bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterial panniculitis caused by Mycobacterium thermoresistibile in a cat
Authors: Vishkautsan Polina , Reagan Krystle L , Keel M Kevin , Sykes Jane E 
Published: October 2016

Case summary A domestic shorthair cat was evaluated for chronic, bilateral, ulcerative dermatitis affecting the inguinal region and lateral aspects of both pelvic limbs. Histopathologic examination of skin biopsies collected throughout the course of disease revealed chronic pyogranulomatous ulcerative dermatitis. Aerobic bacterial skin cultures yielded growth of a methicillin-resistant Staphylococcus aureus and Corynebacterium amycolatum. Upon referral the clinical findings were suggestive of a non-tuberculous Mycobacterium species infection. Previously obtained skin cultures failed to yield growth of mycobacterial organisms. A deep skin biopsy was collected and submitted for mycobacterial culture. At 5 weeks of incubation Mycobacterium thermoresistibile was isolated. In previous reports, M thermoresistibile has been isolated after 2–4 days of incubation, suggesting that this strain may have been a slower growing variant, or other factors (such as prior antimicrobial therapy) inhibited rapid growth of this isolate. The cat was hospitalized for intravenous antibiotic therapy, surgical debridement of wounds, vacuum-assisted wound closure therapy and reconstruction procedures. The wounds were ultimately primarily closed and the cat was discharged to the owner after 50 days of hospitalization. Seven months after hospitalization, the ulcerative skin lesions had healed. Relevance and novel information To our knowledge, only two cases of M thermoresistibile panniculitis have been reported in cats. In the only detailed report of feline M thermoresistibile panniculitis, treatment was not attempted. The second case only reported detection of M thermoresistibile by PCR without a clinical description of the case. In our case report, severe chronic skin infection with M thermoresistibile was addressed using prolonged specific antibiotic therapy, surgical debridement and reconstructions, and treatment of secondary bacterial infections.
A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation
Authors: Hejase Hussein A. , Liu Kevin J. 
Published: October 2016

Abstract
Background
Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a directed acyclic graph known as a phylogenetic network. Both phylogenetic trees and networks are typically reconstructed using computational analysis of multi-locus sequence data. The advent of high-throughput sequencing technologies has brought about two main scalability challenges: (1) dataset size in terms of the number of taxa and (2) the evolutionary divergence of the taxa in a study. The impact of both dimensions of scale on phylogenetic tree inference has been well characterized by recent studies; in contrast, the scalability limits of phylogenetic network inference methods are largely unknown.

Results
In this study, we quantify the performance of state-of-the-art phylogenetic network inference methods on large-scale datasets using empirical data sampled from natural mouse populations and a range of simulations using model phylogenies with a single reticulation. We find that, as in the case of phylogenetic tree inference, the performance of leading network inference methods is negatively impacted by both dimensions of dataset scale. In general, we found that topological accuracy degrades as the number of taxa increases; a similar effect was observed with increased sequence mutation rate. The most accurate methods were probabilistic inference methods which maximize either likelihood under coalescent-based models or pseudo-likelihood approximations to the model likelihood. The improved accuracy obtained with probabilistic inference methods comes at a computational cost in terms of runtime and main memory usage, which become prohibitive as dataset size grows past twenty-five taxa. None of the probabilistic methods completed analyses of datasets with 30 taxa or more after many weeks of CPU runtime.

Conclusions
We conclude that the state of the art of phylogenetic network inference lags well behind the scope of current phylogenomic studies. New algorithmic development is critically needed to address this methodological gap.
Lack of effects of ooplasm transfer on early development of interspecies somatic cell nuclear transfer bison embryos
Authors: González-Grajales L. Antonio , Favetta Laura A. , King W. Allan , Mastromonaco Gabriela F. 
Published: October 2016

Abstract
Background
Successful development of iSCNT (interspecies somatic cell nuclear transfer) embryos depends on complex interactions between ooplasmic and nuclear components, which can be compromised by genetic divergence. Transfer of ooplasm matching the genetic background of the somatic cell in iSCNT embryos is a valuable tool to study the degree of incompatibilities between nuclear and ooplasmic components. This study investigated the effects of ooplasm transfer (OT) on cattle (Bos taurus) and plains bison (Bison bison bison) embryos produced by iSCNT and supplemented with or without ooplasm from cattle or plains bison oocytes.

Results
Embryos in all groups were analysed for developmental competence that included cleavage rates, ATP content, and expression of nuclear- and mitochondrial- encoded genes at 8–16 cell stage. Interestingly, no significant differences were observed in embryo development, ATP content, and expression of nuclear respiratory factor 2 (NRF2), mitochondrial transcription factor A (TFAM) and mitochondrial subunit 2 of cytochrome c oxidase (mt-COX2) among groups. Thus, although OT did not result in any detrimental effects on the reconstructed embryos due to invasive manipulation, significant benefits of OT were not observed up to the 8–16 cell stage.

Conclusions
This study showed that a viable technique for OT + SCNT is possible, however, further understanding of the effects of OT on blastocyst development is necessary.
Human macrophage differentiation induces OCTN2–mediated L-carnitine transport through stimulation of mTOR–STAT3 axis
Authors: Ingoglia Filippo , Visigalli Rossana , Rotoli Bianca Maria , Barilli Amelia , Riccardi Benedetta , Puccini Paola , Milioli Marco , Di Lascia Maria , Bernuzzi Gino , Dall’Asta Valeria 
Published: October 2016

Abstract
l-Carnitine, in addition to playing a fundamental role in the β-oxidation of fatty acids, has been recently identified as a modulator of immune function, although the mechanisms that underlie this role remain to be clarified. In this study, we addressed the modulation of l-carnitine transport and expression of related transporters during differentiation of human monocytes to macrophages. Whereas monocytes display a modest uptake of l-carnitine, GM-CSF–induced differentiation massively increased the saturable Na+-dependent uptake of l-carnitine. Kinetic and inhibition analyses demonstrate that in macrophage l-carnitine transport is mediated by a high-affinity component (Km ∼4 µM) that is identifiable with the operation of OCTN2 transporter and a low-affinity component (Km &gt; 10 mM) that is identifiable with system A for neutral amino acids. Consistently, both SLC22A5/OCTN2 and SLC38A2/SNAT2 are induced during the differentiation of monocytes to macrophages at gene and protein levels. Elucidation of GM-CSF signaling demonstrates that the cytokine causes the activation of mTOR kinase, leading to the phosphorylation and activation of STAT3, which, in turn, is responsible for OCTN2 transcription. SLC22A5/OCTN2 therefore emerges as a novel member of the set of genes markers of macrophage differentiation.
The TNF family member TL1A induces IL-22 secretion in committed human Th17 cells via IL-9 induction
Authors: Thomas Lisa S , Targan Stephan R , Tsuda Masato , Yu Qi T , Salumbides Brenda C , Haritunians Talin , Mengesha Emebet , McGovern Dermot P B , Michelsen Kathrin S 
Published: October 2016

Abstract
TL1A contributes to the pathogenesis of several chronic inflammatory diseases, including those of the bowel by enhancing TH1, TH17, and TH2 responses. TL1A mediates a strong costimulation of these TH subsets, particularly of mucosal CCR9+ T cells. However, the signaling pathways that TL1A induces in different TH subsets are incompletely understood. We investigated the function of TL1A on human TH17 cells. TL1A, together with TGF-β, IL-6, and IL-23, enhanced the secretion of IL-17 and IFN-γ from human CD4+ memory T cells. TL1A induced expression of the transcription factors BATF and T-bet that correlated with the secretion of IL-17 and IFN-γ. In contrast, TL1A alone induced high levels of IL-22 in memory CD4+ T cells and committed TH17 cells. However, TL1A did not enhance expression of IL-17A in TH17 cells. Expression of the transcription factor aryl hydrocarbon receptor, which regulates the expression of IL-22 was not affected by TL1A. Transcriptome analysis of TH17 cells revealed increased expression of IL-9 in response to TL1A. Blocking IL-9 receptor antibodies abrogated TL1A-induced IL-22 secretion. Furthermore, TL1A increased IL-9 production by peripheral TH17 cells isolated from patients with Crohn’s disease. These data suggest that TL1A differentially induces expression of TH17 effector cytokines IL-17, -9, and -22 and provides a potential target for therapeutic intervention in TH17-driven chronic inflammatory diseases.
Prediagnostic Intervals in Retinoblastoma: Experience at an Oncology Center in Brazil
Authors: Mattosinho Clarissa Campolina de Sá , Grigorovski Nathalia , Lucena Evandro , Ferman Sima , Soares de Moura Anna Tereza Miranda , Portes Arlindo Freire 
Published: October 2016

Purpose Retinoblastoma is the most common intraocular malignancy of childhood. In most cases, parents are the first to notice leukocoria and other symptoms before undergoing a prolonged period of stress before diagnosis. The purpose of this study was to determine prediagnostic intervals of patients with retinoblastoma at an oncology tertiary center (Instituto Nacional de Cancer) in Rio de Janeiro, Brazil, and relate them to stage at diagnosis, eye salvage, and survival. Methods Parents or caregivers of children with retinoblastoma registered between January 2006 and September 2013 were interviewed using a semistructured individually applied questionnaire, concerning their trajectory before registration. Results Out of 76 patients, 39 (51%) were girls, 52 (68%) had unilateral retinoblastoma, and 24 (32%) had bilateral retinoblastoma, totaling 100 affected eyes. The most common stage of diagnosis was the intraocular group, with 63 (83%) patients; nine (12%) were extraocular, and four (5%) had metastatic disease. During the follow-up time of 37 ± 24.5 months, 10 (13%) patients died and 70 (70%) eyes were enucleated. Mean family interval was 1.6 ± 2.6 months, mean medical interval was 5.0 ± 6.2 months, mean referral interval was 0.2 ± 1.4 months, and mean overall interval was 7.1 ± 6.9 months. In univariate analysis, age at diagnosis, maternal education, medical interval, and overall interval were significantly related to advanced stage at diagnosis and survival. In multivariate analysis, maternal education and medical interval were significantly related to advanced stage at diagnosis and survival. No variables affected eye salvage. Conclusion Medical interval was responsible for 70% of the overall interval; therefore, programs or campaigns targeting retinoblastoma early diagnosis should focus emphasize in medical awareness.
Default Drug Doses in Anesthesia Information Management Systems
Authors: Rodriquez Luis I. , Smaka Todd J. , Mahla Michael , Epstein Richard H. 
Published: October 2016

BACKGROUND:
In the United States, anesthesia information management systems (AIMS) are well established, especially within academic practices. Many hospitals are replacing their stand-alone AIMS during migration to an enterprise-wide electronic health record. This presents an opportunity to review choices made during the original implementation, based on actual usage. One area amenable to this informatics approach is the configuration in the AIMS of quick buttons for typical drug doses. The use of such short cuts, as opposed to manual typing of doses, simplifies and may improve the accuracy of drug documentation within the AIMS. We analyzed administration data from 3 different institutions, 2 of which had empirically configured default doses, and one in which defaults had not been set up. Our first hypothesis was that most (ie, >50%) of drugs would need at least one change to the existing defaults. Our second hypothesis was that for most (>50%) drugs, the 4 most common doses at the site lacking defaults would be included among the most common doses at the 2 sites with defaults. If true, this would suggest that having default doses did not affect the typical administration behavior of providers.

METHODS:
The frequency distribution of doses for all drugs was determined, and the 4 most common doses representing at least 5% of total administrations for each drug were identified. The appropriateness of the current defaults was determined by the number of changes (0–4) required to match actual usage at the 2 hospitals with defaults. At the institution without defaults, the most frequent doses for the 20 most commonly administered drugs were compared with the default doses at the other institutions.

RESULTS:
At the 2 institutions with defaults, 84.7% and 77.5% of drugs required at least 1 change in the default drug doses (P < 10−6 for both compared with 50%), confirming our first hypothesis. At the institution lacking the default drug doses, 100% of the 20 most commonly administered doses (representing ≥5% of use for that drug) were included in the most commonly administered doses at the other 2 institutions (P < 10−6), confirming our second hypothesis.

CONCLUSIONS:
We recommend that default drug doses should be analyzed when switching to a new AIMS because most drugs needed at least one change. Such analysis is also recommended periodically so that defaults continue to reflect current practice. The use of default dose buttons does not appear to modify the selection of drug doses in clinical practice.
Fragmented Sleep Enhances Postoperative Neuroinflammation but Not Cognitive Dysfunction
Authors: Vacas Susana , Degos Vincent , Maze Mervyn 
Published: October 2016

BACKGROUND:
Sleep is integral to biologic function, and sleep disruption can result in both physiological and psychologic dysfunction including cognitive decline. Surgery activates the innate immune system, inducing neuroinflammatory changes that interfere with cognition. Because surgical patients with sleep disorders have an increased likelihood of exhibiting postoperative delirium, an acute form of cognitive decline, we investigated the contribution of perioperative sleep fragmentation (SF) to the neuroinflammatory and cognitive responses of surgery.

METHODS:
The effects of 24-hour SF and surgery were explored in adult C57BL/6J male mice. The SF procedure started at 7 am with cages being placed on a large platform orbital shaker that cycled every 120 seconds (30 seconds on/90 seconds off) for 24 hours. In separate cohorts, stabilized tibial fracture was performed either before or after the 24-hour SF procedure and assessed for systemic and hippocampal inflammation and cognition.

RESULTS:
SF-induced nonhippocampal memory dysfunction (mean ± standard deviation [SD] of the difference in time spent between novel and familiar object for control was 4.7 ± 1.4 seconds, n = 8 versus SF −0.5 ± 0.2 seconds, n = 11, yielding an estimated treatment effect of 5.2 seconds [95% confidence interval {CI}, 2.6–7.7]; P < .001) and increased systemic interleukin-6 (median [25%–75% quartile] for control 0.0 [0.0–2.4] pg/mL versus 9.7 [6.3–12.9] pg/mL, n = 8/group, yielding an estimated treatment effect of 9.7 pg/mL [95% CI, 5.8–11.8]; P < .0001). SF reduced freezing time in hippocampal-dependent memory test (mean ± SD for control 49.3% ± 5.8% versus for SF 32.9% ± 5.8%, n = 10/group, estimated treatment effect = 16.4% [95% CI, 11.0–21.8]; P < .0001). Although surgery also reduced freezing time (mean ± SD for control 49.3% ± 5.8% versus for surgery 30.3% ± 3.3%, n = 10/group, estimated treatment effect = 19.0% [95% CI, 14.6–23.4]; P < .0001), memory impairment was not further exacerbated by combining SF with surgery. One day after SF, there was an increase in hippocampal messenger RNA expression of tumor necrosis factor-α (relative quantitation [RQ] 5.12-fold, n = 5/group [95% CI, 1.64–15.97]; P < .01), and 1 day after surgery, there was an increase in messenger RNA interleukin-6 (RQ 4.64-fold, n = 5 [95% CI, 1.48–14.56]; P < .05) and tumor necrosis factor-α (RQ 5.54-fold, n = 5 [95% CI, 2.92–10.51]; P < .01). These increments were more pronounced when either pre- or postoperative SF was combined with surgery.

CONCLUSIONS:
Although SF and surgery can independently produce significant memory impairment, perioperative SF significantly increased hippocampal inflammation without further cognitive impairment. The dissociation between neuroinflammation and cognitive decline may relate to the use of a sole memory paradigm that does not capture other aspects of cognition, especially learning.
Perianth symmetry changed at least 199 times in angiosperm evolution
Authors: Reyes Elisabeth , Sauquet Hervé , Nadot Sophie 
Published: October 2016

AbstractPerianth bilateral symmetry (zygomorphy) has evolved repeatedly from radial symmetry (actinomorphy) throughout angiosperms. Zygomorphy has previously been linked with plant‐pollinator specialization and higher species diversification. However, the exact number of transitions to and from zygomorphy has remained so far unknown. We recorded perianth symmetry from 761 species, selected to represent all 61 orders and 426 currently accepted families of angiosperms and to include all presumed origins of perianth zygomorphy. We then reconstructed the evolution of perianth symmetry on a consensus backbone tree, using parsimony. We found perianth zygomorphy in 32 orders and 110 families. There was a minimum of 130 origins, almost double of what was previously estimated, and 69 reversals to actinomorphy. Among the origins, 2 were in magnoliids, 29 in monocots, 17 in basal eudicots, 35 in superrosids and 47 in superasterids. Among the reversals, 8 were in monocots, 4 in basal eudicots, 18 in superrosids and 39 in superasterids. This study shows that there has been many more origins of perianth zygomorphy and reversals to actinomorphy than previously shown. We then use this new framework to review the developmental evidence of changes in floral symmetry, showing convergence in the early stages of zygomorphy across angiosperms at the developmental level. We also review the evidence on the genetic control of floral symmetry, suggesting that a restricted number of genes has been recruited multiple times independently to achieve zygomorphy. In contrast to its relative homogeneity at the early developmental and molecular level, zygomorphy appears to be highly variable in its morphological expression at anthesis, involving various processes such as perianth part displacement and differentiation. We then review recent hypotheses on the relationship between floral symmetry, floral orientation, and pollination mode in terms of selective advantages and constraints. Our comprehensive angiosperm‐wide reconstruction of floral symmetry evolution provides a new context for future studies on the developmental, functional, and macroevolutionary aspects of floral symmetry.
Retrieval of hundreds of nuclear loci from herbarium specimens
Authors: Hart Michelle L. , Forrest Laura L. , Nicholls James A. , Kidner Catherine A. 
Published: October 2016

AbstractHerbaria are unparalleled collections of biodiversity information representing the world's flora. However, this treasure has remained largely inaccessible to genetic studies, frequently limited by the low yields of poor‐quality DNA. Next‐generation sequencing (NGS) has transformed every field of biological research. The different strategies for accessing genetic data using NGS are changing the direction of biodiversity research—we are no longer constrained by a relatively small number of markers for non‐model organisms, by time and cost limited sample sizes, or by incomplete datasets due to recalcitrant DNA extractions or PCR amplification failure. Here we show that targeted enrichment through hybrid capture can be used to generate hundreds of kilobases of nuclear sequence data of the Neotropical genus Inga, from herbarium specimens as old as 180 years and using as little as 16 ng of degraded DNA.
The Value of Nothing: Asymmetric Attention to Opportunity Costs Drives Intertemporal Decision Making
Authors: Read Daniel , Olivola Christopher Y. , Hardisty David J. 
Published: October 2016

This paper proposes a novel account of impatience: People pay more attention to the opportunity costs of choosing larger, later rewards than to the opportunity costs of choosing smaller, sooner ones. Eight studies show that when the opportunity costs of choosing smaller, sooner rewards are subtly highlighted, people become more patient, whereas when the opportunity costs of choosing larger, later rewards are highlighted this has no effect. This pattern is robust to variations in the choice task, to the participant population, and to whether the choices are incentivized or hypothetical. We argue that people are naturally aware of the opportunity costs of delayed rewards but pay less attention to those associated with smaller, sooner ones. We conclude by discussing implications for theory and policy. Data, as supplemental material, are available at https://doi.org/10.1287/mnsc.2016.2547 . This paper was accepted by Yuval Rottenstreich, judgment and decision making.
Fantasy and Dread: The Demand for Information and the Consumption Utility of the Future
Authors: Ganguly Ananda , Tasoff Joshua 
Published: October 2016

We present evidence that intrinsic demand for information about the future is increasing in expected future consumption utility. In the first experiment, subjects may resolve a lottery now or later. The information is useless for decision making, but the larger the reward, the more likely subjects are to pay to resolve the lottery early. In the second experiment, subjects may pay to avoid being tested for herpes simplex virus type 1 (HSV-1) and the more highly feared type 2 (HSV-2). Subjects are three times more likely to avoid testing for HSV-2, suggesting that more aversive outcomes lead to more information avoidance. In a third experiment, subjects make choices about when to get tested for a fictional disease. Some subjects behave in a way consistent with expected utility theory, and others exhibit greater delay of information for more severe diseases. We also find that information choice is correlated with positive affect, ambiguity aversion, and time preference, as some theories predict.Data, as supplemental material, are available at https://doi.org/10.1287/mnsc.2016.2550 .This paper was accepted by Teck-Hua Ho, behavioral economics.