bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic polymorphisms of CYP2C19 and IL1B have no influence on esomeprazole treatment for mild erosive esophagitis
Authors: Hsu Wen‐Hung , Kuo Fu‐Chen , Hu Huang‐Ming , Hsu Ping‐I , Wu Deng‐Chyang , Kuo Chao‐Hung 
Published: March 2015

AbstractInterleukin (IL)‐1β is a potent inhibitor of gastric acid secretion and its genetic polymorphism is linked to the severity of reflux esophagitis. Proton‐pump inhibitor (PPI) metabolized by P450 2C19 (CYP2C19) is the chief medication in reflux esophagitis treatment. The CYP2C19 genotype may influence the therapeutic effect of PPI for reflux esophagitis. From November 2009 to June 2012, 184 patients were enrolled in this study with endoscopy examination, 8 weeks of esomeprazole treatment, and 20 weeks of follow‐up with questionnaire. These patients also received endoscopy examination after 20 weeks. Blood was collected for genetic polymorphism analysis with polymerase chain reaction. After 8 weeks of treatment with esomeprazole, all of these 184 patients had achieved complete symptom relief. However, in the following 12 weeks, 58.70% (108/184) complained of symptom relapse, 45.65% (84/184) patients had persistent esophageal erosion verified by endoscopy, and in total, 76.09% (140/184) patients had treatment failure at the end of 20 weeks. There were no influences between the genetic polymorphisms of CYP2C19 and IL1B to treatment failure (p = 0.896). Therefore, prolonging PPI treatment and further lifestyle modification might be warranted for symptomatic mild esophagitis. There were no relationships between IL‐1β and CYP2C19 in the treatment effect in mild reflux esophagitis.
Clinically acceptable colchicine concentrations have potential for the palliative treatment of human cholangiocarcinoma
Authors: Wu Chun‐Chieh , Lin Zu‐Yau , Kuoc Chao‐Hung , Chuang Wan‐Long 
Published: March 2015

AbstractMicrotubules are an ideal target for anticancer drugs because of their essential role in mitosis. Colchicine is a microtubule destabilizer. Whether the clinically acceptable colchicine concentrations had anticancer effects on human cholangiocarcinoma cells was investigated. Two human cholangiocarcinoma cell lines (C14/KMUH, C51/KMUH) were investigated using clinically acceptable plasma colchicine concentrations (2 ng/mL and 6 ng/mL for the in vitro experiment, 0.07 mg colchicine/kg/d × 14 days for the nude mouse experiment). Our results showed that colchicine caused significantly dose‐dependent antiproliferative effects on both cell lines (all p < 0.0001). Nude mouse (BALB/c‐nu) experiments showed that the increased tumor volume ratios in colchicine‐treated mice were significantly lower than control mice started from the 11th day of treatment (p = 0.0167). The tumor growth rates in colchicine‐treated mice after 14 days of treatment were significantly lower than in control mice (0.147 ± 0.004/d vs. 0.274 ± 0.003/d, p = 0.0015). In addition to the well‐known direct colchicine–tubulin interaction as a common anticancer mechanism of colchicine, microarray and quantitative reverse transcriptase‐polymerase chain reaction showed that the antiproliferative effects of both 2 ng/mL and 6 ng/mL colchicine on C14/KMUH cells could be partially explained by downregulations of both HSD11B2 and MT‐COI. There was no effect of colchicine on MT‐COI expression in C51/KMUH cells, however, 6 ng/mL colchicine also downregulated HSD11B2 in this cell line. In conclusion, clinically acceptable colchicine concentrations can inhibit the proliferation of human cholangiocarcinoma cells. This drug has good potential for the palliative treatment of cholangiocarcinoma due to its low cost and our long‐standing prescription experience.
Predicting the Risk for Hospital-Onset Clostridium difficile Infection (HO-CDI) at the Time of Inpatient Admission: HO-CDI Risk Score
Authors: Tabak Ying P. , Johannes Richard S. , Sun Xiaowu , Nunez Carlos M. , McDonald L. Clifford 
Published: March 2015

OBJECTIVETo predict the likelihood of hospital-onset Clostridium difficile infection (HO-CDI) based on patient clinical presentations at admissionDESIGNRetrospective data analysisSETTINGSix US acute care hospitalsPATIENTSAdult inpatientsMETHODSWe used clinical data collected at the time of admission in electronic health record (EHR) systems to develop and validate a HO-CDI predictive model. The outcome measure was HO-CDI cases identified by a nonduplicate positive C. difficile toxin assay result with stool specimens collected >48 hours after inpatient admission. We fit a logistic regression model to predict the risk of HO-CDI. We validated the model using 1,000 bootstrap simulations.RESULTSAmong 78,080 adult admissions, 323 HO-CDI cases were identified (ie, a rate of 4.1 per 1,000 admissions). The logistic regression model yielded 14 independent predictors, including hospital community onset CDI pressure, patient age ≥65, previous healthcare exposures, CDI in previous admission, admission to the intensive care unit, albumin ≤3 g/dL, creatinine >2.0 mg/dL, bands >32%, platelets ≤150 or >420 109/L, and white blood cell count >11,000 mm3. The model had a c-statistic of 0.78 (95% confidence interval [CI], 0.76–0.81) with good calibration. Among 79% of patients with risk scores of 0–7, 19 HO-CDIs occurred per 10,000 admissions; for patients with risk scores >20, 623 HO-CDIs occurred per 10,000 admissions (P<.0001).CONCLUSIONUsing clinical parameters available at the time of admission, this HO-CDI model demonstrated good predictive ability, and it may have utility as an early risk identification tool for HO-CDI preventive interventions and outcome comparisons.Infect Control Hosp Epidemiol 2015;00(0):1–7
A framework for studying the effect of compliant surfaces on wall turbulence
Authors: Luhar M. , Sharma A. S. , McKeon B. J. 
Published: March 2015

This paper extends the resolvent formulation proposed by McKeon & Sharma (J. Fluid Mech., vol. 658, 2010, pp. 336–382) to consider turbulence–compliant wall interactions. Under this formulation, the turbulent velocity field is expressed as a linear superposition of propagating modes, identified via a gain-based decomposition of the Navier–Stokes equations. Compliant surfaces, modelled as a complex wall admittance linking pressure and velocity, affect the gain and structure of these modes. With minimal computation, this framework accurately predicts the emergence of the quasi-two-dimensional propagating waves observed in recent direct numerical simulations. Further, the analysis also enables the rational design of compliant surfaces, with properties optimized to suppress flow structures energetic in wall turbulence. It is shown that walls with unphysical negative damping are required to interact favourably with modes resembling the energetic near-wall cycle, which could explain why previous studies have met with limited success. Positive-damping walls are effective for modes resembling the so-called very-large-scale motions, indicating that compliant surfaces may be better suited for application at higher Reynolds number. Unfortunately, walls that suppress structures energetic in natural turbulence are also predicted to have detrimental effects elsewhere in spectral space. Consistent with previous experiments and simulations, slow-moving spanwise-constant structures are particularly susceptible to further amplification. Mitigating these adverse effects will be central to the development of compliant coatings that have a net positive influence on the flow.
Salinity transfer in bounded double diffusive convection
Authors: Yang Yantao , van der Poel Erwin P. , Ostilla-Mónico Rodolfo , Sun Chao , Verzicco Roberto , Grossmann Siegfried , Lohse Detlef 
Published: March 2015

The double diffusive convection between two parallel plates is numerically studied for a series of parameters. The flow is driven by the salinity difference and stabilised by the thermal field. Our simulations are directly compared with experiments by Hage & Tilgner (Phys. Fluids, vol. 22, 2010, 076603) for several sets of parameters and reasonable agreement is found. This, in particular, holds for the salinity flux and its dependence on the salinity Rayleigh number. Salt fingers are present in all simulations and extend through the entire height. The thermal Rayleigh number seems to have a minor influence on the salinity flux but affects the Reynolds number and the morphology of the flow. In addition to the numerical calculation, we apply the Grossmann–Lohse theory for Rayleigh–Bénard flow to the present problem without introducing any new coefficients. The theory successfully predicts the salinity flux both with respect to the scaling and even with respect to the absolute value for the numerical and experimental results.
On the benefits of being redundant: low compositional fidelity of diatom death assemblages does not hamper the preservation of environmental gradients in shallow lakes
Authors: Hassan Gabriela S. 
Published: March 2015

AbstractComparisons between death assemblages and their source living communities are among the most common actualistic methods of evaluating the preservation of compositional and environmental information in fossil assemblages. Although live-dead studies have commonly focused on marine mollusks, the potential of diatoms to preserve ecological information in continental settings has been overlooked. Thus, little is known about the nature and magnitude of the taphonomic biases affecting live-dead agreement of diatom assemblages, despite their extensive application as modern and fossil bioindicators in paleoecological and paleoenvironmental reconstructions. In this study, I analyzed three live-dead data sets in order to evaluate the compositional and environmental fidelity exhibited by diatom death assemblages in shallow lakes. I find that diatom death assemblages (DAs) do differ significantly in their taxonomic composition from living assemblages (LAs), mainly as a consequence of (1) differences in the temporal resolution between time-averaged DAs and non-averaged LAs, and (2) differential preservation of diatom taxa related to the intrinsic properties of their valves. Despite compositional dissimilarities, DAs were able to capture the same environmental gradients as LAs, with high significance. This decoupling between live-dead agreement in community composition and community response to gradients can be related to the existence of at least two mutually exclusive subsets of species that significantly captured compositional dissimilarities based on the full set of the species in the three lakes. This functional redundancy implies that the between-sample relationships of living assemblages can be significantly preserved by DAs even if some taxa are removed by taphonomic processes. The preservation of environmental gradients thus does not require good preservation of all living taxa. Structural redundancy compensates for the loss of compositional fidelity caused by postmortem processes in the diatom data set.
A morphospace of planktonic marine diatoms. I. Two views of disparity through time
Authors: Kotrc Benjamin , Knoll Andrew H. 
Published: March 2015

AbstractBoth molecular clocks and the first appearances of major groups in the fossil record suggest that most of the range of diatom morphologies observed today had evolved by the end of the Cretaceous Period. Despite this, a canonical reading of the Cenozoic fossil record suggests a dramatic rise in taxonomic diversity that can be interpreted as an explosion of morphological variety. We investigated this apparent discrepancy by using a discrete-character-based, empirical diatom morphospace, resolved by molecular phylogeny and by fossil occurrences through time. The morphospace shows little correspondence to phylogeny and little Cenozoic change in disparity as measured by mean pairwise distance. There is, however, an increase in the total volume of morphospace occupied. Although the increase in occupied volume through time ostensibly supports a conclusion of increasing morphological variety, sampling biases and other data suggest an underlying stationary pattern more consistent with molecular clock data.
Exploring photosymbiotic ecology of planktic foraminifers from chamber-by-chamber isotopic history of individual foraminifers
Authors: Takagi Haruka , Moriya Kazuyoshi , Ishimura Toyoho , Suzuki Atsushi , Kawahata Hodaka , Hirano Hiromichi 
Published: March 2015

AbstractEvolution of photosymbiotic ecology is an important adaptation for planktic foraminifers that enhances the ecological advantage of living in oligotrophic oceans. Therefore, detecting photosymbiotic ecology in fossil species is one of the keys to understanding the paleobiodiversity dynamics of planktic foraminifers. Because foraminiferal tests record the ontogenetic history of ecological information in geochemical signatures, analyzing individual geochemical profiles with growth can reveal a species’ ecology. This study examined chamber-by-chamber stable isotopes (δ13C and δ18O) of foraminiferal individuals to identify photosymbiotic signals. We observed an ontogenetic δ13C increase of up to 2.4‰, accompanied by relatively stable, negative δ18O, in the symbiotic species Globigerinoides conglobatus and Globigerinoides sacculifer. In contrast, δ13C and δ18O showed significant positive correlation during ontogeny in the asymbiotic species Globorotalia truncatulinoides. These two ecological groups produce contrasting isotopic profiles, thereby allowing us to use our ontogenetic isotopic analyses of individual specimens to identify algal photosymbiosis in fossil foraminifers. The chamber-by-chamber isotope analyses with individual ontogeny have great advantages in analyzing rare species because only one individual is required to describe ontogenetic isotopic history. In addition to photosymbiotic identification, our methods hold great potential to provide new insight into species paleoecological studies such as the ontogenetic history of calcification depth.
Breaking the mold: using biomechanical experiments to assess the life orientation of dorsibiconvex brachiopods
Authors: Barclay Kristina M. , Schneider Chris L. , Leighton Lindsey R. 
Published: March 2015

AbstractUnderstanding the life orientation of fossil organisms, such as brachiopods, is not only important for understanding the biology of the organism in question, but it also can be used to interpret paleoecological information about the assemblages from which the specimens were derived. The dorsibiconvex brachiopod morphology is particularly common, especially among the Order Atrypida, yet there have been few independent, biomechanical studies to assess the life orientation of these brachiopods. In this study, we assess potential orientations of two end-member morphologies of a dorsibiconvex brachiopod, Pseudoatrypa lineata, from the Mid–Late Devonian of North America by placing realistic models in a flume.Using materials with the specific gravity of calcium carbonate, we modeled two well-preserved Pseudoatrypa lineata from the Waterways Formation (Givetian–Frasnian, Alberta, Canada) to represent the original shell. The hydrodynamic stability of the models was assessed by placing the models in a recirculating flume in one of three initial orientations: (1) anterior commissure upstream, (2) umbo upstream, and (3) lateral (specimen perpendicular to flow), each with the dorsal and ventral valve topmost. The entire process was conducted both on a Plexiglas substrate and on well-sorted, mediumgrained sand. All scenarios were repeated five times for a total of sixty trials per specimen (120 total).Flume trials indicate that neither brachiopod had a true hydrodynamically stable orientation.Reorientations occurred at low velocities (~0.2 m/s), with transport occurring soon after (~0.3 m/s).Assuming that a juvenile, pedunculate, dorsibiconvex brachiopod would initially have been oriented with its ventral valve topmost, our results suggest two outcomes: the brachiopods either (1) were attached via pedicles throughout their lives or (2) lived in quiet, undisturbed waters. Given the abundance of dorsibiconvex brachiopods in observed high-energy environments, our results indicate it is more conservative to assume dorsibiconvex brachiopods retained pedicles throughout their lives.
Residents’ Self-Reported Quality of Life in Long-Term Care Facilities in Canada
Authors: Kehyayan Vahe , Hirdes John P. , Tyas Suzanne L. , Stolee Paul 
Published: March 2015

RÉSUMÉLa qualité de vie (QV) dont bénéficient les résidents des centres d'hébergement de soins de longue durée (SLD) est un résultat important des soins. Cette étude descriptive transversale a examiné la qualité de vie auto-declarée de résidents des établissements de SLD au Canada, tout en utilisant l'auto-évaluation interRAI Nursing Home Quality of Life Survey. Un objectif secondaire était de tester les propriétés pschométriques de l'instrument. Les tests psychométriques de l'instrument ont soutenu sa fiabilité et la validité de sa convergence et de son contenu pour l'évaluation de QV des résidents. Les résultats ont montré que les résidents ont évalués positivement plusieurs aspects de leur vie, comme d'avoir la vie privée lors des visites (76,9%) et l'honnêteté du personnel en traitant avec eux (73,6%). Les résidents ont accordé des taux inférieures à d'autres aspects, comme l'autonomie, la liaison entre le personnel et les résidents, et les relations personnelles. Les résultats suggèrent des lacunes importantes entre les philosophies de soins dans les établissements et leur traduction dans un environnement de soins ou les soins sont vraiment dirigés aux résidents. En outre, les résultats ont des implications potentielles pour la planification de soins aux résidents, la programmation de l'installation, le développement de la politique sociale et de la recherche future.
Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses
Authors: Rojo David , Gosalbes María J , Ferrari Rafaela , Pérez-Cobas Ana E , Hernández Ester , Oltra Rosa , Buesa Javier , Latorre Amparo , Barbas Coral , Ferrer Manuel , Moya Andrés 
Published: March 2015

Abstract
Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious emerging health problem. Yet, its progression and functional consequences are unclear. We hypothesised that C. difficile can drive major measurable metabolic changes in the gut microbiota and that a relationship with the production or absence of toxins may be established. We tested this hypothesis by performing metabolic profiling on the gut microbiota of patients with C. difficile that produced (n=6) or did not produce (n=4) toxins and on non-colonised control patients (n=6), all of whom were experiencing diarrhoea. We report a statistically significant separation (P-value &lt;0.05) among the three groups, regardless of patient characteristics, duration of the disease, antibiotic therapy and medical history. This classification is associated with differences in the production of distinct molecules with presumptive global importance in the gut environment, disease progression and inflammation. Moreover, although severe impaired metabolite production and biological deficits were associated with the carriage of C. difficile that did not produce toxins, only previously unrecognised selective features, namely, choline- and acetylputrescine-deficient gut environments, characterised the carriage of toxin-producing C. difficile. Additional results showed that the changes induced by C. difficile become marked at the highest level of the functional hierarchy, namely the metabolic activity exemplified by the gut microbial metabolome regardless of heterogeneities that commonly appear below the functional level (gut bacterial composition). We discuss possible explanations for this effect and suggest that the changes imposed by CDAD are much more defined and predictable than previously thought.
Description of quantum coherence in thermodynamic processes requires constraints beyond free energy
Authors: Lostaglio Matteo , Jennings David , Rudolph Terry 
Published: March 2015

AbstractRecent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
Authors: Cotney Justin , Muhle Rebecca A. , Sanders Stephan J. , Liu Li , Willsey A. Jeremy , Niu Wei , Liu Wenzhong , Klei Lambertus , Lei Jing , Yin Jun , Reilly Steven K. , Tebbenkamp Andrew T. , Bichsel Candace , Pletikos Mihovil , Sestan Nenad , Roeder Kathryn , State Matthew W. , Devlin Bernie , Noonan James P. 
Published: March 2015

AbstractRecent studies implicate chromatin modifiers in autism spectrum disorder (ASD) through the identification of recurrent de novo loss of function mutations in affected individuals. ASD risk genes are co-expressed in human midfetal cortex, suggesting that ASD risk genes converge in specific regulatory networks during neurodevelopment. To elucidate such networks, we identify genes targeted by CHD8, a chromodomain helicase strongly associated with ASD, in human midfetal brain, human neural stem cells (hNSCs) and embryonic mouse cortex. CHD8 targets are strongly enriched for other ASD risk genes in both human and mouse neurodevelopment, and converge in ASD-associated co-expression networks in human midfetal cortex. CHD8 knockdown in hNSCs results in dysregulation of ASD risk genes directly targeted by CHD8. Integration of CHD8-binding data into ASD risk models improves detection of risk genes. These results suggest loss of CHD8 contributes to ASD by perturbing an ancient gene regulatory network during human brain development.
Cobalt-catalysed site-selective intra- and intermolecular dehydrogenative amination of unactivated sp3 carbons
Authors: Wu Xuesong , Yang Ke , Zhao Yan , Sun Hao , Li Guigen , Ge Haibo 
Published: March 2015

AbstractCobalt-catalysed sp2 C–H bond functionalization has attracted considerable attention in recent years because of the low cost of cobalt complexes and interesting modes of action in the process. In comparison, much less efforts have been devoted to the sp3 carbons. Here we report the cobalt-catalysed site-selective dehydrogenative cyclization of aliphatic amides via a C–H bond functionalization process on unactivated sp3 carbons with the assistance of a bidentate directing group. This method provides a straightforward synthesis of monocyclic and spiro β- or γ-lactams with good to excellent stereoselectivity and functional group tolerance. In addition, a new procedure has been developed to selectively remove the directing group, which enables the synthesis of free β- or γ-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp3 carbons is also realized.