bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance, Revision, and Extension of the National Nosocomial Infections Surveillance System's Risk Index in Brazilian Hospitals
Authors: Biscione Fernando Martín , Couto Renato Camargos , Pedrosa Tânia M. G. 
Published: January 2012

Objective.To assess the benefit of using procedure-specific alternative cutoff points for National Nosocomial Infections Surveillance (NNIS) risk index variables and of extending surgical site infection (SSI) risk prediction models with a postdischarge surveillance indicator.Design.Open, retrospective, validation cohort study.Setting.Five private, nonuniversity Brazilian hospitals.Patients.Consecutive inpatients operated on between January 1993 and May 2006 (other operations of the genitourinary system [n = 20,723], integumentary system [n = 12,408], or musculoskeletal system [n = 15,714] and abdominal hysterectomy [n = 11,847]).Methods.For each procedure category, development and validation samples were defined nonrandomly. In the development samples, alternative SSI prognostic scores were constructed using logistic regression: (i) alternative NNIS scores used NNIS risk index covariates and cutoff points but locally derived SSI risk strata and rates, (ii) revised scores used procedure-specific alternative cutoff points, and (iii) extended scores expanded revised scores with a postdischarge surveillance indicator. Performances were compared in the validation samples using calibration, discrimination, and overall performance measures.Results.The NNIS risk index showed low discrimination, inadequate calibration, and predictions with high variability. The most consistent advantage of alternative NNIS scores was regarding calibration (prevalence and dispersion components). Revised scores performed slightly better than the NNIS risk index for most procedures and measures, mainly in calibration. Extended scores clearly performed better than the NNIS risk index, irrespective of the measure or operative procedure.Conclusions.Locally derived SSI risk strata and rates improved the NNIS risk index's calibration. Alternative cutoff points further improved the specification of the intrinsic SSI risk component. Controlling for incomplete postdischarge SSI surveillance provided consistently more accurate SSI risk adjustment.Infect Control Hosp Epidemiol 2012;33(2):124-134
Inclusion of 30-Day Postdischarge Detection Triples the Incidence of Hospital-Onset Methicillin-ResistantStaphylococcus aureus
Authors: Avery Taliser R. , Kleinman Ken P. , Klompas Michael , Aschengrau Ann , Huang Susan S. 
Published: January 2012

Background.Hospitalized patients are at increased risk for acquisition of methicillin-resistantStaphylococcus aureus(MRSA). As hospital length of stay shortens, hospital-acquired MRSA events may be more likely to be detected after discharge.Objective.We assessed the impact of attributing MRSA cases discovered within 30 days after discharge to the most recent hospitalization and identified patient characteristics associated with MRSA detection after discharge.Design.Retrospective cohort study.Setting.Twenty-seven acute care hospitals in Orange County, California.Participants.Adult acute care admissions (2002–2007).Methods.Using a countywide hospital data set containing diagnostic codes with present-on-admission (POA) indicators, we identified the first admission with a MRSA code for each patient. This incident MRSA admission was defined as predischarge-detected (pre-DD) hospital-onset MRSA (HO-MRSA) when MRSA was not POA. If MRSA was POA and a prior admission occurred within 30 days, this prior admission was assigned postdischarge-detected (post-DD) HO-MRSA. We evaluated the impact of including post-DD HO-MRSA in the calculation of hospital HO-MRSA incidence using signed-rank tests and reviewed changes in hospital rankings. We conducted multivariate comparisons of patient characteristics of pre-DD versus post-DD HO-MRSA patients.Results.Among 1,217,253 at-risk hospitalizations, the inclusion of post-DD HO-MRSA tripled the median hospital HO-MRSA incidence, from 12.2 to 35.7 cases per 10,000 at-risk admissions (P<.0001). Hospital ranking changed substantially when including post-DD HO-MRSA. Patients with shorter stays were more likely to have post-DD MRSA.Conclusions.On the basis of administrative claims data, the inclusion of post-DD HO-MRSA significantly increased the estimated HO-MRSA incidence and altered hospital rankings. This finding underscores the limitations of single-facility data when deriving HO-MRSA incidence and rank.Infect Control Hosp Epidemiol2012;33(2):114-121
Performance analysis of AlGaAs/GaAs tunnel junctions for ultra-high concentration photovoltaics
Authors: García I , Rey-Stolle I , Algora C 
Published: January 2012

Abstract
An n++-GaAs/p++-AlGaAs tunnel junction with a peak current density of 10 100 A cm−2 is developed. This device is a tunnel junction for multijunction solar cells, grown lattice-matched on standard GaAs or Ge substrates, with the highest peak current density ever reported. The voltage drop for a current density equivalent to the operation of the multijunction solar cell up to 10 000 suns is below 5 mV. Trap-assisted tunnelling is proposed to be behind this performance, which cannot be justified by simple band-to-band tunnelling. The metal-organic vapour-phase epitaxy growth conditions, which are in the limits of the transport-limited regime, and the heavy tellurium doping levels are the proposed origins of the defects enabling trap-assisted tunnelling. The hypothesis of trap-assisted tunnelling is supported by the observed annealing behaviour of the tunnel junctions, which cannot be explained in terms of dopant diffusion or passivation. For the integration of these tunnel junctions into a triple-junction solar cell, AlGaAs barrier layers are introduced to suppress the formation of parasitic junctions, but this is found to significantly degrade the performance of the tunnel junctions. However, the annealed tunnel junctions with barrier layers still exhibit a peak current density higher than 2500 A cm−2 and a voltage drop at 10 000 suns of around 20 mV, which are excellent properties for tunnel junctions and mean they can serve as low-loss interconnections in multijunction solar cells working at ultra-high concentrations.
A method to infer positive selection from marker dynamics in an asexual population
Authors: Illingworth Christopher J. R. , Mustonen Ville 
Published: January 2012

Abstract
Motivation: The observation of positive selection acting on a mutant indicates that the corresponding mutation has some form of functional relevance. Determining the fitness effects of mutations thus has relevance to many interesting biological questions. One means of identifying beneficial mutations in an asexual population is to observe changes in the frequency of marked subsets of the population. We here describe a method to estimate the establishment times and fitnesses of beneficial mutations from neutral marker frequency data.
Results: The method accurately reproduces complex marker frequency trajectories. In simulations for which positive selection is close to 5% per generation, we obtain correlations upwards of 0.91 between correct and inferred haplotype establishment times. Where mutation selection coefficients are exponentially distributed, the inferred distribution of haplotype fitnesses is close to being correct. Applied to data from a bacterial evolution experiment, our method reproduces an observed correlation between evolvability and initial fitness defect.
Availability: A C++ implementation of the inference tool is available under GNU GPL license (http://www.sanger.ac.uk/resources/software/optimist/).
Contact: vm5@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of Early and High Amino Acid Supplementation on ELBW Infants at 2 Years
Authors: Blanco Cynthia L. , Gong Alice K. , Schoolfield John , Green Belinda K. , Daniels Wanda , Liechty Edward A. , Ramamurthy Rajam 
Published: January 2012

ABSTRACTObjective:The aim of the present study was to examine the effects of early and high intravenous (IV) amino acid (AA) supplementation on growth, health, and neurodevelopment of extremely‐low‐birth‐weight (ELBW) infants throughout their first 2 years of life.Methods:Infants were prospectively randomized in a double‐masked fashion and treated for 7 days with either IV AA starting at 0.5 g · kg−1 · day−1 and increased by 0.5 g · kg−1 every day to 3 g · kg−1 · day−1 or starting at 2 g · kg−1 · day−1 of IV AA and advanced by 1 g · kg−1 every day to 4 g · kg−1 · day−1. Plasma AA concentrations were determined by reverse‐phase high‐performance liquid chromatography. Survivors were longitudinally assessed with Bayley II Scales of Infant Development and physical, social, and global health.Results:Forty‐three of 51 survivors were studied. Mental Developmental Index (MDI) and Psychomotor Developmental Index were similar between groups; however, the early and high AA group had a lower MDI at 18 months. This difference disappeared at 2 years of age. The early and high AA group z score means for weight, length, and head circumferences were significantly lower than the standard AA group at most visits. Cumulative and single plasma AA concentrations correlated negatively with MDI and postnatal growth.Conclusions:ELBW infants who received early and high IV AA during the first week of life were associated with poor overall growth at 2 years.
Review article: a decision‐making algorithm for the management of pregnancy in the inflammatory bowel disease patient
Authors: Habal F. M. , Huang V. W. 
Published: January 2012

AbstractBackgroundInflammatory bowel disease affects patients who are in their reproductive years. There are many questions regarding the management of IBD patients who are considering or who are already pregnant. These include the effect of the disease and the medications on fertility and on the pregnancy outcome.AimTo create an evidence‐based decision‐making algorithm to help guide physicians through the management of pregnancy in the IBD patient.MethodsA literature review using phrases that include: ‘inflammatory bowel disease’, ‘Crohn's disease’, ‘ulcerative colitis’, ‘pregnancy’, ‘fertility’, ‘breast feeding’, ‘delivery’, ‘surgery’, ‘immunomodulators’, ‘azathioprine’, ‘mercaptopurine’, ‘biologics’, ‘infliximab’, ‘adalimumab’, ‘certolizumab’.ConclusionsThe four decision‐making nodes in the algorithm for the management of pregnancy in the IBD patient, and the key points for each one are as follows: (i) preconception counselling – pregnancy outcome is better if patients remain in remission during pregnancy, (ii) contemplating pregnancy or is already pregnant – drugs used to treat IBD appear to be safe during pregnancy, with the exception of methotrexate and thalidomide, (iii) delivery and (iv) breast feeding – drugs used to treat IBD appear to be safe during lactation, except for ciclosporin. Another key point is that biological agents may be continued up to 30 weeks gestation. The management of pregnancy in the IBD patient should be multi‐disciplinary involving the patient and her partner, the family physician, the gastroenterologist and the obstetrician.
Compressional salt tectonics and synkinematic strata of the western Kuqa foreland basin, southern Tian Shan, China
Authors: Li Shiqin , Wang Xin , Suppe John 
Published: January 2012

AbstractThe synkinematic strata of the Kuqa foreland basin record a rich history of Cenozoic reactivation of the Palaeozoic Tian Shan mountain belt. Here, we present new constraints on the history of deformation in the southern Tian Shan, based on an analysis of interactions between tectonics and sedimentation in the western Kuqa basin. We constructed six balanced cross‐sections of the basin, integrating surface geology, well data and a grid of seismic reflection profiles. These profiles show that the Qiulitage fold belt on the southern edge of the Kuqa basin developed by thin‐skinned compression salt tectonics. The structural styles have been influenced by two major factors: the nature of early‐formed diapirs and the basinward depositional limit of the Kumugeliemu salt. Several early diapirs developed in the western Kuqa basin, soon after salt deposition, which acted to localize the subsequent shortening. Where diapirs had low relief and a thick overburden they tended to tighten into salt domes 3000–7000 m in height. Conversely, where the original diapirs had higher relief and a thinner overburden they tended to evolve into salt nappes, with the northern flanks of the diapirs thrusting over their southern flanks. Salt was expelled forward, up dip along the mother salt layer, tended to accumulate at the distal pinch‐out of Kumugeliemu salt located at the Qiulitage fold belt. Furthermore, the synkinematic strata (6–8 km thick) of the Kuqa basin indicate that during the Cenozoic reactivation of the Tian Shan, shortening of the western Kuqa basin was mainly in the hinterland until the early Miocene. Then, compression spread simultaneously southwards to the Dawanqi anticline, the Qiulitage fold belt and the southernmost blind detachment fold at the end of Miocene. The western Kuqa basin has a shortening of ca. 23 km. We consider that ca. 9 km was consumed from the end of the Miocene (5.2/5.8 Ma) to the early Pleistocene (2.58 Ma) and another ca. 14 km have been absorbed since then. Thus, we obtain a ca. 3.4/2.8 mm year−1 average shortening from 5.2/5.8 to 2.58 Ma, followed by a 60–90% increase in average shortening rate to ca. 5.4 mm year−1 since 2.58 Ma. This suggests that the reactivation of the modern Tian Shan has been accelerating up to the present day.
Post‐orogenic evolution of the southernPyrenees: constraints from inverse thermo‐kinematic modelling of low‐temperature thermochronology data
Authors: Fillon Charlotte , van der Beek Peter 
Published: January 2012

AbstractThe late‐stage evolution of the southern centralPyrenees has been well documented but controversies remain concerning potentialNeogene acceleration of exhumation rates and the influence of tectonic and/or climatic processes. A popular model suggests that thePyrenees and their southern foreland were buried below a thick succession of conglomerates during theOligocene, when the basin was endorheic. However, both the amount of post‐orogenic fill and the timing of re‐excavation remain controversial. We address this question by revisiting extensive thermochronological datasets of theAxialZone. We use an inverse approach that couples the thermo‐kinematic modelPecubeand theNeighbourhood inversion algorithm to constrain the history of exhumation and topographic changes since 40 Ma. By comparison with independent geological data, we identified a most probable scenario involving rapid exhumation (>2.5 km Myr−1) between 37 and 30 Ma followed by a strong decrease to very slow rates (0.02 km Myr−1) that remain constant until the present. Therefore, the inversion does not require a previously inferredPliocene acceleration in regional exhumation rates. A clear topographic signal emerges, however: the topography has to be infilled by conglomerates to an elevation of 2.6 km between 40 and 29 Ma and then to remain stable untilca. 9 Ma. We interpret the last stage of the topographic history as recording major incision of the southernPyrenean wedge, due to the Ebro basin connection to theMediterranean, well before previously suggestedMessinian ages. These results thus demonstrate temporally varying controls of different processes on exhumation: rapid rock uplift in an active orogen during lateEocene, whereas base‐level changes in the foreland basin control the post‐orogenic evolution of topography and exhumation in the centralPyrenees. In contrast, climate changes appear to play a lesser role in the post‐orogenic topographic and erosional evolution of this mountain belt.
The Burkholderia cenocepacia BDSF quorum sensing fatty acid is synthesized by a bifunctional crotonase homologue having both dehydratase and thioesterase activities
Authors: Bi Hongkai , Christensen Quin H. , Feng Youjun , Wang Haihong , Cronan John E. 
Published: January 2012

SummarySignal molecules of the diffusible signal factor (DSF) family have been shown recently to be involved in regulation of pathogenesis and biofilm formation in diverse Gram‐negative bacteria. DSF signals are reported to be active not only on their cognate bacteria, but also on unrelated bacteria and the pathogenic yeast, Candida albicans. DSFs are monounsaturated fatty acids of medium chain length containing an unusual cis‐2 double bond. Although genetic analyses had identified genes involved in DSF synthesis, the pathway of DSF synthesis was unknown. The DSF of the important human pathogen Burkholderia cenocepacia (called BDSF) is cis‐2‐dodecenoic acid. We report that BDSF is synthesized from a fatty acid synthetic intermediate, the acyl carrier protein (ACP) thioester of 3‐hydroxydodecanoic acid. This intermediate is intercepted by protein Bcam0581 and converted to cis‐2‐dodecenoyl‐ACP. Bcam0581 is annotated as a homologue of crotonase, the first enzyme of the fatty acid degradation pathway. We demonstrated Bcam0581to be a bifunctional protein that not only catalysed dehydration of 3‐hydroxydodecanoyl‐ACP to cis‐2‐dodecenoyl‐ACP, but also cleaved the thioester bond to give the free acid. Both activities required the same set of active‐site residues. Although dehydratase and thioesterase activities are known activities of the crotonase superfamily, Bcam0581 is the first protein shown to have both activities.
N for AsN – O for StrOcture? A strand–loop–strand motif for prokaryotic O‐glycosylation
Authors: Otzen Daniel 
Published: January 2012

SummarySo far, it has not been possible to identify a general sequence motif for O‐glycosylation in bacteria. In this issue, Charbonneau et al. (2012) demonstrate why O‐glycosylation is mediated by a 13‐residue strand–loop–strand motif which is part of a 19‐residue imperfect repeat in the passenger domain of bacterial autotransporters. This motif provides a convenient ‘glycosylation cassette’ and raises intriguing questions about the structural regulation of the glycosylation pathway.
Wheat WRKY genes TaWRKY2 and TaWRKY19 regulate abiotic stress tolerance in transgenic Arabidopsis plants
Authors: NIU CAN‐FANG , WEI WEI , ZHOU QI‐YUN , TIAN AI‐GUO , HAO YU‐JUN , ZHANG WAN‐KE , MA BIAO , LIN QING , ZHANG ZHENG‐BIN , ZHANG JIN‐SONG , CHEN SHOU‐YI 
Published: January 2012

ABSTRACTWRKY‐type transcription factors are involved in multiple aspects of plant growth, development and stress response. WRKY genes have been found to be responsive to abiotic stresses; however, their roles in abiotic stress tolerance are largely unknown especially in crops. Here, we identified stress‐responsive WRKY genes from wheat (Triticum aestivum L.) and studied their functions in stress tolerance. Forty‐three putative TaWRKY genes were identified and two multiple stress‐induced genes, TaWRKY2 and TaWRKY19, were further characterized. TaWRKY2 and TaWRKY19 are nuclear proteins, and displayed specific binding to typical cis‐element W box. Transgenic Arabidopsis plants overexpressing TaWRKY2 exhibited salt and drought tolerance compared with controls. Overexpression of TaWRKY19 conferred tolerance to salt, drought and freezing stresses in transgenic plants. TaWRKY2 enhanced expressions of STZ and RD29B, and bound to their promoters. TaWRKY19 activated expressions of DREB2A, RD29A, RD29B and Cor6.6, and bound to DREB2A and Cor6.6 promoters. The two TaWRKY proteins may regulate the downstream genes through direct binding to the gene promoter or via indirect mechanism. Manipulation of TaWRKY2 and TaWRKY19 in wheat or other crops should improve their performance under various abiotic stress conditions.
Neuropathy in a patient with lymphocytic thrombophilic arteritis
Authors: Shen Sarah , Williams Richard A , Kelly Robert I 
Published: January 2012

ABSTRACTA 35‐year‐old Lebanese woman presented with a 3‐year history of persistent, localized livedo racemosa over her feet, distal legs and forearms that was associated with the development of lower limb sensorimotor neuropathy. Investigations revealed the patient was heterozygous for prothrombin gene mutation and was also found to have a T‐cell receptor gamma chain gene rearrangement. Histological examination revealed a mid‐lower dermal medium vessel lymphocytic vasculitis with prominent fibrinoid ring within its wall. These findings are consistent with a recently described condition known as lymphocytic thrombophilic arteritis. This has so far been considered to be a benign clinical condition not associated with extra cutaneous manifestations. The novel findings in the present case are the associated sensorimotor neuropathy and the characteristic fibrin ring appears to be intramural rather intraluminal in location. The findings of a T cell gene rearrangement and a prothombin gene mutation suggest that both immunological and thrombophilic factors might contribute to the development of this condition.
N and C control of ABC‐type bicarbonate transporter Cmp and its LysR‐type transcriptional regulator CmpR in a heterocyst‐forming cyanobacterium, Anabaena sp.
Authors: López‐Igual Rocío , Picossi Silvia , López‐Garrido Javier , Flores Enrique , Herrero Antonia 
Published: January 2012

SummaryIn the model, heterocyst‐forming cyanobacterium Anabaena sp. PCC 7120, gene cluster alr2877‐alr2880, which encodes an ABC‐type transport system, was induced under conditions of carbon limitation and its inactivation impaired the uptake of bicarbonate. Thus, this gene cluster encodes a Cmp bicarbonate transporter. ORF all0862, encoding a LysR‐type transcriptional regulator, was expressed under carbon limitation and at higher levels in the absence than in the presence of combined nitrogen, with a positive effect of the N‐control transcription factor NtcA. all0862 was expressed from two putative transcription start sites located 164 and 64 bp upstream from the gene respectively. The latter was induced under carbon limitation and was dependent on positive autoregulation by All0862. All0862 was required for the induction of the Cmp bicarbonate transporter, thus representing a CmpR regulator of Anabaena sp. These results show a novel mode of co‐regulation by C and N availability through the concerted action of N‐ and C‐responsive transcription factors.
Ovarian maturation and oogenesis in the blue swimmer crab, Portunus pelagicus (Decapoda: Portunidae)
Authors: Ravi Raghunath , Manisseri Mary K. , Sanil Nandiath Karayi 
Published: January 2012

AbstractThe study was aimed at understanding the process of reproduction and the changes happening in the ovary of Portunus pelagicus during maturation, which would be useful for its broodstock development for hatchery purposes. For that, tissue samples from different regions of the ovary at various stages of maturation were subjected to light and electron microscopy, and based on the changes revealed and the differences in ovarian morphology, the ovary was divided into five stages such as immature (previtellogenic oocytes), early maturing (early vitellogenic oocytes), late maturing (late vitellogenic oocytes), mature (vitellogenic oocytes), and spent (resorbing oocytes). The ovarian wall comprised of an outermost thin pavement epithelium, a middle layer of connective tissue, and an innermost layer of germinal epithelium. The oocytes matured as they moved from the centrally placed germinal zone toward the ovarian wall. The peripheral arrangement of nucleolar materials and the high incidence of cell organelles during the initial stages indicated vitellogenesis I. Movement of follicle cells toward oocytes in the early maturing stage and low incidence of mitochondria and endoplasmic reticulum in the ooplasm during late vitellogenic stage marked the commencement and end of vitellogenesis II, respectively. Yolk granules at various stages of development were seen in the ooplasm from late vitellogenic stage onwards. The spent ovary had an area with resorbing oocytes and empty follicle cells denoting the end of one reproductive cycle and another area with oogonial cells and previtellogenic oocytes indicating the beginning of the next.