bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elemental Contrast X-ray Tomography Using Ross Filter Pairs with a Polychromatic Laboratory Source
Authors: Arhatari Benedicta D. , Gureyev Timur E. , Abbey Brian 
Published: March 2017

AbstractThe majority of current laboratory based X-ray sources are polychromatic and are not tuneable. This lack of monochromaticity limits the range of applications for these sources and in particular it reduces the elemental specificity of laboratory based X-ray imaging experiments. Here we present a solution to this problem based on the use of Ross filter pairs. Although such Ross filter arrangements have been applied in proof-of-principle spectroscopy experiments, to date there have been no reports of this approach used for full-field X-ray imaging. Here we report on the experimental demonstration of Ross filter pairs being used for quasi-monochromatic, full-field imaging. This arrangement has several important benefits for laboratory based X-ray imaging including, as we demonstrate, elemental contrast enhancement. The method is demonstrated both for two-dimensional radiography and for three-dimensional X-ray tomography.
An analysis of Echinacea chloroplast genomes: Implications for future botanical identification
Authors: Zhang Ning , Erickson David L. , Ramachandran Padmini , Ottesen Andrea R. , Timme Ruth E. , Funk Vicki A. , Luo Yan , Handy Sara M. 
Published: March 2017

AbstractEchinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.
Modeling the air-soil exchange, secondary emissions and residues in soil of polychlorinated biphenyls in China
Authors: Cui Song , Fu Qiang , Li Yi-Fan , Ma Jianmin , Tian Chongguo , Liu Liyan , Zhang Leiming 
Published: March 2017

AbstractThe present study investigated the environmental distribution and fate of low molecular weight (LMW) polychlorinated biphenyls (PCBs) in China using the ChnGIPERM (Chinese Gridded Industrial Pollutants Emission and Residue Model), in which the air-soil exchange, spatial-temporal variations and the heterogeneity of secondary emission and residue in the non-source areas were studied. The model simulated the temporal and spatial variations of the PCB28 concentration in soils and air which agreed well with historical monitoring data across China. The long-range atmospheric transport (LRAT) and temperature was identified as the major factor affecting the distribution patterns of the secondary emissions and residues. Soil residue was considered as important environmental fate of PCB28. However, the intensity of an emissions source and the distance with non-source area strongly affected the spatial and temporal variations of PCB28 residues in soil. Several factors strongly impacted the distribution characteristics and air-soil exchange of PCB28, including emission patterns, atmospheric transport, soil organic carbon (SOC), soil vertical transfer, ambient temperature, and precipitation.
Comparison of orofacial pain of patients with different stages of precancer and oral cancer
Authors: Yang Yanjie , Zhang Peipei , Li Wenlu 
Published: March 2017

AbstractOrofacial pain impairs a patient's speech, swallowing, eating and interpersonal relations. Thirty-seven patients with a premalignant oral lesion, 124 patients with oral squamous cell carcinoma (OSSC), and 21 patients with a recurrence of OSSC were evaluated for their orofacial pain. The University of California San Francisco Oral Cancer Pain Questionnaire was administered to these patients at their initial visit, before they were prescribed analgesics for pain and before any treatment. Significant differences with respect to orofacial pain between the groups could be evaluatedwere observed. Patients with recurrence had the highest facial pain and patients with precancer had the lowest. Patients with OSSC and recurrence of OSSC reported significant levels of orofacial pain and functional restriction because of pain. Moreover, patients with recurrence of OSSC experienced significantly higher function-related pain, rather than pain qualities. These findings suggest that an important predictor for recurrence of OSSC may be the onset of orofacial pain that is exacerbated during function. The present study examined orofacial pain depending on the disease severity of precancer and oral cancer patients. Earlier recognition of symptoms of OSSC may improve early detection of its recurrence.
Clinical and radiographic response following targeting of BCAN-NTRK1 fusion in glioneuronal tumor
Authors: Alvarez-Breckenridge Christopher , Miller Julie J. , Nayyar Naema , Gill Corey M. , Kaneb Andrew , D’Andrea Megan , Le Long P. , Lee Jesse , Cheng Ju , Zheng Zongli , Butler William E. , Multani Pratik , Chow Maneval Edna , Ha Paek Sun , Toyota Brian D. , Dias-Santagata Dora , Santagata Sandro , Romero Javier , Shaw Alice T. , Farago Anna F. , Yip Stephen , Cahill Daniel P. , Batchelor Tracy T. , Iafrate A. John , Brastianos Priscilla K. 
Published: March 2017

AbstractGlioneuronal tumors constitute a histologically diverse group of primary central nervous system neoplasms that are typically slow-growing and managed conservatively. Genetic alterations associated with glioneuronal tumors include BRAF mutations and oncogenic fusions. To further characterize this group of tumors, we collected a cohort of 26 glioneuronal tumors and performed in-depth genomic analysis. We identified mutations in BRAF (34%) and oncogenic fusions (30%), consistent with previously published reports. In addition, we discovered novel oncogenic fusions involving members of the NTRK gene family in a subset of our cohort. One-patient with BCAN exon 13 fused to NTRK1 exon 11 initially underwent a subtotal resection for a 4th ventricular glioneuronal tumor but ultimately required additional therapy due to progressive, symptomatic disease. Given the patient’s targetable fusion, the patient was enrolled on a clinical trial with entrectinib, a pan-Trk, ROS1, and ALK (anaplastic lymphoma kinase) inhibitor. The patient was treated for 11 months and during this time volumetric analysis of the lesion demonstrated a maximum reduction of 60% in the contrast-enhancing tumor compared to his pre-treatment magnetic resonance imaging study. The radiologic response was associated with resolution of his clinical symptoms and was maintained for 11 months on treatment. This report of a BCAN-NTRK1 fusion in glioneuronal tumors highlights its clinical importance as a novel, targetable alteration.
Central role of lactate and proton in cancer cell resistance to glucose deprivation and its clinical translation
Authors: Hu Xun , Chao Ming , Wu Hao 
Published: March 2017

AbstractTargeting common weaknesses of cancer is an important strategy for cancer therapy. Glucose is a nutrient that maintains essential cellular metabolism, supporting cancer cell survival, growth and proliferation. Depriving glucose rapidly kills cancer cells. Most cancer cells possess a feature called Warburg effect, which refers to that cancer cells even with ample oxygen exhibit an exceptionally high glycolysis rate and convert most incoming glucose to lactate. Although it is recognized that Warburg effect confers growth advantage to cancer cells when glucose supply is sufficient, this feature could be considered as a fatal weakness of cancer cells when glucose supply is a problem. As glucose supply in many solid tumors is poor, and as most cancer cells have exceptionally high glycolytic capacity, maximizing cancer cell glycolysis rate would possibly exhaust intratumoral glucose, leading cancer cell to death. Lactate and proton are two common factors in solid tumors, they jointly protect cancer cells against glucose deprivation, and they are also powerful regulators dictating glucose metabolic phenotypes of cancer cells. Disrupting the joint action of lactate and proton, for example, by means of bicarbonate infusion into tumor, could maximize cancer cell glycolytic rate to rapidly use up glucose, expose their vulnerability to glucose deprivation and ultimately kill cancer cells. A pilot clinical study demonstrated that this approach achieved a remarkable improvement in local control of large and huge hepatocellular carcinoma.
IL-17 induces reactive astrocytes and up-regulation of vascular endothelial growth factor (VEGF) through JAK/STAT signaling
Authors: You Tao , Bi Yihui , li Jun , Zhang Mingkai , Chen Xuezhou , Zhang Keke , Li Jun 
Published: March 2017

AbstractSpinal cord injury is a grave neurological disability resulting in neuron degeneration and permanent paralysis. The inflammation triggered by the injury would promote the spinal cord lesion in turn. Activated astrocytes during inflammatory response could promote glial scar formation and contribute to the progression of the spinal cord injury. Interleukin 17 (IL-17) was upregulated in inflammatory responses to contusion or compression of the spinal cord. in this study, IL-17 could induce reactive astrocytes which was indicated by a well-known hallmark glial fibrillary acidic protein (GFAP)in vitroandin vivo. Moreover, we demonstrated that the upregulation of VEGF was induced by IL-17 human astrocytoma cells. In our further investigation, IL-17 induced the expression of VEGF in spinal cord injury by activating JAK/STAT signaling pathway bothin vitroandin vivo. In addition, we also found that IL-17 significantly changed tissue preservation and residual urine volumes and blood-spinal cord-barrier integrityin vivo. This newly found IL-17-JAK/STAT-VEGF axis improves our understanding of the molecular mechanism of spinal cord injury during inflammatory response and provides another potential target of spinal cord injury.
Standardized and flexible eight colour flow cytometry panels harmonized between different laboratories to study human NK cell phenotype and function
Authors: Veluchamy John P. , Delso-Vallejo María , Kok Nina , Bohme Fenna , Seggewiss-Bernhardt Ruth , van der Vliet Hans J. , de Gruijl Tanja D. , Huppert Volker , Spanholtz Jan 
Published: March 2017

AbstractAdvancements in multi-colour fluorescence activated cell sorting (FACS) panel warrant harmonized procedures to obtain comparable data between various laboratories. The intensifying clinical exploration of Natural Killer (NK) cell-based immunotherapy demands standardized and harmonized NK cell FACS panels and acquisition protocols. Eight colour FACS panels were designed to study human NK cell phenotype and function within peripheral blood mononuclear cells (PBMC). The panels were designed around fixed backbone markers and channels, covering antigens for non-NK lineage exclusion (CD3, TCRγδ, CD19, CD14, SYTOX® Blue) and NK cell selection (CD45, CD56, CD16), complemented with variable drop-in markers/channels to study NK cell phenotype (NKG2A, NKG2C, NKG2D and KIR2D) or NK cell function and activation (CD25, NKp44 and CD107a). Harmonized FACS set-up and data analysis for three different flow cytometers has been established, leading to highly comparable and reproducible data sets using the same PBMC reference samples (n = 6). Further studies of NK cells in fresh or cryopreserved PBMC samples (n = 12) confirmed that freezing and thawing of PBMC samples did not significantly affect NK phenotype or function. In conclusion, our data demonstrate that cryopreserved PBMC samples analysed by standardized FACS panels and harmonized analysis protocols will generate highly reliable data sets for multi-center clinical trials under validated conditions.
Advanced analytical methodologies for measuring healthy ageing and its determinants, using factor analysis and machine learning techniques: the ATHLOS project
Authors: Caballero Francisco Félix , Soulis George , Engchuan Worrawat , Sánchez-Niubó Albert , Arndt Holger , Ayuso-Mateos José Luis , Haro Josep Maria , Chatterji Somnath , Panagiotakos Demosthenes B. 
Published: March 2017

AbstractA most challenging task for scientists that are involved in the study of ageing is the development of a measure to quantify health status across populations and over time. In the present study, a Bayesian multilevel Item Response Theory approach is used to create a health score that can be compared across different waves in a longitudinal study, using anchor items and items that vary across waves. The same approach can be applied to compare health scores across different longitudinal studies, using items that vary across studies. Data from the English Longitudinal Study of Ageing (ELSA) are employed. Mixed-effects multilevel regression and Machine Learning methods were used to identify relationships between socio-demographics and the health score created. The metric of health was created for 17,886 subjects (54.6% of women) participating in at least one of the first six ELSA waves and correlated well with already known conditions that affect health. Future efforts will implement this approach in a harmonised data set comprising several longitudinal studies of ageing. This will enable valid comparisons between clinical and community dwelling populations and help to generate norms that could be useful in day-to-day clinical practice.
Exploring RNA conformational space under sparse distance restraints
Authors: Taylor William R. , Hamilton Russell S. 
Published: March 2017

AbstractWe show that the application of a small number of restraints predicted by coevolution analysis can provide a powerful restriction on the conformational freedom of an RNA molecule. The greatest degree of restriction occurs when a contact is predicted between the distal ends of a pair of adjacent stemloops but even with this location additional flexibilities in the molecule can mask the contribution. Multiple cross-links, especially those including a pseudoknot provided the strongest restraint on conformational freedom with the effect being most apparent in topologically simple folds and less so if the fold is more topologically entwined. Little was expected for large structures (over 300 bases) and although a few strong localised restrictions were observed, they contributed little to the restraint of the overall fold. Although contacts predicted using a correlated mutation analysis can provide some powerful restrictions on the conformational freedom of RNA molecules, they are too erratic in their occurrence and distribution to provide a general approach to the problem of RNA 3D structure prediction from sequence.
Prevalence and magnitude of groundwater use by vegetation: a global stable isotope meta-analysis
Authors: Evaristo Jaivime , McDonnell Jeffrey J. 
Published: March 2017

AbstractThe role of groundwater as a resource in sustaining terrestrial vegetation is widely recognized. But the global prevalence and magnitude of groundwater use by vegetation is unknown. Here we perform a meta-analysis of plant xylem water stable isotope (δ2H and δ18O, n = 7367) information from 138 published papers – representing 251 genera, and 414 species of angiosperms (n = 376) and gymnosperms (n = 38). We show that the prevalence of groundwater use by vegetation (defined as the number of samples out of a universe of plant samples reported to have groundwater contribution to xylem water) is 37% (95% confidence interval, 28–46%). This is across 162 sites and 12 terrestrial biomes (89% of heterogeneity explained; Q-value = 1235; P < 0.0001). However, the magnitude of groundwater source contribution to the xylem water mixture (defined as the proportion of groundwater contribution in xylem water) is limited to 23% (95% CI, 20–26%; 95% prediction interval, 3–77%). Spatial analysis shows that the magnitude of groundwater source contribution increases with aridity. Our results suggest that while groundwater influence is globally prevalent, its proportional contribution to the total terrestrial transpiration is limited.
A De Novo Nonsense Mutation in MAGEL2 in a Patient Initially Diagnosed as Opitz-C: Similarities Between Schaaf-Yang and Opitz-C Syndromes
Authors: Urreizti Roser , Cueto-Gonzalez Anna Maria , Franco-Valls Héctor , Mort-Farre Sílvia , Roca-Ayats Neus , Ponomarenko Julia , Cozzuto Luca , Company Carlos , Bosio Mattia , Ossowski Stephan , Montfort Magda , Hecht Jochen , Tizzano Eduardo F. , Cormand Bru , Vilageliu Lluïsa , Opitz John M. , Neri Giovanni , Grinberg Daniel , Balcells Susana 
Published: March 2017

AbstractOpitz trigonocephaly C syndrome (OTCS) is a rare genetic disorder characterized by craniofacial anomalies, variable intellectual and psychomotor disability, and variable cardiac defects with a high mortality rate. Different patterns of inheritance and genetic heterogeneity are known in this syndrome. Whole exome and genome sequencing of a 19-year-old girl (P7), initially diagnosed with OTCS, revealed a de novo nonsense mutation, p.Q638*, in the MAGEL2 gene. MAGEL2 is an imprinted, maternally silenced, gene located at 15q11-13, within the Prader-Willi region. Patient P7 carried the mutation in the paternal chromosome. Recently, mutations in MAGEL2 have been described in Schaaf-Yang syndrome (SHFYNG) and in severe arthrogryposis. Patient P7 bears resemblances with SHFYNG cases but has other findings not described in this syndrome and common in OTCS. We sequenced MAGEL2 in nine additional OTCS patients and no mutations were found. This study provides the first clear molecular genetic basis for an OTCS case, indicates that there is overlap between OTCS and SHFYNG syndromes, and confirms that OTCS is genetically heterogeneous. Genes encoding MAGEL2 partners, either in the retrograde transport or in the ubiquitination-deubiquitination complexes, are promising candidates as OTCS disease-causing genes.
Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus
Authors: Murata Kazuyoshi , Zhang Qinfen , Gerardo Galaz-Montoya Jesús , Fu Caroline , Coleman Maureen L. , Osburne Marcia S. , Schmid Michael F. , Sullivan Matthew B. , Chisholm Sallie W. , Chiu Wah 
Published: March 2017

AbstractMarine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events. Subtomogram classification and averaging revealed three main conformations characterized by different angles between the phage tail and the cell surface. Namely, phage tails were (i) parallel to, (ii) ~45 degrees to, or (iii) perpendicular to the cell surface. Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. We also observed density beyond the tail tip in vertically-oriented phages that had penetrated the cell wall, capturing the final stage of adsorption. Together, our data provide a quantitative characterization of the orientation of phages as they adsorb onto cells, and suggest that cyanophages that abut their cellular targets are only transiently in the “perpendicular” orientation required for successful infection.
Ibuprofen results in alterations of human fetal testis development
Authors: Ben Maamar Millissia , Lesné Laurianne , Hennig Kristin , Desdoits-Lethimonier Christèle , Kilcoyne Karen R. , Coiffec Isabelle , Rolland Antoine D. , Chevrier Cécile , Kristensen David M. , Lavoué Vincent , Antignac Jean-Philippe , Le Bizec Bruno , Dejucq-Rainsford Nathalie , Mitchell Rod T. , Mazaud-Guittot Séverine , Jégou Bernard 
Published: March 2017

AbstractAmong pregnant women ibuprofen is one of the most frequently used pharmaceutical compounds with up to 28% reporting use. Regardless of this, it remains unknown whether ibuprofen could act as an endocrine disruptor as reported for fellow analgesics paracetamol and aspirin. To investigate this, we exposed human fetal testes (7–17 gestational weeks (GW)) to ibuprofen using ex vivo culture and xenograft systems. Ibuprofen suppressed testosterone and Leydig cell hormone INSL3 during culture of 8–9 GW fetal testes with concomitant reduction in expression of the steroidogenic enzymes CYP11A1, CYP17A1 and HSD17B3, and of INSL3. Testosterone was not suppressed in testes from fetuses younger than 8 GW, older than 10–12 GW, or in second trimester xenografted testes (14–17 GW). Ex vivo, ibuprofen also affected Sertoli cell by suppressing AMH production and mRNA expression of AMH, SOX9, DHH, and COL2A1. While PGE2 production was suppressed by ibuprofen, PGD2 production was not. Germ cell transcripts POU5F1, TFAP2C, LIN28A, ALPP and KIT were also reduced by ibuprofen. We conclude that, at concentrations relevant to human exposure and within a particular narrow ‘early window’ of sensitivity within first trimester, ibuprofen causes direct endocrine disturbances in the human fetal testis and alteration of the germ cell biology.
Albedo feedbacks to future climate via climate change impacts on dryland biocrusts
Authors: Rutherford William A. , Painter Thomas H. , Ferrenberg Scott , Belnap Jayne , Okin Gregory S. , Flagg Cody , Reed Sasha C. 
Published: March 2017

AbstractDrylands represent the planet’s largest terrestrial biome and evidence suggests these landscapes have large potential for creating feedbacks to future climate. Recent studies also indicate that dryland ecosystems are responding markedly to climate change. Biological soil crusts (biocrusts) ‒ soil surface communities of lichens, mosses, and/or cyanobacteria ‒ comprise up to 70% of dryland cover and help govern fundamental ecosystem functions, including soil stabilization and carbon uptake. Drylands are expected to experience significant changes in temperature and precipitation regimes, and such alterations may impact biocrust communities by promoting rapid mortality of foundational species. In turn, biocrust community shifts affect land surface cover and roughness—changes that can dramatically alter albedo. We tested this hypothesis in a full-factorial warming (+4 °C above ambient) and altered precipitation (increased frequency of 1.2 mm monsoon-type watering events) experiment on the Colorado Plateau, USA. We quantified changes in shortwave albedo via multi-angle, solar-reflectance measurements. Warming and watering treatments each led to large increases in albedo (>30%). This increase was driven by biophysical factors related to treatment effects on cyanobacteria cover and soil surface roughness following treatment-induced moss and lichen mortality. A rise in dryland surface albedo may represent a previously unidentified feedback to future climate.