bluuebunny/crossref_metadata_2025_split huggingface dataset:
Successful Primary Therapy With Posaconazole for Fulminant Progressive Disseminated Histoplasmosis in a Renal Transplant Recipient
Authors: Akram Sami , Sundareshan Vidya , West Bradford , Prakash Vidhya , Bergman Scott , Koirala Janak 
Published: July 2017

Abstract
For severe cases of progressive disseminated histoplasmosis (PDH), Infectious Diseases Society of America recommends treatment with liposomal amphotericin B for 2 weeks followed by itraconazole. In patients who are at risk for renal failure and for renal transplant patients on multiple nephrotoxic medications, there are no alternatives currently in clinical use. Posaconazole has shown promise in the animal experiments and also as salvage therapy in patients who have failed therapy with polyene and azole antifungal agents. Posaconazole has seldom been used as an initial drug for severe cases of PDH. We report a case of a renal transplant patient with severe PDH, on immunosuppressive therapy, successfully treated with posaconazole.
Dual-Energy Computed Tomography in Stroke Imaging: Technical and Clinical Considerations of Virtual Noncontrast Images for Detection of the Hyperdense Artery Sign
Authors: Winklhofer Sebastian , Vittoria De Martini Ilaria , Nern Chrisitian , Blume Iris , Wegener Susanne , Pangalu Athina , Valavanis Antonios , Alkadhi Hatem , Guggenberger Roman 
Published: July 2017

Objective
The technical feasibility of virtual noncontrast (VNC) images from dual-energy computed tomography (DECT) for the detection of the hyperdense artery sign (HAS) in ischemic stroke patients was investigated.

Methods
True noncontrast (TNC) scans of 60 patients either with or without HAS (n = 30 each) were investigated. Clot presence and characteristics were assessed on VNC images from DECT angiography and compared with TNC images. Clot characterization included the level of confidence for diagnosing HAS, a qualitative clot burden score, and quantitative attenuation (Hounsfield unit [HU]) measurements.

Results
Sensitivity, specificity, and accuracy of VNC for diagnosing HAS were 97%, 90%, and 93%, respectively. No significant differences were found regarding the diagnostic confidence (P = 0.18) and clot burden score (P = 0.071). No significant HU differences were found among vessels with HAS in VNC (56 ± 7HU) and TNC (57 ± 8HU) (P = 0.691) images.

Conclusions
Virtual noncontrast images derived from DECT enable an accurate detection and characterization of HAS.
Versatile open software to quantify cardiomyocyte and cardiac muscle contractionin vitroandin vivo
Authors: Sala L. , van Meer B.J. , Tertoolen L.G.J. , Bakkers J. , Bellin M. , Davis R.P. , Denning C. , Dieben M.A.E. , Eschenhagen T. , Giacomelli E. , Grandela C. , Hansen A. , Holman E.R. , Jongbloed M.R. M. , Kamel S.M. , Koopman C.D. , Lachaud Q. , Mannhardt I. , Mol M.P.H. , Orlova V.V. , Passier R. , Ribeiro M.C. , Saleem U. , Smith G.L. , Mummery C.L. , Burton F.L. 
Published: July 2017

AbstractContraction of muscle reflects its physiological state. Methods to quantify contraction are often complex, expensive and tailored to specific models or recording conditions, or require specialist knowledge for data extraction. Here we describe an automated, open-source software tool (MUSCLEMOTION) adaptable for use with standard laboratory and clinical imaging equipment that enables quantitative analysis of normal cardiac contraction, disease phenotypes and pharmacological responses. MUSCLEMOTION allowed rapid and easy measurement of contractility in (i) single cardiomyocytes from primary adult heart and human pluripotent stem cells, (ii) multicellular 2D-cardiomyocyte cultures, 3D engineered heart tissues and cardiac organoids/microtissuesin vitroand (iii) intact hearts of zebrafish and humansin vivo. Good correlation was found with conventional measures of contraction in each system. Thus, using a single method for processing video recordings, we obtained reliable pharmacological data and measures of cardiac disease phenotype in experimental cell- and animal models and human echocardiograms.
Transmission trees on a known pathogen phylogeny: enumeration and sampling
Authors: Hall Matthew , Colijn Caroline 
Published: July 2017

AbstractOne approach to the reconstruction of infectious disease transmission trees from pathogen genomic data has been to use a phylogenetic tree, reconstructed from pathogen sequences, and annotate its internal nodes to provide a reconstruction of which host each lineage was in at each point in time. If only one pathogen lineage can be transmitted to a new host (i.e. the transmission bottleneck is complete), this corresponds to partitioning the nodes of the phylogeny into connected regions, each of which represents evolution in an individual host. These partitions define the possible transmission trees that are consistent with a given phylogenetic tree. However, the mathematical properties of the transmission trees given a phylogeny remain largely unexplored. Here, we describe a procedure to calculate the number of possible transmission trees for a given phylogeny, and we show how to uniformly sample from these transmission trees. The procedure is outlined for situations where one sample is available from each host and trees do not have branch lengths, and we also provide extensions for incomplete sampling, multiple sampling, and the application to time trees in a situation where limits on the period during which each host could have been infected are known. The sampling algorithm is available as an R package (STraTUS).
Gene isoforms as expression-based biomarkers predictive of drug response in vitro
Authors: Safikhani Zhaleh , Thu Kelsie L. , Silvester Jennifer , Smirnov Petr , Lupien Mathieu , Mak Tak W. , Cescon David , Haibe-Kains Benjamin 
Published: July 2017

ABSTRACTBackgroundOne of the main challenges in precision medicine is the identification of molecular features associated to drug response to provide clinicians with tools to select the best therapy for each individual cancer patient. The recent adoption of next-generation sequencing technologies enables accurate profiling of not only gene expression but also alternatively-spliced transcripts in large-scale pharmacogenomic studies. Given that altered mRNA splicing has been shown to be prominent in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery.MethodsTo address the lack of reproducibility of drug sensitivity measurements across studies, we developed a meta-analytical framework combining the pharmacological data generated within the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC). Predictive models are fitted with CCLE RNA-seq data as predictor variables, controlled for tissue type, and combined GDSC and CCLE drug sensitivity values as dependent variables.ResultsWe first validated the biomarkers identified from GDSC and CCLE using an existing pharmacogenomic dataset of 70 breast cancer cell lines. We further selected four drugs with the most promising biomarkers to test whether their predictive value is robust to change in pharmacological assay. We successfully validated 10 isoform-based biomarkers predictive of drug response in breast cancer, including TGFA-001 for the MEK tyrosine kinase inhibitor (TKI) AZD6244, DUOX-001 for the EGFR inhibitor erlotinib, and CPEB4-001 transcript expression associated with lack of sensitivity to paclitaxel.ConclusionThe results of our meta-analysis of pharmacogenomic data suggest that isoforms represent a rich resource for biomarkers predictive of response to chemo- and targeted therapies. Our study also showed that the validation rate for this type of biomarkers is low (<50%) for most drugs, supporting the requirements for independent datasets to identify reproducible predictors of response to anticancer drugs.
The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian CricketLaupala
Authors: Blankers Thomas , Oh Kevin P. , Bombarely Aureliano , Shaw Kerry L. 
Published: July 2017

ABSTRACTPhenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, cross-over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed recombination due to genomic rearrangements, modifier alleles, and intrinsic chromosomal properties may offer a shield against maladaptive gene flow eroding co-adapted gene complexes. Both theoretical and empirical results support this relationship. However, little is known about this relationship in the context of behavioral isolation, where co-evolving signals and preferences are the major hybridization barrier. Here we examine the genomic architecture of recently diverged, sexually isolated Hawaiian swordtail crickets (Laupala). We assemble ade novogenome and generate three dense linkage maps from interspecies crosses. In line with expectations based on the species’ recent divergence and successful interbreeding in the lab, the linkage maps are highly collinear and show no evidence for large-scale chromosomal rearrangements. The maps were then used to anchor the assembly to pseudomolecules and estimate recombination rates across the genome. We tested the hypothesis that loci involved in behavioral isolation (song and preference divergence) are in regions of low interspecific recombination. Contrary to our expectations, a genomic region where a male song QTL co-localizes with a female preference QTL was not associated with particularly low recombination rates. This study provides important novel genomic resources for an emerging evolutionary genetics model system and suggests that trait-preference co-evolution is not necessarily facilitated by locally suppressed recombination.
Unpaid extinction debts for endemic plants and invertebrates as a legacy of habitat loss on oceanic islands
Authors: Otto Rüdiger , Garzón‐Machado Víctor , del Arco Marcelino , Fernández‐Lugo Silvia , de Nascimento Lea , Oromí Pedro , Báez Marcos , Ibáñez Miguel , Alonso María R. , Fernández‐Palacios José María 
Published: July 2017

AbstractAimThe majority of documented extinctions world‐wide in the last four centuries are of species endemic to islands. However, the phenomenon of delayed extinctions as a result of habitat loss has rarely been assessed on oceanic islands. In this study, we tested whether extinction debt (ED), in general, occurs on islands and for which taxonomical groups this phenomenon is most pronounced by assessing ED for multiple endemic taxa and for each of the main altitudinal ecosystems in a well‐studied oceanic archipelago.LocationCanary Islands.MethodsWe characterized habitat preferences for all endemic species of several taxonomic groups (vascular plants, ground and darkling beetles, flies and land snails). Using generalized linear mixed models and available data about habitat distributions, we tested for all taxa and habitat types to determine whether past habitat area better explained current richness of habitat specialists than current habitat area. If so, an extinction debt can be assumed.ResultsFor all five major habitat types and five taxonomic groups studied, present‐day richness of habitat specialists fitted better with past than current habitat area, evidencing habitat‐ and taxon‐specific extinction debts. This pattern was consistent for both long‐lived vascular plants and short‐lived invertebrates. Single island endemics in each taxonomic group showed steeper slopes of the species–area relationship (SAR) compared to archipelago endemics indicating higher sensitivity to habitat loss which might increase sizes of ED.ConclusionDespite differences in species’ generation times, plants and invertebrates showed delayed extinctions after habitat destruction in the Canary Islands. Our SAR approach suggests that a considerable number of Canary Island endemics will eventually become extinct in the future without further habitat loss. The case of the Canary archipelago is probably not unique. Hence, we interpret our results as a warning for island conservationists that the worst of the extinction crisis on oceanic islands might be yet to come. Conservation actions should focus on habitat restoration to attenuate or reverse current extinction processes.
Individual and partner's level of occupation and the association with HbA1c levels in people with Type 2 diabetes mellitus: the Dutch Diabetes Pearl cohort
Authors: Rutte A. , Rauh S. P. , Schram M. T. , Nijpels G. , DeVries J. H. , Holleman F. , Pijl H. , Dekkers O. M. , Özcan B. , Sijbrands E. J. G. , Tack C. J. , Abbink E. J. , de Valk H. W. , Silvius B. , Wolffenbuttel B. H. R. , Stehouwer C. D. A. , Schaper N. C. , Dekker J. M. , Beulens J. W. , Elders P. J. M. , Rutters F. ,   the Diabetes Pearl from the Parelsnoer Initiative
Published: July 2017

AbstractAimsIndividual indicators of socio‐economic status have been associated with glycaemic control in people with Type 2 diabetes, but little is known about the association between partner’s socio‐economic status and HbA1c levels. We therefore examined the cross‐sectional association between individual and partner’s level of occupation on HbA1c levels in people with Type 2 diabetes in the Netherlands.MethodsWe included people with Type 2 diabetes with a partner who were treated in primary, secondary and tertiary care in the Diabetes Pearl cohort. Occupational level was classified according to International Standard Classification of Occupations (ISCO)‐08 skill levels. Linear regression analyses were performed stratified for sex, and corrected for age, recruitment centre and diabetes medication.ResultsIn total, 3257 participants (59.8% men, mean 62.2±9.4 years) were included. For men, having a partner with an intermediate level of occupation was associated with lower HbA1c levels [e.g. ISCO level 3: –2 mmol/mol (95% CI –4;–1) or ‐0.2% (95% CI –0.4;–0.1)], compared with having a partner of the highest occupational level (ISCO level 4). In women, having an unemployed partner was associated with higher HbA1c levels [14 mmol/mol (95% CI 6; 22) or 1.3% (95% CI 0.6; 2.0)], compared with having a partner of the highest occupational level.ConclusionsPartner's occupational status provided additional information on the association between socio‐economic status and HbA1c levels in people with Type 2 diabetes. Women seemed to benefit from a partner with a higher occupational status, while men seemed to benefit from a partner with a lower status. Because of the cross‐sectional nature of the present study, more research is necessary to explore this association.
Effect of sodium‐glucose co‐transporter‐2 inhibitors on impaired ventricular repolarization in people with Type 2 diabetes
Authors: Sato T. , Miki T. , Ohnishi H. , Yamashita T. , Takada A. , Yano T. , Tanno M. , Tsuchida A. , Miura T. 
Published: July 2017

AbstractAimsTo test the hypothesis that treatment with a sodium‐glucose co‐transporter‐2 inhibitor would reverse ventricular repolarization heterogeneity, a predictor of cardiovascular mortality, in people with Type 2 diabetes.MethodsWe retrospectively analysed changes in indices of ventricular repolarization before and after treatment with a sodium‐glucose co‐transporter‐2 inhibitor in 46 people with Type 2 diabetes.ResultsSodium‐glucose co‐transporter‐2 inhibitor treatment reduced HbA1c concentration [62±13 mmol/mol (7.7±1.2%) vs 59±16 mmol/mol (7.5±1.4%)], body weight (77.8±13.9 vs 74.7±12.5 kg) and systolic blood pressure (133±18 vs 126±12 mmHg) in the study participants. Heart rate and QTc interval were not changed by sodium‐glucose co‐transporter‐2 inhibitor treatment, but QTc dispersion was significantly reduced (median, 48.8 vs 44.2 ms). Sodium‐glucose co‐transporter‐2 inhibitor treatment reversed QTc dispersion more in participants who had larger QTc dispersion before the treatment. Changes in systolic blood pressure (Spearman's ρ= 0.319; P=0.031), but not in HbA1c concentration, were correlated with changes in QTc dispersion after sodium‐glucose co‐transporter‐2 inhibitor treatment.ConclusionsThe findings suggest that sodium‐glucose co‐transporter‐2 inhibitor treatment reverses ventricular repolarization heterogeneity in people with Type 2 diabetes, independently of its effect on glycaemic control. The favourable effect on ventricular repolarization heterogeneity could be the mechanism by which empaglifozin reduced cardiovascular events in a recent study.
Colorimetric analysis of soil with flatbed scanners
Authors: Kirillova N. P. , Kemp D. B. , Artemyeva Z. S. 
Published: July 2017

Colour is an important physical property in the characterization of soil type and the description of soil profiles. Quantitative data from spectrophotometers and colorimeters have been used in soil research for this purpose, but semi‐quantitative Munsell colour description remains the main method of soil colour evaluation. Low‐cost digital devices (cameras and scanners) could largely replace the semi‐quantitative assessment of colour by Munsell charts if such devices can be calibrated colorimetrically to provide accurate and reproducible data. Robust application of such tools, however, requires standardized light sources, which precludes the use of digital cameras as viable devices for use in the field. Flatbed scanners, on the other hand, enable 2‐D imaging by a contact method under consistent lighting conditions. Power can be provided to such scanners through a USB port by a laptop computer, so they can be used as viable devices in the field. In this study, we explored the feasibility of using flatbed scanners to derive colorimetrically accurate images and data from a set of 161 soil samples. The efficacy of our approach was tested with two low‐cost scanners, and included analysis of two commercial colour charts, six printed colour charts and three editions of the Munsell Soil Colour chart to assess the optimum methods of colorimetric calibration. For both scanners tested, we found that accurate colour characterization could be achieved for > 95% of the soil samples studied (i.e. with colour errors barely perceptible by the human eye). These results illustrate the merit and efficacy of this rapid and low‐cost approach for soil colour evaluation.HighlightsCan soil colour be measured accurately with commercial scanners?
Scanners can replace semi‐quantitative Munsell chart comparison or spectrophotometers.
With careful calibration, scanners can be used to measure soil colour.
Colour can be measured with an accuracy close to that achievable with spectrophotometers.
The quality of evidence in tablet‐assisted interventions for students with disabilities
Authors: Kim Min Kyung , Park Yujeong , Coleman Mari Beth 
Published: July 2017

AbstractThe purpose of this review is to weigh the evidence of the effectiveness of tablet‐assisted instructions (TAIs) at improving academic outcomes of students with disabilities. An extensive search process with inclusion and exclusion criteria yielded a total of 17 studies to be included in the present study: three group design studies and 14 single‐subject design studies. The quality indicators proposed by Gersten et al. () and Horner et al. () were applied to evaluate the methodological rigour of TAI studies and their feasibility to be considered evidence‐based. Results revealed that (a) most group design studies provided little information about the intervention agent and equivalence of groups across conditions, (b) the social validity of using tablets for students with disabilities was strongly established across all single‐subject design studies and (c) procedural fidelity in assessment and intervention implementation was inadequately addressed in group design studies. Although this review suggests that TAI used in single‐subject design studies can be a potentially evidence‐based practice for students with disabilities, there still remains to be established whether the group design studies can be considered evidence‐based, because of the lack of methodological rigour in group design studies. Finally, implications for future directions and practical ideas are discussed.
Selective Expression of CCR10 and CXCR3 by Circulating Human Herpes Simplex Virus-Specific CD8 T Cells
Authors: Hensel Michael T. , Peng Tao , Cheng Anqi , De Rosa Stephen C. , Wald Anna , Laing Kerry J. , Jing Lichen , Dong Lichun , Magaret Amalia S. , Koelle David M. 
Published: July 2017

ABSTRACTHerpes simplex virus (HSV) infection is restricted to epithelial cells and neurons and is controlled by CD8 T cells. These cells both traffic to epithelial sites of recurrent lytic infection and to ganglia and persist at the dermal-epidermal junction for up to 12 weeks after lesion resolution. We previously showed that cutaneous lymphocyte-associated antigen (CLA), a functional E-selectin ligand (ESL), is selectively expressed on circulating HSV-2-specific CD8 T cells. CLA/ESL mediates adhesion of T cells to inflamed vascular endothelium. Later stages in T-cell homing involve chemokines (Ch) and lymphocyte chemokine receptors (ChR) for vascular wall arrest and diapedesis. Several candidate ChR have been implicated in skin homing. We measured cell surface ChR on HSV-specific human peripheral blood CD8 T cells and extended our studies to HSV-1. We observed preferential cell surface expression of CCR10 and CXCR3 by HSV-specific CD8 T cells compared to CD8 T cells specific for control viruses, Epstein-Barr virus (EBV) and cytomegalovirus (CMV), and compared to bulk memory CD8 T cells. CXCR3 ligand mRNA levels were selectively increased in skin biopsy specimens from persons with recurrent HSV-2, while the mRNA levels of the CCR10 ligand CCL27 were equivalent in lesion and control skin. Our data are consistent with a model in which CCL27 drives baseline recruitment of HSV-specific CD8 T cells expressing CCR10, while interferon-responsive CXCR3 ligands recruit additional cells in response to virus-driven inflammation.IMPORTANCEHSV-2 causes very localized recurrent infections in the skin and genital mucosa. Virus-specific CD8 T cells home to the site of recurrent infection and participate in viral clearance. The exit of T cells from the blood involves the use of chemokine receptors on the T-cell surface and chemokines that are present in infected tissue. In this study, circulating HSV-2-specific CD8 T cells were identified using specific fluorescent tetramer reagents, and their expression of several candidate skin-homing-associated chemokine receptors was measured using flow cytometry. We found that two chemokine receptors, CXCR3 and CCR10, are upregulated on HSV-specific CD8 T cells in blood. The chemokines corresponding to these receptors are also expressed in infected tissues. Vaccine strategies to prime CD8 T cells to home to HSV lesions should elicit these chemokine receptors if possible to increase the homing of vaccine-primed cells to sites of infection.