bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new dipole index of the salinity anomalies of the tropical Indian Ocean
Authors: Li Junde , Liang Chujin , Tang Youmin , Dong Changming , Chen Dake , Liu Xiaohui , Jin Weifang 
Published: April 2016

AbstractWith the increased interest in studying the sea surface salinity anomaly (SSSA) of the tropical Indian Ocean during the Indian Ocean Dipole (IOD), an index describing the dipole variability of the SSSA has been pursued recently. In this study, we first use a regional ocean model with a high spatial resolution to produce a high-quality salinity simulation during the period from 1982 to 2014, from which the SSSA dipole structure is identified for boreal autumn. On this basis, by further analysing the observed data, we define a dipole index of the SSSA between the central equatorial Indian Ocean (CEIO: 70°E-90°E, 5°S-5°N) and the region off the Sumatra-Java coast (SJC: 100°E-110°E, 13°S-3°S). Compared with previous SSSA dipole indices, this index has advantages in detecting the dipole signals and in characterizing their relationship to the sea surface temperature anomaly (SSTA) dipole variability. Finally, the mechanism of the SSSA dipole is investigated by dynamical diagnosis. It is found that anomalous zonal advection dominates the SSSA in the CEIO region, whereas the SSSA in the SJC region are mainly influenced by the anomalous surface freshwater flux. This SSSA dipole provides a positive feedback to the formation of the IOD events.
Expression of Estrogen Receptor Beta Predicts Oncologic Outcome of pT3 Upper Urinary Tract Urothelial Carcinoma Better Than Aggressive Pathological Features
Authors: Luo Hao Lun , Sung Ming Tse , Tsai Eing Mei , Lin Chang Shen , Lee Nai Lun , Chung Yueh-Hua , Chiang Po Hui 
Published: April 2016

AbstractUpper urinary tract urothelial carcinoma (UT-UC) is rare and treatment options or prognostic markers are limited. There is increasing evidence indicating that urothelial carcinoma may be an endocrine-related cancer. The aim of this study was to analyze the prognostic effect of estrogen receptor beta (ERβ) on the outcome of UT-UC. From 2005 to 2012, this study included 105 patients with pT3 UT-UC. Perioperative factors, pathological features and ERβ immunostaining were reviewed and prognostic effects were examined by multivariate analysis. This study divided patients into either the ERβ-high (n = 52) or ERβ-low (n = 53) group and analyzed their oncologic outcomes. All pathological features except infiltrating tumor architecture (significantly higher incidence in ERβ-low group, p = 0.004) are symmetric in both groups. Low ERβ expression was significantly correlated with local recurrence and distant metastasis in univariate analysis (p = 0.035 and 0.004, respectively) and multivariate analysis (p = 0.05 and 0.008, respectively). Cell line study also proved that knock down of ERβ cause less UTUC proliferation and migration. In addition, ERβ agonist also enhanced the cytotoxic and migration inhibition effect of cisplatin and ERβ antagonist cause the UTUC cell more resistant to cisplatin. This result may help identify patients in need of adjuvant therapy or develop potential targeted therapy.
Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii
Authors: Najnin T. , Siddiqui K. S. , Taha  , Elkaid N. , Kornfeld G. , Curmi P. M. G. , Cavicchioli R. 
Published: April 2016

AbstractCold environments dominate the Earth’s biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and regulate cellular processes. Two component regulatory systems have been inferred to function in thermal regulation of gene expression, but biochemical studies assessing these systems inBacteriaare rare, and none have been performed inArchaeaor psychrophiles. Here we examined the LtrK/LtrR two component regulatory system from the Antarctic archaeon,Methanococcoides burtonii, assessing kinase and phosphatase activities of wild-type and mutant proteins. LtrK was thermally unstable and had optimal phosphorylation activity at 10 °C (the lowest optimum activity for any psychrophilic enzyme), high activity at 0 °C and was rapidly thermally inactivated at 30 °C. These biochemical properties match well with normal environmental temperatures ofM. burtonii(0–4 °C) and the temperature this psychrophile is capable of growing at in the laboratory (−2 to 28 °C). Our findings are consistent with a role for LtrK in performing phosphotransfer reactions with LtrR that could lead to temperature-dependent gene regulation.
Generation and detection of orbital angular momentum via metasurface
Authors: Jin Jinjin , Luo Jun , Zhang Xiaohu , Gao Hui , Li Xiong , Pu Mingbo , Gao Ping , Zhao Zeyu , Luo Xiangang 
Published: April 2016

AbstractBeams carrying orbital angular momentum possess a significant potential for modern optical technologies ranging from classical and quantum communication to optical manipulation. In this paper, we theoretically design and experimentally demonstrate an ultracompact array of elliptical nanoholes, which could convert the circularly polarized light into the cross-polarized vortex beam. To measure the topological charges of orbital angular momentum in a simple manner, another elliptical nanoholes array is designed to generate reference beam as a reference light. This approach may provide a new way for the generation and detection of orbital angular momentum in a compact device.
Impact of Surgical Approach on Clinical Outcomes in the Treatment of Lumbar Pseudarthrosis
Authors: Owens R. Kirk , Djurasovic Mladen , Crawford Charles H. , Glassman Steven D. , Dimar John R. , Carreon Leah Y. 
Published: April 2016

Study Design Retrospective comparative cohort. Objective Pseudarthrosis following fusion for degenerative lumbar spine pathologies remains a substantial problem. Current data shows that patients who develop a pseudarthrosis have suboptimal outcomes. This study evaluates if treatment of pseudarthrosis can be affected by surgical approach. Methods Medical records of 63 female and 65 male patients (mean age 50.37) who were treated for nonunion following lumbar fusion were reviewed. Sixty patients underwent posterolateral fusion (PSF), 18 underwent PSF with transforaminal interbody fusion (TLIF), 32 underwent anterior and posterior spinal fusion (AP), and 24 underwent anterior lumbar interbody fusion (ALIF). Results Significant differences between the treatment groups were observed in length of stay ( p = 0.000), blood loss ( p = 0.000), and operative time ( p = 0.000). In the AP fusion group, minimal clinically important difference (MCID) was reached in 47% of patients for back pain, 28% for leg pain, and 28% for Oswestry Disability Index (ODI). PSF had the highest percentage of patients reaching MCID for Short Form-36 (SF-36) physical composite score at 25%. ALIF and TLIF subgroups reached MCID for ODI in 17% of patients. Linear regression analysis showed that type of surgical approach did not impact change in ODI scores. Conclusion Although not statistically significant, the AP fusion group reached MCID more frequently in all outcomes except SF-36 Physical Component Summary. All surgical approaches examined for treatment of lumbar pseudarthrosis resulted in only poor to modest improvement in ODI. This result further emphasizes the importance of achieving a solid fusion with the index surgery.
Prospects of eLISA for detecting Galactic binary black holes similar to GW150914
Authors: Seto Naoki 
Published: April 2016

Abstract
We discuss the prospects of eLISA for detecting gravitational waves (GWs) from Galactic binary black holes (BBHs) similar to GW150914. For a comoving merger rate that is consistent with current observation, eLISA is likely to identify at least one BBH with a sufficient signal-to-noise ratio. In addition, eLISA has a potential to measure the eccentricity of the BBH as small as e ∼ 0.02, corresponding to the residual value e ∼ 10−6 at 10 Hz. Therefore, eLISA could provide us with a crucial information to understand the formation processes of relatively massive BBHs like GW150914. We also derive a simple scaling relation for the expected number of detectable Galactic BBHs.
Identification of Diaporthe longicolla on Dry Edible Pea, Dry Edible Bean, and Soybean in North Dakota
Authors: Mathew Febina M. , Castlebury Lisa A. , Alananbeh Kholoud , Jordahl James G. , Taylor Chris A. , Meyer Scott M. , Lamppa Robin S. , Pasche Julie A. , Markell Samuel G. 
Published: April 2016

North Dakota soybean production has expanded geographically, and possible short rotations with dry edible bean and pea raise concerns of pathogens (such as Diaporthe longicolla, cause of Phomopsis seed decay and stem disease of soybean) developing overlapping host ranges. To the best of our knowledge, this is the first report of D. longicolla causing stem disease on dry edible beans and dry edible peas, and stem disease on soybean in North Dakota. Its impact on dry edible beans and dry edible peas is uncertain. Accepted for publication 16 February 2015. Published 15 April 2015.
Role of Specificity Protein-1 and Activating Protein-2 Transcription Factors in the Regulation of the Gap Junction Protein Beta-2 Gene in the Epididymis of the Rat1
Authors: Adam Cécile , Cyr Daniel G. 
Published: April 2016

Abstract
In prepubertal rats, connexin 26 (GJB2) is expressed between adjacent columnar cells of the epididymis. At 28 days of age, when columnar cells differentiate into adult epithelial cell types, Gjb2 mRNA levels decrease to barely detectable levels. There is no information on the regulation of GJB2 in the epididymis. The present study characterized regulation of the Gjb2 gene promoter in the epididymis. A single transcription start site at position −3829 bp relative to the ATG was identified. Computational analysis revealed several TFAP2A, SP1, and KLF4 putative binding sites. A 1.5-kb fragment of the Gjb2 promoter was cloned into a vector containing a luciferase reporter gene. Transfection of the construct into immortalized rat caput epididymal (RCE-1) cells indicated that the promoter contained sufficient information to drive expression of the reporter gene. Deletion constructs showed that the basal activity of the promoter resides in the first −230 bp of the transcriptional start site. Two response elements necessary for GJB2 expression were identified: an overlapping TFAP2A/SP1 site (−136 to −126 bp) and an SP1 site (−50 bp). Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays confirmed that SP1 and TFAP2A were bound to the promoter. ChIP analysis of chromatin from young and pubertal rats indicated that TFAP2A and SP1 binding decreased with age. SP1 and TFAP2A knockdown indicated that SP1 is necessary for Gjb2 expression. DNA methylation did not appear to be involved in the regulation of Gjb2 expression. Results indicate that SP1 and TFAP2A regulate Gjb2 promoter activity during epididymal differentiation in rat.
Integrative pharmacogenomics to infer large-scale drug taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin 
Published: April 2016

ABSTRACTIdentification of drug targets and mechanism of action (MoA) for new and uncharacterlzed drugs is important for optimization of drug efficacy. Current MoA prediction approaches largely rely on prior information including side effects, therapeutic indication and/or chemo-informatics. Such information is not transferable or applicable for newly identified, previously uncharacterlzed small molecules. Therefore, a shift in the paradigm of MoA predictions is necessary towards development of unbiased approaches that can elucidate drug relationships and efficiently classify new compounds with basic input data. We propose a new integrative computational pharmacogenomlc approach, referred to as Drug Network Fusion (DNF), to infer scalable drug taxonomies that relies only on basic drug characteristics towards elucidating drug-drug relationships. DNF is the first framework to integrate drug structural information, high-throughput drug perturbation and drug sensitivity profiles, enabling drug classification of new experimental compounds with minimal prior information. We demonstrate that the DNF taxonomy succeeds in identifying pertinent and novel drug-drug relationships, making it suitable for investigating experimental drugs with potential new targets or MoA. We highlight how the scalability of DNF facilitates identification of key drug relationships across different drug categories, and poses as a flexible tool for potential clinical applications in precision medicine. Our results support DNF as a valuable resource to the cancer research community by providing new hypotheses on the compound MoA and potential insights for drug repurposlng.
KinLinks: Software Toolkit for Kinship Analysis and Pedigree Generation from HTS Datasets
Authors: Shcherbina Anna , Ricke Darrell O. , Schwoebel Eric , Boettcher Tara , Zook Christina , Bobrow Johanna , Petrovick Martha , Wack Edward 
Published: April 2016

AbstractThe ability to predict familial relationships from source DNA in multiple samples has a number of forensic and medical applications. Kinship testing of suspect DNA profiles against relatives in a law enforcement database can provide valuable investigative leads, determination of familial relationships can inform immigration decisions, and remains identification can provide closure to families of missing individuals. The proliferation of High-Throughput Sequencing technologies allows for enhanced capabilities to accurately predict familial relationships to the third degree and beyond. KinLinks, developed by MIT Lincoln Laboratory, is a software tool that predicts pairwise relationships and reconstructs kinship pedigrees for multiple input samples using single-nucleotide polymorphism (SNP) profiles. The software has been trained and evaluated on a set of 175 subjects (30,450 pairwise relationships), consisting of three multi-generational families and 52 geographically diverse subjects. Though a panel of 5396 SNPs was selected for kinship prediction, KinLinks is highly modular, allowing for the substitution of expanded SNP panels and additional training models as sequencing capabilities continue to progress. KinLinks builds on the SNP-calling capabilities of Sherlocks Toolkit, and is fully integrated with the Sherlocks Toolkit pipeline.
An evolutionary medicine perspective on Neandertal extinction
Authors: Sullivan Alexis P. , de Manuel Marc , Marques-Bonet Tomas , Perry George H. 
Published: April 2016

AbstractThe Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and lasting for more than 5,000 years – has long sparked anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture – and thus direct contact – between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (six chromosomes per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates – genes with the highest 1% genetic diversity genome-wide in non-human apes. In contrast, Neandertals had similar to higher levels of genetic diversity than humans in 13 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, this model does have limitations.
Language impairment resulting from a de novo deletion of 7q32.1-q33: a case report
Authors: Jiménez-Romero Ma Salud , Barcos-Martínez Montserrat , Espejo-Portero Isabel , Benítez-Burraco Antonio 
Published: April 2016

ABSTRACTChromosome 7 is a hot spot for cognitive disorders involving language deficits. We report on a girl who presents with a cognitive and speech delay, motor problems, hearing loss, and behavioral disturbances, and a de novo deletion within 7q32.1-q33 (chromosome position: chr7:127109685-132492196, hg 18). Several genes involved in brain development and function are located within the deleted region. Many of them are related to developmental disorders encompassing language deficits (dyslexia, speech-sound disorder, and autism). The proband’s phenotype may result from a change in the expression level of some of these genes.
Nanoscale mechanical stimulation method for quantifyingC. elegansmechanosensory behavior and memory
Authors: Sugi Takuma , Okumura Etsuko , Kiso Kaori , Igarashi Ryuji 
Published: April 2016

AbstractHere, we establish a novel economic system to quantifyC. elegansmechanosensory behavior and memory by a controllable nanoscale mechanical stimulation. Using piezoelectric sheet speaker, we can flexibly change the vibration properties at a nanoscale displacement level and quantify behavioral responses and memory under the control of each vibration property. This system will facilitate understanding of physiological aspects ofC. elegansmechanosensory behavior and memory.
Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia
Authors: Marrero Patricia , Abu-Amero Khaled K. , Larruga Jose M , Cabrera Vicente M 
Published: April 2016

ABSTRACTObjetivesWe suggest that the phylogeny and phylogeography of mtDNA macrohaplogroup M in Eurasia and Australasia is better explained supposing an out of Africa of modern humans following a northern route across the Levant than the most prevalent southern coastal route across Arabia and India proposed by others.MethodsA total 206 Saudi samples belonging to macrohaplogroup M have been analyzed. In addition, 4107 published complete or nearly complete Eurasian and Australasian mtDNA genomes ascribed to the same macrohaplogroup have been included in a global phylogeographic analysis.ResultsMacrohaplogroup M has only historical implantation in West Eurasia including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.ConclusionsThe existence of a northern route previously advanced by the phylogeography of mtDNA macrohaplogroup N is confirmed here by that of macrohaplogroup M. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.
Morphological diversity of blastula formation and gastrulation in temnopleurid sea urchins
Authors: Kitazawa Chisato , Fujii Tsubasa , Egusa Yuji , Komatsu Miéko , Yamanaka Akira 
Published: April 2016

ABSTRACTEmbryos of temnopleurid sea urchins exhibit species-specific morphologies. WhileTemnopleurus toreumaticushas a wrinkled blastula, others have a smooth blastula. Embryos ofT. toreumaticusinvaginate continuously at gastrulation, whereas in some others invagination is stepwise. We studied blastula and gastrula formation in four temnopleurids using light and scanning electron microscopy to clarify the mechanisms producing these differences. UnlikeT. toreumaticus, blastomeres of mid-blastulae inT. reevesii,T. hardwickiiandMespilia globulusformed pseudopods. Before primary mesenchyme cells ingressed, embryos developed an area of orbicular cells in the vegetal plate. The cells surrounding the orbicular cells extended pseudopods toward the orbicular cell area inT. toreumaticus,T. reevesiiandT. hardwickii. InT. toreumaticus, the extracellular matrix was well-developed and developed a hole-like structure that was not formed in others. Gastrulation ofT. reevesii,T. hardwickiiandM. globuluswas stepwise, suggesting that differences of gastrulation are caused by all or some of factors: change of cell shape, rearrangement, pushing up and towing of cells. These species-specific morphologies may be caused by the shape and surface structure of blastomeres with cell-movement.Summary statement:Temonopleurid embryology
Genome-wide evidence for a hybrid origin of modern polar bears
Authors: Lan Tianying , Cheng Jade , Ratan Aakrosh , Miller Webb , Schuster Stephan C , Farley Sean , Shideler Richard T , Mailund Thomas , Lindqvist Charlotte 
Published: April 2016

AbstractInterspecific hybridization is recognized as a widespread phenomenon but measuring its extent, directionality, and adaptive importance in the evolution of species remain challenging. Polar bears possess unique adaptations to life on the Arctic sea ice, whereas their closest relatives -brown bears - are boreal and subarctic generalists. Despite largely non-overlapping modern distributions, genomic evidence demonstrates ancient admixture between these species. Here, we analyze new genomes from contemporary zones of species overlap as well as a previously sequenced 120,000-year old polar bear subfossil. We use explicit statistical fitting of data to admixture graphs to provide a framework for testing alternative scenarios of population relationships and gene flow directionality. Our analyses favor a single, parsimonious introgression event from relatives of extant Southeast Alaskan coastal brown bears into the ancestor of extant polar bears, which inverts the current paradigm of unidirectional gene flow from polar into brown bear. This conclusion has clear implications for our understanding of the impact of climate change: a specialist Arctic lineage may have been the recipient of generalist, boreal genetic variants at crucial times during critical phases of Northern Hemisphere glacial oscillations.