB4 and ATRA-resistant NB4-MR2 APL cells during treatment versus post treatment termination. After treatment termination, NB4 cells treated with ATRA or ATO reverted to non-differentiated cells, while combination-treated cells remained terminally differentiated. This effect was diminished in NB4-MR2 cells. This suggests combination treatment induced more permanent changes. Combination treatment induced higher expression of target genes (e.g., transglutaminase 2 and retinoic acid receptor beta), which in NB4 cells was sustained post treatment termination. To determine whether sustained epigenetic changes were responsible, we quantified the enrichment of histone modifications by chromatin immunoprecipitation, and CpG methylation by bisulfite-pyrosequencing. While ATRA and combination treatment induced similar histone acetylation enrichment, combination treatment induced greater demethylation of target genes, which was sustained. Therefore, sustained demethylation of target genes by ATRA and ATO combination treatment is associated with lasting differentiation and gene expression changes.
Bioaccumulation of metals in calanoid copepods by oral intake
Authors: Kadiene Esther U. , Ouddane Baghdad , Hwang Jiang-Shiou , Souissi Sami 
Published: July 2019

AbstractWe demonstrated that oral intake of water by two calanoid copepods, Pseudodiaptomus annandalei and Eurytemora affinis takes place and has implications for their ecotoxicology. In the first experiment, copepods were exposed to a dyed medium, which allowed us to visually examine the possibility of water uptake by the copepod. We observed that both copepod species were taking in water orally and evacuated dye at different speeds. This exposure left concentrated dye in the guts of the copepods indicating adsorption into the gut epithelium. This was further demonstrated by exposing both copepod species independently to dissolved metals (Cd,17 µg/L; Cu,13.8 µg/L; Ni, 29.3 µg/L) and to dietary metals (Cd,18.8 µg/g; Cu, 35.3 µg/g; Ni, 32.5 µg/g). The results showed that although the concentration of dissolved metals they were exposed to were lower than those of the dietary metals, nevertheless, uptake of metals by both copepod species from the dissolved phase alone was substantially higher than from dietary exposure. This provides clear evidence to support our hypothesis that higher metal body burden observed in copepods exposed to dissolved metals than in those exposed to dietary metals is an implication of oral intake of water. P. annandalei showed higher excretion rate of metals when exposed to dissolved metals than E. affinis. However, the excretion rate of metals from both copepod species exposed to dietary metal was similar. We conclude here that both copepod species take in water orally. Our study further showed that metal uptake depends on the exposure routes and the uptake and excretion rates are dependent on the type of metals, amounts and the species.
Favorable Changes in Fasting Glucose in a 6-month Self-Monitored Lifestyle Modification Programme Inversely Affects Spexin Levels in Females with Prediabetes
Authors: Al-Daghri Nasser M. , Wani Kaiser , Yakout Sobhy M. , Al-Hazmi Hazim , Amer Osama E. , Hussain Syed Danish , Sabico Shaun , Ansari Mohammed Ghouse Ahmed , Al-Musharaf Sara , Alenad Amal M. , Alokail Majed S. , Clerici Mario 
Published: July 2019

AbstractSpexin (SPX) is a novel peptide thought to have a role in various metabolic regulations. Given its presumed body-weight regulatory functions, we aimed to determine whether lifestyle intervention programs on weight loss and fasting glucose (FG) improvement among people with impaired glucose regulation also alter levels of circulating SPX. A total of 160 Saudi adult males and females with prediabetes were randomly selected from a larger cohort (N = 294) who underwent a 6-month lifestyle modification program to improve their glycemic status. Participants were split into two groups based on differences in glucose levels post-intervention, with the first 50% (improved group) having the most significant reduction in FG. SPX was measured at baseline and after 6 months. Changes in SPX was significant only in the improved group [baseline: median (Q1–Q3) of 164 pg/ml (136–227) vs follow-up: 176 pg/ml (146–285); p < 0.01]. When stratified by sex, the significant increase was observed only in females [159 pg/ml (127–252) vs 182.5 (152,369.1); p < 0.01]. Furthermore, SPX levels showed a significant inverse association with FG (β = −0.22, p = 0.003) even after adjustment with age and BMI, again only in females. Circulating SPX levels increase over time in people with prediabetes, particularly women who responded favorably in a 6-month lifestyle intervention program. Whether an unknown mechanism regulating the sexual disparity seen in SPX levels post-intervention exists should be further investigated using a larger sample size.