bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three new basidiomycetous yeasts, Pseudozyma alboarmeniaca sp. nov., Pseudozyma crassa sp. nov. and Pseudozyma siamensis sp. nov. isolated from Thai patients
Authors: Mekha Nanthawan , Takashima Masako , Boon‐long Jotika , Cho Otomi , Sugita Takashi 
Published: November 2013

ABSTRACTWe previously reported the first isolation of Pseudozyma species from the blood of Thai patients. In this study, three additional new Pseudozyma species were isolated from clinical specimens from Thai patients. The Pseudozyma species showed relatively low sensitivity to azole antifungal agents. The names proposed for these isolates are Pseudozyma alboarmeniaca (DMST 17135T = JCM 12454T = CBS 9961T), Pseudozyma crassa (DMST 17136T = JCM 12455T = CBS 9959T) and Pseudozyma siamensis (DMST 17137T = JCM 12456T CBS 9960T), where DMST is Department of Medical Sciences Culture Collection, JCM is Japan Collection of Microorganisms and CBS is Centraalbureau voor Schimmelcultures.
Human Rights, Universality and Sovereignty: The Irrelevance and Relevance of Sharia
Authors: An‐Naim Abdullahi Ahmed 
Published: November 2013

AbstractIn this article I argue that the paradoxes of universality and self‐regulation by the state are inherent to the human rights paradigm itself in its application to every cultural, religious and ideological context. By the paradox of universality I refer to the expectation of global agreement on universal human rights norms among peoples of radically different cultural (including religious and ideological) traditions around the world. The paradox of self‐regulation by the state is in expecting any state to adopt human rights norms to limit its own powers, and then to effectively enforce those limitations against the officials of the same state. This article focuses on the internal dimension of this process in relation to Islamic societies. The case of Sharia is examined here to illustrate how the paradoxes of universality and self‐regulation can be mediated through an internal discourse within Islamic societies. I examine the prospects of Islamic reform in light of the cultural relevance and the legal irrelevance of Sharia norms and the possibility of their internal transformation from an Islamic point of view.
A model‐based approach to studying changes in compositional heterogeneity
Authors: Baeten Lander , Warton David I. , Van Calster Hans , De Frenne Pieter , Verstraeten Gorik , Bonte Dries , Bernhardt‐Römermann Markus , Cornelis Johnny , Decocq Guillaume , Eriksson Ove , Hédl Radim , Heinken Thilo , Hermy Martin , Hommel Patrick , Kirby Keith , Naaf Tobias , Petřík Petr , Walther Gian‐Reto , Wulf Monica , Verheyen Kris 
Published: November 2013

Summary

Non‐random species loss and gain in local communities change the compositional heterogeneity between communities over time, which is traditionally quantified with dissimilarity‐based approaches. Yet, dissimilarities summarize the multivariate species data into a univariate index and obscure the species‐level patterns of change, which are central to understand the causes and consequences of the community changes.

Here, we propose a model‐based approach that looks for species‐level effects of time period and construct a multiple‐site metric as a sum across species to test the consistency of the individual species responses. Species fall into different response types, showing how they influence the changes in community heterogeneity.

In a comparison with other multiple‐site metrics, we illustrate the properties of our method and the differences and similarities with other approaches. For instance, our metric estimates the total variation in a community data set based on species‐level contributions, not the compositional dissimilarities between particular sites. Similar to some other approaches, we can distinguish between heterogeneity derived from turnover or richness differences.

Our approach was applied to a set of 23 forest understorey resurvey studies spread across Europe. We show the species gains and losses may as well decrease or increase levels of community heterogeneity. Although species occurrences and communities have not changed in a consistent way along continental‐scale environmental gradients such as climatic conditions, several species shifted in a similar way across the different data sets.

Testing the significance of shifts in species prevalence over time to infer corresponding changes in the compositional heterogeneity among sites provides a very intuitive tool for community resurvey studies. The main strengths of our framework are the explicit consideration of the relative roles of species gains and losses and the straightforward generalization to different sets of hypotheses related to community changes.
Programming effects of FTO in the development of obesity
Authors: Sebert S. , Salonurmi T. , Keinänen‐Kiukaanniemi S. , Savolainen M. , Herzig K.‐H. , Symonds M. E. , Järvelin M.‐R. 
Published: November 2013

AbstractIt is becoming increasingly recognized that early‐life nutritional, metabolic and environmental factors can have a long‐term impact on the early onset of obesity, type 2 diabetes and cardiovascular diseases. Numerous experimental and epidemiological observations support the concept that an individual's response to their adult lifestyle and nutritional environment depends not only on their genetic susceptibility but also on their previous early‐life experiences. The current research challenge is to determine the primary pathways contributing to ‘non‐ or epi‐genetic’ causes of excess adult weight gain and adiposity. Evidence from the fields of genetic epidemiology, life course modelling and diet‐induced foetal programming all support a role for the FTO gene in this complex biological interaction. It may provide a missing link in the developmental regulation of energy metabolism. Our review therefore considers the role of the FTO gene in the early‐life determination of body weight, body composition and energy balance. We will summarize current knowledge on FTO biology combining human genetic epidemiology, molecular models and findings from animal studies. Notably, we will focus on the role of FTO in energy balance in humans, the importance of FTO polymorphisms in childhood growth and the impact of foetal nutrition. Ultimately, we propose a new hypothesis for future research designed to understand the role of FTO in setting gene expression in metabolically active tissues.
Evaluation of pain scores after single‐incision and conventional laparoscopic cholecystectomy: A randomized control trial in a rural Indian population
Authors: Borle Firoz R , Mehra Bhupendra K , Jain Sheelchand 
Published: November 2013

AbstractIntroductionSingle‐incision laparoscopic cholecystectomy (SILC) is considered to be less invasive and have less morbidity than conventional laparoscopic cholecystectomy (CLC). However, there is a relative paucity of data regarding postoperative pain scores in rural Indian populations following SILC. Also, data pertaining to the applicability of SILC in rural Indian population are scant.MethodsIn the present randomized control trial, pain scores after SILC and CLC were evaluated. Sixty patients with gallstone disease were randomly assigned to one of two groups with 30 patients each: the CLC group and the SILC group. Postoperative pain scores were recorded on the visual analog scale at 8 hours, 24 hours and 7 days after surgery.ResultsThe patients were comparable with respect to age, sex and BMI. Operative time was longer for the SILC group (47.73 ± 5.57 min vs 69.53 ± 8.96 min; P < 0.0001).The pain scores were similar in both groups at 8 hours (3.61 ± 0.41 vs 3.50 ± 0.51; P = 0.36) and 24 hours (3.30 ± 0.59 vs 3.20 ± 0.40; P = 0.44) postoperatively. On day 7, the SILC group had lower pain scores than the CLC group (2.56 ± 0.56 vs 1.16 ± 0.37; P < 0.01).ConclusionThere was no distinct advantage to SILC with regard to immediate postoperative pain. Pain was significantly less (P < 0.01) in the SILC group on postoperative day 7.
In vitro fragmentation efficiency of holmium: yttrium‐aluminum‐garnet (YAG) laser lithotripsy – a comprehensive study encompassing different frequencies, pulse energies, total power levels and laser fibre diameters
Authors: Kronenberg Peter , Traxer Olivier 
Published: November 2013

ObjectiveTo assess the fragmentation (ablation) efficiency of laser lithotripsy along a wide range of pulse energies, frequencies, power settings and different laser fibres, in particular to compare high‐ with low‐frequency lithotripsy using a dynamic and innovative testing procedure free from any human interaction bias.Materials and MethodsAn automated laser fragmentation testing system was developed.The unmoving laser fibres fired at the surface of an artificial stone while the stone was moved past at a constant velocity, thus creating a fissure.The lithotripter settings were 0.2–1.2 J pulse energies, 5–40 Hz frequencies, 4–20 W power levels, and 200 and 550 μm core laser fibres.Fissure width, depth, and volume were analysed and comparisons between laser settings, fibres and ablation rates were made.ResultsLow frequency‐high pulse energy (LoFr‐HiPE) settings were (up to six times) more ablative than high frequency‐low pulse energy (HiFr‐LoPE) at the same power levels (P < 0.001), as they produced deeper (P < 0.01) and wider (P < 0.001) fissures.There were linear correlations between pulse energy and fragmentation volume, fissure width, and fissure depth (all P < 0.001).Total power did not correlate with fragmentation measurements.Laser fibre diameter did not affect fragmentation volume (P = 0.81), except at very low pulse energies (0.2 J), where the large fibre was less efficient (P = 0.015).ConclusionsAt the same total power level, LoFr‐HiPE lithotripsy was most efficient. Pulse energy was the key variable that drove fragmentation efficiency.Attention must be paid to prevent the formation of time‐consuming bulky debris and adapt the lithotripter settings to one's needs.As fibre diameter did not affect fragmentation efficiency, small fibres are preferable due to better scope irrigation and manoeuvrability.
A myelopoiesis gene signature during remission in anti-neutrophil cytoplasm antibody-associated vasculitis does not predict relapses but seems to reflect ongoing prednisolone therapy
Authors: Kurz T , Weiner M , Skoglund C , Basnet S , Eriksson P , Segelmark M 
Published: November 2013

SummaryA myelopoiesis gene signature in circulating leucocytes, exemplified by increased myeloperoxidase (MPO) and proteinase 3 (PR3) mRNA levels, has been reported in patients with active anti-neutrophil cytoplasm antibody-associated vasculitis (AAV), and to a lesser extent during remission. We hypothesized that this signature could predict disease relapse. mRNA levels of PR3, MPO, selected myelopoiesis transcription factors [CCAAT/enhancer binding protein α (CEBP-α), CCAAT/enhancer binding protein β (CEBP-β), SPI1/PU.1-related transcription factor (SPIB), spleen focus forming virus proviral integration oncogene, PU.1 homologue (SPI1)] and microRNAs (miRNAs) from patient and control peripheral blood mononuclear cells (PBMC) and polymorphonuclear cells (PMN) were analysed and associated with clinical data. Patients in stable remission had higher mRNA levels for PR3 (PBMC, PMN) and MPO (PBMC). PR3 and SPIB mRNA correlated positively in controls but negatively in patient PBMC. Statistically significant correlations existed between PR3 mRNA and several miRNAs in controls, but not in patients. PR3/MPO mRNA levels were not associated with previous or future relapses, but correlated with steroid treatment. Prednisolone doses were negatively linked to SPIB and miR-155-5p, miR-339-5p (PBMC) and to miR-221, miR-361 and miR-505 (PMN). PR3 mRNA in PBMC correlated with time since last flare, blood leucocyte count and estimated glomerular filtration rate. Our results show that elevated leucocyte PR3 mRNA levels in AAV patients in remission do not predict relapse. The origin seems multi-factorial, but to an important extent explainable by prednisolone action. Gene signatures in patients with AAV undergoing steroid treatment should therefore be interpreted accordingly.
T helper type 17 pathway suppression by appendicitis and appendectomy protects against colitis
Authors: Cheluvappa R , Luo A S , Grimm M C 
Published: November 2013

Summary
Appendicitis followed by appendectomy (AA) at a young age protects against inflammatory bowel disease (IBD). We wanted to characterize the role of the T helper type 17 (Th17) system involved in this protective effect. AA was performed on 5-week-old male BALB/c mice and distal-colon samples were harvested. Mice with two laparotomies each served as sham–sham (SS) controls. RNA was extracted from four individual colonic samples per group (AA and SS groups) and each sample microarray-analysed and reverse transcription–polymerase chain reaction (RT–PCR)-validated. Gene-set enrichment analysis (GSEA) showed that the Th17 recruitment factor gene CCL20 was significantly suppressed at both 3 days post-AA and 28 days post-AA. Although Th17 cell development differentiation factor genes TGF-β2 and TGF-β3 were significantly up-regulated 3 days post-AA, GSEA 28 days post-AA showed that AA down-regulated 29 gene-sets associated with TGF-β1, TGF-β2 and TGF-β3 in contrast to none up-regulated with any of these genes. GSEA showed substantial down-regulation of gene-sets associated with Th17 lymphocyte recruitment, differentiation, activation and cytokine expression in the AA group 28 days post-AA. We conclude that Th17-system cytokines are kept under control by AA via down-regulation of proinflammatory CCL20, a rapid down-regulation of pro-Th17 cell differentiation genes TGF-β2 and TGF-β3, suppression of RORC-associated gene-sets, increased protective STAT1 expression and suppression of 81 ‘pro-Th17’ system gene-sets. AA suppresses the Th17 pathway leading to colitis amelioration. Further characterization of Th17-associated genes and biological pathways will assist in the development of better therapeutic approaches in IBD management.
Language Helps Children Succeed on a Classic Analogy Task
Authors: Christie Stella , Gentner Dedre 
Published: November 2013

AbstractAdult humans show exceptional relational ability relative to other species. In this research, we trace the development of this ability in young children. We used a task widely used in comparative research—the relational match‐to‐sample task, which requires participants to notice and match the identity relation: for example,AAshould matchBBinstead ofCD. Despite the simplicity of this relation, children under 4 years of age failed to pass this test (Experiment 1), and their performance did not improve even with initial feedback (Experiment 2). In Experiments 3 and 4, we found that two kinds of symbolic‐linguistic experience can facilitate relational reasoning in young children. Our findings suggest that children learn to become adept analogical thinkers, and that language fosters this learning in at least two distinct ways.
Perception from the First‐Person Perspective
Authors: Howell Robert J. 
Published: November 2013

AbstractThis paper develops a view of the content of perceptual states that reflects the cognitive significance those states have for the subject. Perhaps the most important datum for such a theory is the intuition that experiences are ‘transparent’, an intuition promoted by philosophers as diverse as Sartre and Dretske. This paper distinguishes several different transparency theses, and considers which ones are truly supported by the phenomenological data. It is argued that the only thesis supported by the data is much weaker than those typically considered in the literature, and has no obvious implications for the existence of sensory intermediaries. It does, however, have implications for the content of perceptual experience. It is argued that combining the first personal project with the transparency intuition yields an error theory of perception. The counterintuitive implications of this error theory are mitigated, however, by an account of perceptual beliefs which allows for them to be true even if the perceptual states are non‐veridical.
Evolution of age and length at maturation of Alaskan salmon under size‐selective harvest
Authors: Kendall Neala W. , Dieckmann Ulf , Heino Mikko , Punt André E. , Quinn Thomas P. 
Published: November 2013

AbstractSpatial and temporal trends and variation in life‐history traits, including age and length at maturation, can be influenced by environmental and anthropogenic processes, including size‐selective exploitation. Spawning adults in many wild Alaskan sockeye salmon populations have become shorter at a given age over the past half‐century, but their age composition has not changed. These fish have been exploited by a gillnet fishery since the late 1800s that has tended to remove the larger fish. Using a rare, long‐term dataset, we estimated probabilistic maturation reaction norms (PMRNs) for males and females in nine populations in two basins and correlated these changes with fishery size selection and intensity to determine whether such selection contributed to microevolutionary changes in maturation length. PMRN midpoints decreased in six of nine populations for both sexes, consistent with the harvest. These results support the hypothesis that environmental changes in the ocean (likely from competition) combined with adaptive microevolution (decreased PMRNs) have produced the observed life‐history patterns. PMRNs did not decrease in all populations, and we documented differences in magnitude and consistency of size selection and exploitation rates among populations. Incorporating evolutionary considerations and tracking further changes in life‐history traits can support continued sustainable exploitation and productivity in these and other exploited natural resources.
Understanding polyspecificity within the substrate‐binding cavity of the human multidrug resistance P‐glycoprotein
Authors: Martinez Lorena , Arnaud Ophélie , Henin Emilie , Tao Houchao , Chaptal Vincent , Doshi Rupak , Andrieu Thibault , Dussurgey Sébastien , Tod Michel , Di Pietro Attilio , Zhang Qinghai , Chang Geoffrey , Falson Pierre 
Published: November 2013

Human P‐glycoprotein (P‐gp) controls drugs bioavailability by pumping structurally unrelated drugs out of cells. The X‐ray structure of the mouse P‐gp ortholog has been solved, with two SSS enantiomers or one RRR enantiomer of the selenohexapeptide inhibitor QZ59, found within the putative drug‐binding pocket (Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, Zhuo R, Harrell PM, Trinh YT, Zhang Q, Urbatsch IL et al. (2009). Science 323, 1718–1722). This offered the first opportunity to localize the well‐known H and R drug‐binding sites with respect to the QZ59 inhibition mechanisms of Hoechst 33342 and daunorubicin transports, characterized here in cellulo. We found that QZ59‐SSS competes efficiently with both substrates, with KI,app values of 0.15 and 0.3 μm, which are 13 and 2 times lower, respectively, than the corresponding Km,app values. In contrast, QZ59‐RRR non‐competitively inhibited daunorubicin transport with moderate efficacy (KI,app = 1.9 μm); it also displayed a mixed‐type inhibition of the Hoechst 33342 transport, resulting from a main non‐competitive tendency (Ki2,app = 1.6 μm) and a limited competitive tendency (Ki1,app = 5 μm). These results suggest a positional overlap of QZ59 and drugs binding sites: full for the SSS enantiomer and partial for the RRR enantiomer. Crystal structure analysis suggests that the H site overlaps both QZ59‐SSS locations while the R site overlaps the most embedded location.
Risk factors of postoperative urinary retention after hip surgery for femoral neck fracture in elderly women
Authors: Tobu Shohei , Noguchi Mitsuru , Hashikawa Takeshi , Uozumi Jiro 
Published: November 2013

AimThe aim of the present study was to evaluate risk factors for postoperative urinary retention (POUR) in female patients with femoral neck fractures.MethodsWe recruited 72 female patients (age 86.5 ± 6.7 years) from among 90 cases of hip surgery carried out between January and December 2011 at Goto Chuo Hospital. We evaluated the risk factors for POUR, including the administration of anticholinergic drugs, diabetes mellitus, preoperative dementia and/or delirium, neurological disorders, age, hypertension, overactive bladder, and the postoperative duration of the use of an indwelling urethral catheter using a multiple logistic regression analysis.ResultsIn the present study, POUR occurred in eight out of 72 cases (11.1%). The multivariate analysis showed that the indwelling period of the urethral catheter (per 1‐day increase; P = 0.04, OR 0.33 95% CI 0.11–0.96), and preoperative dementia and/or delirium (P = 0.03, OR10.4, 95%CI 1.21–89.2) correlated with the occurrence of POUR. Diabetes mellitus (P = 0.78), anticholinergic agents (P = 0.23), neurological disorders (P = 0.83), age (P = 0.86), hypertension (P = 0.76) and overactive bladder (P = 0.34) did not significantly correlate with the occurrence of POUR.ConclusionsThe present study showed that the early removal of the urethral catheter, and preoperative dementia and/or delirium had significant correlations with POUR. The femoral neck fractures and the surgical procedure used for the hip surgery do not induce damage to the bladder and nerve system related to the voiding function, and the voiding function in all of the patients recovered after short‐term intermittent catheterization. Physicians should not place permanent indwelling urethral catheters without carrying out urological assessments. Geriatr Gerontol Int 2014; 14: 636–639.
A Summary of Attack Methods and Confidentiality Protection Measures for Fully Automated Remote Analysis Systems
Authors: O'Keefe Christine M. , Chipperfield James O. 
Published: November 2013

SummaryThis paper presents a summary of the current state of research on reducing the risk of disclosure related to what may be called “non‐traditional” outputs for statistical agencies. Whereas traditional outputs include frequency tables, magnitude tables and public use microdata files, non‐traditional outputs include outputs associated with user‐defined exploratory data analysis and statistical modelling offered through a remote analysis system. In remote analysis, a system accepts a query from an analyst, runs it on data held in a secure environment, and then returns the results to the analyst. There is a considerable current interest in fully automated remote analysis systems, because these have the potential to enable agencies to respond to growing researcher demand for more and more detailed data. In practice, a range of protective measures is most effective in remote analysis, and the choice of this range depends heavily on the context including the regulatory environment, the dataset itself, and the purpose of the access.This paper provides a summary of known attack methods on remote analysis system outputs, focussing on exploratory data analysis and linear regression. The paper also summarizes the associated suggested protective measures designed to prevent disclosures and thwart attacks in fully automated remote analysis systems. Some commentary on the attacks and measures is provided.