bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenomic profiling of neuroblastoma cell lines
Authors: Upton Kristen , Modi Apexa , Patel Khushbu , Kendsersky Nathan M. , Conkrite Karina L. , Sussman Robyn T. , Way Gregory P. , Adams Rebecca N. , Sacks Gregory I. , Fortina Paolo , Diskin Sharon J. , Maris John M. , Rokita Jo Lynne 
Published: April 2020

AbstractUnderstanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
Syncytiotrophoblast extracellular microvesicle profiles in maternal circulation for noninvasive diagnosis of preeclampsia
Authors: Levine Lisa , Habertheuer Andreas , Ram Chirag , Korutla Laxminarayana , Schwartz Nadav , Hu Robert W. , Reddy Sanjana , Freas Andrew , Zielinski Patrick D. , Harmon Joey , Molugu Sudheer Kumar , Parry Samuel , Vallabhajosyula Prashanth 
Published: April 2020

AbstractPreeclampsia is the most common placental pathology in pregnant females, with increased morbidity and mortality incurred on the mother and the fetus. There is a need for improved biomarkers for diagnosis and monitoring of this condition. Placental syncytiotrophoblasts at the maternal-fetal interface release nanoparticles, including extracellular microvesicles, into the maternal blood during pregnancy. Syncytiotrophoblast extracellular microvesicles (STEVs) are being studied for their diagnostic potential and for their potential physiologic role in preeclampsia. We hypothesized that STEV profiles in maternal circulation would be altered under conditions of preeclampsia compared to normal pregnancy. Extracellular vesicles (EVs) released by BeWo cells in vitro showed high expression of syncytin-1, but no plac1 expression, demonstrating that trophoblast cell EVs express syncytin-1 on their surface. Placental alkaline phosphatase also showed high expression on BeWo EVs, but due to concern for cross reactivity to highly prevalent isoforms of intestinal and bone alkaline phosphatase, we utilized syncytin-1 as a marker for STEVs. In vivo, syncytin-1 protein expression was confirmed in maternal plasma EVs from Control and Preeclampsia subjects by Western blot, and overall, lower expression was noted in samples from patients with preeclampsia (n = 8). By nanoparticle analysis, EV profiles from Control and Preeclampsia groups showed similar total plasma EV quantities (p = 0.313) and size distribution (p = 0.415), but STEV quantitative signal, marked by syncytin-1 specific EVs, was significantly decreased in the Preeclampsia group (p = 2.8 × 10−11). Receiver operating characteristic curve demonstrated that STEV signal threshold cut-off of <0.316 was 95.2% sensitive and 95.6% specific for diagnosis of preeclampsia in this cohort (area under curve = 0.975 ± 0.020). In conclusion, we report that the syncytin-1 expressing EV profiles in maternal plasma might serve as a placental tissue specific biomarker for preeclampsia.
A Scalable Similarity-Popularity Link Prediction Method
Authors: Kerrache Said , Alharbi Ruwayda , Benhidour Hafida 
Published: April 2020

AbstractLink prediction is the task of computing the likelihood that a link exists between two given nodes in a network. With countless applications in different areas of science and engineering, link prediction has received the attention of many researchers working in various disciplines. Considerable research efforts have been invested into the development of increasingly accurate prediction methods. Most of the proposed algorithms, however, have limited use in practice because of their high computational requirements. The aim of this work is to develop a scalable link prediction algorithm that offers a higher overall predictive power than existing methods. The proposed solution falls into the class of global, parameter-free similarity-popularity-based methods, and in it, we assume that network topology is governed by three factors: popularity of the nodes, their similarity and the attraction induced by local neighbourhood. In our approach, popularity and neighbourhood-caused attraction are computed directly from the network topology and factored out by introducing a specific weight map, which is then used to estimate the dissimilarity between non-adjacent nodes through shortest path distances. We show through extensive experimental testing that the proposed method produces highly accurate predictions at a fraction of the computational cost required by existing global methods and at a low additional cost compared to local methods. The scalability of the proposed algorithm is demonstrated on several large networks having hundreds of thousands of nodes.
Glutamate dehydrogenase: a novel candidate to diagnose Plasmodium falciparum through rapid diagnostic test in blood specimen from fever patients
Authors: Kori Lokesh D. , Valecha Neena , Anvikar Anupkumar R. 
Published: April 2020

AbstractIn recent years, Plasmodium falciparum histidine-rich protein 2 gene deletion has been reported in India. Such isolates are prone to selective transmission and thus form a challenge to case management. As most of the rapid malaria diagnostic tests are based on the detection of HRP2 protein in the blood, we attempted to use Glutamate Dehydrogenase (GDH) as a biomarker for the diagnosis of P. falciparum. Recombinant PfGDH was successfully cloned, expressed and purified using the Ni-NTA approach. Polyclonal antibodies were raised against full-length rPfGDH and its peptides. Antibodies for rPfGDH showed a strong immune response against the recombinant protein. However, antibody showed no affinity towards the peptides, which suggests they failed as antigen. Antibodies for rPfGDH significantly detected the GDH in human blood specimens. This is the first report where P. falciparum GDH was detected in malaria cases from various parts of India. The raised polyclonal antibodies had shown an affinity for PfGDH in quantitative ELISA and are capable to be exploited for RDTs. This research needs further statistical validation on a large number and different sample types from candidates infected with P. falciparum and other species.
Simultaneous Measurement of Perfusion and T2* in Calf Muscle at 7T with Submaximal Exercise using Radial Acquisition
Authors: Mahmud Sultan Z. , Gladden L. Bruce , Kavazis Andreas N. , Motl Robert W. , Denney Thomas S. , Bashir Adil 
Published: April 2020

AbstractImpairments in oxygen delivery and consumption can lead to reduced muscle endurance and physical disability. Perfusion, a measure of microvascular blood flow, provides information on nutrient delivery. T2* provides information about relative tissue oxygenation. Changes in these parameters following stress, such as exercise, can yield important information about imbalance between delivery and consumption. In this study, we implemented novel golden angle radial MRI acquisition technique to simultaneously quantify muscle perfusion and T2* at 7T with improved temporal resolution, and demonstrated assessment of spatial and temporal changes in these parameters within calf muscles during recovery from plantar flexion exercise. Nine healthy subjects participated the studies. At rest, perfusion and T2* in gastrocnemius muscle group within calf muscle were 5 ± 2 mL/100 g/min and 21.1 ± 3 ms respectively. Then the subjects performed plantar flexion exercise producing a torque of ~8ft-lb. Immediately after the exercise, perfusion was elevated to 79.3 ± 9 mL/100 g/min and T2* was decreased by 6 ± 3%. The time constants for 50% perfusion and T2* recovery were 54.1 ± 10 s and 68.5 ± 7 s respectively. These results demonstrate successful simultaneous quantification of perfusion and T2* in skeletal muscle using the developed technique.
Protease Inhibition Improves Healing of The Vaginal Wall after Obstetrical Injury: Results from a Preclinical Animal Model
Authors: Hamner Jennifer , Florian-Rodriguez Maria , Acevedo Jesus , Shi Haolin , Word R. Ann 
Published: April 2020

AbstractVaginal delivery with obstetrical trauma is a risk factor for pelvic organ prolapse later in life. Loss of fibulin-5 (FBLN5), an elastogenesis-promoting cellular matrix protein, results in prolapse in mice. Here, we evaluated effects of pregnancy, parturition, and obstetrical injury on FBLN5 content, elastic fibers, biomechanics, and histomorphology of the vaginal wall in rats. Further, we analyzed the effects of actinonin, a protease inhibitor, on obstetrical injury of the vaginal wall. Vaginal FBLN5 decreased significantly in pregnancy, and injury resulted in further downregulation. Stiffness of the vaginal wall decreased 82% in pregnant rats and 74% (p = 0.019) with injury relative to uninjured vaginal delivery controls at 3d. Actinonin ameliorated loss of FBLN5, rescued injury-induced loss of elastic fibers and biomechanical properties after parturition, and reduced the area of injury 10-fold. We conclude that pregnancy and parturition have a profound impact on vaginal FBLN5 and biomechanics of the vaginal wall. Further, obstetrical injury has significant deleterious impact on recovery of the vaginal wall from pregnancy. Actinonin, a non-specific matrix metalloprotease inhibitor, improved recovery of the parturient vaginal wall after obstetrical injury.
Prognostic role of serum high mobility group box 1 concentration in cardiac surgery
Authors: Kim Namo , Lee Sak , Lee Jeong-Rim , Kwak Young-Lan , Jun Ji-Hae , Shim Jae-Kwang 
Published: April 2020

AbstractOutcomes of cardiac surgery are influenced by systemic inflammation. High mobility group box 1 (HMGB1), a pivotal inflammatory mediator, plays a potential role as a prognostic biomarker in cardiovascular disease. The aim of this prospective, observational study was to investigate the relationship between serum HMGB1 concentrations and composite of morbidity endpoints in cardiac surgery. Arterial blood samples for HMGB1 measurement were collected from 250 patients after anaesthetic induction (baseline) and 1 h after weaning from cardiopulmonary bypass (post-CPB). The incidence of composite of morbidity endpoints (death, myocardial infarction, stroke, renal failure and prolonged ventilator care) was compared in relation to the tertile distribution of serum HMGB1 concentrations. The incidence of composite of morbidity endpoints was significantly different with respect to the tertile distribution of post-CPB HMGB1 concentrations (p = 0.005) only, and not to the baseline. Multivariable analysis revealed post-CPB HMGB1 concentration (OR, 1.072; p = 0.044), pre-operative creatinine and duration of CPB as independent risk factors of adverse outcome. Accounting for its prominent role in mediating sterile inflammation and its relation to detrimental outcome, HMGB1 measured 1 h after weaning from CPB would serve as a useful biomarker for accurate risk stratification in cardiac surgical patients and may guide tailored anti-inflammatory therapy.
OsNPR3.3-dependent salicylic acid signaling is involved in recessive gene xa5-mediated immunity to rice bacterial blight
Authors: Jiang Guanghuai , Yin Dedong , Shi Yue , Zhou Zhuangzhi , Li Chunrong , Liu Pengcheng , Jia Yanfeng , Wang Yanyan , Liu Zhenzhen , Yu Minxiang , Wu Xianghong , Zhai Wenxue , Zhu Lihuang 
Published: April 2020

AbstractSalicylic acid (SA) is a key natural component that mediates local and systemic resistance to pathogens in many dicotyledonous species. However, its function is controversial in disease resistance in rice plants. Here, we show that the SA signaling is involved in both pathogen-associated-molecular-patterns triggered immunity (PTI) and effector triggered immunity (ETI) to Xanthomonas oryzae pv. Oryzae (Xoo) mediated by the recessive gene xa5, in which OsNPR3.3 plays an important role through interacting with TGAL11. Rice plants containing homozygous xa5 gene respond positively to exogenous SA, and their endogenous SA levels are also especially induced upon infection by the Xoo strain, PXO86. Depletion of endogenous SA can significantly attenuate plant resistance to PXO86, even to 86∆HrpXG (mutant PXO86 with a damaged type III secretion system). These results indicated that SA plays an important role in disease resistance in rice plants, which can be clouded by high levels of endogenous SA and the use of particular rice varieties.
An epigenetic map of malaria parasite development from host to vector
Authors: Witmer Kathrin , Fraschka Sabine A. , Vlachou Dina , Bártfai Richárd , Christophides George K. 
Published: April 2020

AbstractThe malaria parasite replicates asexually in the red blood cells of its vertebrate host employing epigenetic mechanisms to regulate gene expression in response to changes in its environment. We used chromatin immunoprecipitation followed by sequencing in conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental transition from asexual blood stages to male and female gametocytes and to ookinetes in the rodent malaria parasite Plasmodium berghei. Across the developmental stages examined, heterochromatin protein 1 associates with variantly expressed gene families localised at subtelomeric regions and variant gene expression based on heterochromatic silencing is observed only in some genes. Conversely, the euchromatin mark histone 3 lysine 9 acetylation (H3K9ac) is abundant in non-heterochromatic regions across all developmental stages. H3K9ac presents a distinct pattern of enrichment around the start codon of ribosomal protein genes in all stages but male gametocytes. Additionally, H3K9ac occupancy positively correlates with transcript abundance in all stages but female gametocytes suggesting that transcription in this stage is independent of H3K9ac levels. This finding together with known mRNA repression in female gametocytes suggests a multilayered mechanism operating in female gametocytes in preparation for fertilization and zygote development, coinciding with parasite transition from host to vector.
Distal spinal nerve development and divergence of avian groups
Authors: Rashid Dana J. , Bradley Roger , Bailleul Alida M. , Surya Kevin , Woodward Holly N. , Wu Ping , Wu Yun-Hsin , Menke Douglas B. , Minchey Sergio G. , Parrott Ben , Bock Samantha L. , Merzdorf Christa , Narotzky Emma , Burke Nathan , Horner John R. , Chapman Susan C. 
Published: April 2020

AbstractThe avian transition from long to short, distally fused tails during the Mesozoic ushered in the Pygostylian group, which includes modern birds. The avian tail embodies a bipartite anatomy, with the proximal separate caudal vertebrae region, and the distal pygostyle, formed by vertebral fusion. This study investigates developmental features of the two tail domains in different bird groups, and analyzes them in reference to evolutionary origins. We first defined the early developmental boundary between the two tail halves in the chicken, then followed major developmental structures from early embryo to post-hatching stages. Differences between regions were observed in sclerotome anterior/posterior polarity and peripheral nervous system development, and these were consistent in other neognathous birds. However, in the paleognathous emu, the neognathous pattern was not observed, such that spinal nerve development extends through the pygostyle region. Disparities between the neognaths and paleognaths studied were also reflected in the morphology of their pygostyles. The ancestral long-tailed spinal nerve configuration was hypothesized from brown anole and alligator, which unexpectedly more resembles the neognathous birds. This study shows that tail anatomy is not universal in avians, and suggests several possible scenarios regarding bird evolution, including an independent paleognathous long-tailed ancestor.
Synthesis, crystal structure, photoluminescence and catalytic properties of a novel cuprous complex with 2,3-pyrazinedicarboxylic acid ligands
Authors: Zheng Xingxing , Chen Yanmei , Ran Jingwen , Li Li 
Published: April 2020

AbstractA copper (I) polymer, [Cu2Mg(pzdc)2(H2O)5•2H2O]n (pzdc = 2,3-Pyrazinedicarboxylic acid), was synthesized by solvothermal method. The complex was characterized using X-ray diffraction (XRD), fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectrophotometry (UV-Vis), and element analysis. X-ray crystal structure analysis reveals that the complex is a two-dimensional coordination polymer. The photophysical and luminescent properties of the complex were investigated. At room temperature, the complex exhibits reversible double strands cyclic voltammogram and displays efficient blue emission with peak maxima at 468 nm. Catalytic liquid phase oxidation of dyes and glyphosate was carried out using the copper (I) polymer as catalyst and H2O2 as oxidant. Degradation efficiencies were evaluated by varying the reaction conditions (i.e. illumination and oxidant). In the degradation reactions, the polymer exhibits high degradation efficiency within a short reaction time under the optimum reaction conditions. Furthermore, the reusability of the catalyst is excellent, showing no activity loss in four repeated cycles. The possible reaction mechanism catalyzed by the polymer was inferred on the basis of the results of electron spin resonance (ESR), electrochemical and ion chromatography analyses (IC).
Temporal trends and geographical variability of the prevalence and incidence of attention deficit/hyperactivity disorder diagnoses among children in Catalonia, Spain
Authors: Pérez-Crespo Laura , Canals-Sans Josefa , Suades-González Elisabet , Guxens Mònica 
Published: April 2020

AbstractAttention deficit/hyperactivity disorder (ADHD) is one of the most common behavioral disorders in childhood. According to a recent systematic review, the worldwide estimate of ADHD prevalence is 7.2% in children. This study aims to assess the prevalence of ADHD diagnoses in 2017 and the incidence of ADHD diagnoses in 2009–2017 in children living in Catalonia, Spain, as well as their temporal and geographical variability, and stratifying by sex and age. We used administrative data for all children aged 4 to 17 years who were insured in the public Catalan Health System in 2009–2017. We identified all ADHD cases diagnosed in 2009–2017 (ICD-9 code 314). We estimated the prevalence of ADHD diagnoses in 2017 and the overall annual incidence of ADHD diagnoses in 2009–2017. We used Poisson regression models to assess temporal trends in the incidence. We estimated a prevalence of ADHD diagnoses of 4.06% (95%CI 4.03, 4.10) in 2017, being 5.81% (95%CI 5.75, 5.87) for boys and 2.20% (95%CI 2.16, 2.24) for girls, the highest prevalence being in 13-to-17-year-olds (7.28% (95%CI 7.20, 7.36)). We did not observe a statistically significant increase of the incidence of ADHD diagnoses during the study period. Geographical differences were found across the healthcare areas in both prevalence and annual incidence and constant during the study period. In conclusion, the prevalence of ADHD diagnoses observed in this study was 4.06%, which was lower than the estimates reported in previous systematic reviews, but in line with the prevalence estimates from other recent European studies. The prevalence was higher in boys than girls, with a sex ratio consistent with previous studies. We did not observe an increase in the temporal trend of incidence of ADHD diagnoses in recent years, but we found geographical differences.
Effects of parental exposure to glyphosate-based herbicides on embryonic development and oxidative status: a long-term experiment in a bird model
Authors: Ruuskanen Suvi , Rainio Miia J. , Uusitalo Maiju , Saikkonen Kari , Helander Marjo 
Published: April 2020

AbstractControversial glyphosate-based herbicides (GBHs) are the most frequently used herbicides globally. GBH residues are detected in soil, water, crops, and food products, potentially exposing non-target organisms to health risks; these organisms include wildlife, livestock, and humans. However, the potential for GBH-related parental effects are poorly understood. In the case of birds, GBHs may be transferred directly from mothers to eggs, or they may indirectly influence offspring performance by altered maternal resource allocation to eggs. We experimentally exposed a parental generation of Japanese quails (Coturnix japonica) to GBHs (200 mg/kg feed) or respective controls. Glyphosate residues were found in eggs (ca 0.76 kg/mg). Embryonic development tended to be poorer in the eggs of GBH-exposed parents (76% of eggs showed normal development) compared to control parents (89% normal eggs). Embryonic brain tissue from GBH-exposed parents tended to express more lipid damage (20% higher), yet other biomarkers showed no apparent differences. We detected no differences in egg quality (egg, yolk, or shell mass, egg hormone concentration) across the treatment groups. Given this is the first long-term study testing parental effects of GBHs with birds, more studies are needed characterizing GBH-associated changes in maternal allocation and for example epigenetic programming.
Identification errors in camera-trap studies result in systematic population overestimation
Authors: Johansson Örjan , Samelius Gustaf , Wikberg Ewa , Chapron Guillaume , Mishra Charudutt , Low Matthew 
Published: April 2020

AbstractReliable assessments of animal abundance are key for successful conservation of endangered species. For elusive animals with individually-unique markings, camera-trap surveys are a benchmark standard for estimating local and global population abundance. Central to the reliability of resulting abundance estimates is the assumption that individuals are accurately identified from photographic captures. To quantify the risk of individual misidentification and its impact on population abundance estimates we performed an experiment under controlled conditions in which 16 captive snow leopards (Panthera uncia) were camera-trapped on 40 occasions and eight observers independently identified individuals and recaptures. Observers misclassified 12.5% of all capture occasions, resulting in systematically inflated population abundance estimates on average by one third (mean ± SD = 35 ± 21%). Our results show that identifying individually-unique individuals from camera-trap photos may not be as reliable as previously believed, implying that elusive and endangered species could be less abundant than current estimates indicate.