bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptome‐based analytical workflow for identifying loci for species diagnosis: a case study with Bactrocera fruit flies (Diptera: Tephritidae)
Authors: Krosch Matt N , Schutze Mark K , Strutt Francesca , Clarke Anthony R , Cameron Stephen L 
Published: November 2017

AbstractDevelopment of novel molecular methods for accurate and economical identification of species has become critical both for pure biological research and for a wide range of applied areas. The most widely used current molecular diagnostic tool, the mitochondrial cytochrome c oxidase subunit 1 gene (COI), the so‐called DNA barcode, has been highly criticised and is known to be ineffective at distinguishing species in many groups. Alternative markers are needed to circumvent these issues and provide diagnosticians with a greater range of tools for making accurate identifications. To address this, we describe here a novel analytical workflow for diagnostic marker development that utilises near‐genomic‐scale data to search for potential informative loci. The workflow takes advantage of orthologous gene databases, in combination with tests of phylogenetic resolution, and benchmarking of nucleotide variation against COI, to determine putative loci that might outperform COI. We use transcriptomes of 14 tephritid fruit flies and especially the taxonomically complex genus Bactrocera, as a case study. Of 1646 orthologues searched, our workflow retained a total of five loci following our conservative filtering strategy. One locus, POP4, had strong potential as a novel diagnostic marker for Bactrocera fruit flies. POP4 discriminates most species in the training set of taxa, but like COI fails to separate the sibling species Bactrocera tryoni and Bactrocera neohumeralis. Further validation of this potential new marker against a broader taxonomic sample is ongoing. We advocate that this simple and efficient workflow is, with minor modification, customisable for diagnostic development in almost any taxonomic group.
Categorization of the pelvic limb standing posture in nine breeds of dogs
Authors: Sabanci S. S. , Ocal M. K. 
Published: November 2017

SummaryThe objective of the study was to categorize objectively nine breeds of healthy dogs according to pelvic limb standing posture. A total of 135 dogs from different breeds were used and the standing angles of the hip, stifle, and tarsal joints, together with the percentages of the greater trochanter, patella and tuber calcanei heights, with respect to crista iliaca height, were used as discriminant variables for the categorization of pelvic limb posture. All included breeds were allocated to three groups of the standing pelvic limb posture. The best discriminant variables between the three groups were the percentage of patellar height, and the standing angles of the stifle and tarsal joints. German shepherds, Anatolian shepherds, golden retrievers, Rottweilers, Belgian Malinois and Dobermann pinschers were well separated between 89% and 100% success rate for the categorization. The minimal success rate was determined in Berner sennenhunds as the ratio of 75%. It was also determined that Dobermann pinschers had the straightest pelvic limbs, while German shepherds had the most angulated pelvic limbs. Further studies are required to document the impact of postural differences in active and passive structure diseases of the locomotor system of the pelvic limb among dog breeds.
Deletion of the EGF receptor in vascular smooth muscle cells prevents chronic angiotensin II‐induced arterial wall stiffening and media thickening
Authors: Schreier B. , Hünerberg M. , Mildenberger S. , Rabe S. , Bethmann D. , Wickenhauser C. , Gekle M. 
Published: November 2017

AbstractAimIn vivo vascular smooth muscle cell (VSMC) EGF receptor (EGFR) contributes to acute angiotensin II (AII) effects on vascular tone and blood pressure. The ubiquitously expressed EGFR has been implicated in vascular remodelling preceding end‐organ damage by pharmacological inhibition, and AII signalling in cultured vascular cells is partly EGFR‐dependent. However, the role of VSMC‐EGFR in vivo during AII‐induced pathophysiological processes is not known.MethodsThis study assesses the in vivo relevance of VSMC‐EGFR during chronic AII challenge without further stressors, using a mouse model with inducible, VSMC‐specific EGFR knock out (VSMC‐EGFR‐KO). In these mice functional and structural vascular, renal and cardiac effects or biomarkers were investigated in vivo and ex vivo.ResultsVascular smooth muscle cell‐EGFR‐KO prevented AII‐induced media hypertrophy of mesenteric arteries, renal arterioles and the aorta, VSMC ERK1/2‐phosphorylation as well as the impairment of vascular compliance. Furthermore, induction of vascular fibrosis, creatinineamia, renal interstitial fibrosis as well as the increase in fractional water excretion was prevented. AII‐induced increase in systolic blood pressure was mitigated. By contrast, endothelial dysfunction, induction of vascular inflammatory marker mRNA and albuminuria were not inhibited. Cardiac and cardiomyocyte hypertrophy were also not prevented by VSMC‐EGFR‐KO.ConclusionVascular smooth muscle cell‐EGFRs are relevant for pathological AII action in vivo. Our data show in vivo and ex vivo the necessity of VSMC‐EGFR for AII‐induced structural and functional vascular remodelling, not including endothelial dysfunction. Hereby, VSMC‐EGFR gains importance for complete AII‐induced renal end‐organ damage succeeding vascular remodelling.
Fibrin thrombi in deceased donor kidneys: Prevalence and influence on graft function and graft survival in transplanted patients
Authors: Hansen Ditte , Rørvig Sara , Andersen Claus B. , Sørensen Søren S. 
Published: November 2017

Fibrin thrombi (FT) are occasionally found in the pre‐implantation biopsy of kidneys from deceased donors. The aim of this study was to monitor the prevalence and answer the question whether FT has any impact on future graft function in a Danish patient cohort. We looked for FT in all donor kidney biopsies taken at the time of renal transplantation in a Danish transplantation unit during a 10‐year period. Every recipient transplanted with a FT donor kidney (n = 15) were matched with up to five control recipients (n = 69), and graft function and graft survival were assessed. FT was present in 3% of the transplanted donor kidneys. Graft function was reduced in the FT group 6 months after transplantation (median estimated glomerular filtration rate (eGFR): 29 mL/min vs 46 mL/min; p = 0.017), but at 12 months, an apparent difference did not reach statistical significance. More patients were on dialysis in the FT group after 12 months compared with the control group (27% vs 6%; p = 0.049). In conclusion, FT in donor kidney biopsies at time of transplantation is a risk factor for the development of reduced renal function during the first year of transplantation.
The value of microscopic‐observation drug susceptibility assay in the diagnosis of tuberculosis and detection of multidrug resistance
Authors: Sertel Şelale Denİz , Uzun Meltem 
Published: November 2017

Inexpensive, rapid, and reliable tests for detecting the presence and drug susceptibility of Mycobacterium tuberculosis complex (MTBC) are urgently needed to control the transmission of tuberculosis. In this study, we aimed to assess the accuracy and speed of the microscopic‐observation drug susceptibility (MODS) assay in the identification of MTBC and detection of multidrug resistance. Sputum samples from patients suspected to have tuberculosis were simultaneously tested with MODS and conventional culture [Löwenstein‐Jensen (LJ) culture, BACTEC MGIT™ 960 (MGIT) system], and drug susceptibility testing (MGIT system) methods. A total of 331 sputum samples were analyzed. Sensitivity and specificity of MODS assay for detection of MTBC strains were 96% and 98.8%, respectively. MODS assay detected multidrug resistant MTBC isolates with 92.3% sensitivity and 96.6% specificity. Median time to culture positivity was similar for MGIT (8 days) and MODS culture (8 days), but was significantly longer with LJ culture (20 days) (p < 0.0001 for both comparisons). Median time to availability of the susceptibility results was significantly (p < 0.0001) shorter with MODS assay (8 days) than MGIT system (20 days). In conclusion, MODS is an inexpensive and rapid test with good performance characteristics for direct diagnosis of tuberculosis and detection of multidrug resistance.
Development of furnished cages re‐using conventional cages for laying hens: Behaviour, physical condition and productivity
Authors: Shimmura Tsuyoshi , Maekawa Naoko , Hirahara Satoshi , Tanaka Toshio , Appleby Michael C. 
Published: November 2017

AbstractFurnished cages for laying hens have advantages in allowing normal behaviors and maintaining productivity. As the cost of introduction is a barrier for farms, we developed furnished cages that re‐use conventional cages. To determine the minimum and functional cage design, we compared six designs, combinations of two floor designs (artificial turf or wire cage floor) and three screening designs in the integrated area (no screening, one entrance side or four sides). In total, 144 hens were used, and we measured behavior, physical condition and productivity. Comparing the floors, the percentages of hens performing dust‐bathing and laying eggs in the integrated area were higher in cages with turf than wire floor (P < 0.05 for both). Comparing the screening, dust‐bathing, litter‐exploring and active behavior tended to be more frequent in cages with the integrated area screened on one side than four sides. Feather damage was lower in cages with the integrated area screened on one side than with no screening (P < 0.05). These results suggest that the cage design with an integrated area with artificial turf floor, screened on one side, was effective for furnished cages that re‐use conventional cages.
Measuring automatic value orientations: The Achievement–Benevolence Implicit Association Test
Authors: Dentale Francesco , Vecchione Michele , Gebauer Jochen E. , Barbaranelli Claudio 
Published: November 2017

The construct and criterion validity of an Implicit Association Test designed to rate the importance ascribed to Achievement–Benevolence oriented goals (AB‐IAT) according to Schwartz's model were investigated. In a first study (N = 113), the AB‐IAT and three other value‐IATs (Power–Universalism, Security–Self‐direction, and Tradition–Stimulation) were administered along with the corresponding self‐report scales. The AB‐IAT showed the following: (1) an adequate internal consistency; (2) a small correlation and a different pattern of means with respect to the corresponding self‐report scale; (3) a pattern of correlations with the other value‐IATs that is consistent with Schwartz's model. In a second study (N = 99), results showed that (1) in contrast to self‐report measures of values, the AB‐IAT appeared unrelated to social desirability; (2) the AB‐IAT was significantly correlated with an actual behaviour expressing Benevolence values; (3) in accordance with a double dissociation pattern of prediction, implicit and explicit values are best predictors of actual and self‐rated behaviours, respectively. Overall, results of the studies support the construct and criterion validity of the AB‐IAT. Moreover, they provide a first support for the generalizability of Schwartz's model in the realm of implicit social cognition, and for the applicability of dual‐process models in value research.
Multiple role of 3‐mercaptopyruvate sulfurtransferase: antioxidative function, H2S and polysulfide production and possible SOx production
Authors: Nagahara Noriyuki 
Published: November 2017

Rat 3‐mercaptopyruvate sulfurtransferase (MPST) is a 32 808 Da simple protein. Cys247 is a catalytic site, and Cys154 and Cys263 are on the enzyme surface. MPST is found in all tissues, particularly in the kidneys, although the localization of its activity differs in each tissue. In this review, four functions of MPST are reviewed: (i) antioxidative function: Cys247 is redox‐sensitive and serves as a redox‐sensing switch. It is oxidized to cysteine sulfenate, which has a low redox potential, upon which the enzyme is inactivated. Then, reduced thioredoxin (Trx) with a reducing system (Trx reductase and NADPH) reduces the sulfenate to restore activity; meanwhile, Cys154 and Cys263 form an intermolecular disulfide bond, which serves as another redox‐sensing switch. Consequently, Trx specifically cleaves the intermolecular disulfide bond by converting it from the inactive form (dimer) to the active form (monomer). (ii) Hydrogen sulfide and polysulfide production: hydrogen sulfide is produced via reduction of the persulfurated sulfur‐acceptor substrate by reduced Trx or Trx with a reducing system; as an alternative process, stable polysulfurated or persulfurated Cys247 as a reaction intermediate is reduced by Trx with a reducing system to release hydrogen sulfide and polysulfides. (iii) Possible sulfur oxide production: sulfur oxides (SO, SO2 and SO3) can be produced in the redox cycle of sulfane sulfur formed at the catalytic site Cys247 (Cys–SO−, Cys–SO2− and Cys–SO3−) as reaction intermediates and released by reduced Trx or Trx with a reducing system. (iv) Possible anxiolytic‐like effects: MPST‐knockout mice exhibited anxiolytic‐like effects.
Identification of de novo germline mutations and causal genes for sporadic diseases using trio‐based whole‐exome/genome sequencing
Authors: Jin Zi‐Bing , Li Zhongshan , Liu Zhenwei , Jiang Yi , Cai Xue‐Bi , Wu Jinyu 
Published: November 2017

ABSTRACTWhole‐genome or whole‐exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease‐causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general‐purpose discussion of important issues related to pathogenic gene identification based on trio‐based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio‐based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
The state of European research in tropical biology
Authors: Cayuela Luis , Granzow‐de la Cerda Íñigo , Méndez Marcos 
Published: November 2017

AbstractResearch institutions from the Global North have made significant contributions to the knowledge of tropical ecosystems, but contributions have varied greatly between countries. We show that European nations that share a language, cultural affinity, and/or retain social and political ties with tropical countries (e.g., those with an overseas history) make larger contributions to tropical biological research than countries without these ties. However, exceptions to this pattern demonstrate how science policy agendas can skew the capacity of countries to conduct biological research in the tropics. We conclude that some countries could make a far more important contribution to tropical biological knowledge, but for this to materialize, greater commitment by a country's scientific community is needed, along with better financial and intellectual support from its public administrations.
Promoting Resilience Among African American Girls: Racial Identity as a Protective Factor
Authors: Butler‐Barnes Sheretta T. , Leath Seanna , Williams Amber , Byrd Christy , Carter Rona , Chavous Tabbye M. 
Published: November 2017

This study examines school climate, racial identity beliefs, and achievement motivation beliefs within a cultural‐ecological and risk and resilience framework. Data were drawn from a longitudinal study of 733 (Mage = 14.49) African American adolescent girls. A linear mixed effects model was used to determine if racial identity dimensions moderated the relationship between school climate and achievement motivation beliefs across four waves. Results revealed that racial identity (private regard and racial centrality) and ideology (nationalist) beliefs were associated with higher achievement motivation beliefs over time, while racial centrality and private regard, and a sense of belonging served as protective factors. The findings contribute to the importance of racial identity beliefs and increase the visibility of African American girls.
Giant taxon‐character matrices II: a response to Laing et al. (2017)
Authors: Simões Tiago R. , Caldwell Michael W. , Palci Alessandro , Nydam Randall L. 
Published: November 2017

AbstractThe trend towards big data analyses in evolutionary biology has been observed in phylogenetics via the assembly of giant datasets composed of genomic and phenotypic data. We recently (Simões et al., 2017. Giant taxon‐character matrices: Quality of character constructions remains critical regardless of size. Cladistics 33, 198–219) presented a critique of the phylogenetic character concepts used in current morphological datasets, with the caution that giant datasets did not obviate the empirical requirement of rigor in character construction. Laing et al. (2017. Giant taxon‐character matrices: The future of morphological systematics. Cladistics, https://doi.org/10.1111/cla.12197) have since argued that we had ‘suggested’ that large datasets inherently contain flawed characters, and that we had presented a substandard methodology of phylogenetic analysis. Laing et al. concluded by discussing their approach to phylogenetic signal, total evidence and the inevitability of large datasets. We here reply to Laing et al. by reviewing what we actually wrote regarding dataset size, characters and methodology. We show that Laing et al.'s. central premise is unsupported, thus characterizing a Straw Man argument, and deeply misrepresents our original study. In part two, we discuss total evidence and phylogenetic signal issues raised by Laing et al. that are of major consequence to the appropriate construction of large morphological datasets.
Antibiotics and antibiotic resistance from animal manures to soil: a review
Authors: Xie W.‐Y. , Shen Q. , Zhao F. J. 
Published: November 2017

SummaryThe overuse of veterinary antibiotics in animal production and the subsequent land applications of manures contribute to the elevated antibiotic resistance in the soil environment. To minimize the risk of antibiotic resistance, it is important to understand the fate of antibiotics and the spread of antibiotic resistance genes (ARGs) from animal production systems to soil. In this paper, we review recent studies on veterinary antibiotic use, the concentrations of antibiotics and the abundance and diversity of AGRs in animal manures and in soil that receives manures or manure composts. The mechanisms of ARG dissemination in the environment are also discussed. Although we focus on China where around 3 billion tons of animal manures are produced and more than 84 000 tons of antibiotics are consumed annually in animal production industries, the problem is worldwide. Approximately 58% of the veterinary antibiotics consumed are excreted into the environment, more than half of which end up in the soil. The abundance of ARGs in manures can reach up to 10−1 of the 16S rRNA genes. Applications of manures or manure composts can enrich soil ARGs in at least three ways: (i) by the direct introduction of manure‐derived ARGs, (ii) by elevating the intrinsic soil ARGs and (iii) by imposing a selection of ARGs with the antibiotics in the manures. We also discuss the need for more stringent regulations on the use of veterinary antibiotics and future research directions on the mechanisms of antibiotic resistance and resistance management.Highlights

Soil is a natural reservoir of antibiotics and antibiotic resistance genes (ARGs).
Manure applications introduce antibiotics and enrich soil ARGs through different mechanisms.
Horizontal gene transfer plays an important role in the spread of ARGs from manures.
More stringent regulations are needed to reduce the spread of ARG from animal sources.
6 Hz corneal kindling in mice triggers neurobehavioral comorbidities accompanied by relevant changes in c‐Fos immunoreactivity throughout the brain
Authors: Albertini Giulia , Walrave Laura , Demuyser Thomas , Massie Ann , De Bundel Dimitri , Smolders Ilse 
Published: November 2017

SummaryObjectiveBesides seizures, patients with epilepsy are affected by a variety of cognitive and psychiatric comorbidities that further impair their quality of life. The present study provides an in‐depth characterization of the behavioral alterations induced by 6 Hz corneal kindling. Furthermore, we correlate these behavioral changes to alterations in c‐Fos protein expression throughout the brain following kindling.MethodsAdolescent male Naval Medical Research Institute (NMRI) mice were kindled via repetitive subconvulsive 6 Hz corneal stimulations until they reached the fully kindled state (defined as 10 consecutive generalized seizures). Afterwards we performed an elaborate battery of behavioral tests and we evaluated c‐Fos expression throughout the brain using immunohistochemistry.ResultsFully kindled mice display an abnormal behavioral phenotype, characterized by basal and amphetamine‐induced hyperlocomotion, anhedonia, social withdrawal, and deficits in short‐ and long‐term memory. Moreover, 6 Hz corneal kindling enhances c‐Fos immunoreactivity in the visual, parahippocampal, and motor cortices and the limbic system, whereas c‐Fos+ cells are decreased in the orbital cortex of fully kindled mice.SignificanceThe behavioral outcomes of 6 Hz corneal kindling cluster into 3 main categories: positive symptoms, negative symptoms, and cognitive impairment. These symptoms are accompanied by c‐Fos activation in relevant brain regions once the fully kindled state is established. Based on the face validity of this model, we speculate that 6 Hz corneal kindling can be used to model not only pharmacoresistant limbic seizures, but also several neurobehavioral comorbidities that affect patients with epilepsy.