bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site‐associated DNA sequencing
Authors: Ren Guangpeng , Mateo Rubén G. , Liu Jianquan , Suchan Tomasz , Alvarez Nadir , Guisan Antoine , Conti Elena , Salamin Nicolas 
Published: October 2016

Summary

The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species’ spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs).

Genomic data were obtained for 293 samples of P. tibetica using restriction site‐associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges.

Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes.

These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.
Sonifying science: listening to cancer
Authors: Ihde Don 
Published: October 2016

AbstractAs a long‐time scholar of science and art practices, I look particularly at the role of tools and instruments which make these practices possible. I note that science, historically, has favoured visualist imaging, but art, particularly in performance modes, often uses acoustic imaging. Early modern science was dominantly optical in instrumentation, but uses of optics often preceded science use in early modern times. In late modern times, much more complex instrumentation often originated in the sciences, but artists frequently adapted to acoustic practices. Sonifying science, from imaging space phenomena to medical phenomena, is traced here, focusing upon medical sonification in detecting cancers.
Postcanine microstructure in Cricodon metabolus, a Middle Triassic gomphodont cynodont from south‐eastern Africa
Authors: Hendrickx Christophe , Abdala Fernando , Choiniere Jonah 
Published: October 2016

AbstractCricodon metabolus is a trirachodontid cynodont from the Anisian (Middle Triassic) of eastern and southern Africa. It has labiolingually expanded (gomphodont) postcanines but also a sectorial tooth in the last postcanine locus. In this paper, we examine the crown microstructure of isolated sectorial and gomphodont postcanines belonging to the holotype specimen of this taxon using scanning electron microscopy. The enamel of both teeth is prismless and composed of discontinuous columnar divergence units, supporting the consistent presence of synapsid columnar enamel in cynognathians. Abundant tubules and numerous irregularly spaced incremental lines are also visible in the enamel and dentine layers in each tooth. This study reveals that the enamel thickness varies along the tooth row in Cricodon as the enamel layer of the gomphodont postcanines is 11.5 times thicker than that of the sectorial crown. It is likely that this difference reflects occlusal stresses and fewer replacements in gomphodont postcanines relative to sectorial teeth. Approximately 100 incremental growth lines of von Ebner are present in the dentine layer, indicating that the deposition of the dentine by odontoblasts occurred for three months before the animal's death.
What The Tortoise Has To Say About Diachronic Rationality
Authors: Valaris Markos 
Published: October 2016

AbstractEven if you believe just what you rationally ought to believe, you may be open to rational criticism if you do so ‘for the wrong reasons’, as we say. Some have thought that this familiar observation supports the idea that there are diachronic norms of epistemic rationality – namely, norms of good reasoning. Partly drawing upon Carroll's story of Achilles and the Tortoise, this article criticises this line of thought on the grounds that it rests on a mistaken conception of inference.
Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application
Authors: Scheben Armin , Batley Jacqueline , Edwards David 
Published: October 2016

SummaryIn the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high‐throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping‐by‐sequencing (GBS) methods include over a dozen reduced‐representation sequencing (RRS) approaches and at least four whole‐genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best‐suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker‐assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small‐ to moderate‐sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost‐effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost‐effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
Orbital pacing of the Early Jurassic carbon cycle, black‐shale formation and seabed methane seepage
Authors: Xu Weimu , Ruhl Micha , Hesselbo Stephen P. , Riding James B. , Jenkyns Hugh C. 
Published: October 2016

AbstractThe Early Jurassic (ca 201 to 174 Ma) was marked by a series of rapid perturbations in climate, the environment and global geochemical cycles, which have been linked to volcanic outgassing and the release of biogenic or thermogenic methane into the ocean–atmosphere system. The state of the global carbon cycle and prevailing climatic and environmental conditions that existed at this time are, however, poorly constrained. Here, mudrocks of the Lower Sinemurian Arietites bucklandi ammonite Biozone at coastal exposures at Kilve, Somerset, UK, have been studied. This succession includes laminated organic‐rich black shales, which are present throughout the Bristol Channel Basin, and coincides with a 2 to 3‰ negative carbon‐isotope excursion, distinct changes in inferred land vegetation and abundant marine prasinophytes (green algae). The event itself does not represent a single perturbation of the regional environment, but follows in a sequence of eccentricity‐modulated, precession‐paced perturbations that occur throughout the preceding Hettangian stage, with the periodic formation of organic‐rich laminated black shales in the Bristol Channel Basin. However, the Early Sinemurian event studied herein is more extreme in nature, with sedimentary total organic carbon values of 5 to 11% persisting over about 2 m, representing ca 100 kyr, possibly in phase with short (ca 100 kyr) and long (ca 405 kyr) eccentricity forcing. The formation of methane‐seep carbonate‐cemented mounds took place relatively soon after the deposition of laminated black shales. Biogenic methane probably formed in response to microbial methanogenesis in the organic‐rich black shale, which was subsequently channelled to the sediment–water interface approximately 5 m above the source bed, and ca 200 kyr after cessation of formation of the black shale.
Three‐dimensional seismic characterization of a complex sediment drift in the South China Sea: Evidence for unsteady flow regime
Authors: Sun Qiliang , Cartwright Joe , Lüdmann Thomas , Wu Shiguo , Yao Genshun 
Published: October 2016

AbstractThis study describes a previously unobserved reflection seismic configuration comprising a honeycomb planform and a repeated erosion/infill cross‐section, based on high‐resolution three‐dimensional/two‐dimensional seismic data and bathymetric data. The honeycomb structures cover an area of more than 5000 km2 and are developed within the Late Miocene to recent deep‐water sediments of the north‐western South China Sea. Linear erosional troughs up to 10 km long and 1 km wide are widely developed in this area, are intimately related to the particular seismic configuration and interpreted to represent a new type of sediment drift that is caused by unsteady bottom current regimes operating since the Late Miocene. The unsteady bottom current regimes are suggested to be triggered by irregular seabed morphologies. Considerable sea‐floor topography was generated as a direct result of tectonic movements in the area since the Late Miocene, and this topography then influenced the pathways of strong bottom currents. This study highlights that: (i) an unsteady bottom current regime can be laterally extensive and persist for millions of years; (ii) structurally controlled sea‐floor relief plays an important role in controlling the depositional pattern; and (iii) the bottom currents were active since the Late Miocene, flowing from the south‐east through the Xisha–Guangle Gateway and crossing the honeycomb structure zone. This study documents a new style of drift and will help to improve current knowledge of palaeoceanography and understanding of the South China Sea deep‐water circulation which is at present still poorly understood.
Transplantation of organs from deceased donors with meningitis and encephalitis: a UK registry analysis
Authors: Trotter Patrick B. , Robb Matthew , Hulme William , Summers Dominic M. , Watson Christopher J. E. , Bradley J. Andrew , Neuberger James 
Published: October 2016

AbstractBackgroundDeceased organ donors, where the cause of death is meningitis or encephalitis, are a potential concern because of the risks of transmission of a potentially fatal infection to recipients.MethodsUsing the UK Transplant Registry, a retrospective cohort analysis of deceased organ donors in the UK was undertaken to better understand the extent to which organs from deceased donors with meningitis and/or encephalitis (M/E) (of both known and unknown cause) have been used for transplantation, and to determine the associated recipient outcomes.ResultsBetween 2003 and 2015, 258 deceased donors with M/E were identified and the causative agent was known in 188 (72.9%). These donors provided 899 solid organs for transplantation (455 kidneys and 444 other organs). The only recorded case of disease transmission was from a donor with encephalitis of unknown cause at time of transplantation who transmitted a fatal nematode infection to 2 kidney transplant recipients. A further 3 patients (2 liver and 1 heart recipient) died within 30 days of transplantation from a neurological cause (cerebrovascular accident) with no suggestion of disease transmission. Overall, patient and graft survival in recipients of organs from donors with M/E were similar to those for all other types of deceased organ donor.ConclusionDonors dying with M/E represent a valuable source of organs for transplantation. The risk of disease transmission is low but, where the causative agent is unknown, caution is required.
Norovirus infection in solid organ transplant recipients: a single‐center retrospective study
Authors: Lee Lauren Y. , Ladner Daniela P. , Ison Michael G. 
Published: October 2016

AbstractBackgroundNorovirus (NoV) is gaining recognition as an important cause of diarrhea among solid organ transplant (SOT) recipients, but existing studies have been limited by a small sample size.MethodsWe conducted a retrospective study of all adult SOT recipients diagnosed with NoV between 2006 and 2013 and compared their data to that of adult SOT recipients with diarrhea who tested negative for NoV during that time.ResultsA total of 192 patients with diarrhea had stool NoV testing as part of their work‐up during the study period; of these patients, 35% (67) tested positive for NoV. Of patients with diarrhea without NoV, Clostridium difficile (25%) and cytomegalovirus (12%) were the most commonly identified infectious cause of diarrhea. Diarrheal duration was significantly protracted in NoV patients, with an average of 241 days vs 75 days in the control group (P=.0007). One patient death and 2 graft failures were related to the NoV illness within the first month after the onset of diarrhea, and 30% of NoV patients had a ≥20% increase in creatinine within 1 year of diagnosis. These outcomes did not differ significantly from those of SOT patients with diarrhea in the non‐NoV group.ConclusionsNoV is a common cause of diarrhea among SOT recipients at our institution and is responsible for a very prolonged course of chronic diarrhea.
Combined analysis of cross‐reacting antibodies anti‐β1AR and anti‐B13 in advanced stages of Chagas heart disease
Authors: Rodeles Luz M. , Vicco Miguel H. , Bontempi Iván A. , Siano Alvaro , Tonarelli Georgina , Bottasso Oscar A. , Arias Pablo , Marcipar Iván S. 
Published: October 2016

AbstractObjectiveAutoantibodies cross‐reacting with the β1 adrenergic receptor (anti‐β1AR and anti‐p2β) and cardiac myosin antigens (anti‐B13) have been related to the pathogenesis of chronic Chagas heart disease (CCHD). Studies exploring their levels in different stages are scarce. We aimed to evaluate the relationship of these autoantibodies with the clinical profile of chronic patients, especially regarding their classificatory accuracy in severe presentation with heart failure.Methods and resultsWe conducted a cross‐sectional study of 155 T. cruzi‐seropositive patients and 26 age‐ and gender‐matched healthy controls. They were categorised in three stages of CCHD. Serum antibodies were measured by specific immunoassays. Symptomatic individuals showed increased levels of anti‐β1AR and anti‐B13, while anti‐p2β antibodies were similar between groups. A composite logistic regression model including anti‐B13, anti‐β1AR antibody levels and age was able to predict systolic heart failure yielding an area under the curve of 83% (sensitivity of 67% and specificity of 89%).ConclusionsIn our study, anti‐β1AR and anti‐B13 antibodies were higher in individuals with chronic Chagas heart disease stage III, mainly in those with dilated cardiomyopathy associated with systolic heart failure. Logistic regression analysis showed that both antibodies were good predictors of severe CCHD. As well as being involved in disease progression, anti‐β1AR and anti‐B13 antibodies may be used as a serum marker of poor prognosis in terms of heart compromise.
IMAGING DIAGNOSIS—ULTRASONOGRAPHIC APPEARANCE OF SKELETAL MUSCLE METASTASES IN A DOG WITH HEMANGIOSARCOMA
Authors: Fabbi Martina , Di Palma Stefano , Manfredi Sabrina , Gnudi Giacomo , Miduri Francesca , Daga Eleonora , Melis Gabriele Costantino , Bianchi Ezio , Voccia Simone , Volta Antonella 
Published: October 2016

AbstractA 13‐year‐old spayed female German shepherd dog was presented for acute onset of lethargy, anorexia, and disseminated erythematous skin lesions. Thoracic radiographs and abdominal ultrasonographic findings were consistent with metastatic hemangiosarcoma. Multiple, ill‐defined, irregularly shaped hypoechoic nodules were also detected within the thoracic and abdominal wall. Hemangiosarcoma metastases to the skeletal muscle were confirmed based on histopathological examination. Multivisceral involvement was also confirmed by necropsy. Metastatic neoplasia should be considered as a differential diagnosis for dogs with ill‐defined, irregular, hypoechoic, intramuscular nodules.
Plasticity in mitochondrial cristae density allows metabolic capacity modulation in human skeletal muscle
Authors: Nielsen Joachim , Gejl Kasper D. , Hey‐Mogensen Martin , Holmberg Hans‐Christer , Suetta Charlotte , Krustrup Peter , Elemans Coen P. H. , Ørtenblad Niels 
Published: October 2016

Key points
In human skeletal muscles, the current view is that the capacity for mitochondrial energy production, and thus endurance capacity, is set by the mitochondria volume.
However, increasing the mitochondrial inner membrane surface comprises an alternative mechanism for increasing the energy production capacity.
In the present study, we show that mitochondrial inner membranes in leg muscles of endurance‐trained athletes have an increased ratio of surface per mitochondrial volume.
We show a positive correlation between this ratio and whole body oxygen uptake and muscle fibre mitochondrial content.
The results obtained in the present study help us to understand modulation of mitochondrial function, as well as how mitochondria can increase their oxidative capacity with increased demand.
AbstractMitochondrial energy production involves the movement of protons down a large electrochemical gradient via ATP synthase located on the folded inner membrane, known as cristae. In mammalian skeletal muscle, the density of cristae in mitochondria is assumed to be constant. However, recent experimental studies have shown that respiration per mitochondria varies. Modelling studies have hypothesized that this variation in respiration per mitochondria depends on plasticity in cristae density, although current evidence for such a mechanism is lacking. In the present study, we confirm this hypothesis by showing that, in human skeletal muscle, and in contrast to the current view, the mitochondrial cristae density is not constant but, instead, exhibits plasticity with long‐term endurance training. Furthermore, we show that frequently recruited mitochondria‐enriched fibres have significantly increased cristae density and that, at the whole‐body level, muscle mitochondrial cristae density is a better predictor of maximal oxygen uptake rate than muscle mitochondrial volume. Our findings establish an elevating mitochondrial cristae density as a regulatory mechanism for increasing metabolic power in human skeletal muscle. We propose that this mechanism allows evasion of the trade‐off between cell occupancy by mitochondria and other cellular constituents, as well as improved metabolic capacity and fuel catabolism during prolonged elevated energy requirements.
A Novel Fluorescence Resonance Energy Transfer-Based Screen in High-Throughput Format To Identify Inhibitors of Malarial and Human Glucose Transporters
Authors: Kraft Thomas E. , Heitmeier Monique R. , Putanko Marina , Edwards Rachel L. , Ilagan Ma Xenia G. , Payne Maria A. , Autry Joseph M. , Thomas David D. , Odom Audrey R. , Hruz Paul W. 
Published: October 2016

ABSTRACT

The glucose transporter PfHT is essential to the survival of the malaria parasite
Plasmodium falciparum
and has been shown to be a druggable target with high potential for pharmacological intervention. Identification of compounds against novel drug targets is crucial to combating resistance against current therapeutics. Here, we describe the development of a cell-based assay system readily adaptable to high-throughput screening that directly measures compound effects on PfHT-mediated glucose transport. Intracellular glucose concentrations are detected using a genetically encoded fluorescence resonance energy transfer (FRET)-based glucose sensor. This allows assessment of the ability of small molecules to inhibit glucose uptake with high accuracy (Z′ factor of >0.8), thereby eliminating the need for radiolabeled substrates. Furthermore, we have adapted this assay to counterscreen PfHT hits against the human orthologues GLUT1, -2, -3, and -4. We report the identification of several hits after screening the Medicines for Malaria Venture (MMV) Malaria Box, a library of 400 compounds known to inhibit erythrocytic development of
P. falciparum
. Hit compounds were characterized by determining the half-maximal inhibitory concentration (IC
50
) for the uptake of radiolabeled glucose into isolated
P. falciparum
parasites. One of our hits, compound MMV009085, shows high potency and orthologue selectivity, thereby successfully validating our assay for antimalarial screening.
Randomized, Open-Label Study of the Pharmacokinetics and Safety of Oral and Intravenous Administration of Omadacycline to Healthy Subjects
Authors: Sun Haiying , Ting Lillian , Machineni Surendra , Praestgaard Jens , Kuemmell Andreas , Stein Daniel S. , Sunkara Gangadhar , Kovacs Steven J. , Villano Stephen , Tanaka S. Ken 
Published: October 2016

ABSTRACT

Omadacycline is a first-in-class aminomethylcycline antibiotic with microbiological activity against Gram-positive and Gram-negative aerobes and anaerobes and atypical bacteria that is being developed for the treatment of acute bacterial skin and skin structure infections (ABSSSI) and community-acquired bacterial pneumonia (CABP). The bioavailability of a phase 3 tablet formulation relative to that obtained via intravenous (i.v.) administration (and of other oral formulations relative to that of the phase 3 tablet) was investigated in an open-label, randomized, four-period, crossover study with healthy subjects age 18 to 50 years. Subjects received omadacycline at 100 mg i.v., 300 mg orally as two different tablet formulations with different dissolution profiles, and 300 mg as an oral solution. Plasma omadacycline concentrations were determined using a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Twenty of 24 subjects completed all treatment periods. The two tablet formulations produced equivalent total exposures. The phase 3 tablet produced an exposure equivalent to that of the 100-mg i.v. dose, with a geometric mean ratio (90% confidence intervals [CI]) for area under the concentration-time curve from 0 h to infinity [AUC
∞
]) of 1.00 (0.93, 1.07). The absolute bioavailability of the tablets was approximately 34.5%. Intersubject variability was consistent among the oral formulations (∼20 to 25%). Single oral and i.v. doses of omadacycline were well tolerated; three subjects experienced mild adverse events (dizziness, nausea, and vomiting) that resolved without intervention. A 300-mg dose of the tablet formulation of omadacycline intended for use in phase 3 studies produced a total exposure equivalent to that of a 100-mg i.v. dose.