bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Interdependence of Subtype and Severity: Contributions of Clinical and Neuropsychological Features to Melancholia and Non-melancholia in an Outpatient Sample
Authors: Quinn Candice , Harris Anthony , Kemp Andrew 
Published: February 2012

AbstractMajor depressive disorder is often considered to be a homogenous disorder that changes in terms of severity; however, the presence of distinct subtypes and a variety of presenting symptoms suggests much heterogeneity. Aiming to better understand the relationship between heterogeneity and diagnosis we used an exploratory approach to identify subtypes of depression on the basis of clinical symptoms and neuropsychological performance. Cluster analysis identified two groups of patients distinguished by level of cognitive dysfunction with the more severe cluster being associated with melancholic depression. While the relationship between cluster and subtype was significant, only 58% of melancholic patients were assigned to cluster 1 (the more severe cluster) and 66% of non-melancholic patients assigned to cluster 2. Subtypes also displayed a distinctive profile of impairment such that melancholic patients (n = 65) displayed more variability in attention while non-melancholic patients (n = 59) displayed memory recall impairment. While melancholia and non-melancholia are associated with a more severe and less severe form of depression respectively, findings indicate that differences between melancholia and non-melancholia are more than simple variation on severity. In summary, findings provide support for the heterogeneity of depression. (JINS, 2012, 18, 361–369)
A New Approach to the Determination of Concentration Profiles in Atom Probe Tomography
Authors: Felfer Peter J. , Gault Baptiste , Sha Gang , Stephenson Leigh , Ringer Simon P. , Cairney Julie M. 
Published: February 2012

AbstractAtom probe tomography (APT) provides three-dimensional analytical imaging of materials with near-atomic resolution using pulsed field evaporation. The processes of field evaporation can cause atoms to be placed at positions in the APT reconstruction that can deviate slightly from their original site in the material. Here, we describe and model one such process—that of preferential retention of solute atoms in multicomponent systems. Based on relative field evaporation probabilities, we calculate the point spread function for the solute atom distribution in the “z,” or in-depth direction, and use this to extract more accurate solute concentration profiles.
Diverse microbial species survive high ammonia concentrations
Authors: Kelly Laura C. , Cockell Charles S. , Summers Stephen 
Published: February 2012

AbstractPlanetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3from 5 to 35% (v/v) at −80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of theFirmicutes(Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, StaphylococcusandBrevibacillus) andActinobacteria(Streptomyces). Non-spore forming organisms also survived, includingProteobacteria(Pseudomonas) andActinobacteria(Arthrobacter) that are known to have environmentally resistant resting states.Clostridiumspp. were isolated from the exposed soil under anaerobic culture. High NH3was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.
The role of air‐sea fluxes in Subantarctic Mode Water formation
Authors: Holte James W. , Talley Lynne D. , Chereskin Teresa K. , Sloyan Bernadette M. 
Published: February 2012

Two hydrographic surveys and a one‐dimensional mixed layer model are used to assess the role of air‐sea fluxes in forming deep Subantarctic Mode Water (SAMW) mixed layers in the southeast Pacific Ocean. Forty‐two SAMW mixed layers deeper than 400 m were observed north of the Subantarctic Front during the 2005 winter cruise, with the deepest mixed layers reaching 550 m. The densest, coldest, and freshest mixed layers were found in the cruise's eastern sections near 77°W. The deep SAMW mixed layers were observed concurrently with surface ocean heat loss of approximately −200 W m−2. The heat, momentum, and precipitation flux fields of five flux products are used to force a one‐dimensional KPP mixed layer model initialized with profiles from the 2006 summer cruise. The simulated winter mixed layers generated by all of the forcing products resemble Argo observations of SAMW; this agreement also validates the flux products. Mixing driven by buoyancy loss and wind forcing is strong enough to deepen the SAMW layers. Wind‐driven mixing is central to SAMW formation, as model runs forced with buoyancy forcing alone produce shallow mixed layers. Air‐sea fluxes indirectly influence winter SAMW properties by controlling how deeply the profiles mix. The stratification and heat content of the initial profiles determine the properties of the SAMW and the likelihood of deep mixing. Summer profiles from just upstream of Drake Passage have less heat stored between 100 and 600 m than upstream profiles, and so, with sufficiently strong winter forcing, form a cold, dense variety of SAMW.
Changing Nonmainstream American English Use and Early Reading Achievement From Kindergarten to First Grade
Authors: Terry Nicole Patton , McDonald Connor Carol 
Published: February 2012

Purpose
This study had 2 principal aims: (a) to examine whether children who spoke Nonmainstream American English (NMAE) frequently in school at the end of kindergarten increased their production of Mainstream American English (MAE) forms by the end of first grade, and (b) to examine concurrent and predictive relations between children’s NMAE use and reading skills.

Method
A longitudinal design was implemented with 49 children who varied in their spoken NMAE production in kindergarten. Word reading, phonological awareness, and receptive vocabulary skills were measured at both time points.

Results
Analyses indicated that most children significantly increased their production of MAE forms between the 2 time points; however, this change was not associated with change in letter-word reading and phonological awareness skills. Regression analyses showed that NMAE use in kindergarten contributed significantly and independently to the variance in word reading in first grade, even after accounting for phonological awareness (although word reading in kindergarten was the best predictor of word reading in first grade).

Conclusions
The findings extend previous reports of a significant relation between NMAE use and reading among young children. Theoretical, research, and educational implications of the findings are discussed.
Blueberry field management and harvesting.
Authors: Hancock J. , Retamales J. 
Published: February 2012

Abstract

This chapter covers various management practices that are important in blueberry (Vaccinium spp.) cultivation, including mulching (with plastic film or organic mulch), irrigation, pruning, pollination and mechanical harvesting. Plant water relations, and blueberry response to water stress and water excess (flooding) are briefly discussed.
Electronic-Eye Faucets:LegionellaSpecies Contamination in Healthcare Settings
Authors: Sydnor Emily R. M. , Bova Gregory , Gimburg Anatoly , Cosgrove Sara E. , Perl Trish M. , Maragakis Lisa L. 
Published: February 2012

Objective.To compare heterotrophic plate counts (HPCs) andLegionellaspecies growth from electronic and manual faucet water samples.Design.Proportions of water samples with growth and colony-forming units were compared using Fisher's exact test and the Wilcoxon rank-sum test, respectively.Setting.Two psychiatric units and 1 medical unit in a 1,000-bed university hospital.Methods.Water samples were collected from 20 newly installed electronic faucets and 20 existing manual faucets in 3 hospital units. Manual faucets were located in rooms adjacent to the electronic faucets and received water from the same source. Water samples were collected between December 15, 2008, and January 29, 2009. Four electronic faucets were dismantled, and faucet components were cultured.Legionellaspecies and HPC cultures were performed using standard methods.Results.Nearly all electronic faucets (19/20 [95%]) grewLegionellaspecies from at least 1 water sample, compared with less than half (9/20 [45%]) of manual faucets (P= .001). Fifty-four (50%) of 108 electronic faucet water cultures grewLegionellaspecies, compared with 11 (15%) of 75 manual faucet water cultures (P< .001). After chlorine dioxide remediation, 4 (14%) of 28 electronic faucet and 1 (3%) of 30 manual faucet water cultures grewLegionellaspecies (P= .19), and 8 (29%) electronic faucet and 2 (7%) manual faucet cultures had significant HPC growth (P= .04). All 12 (100%) of die internal faucet components from 2 electronic faucets grewLegionellaspecies.Conclusions.Electronic faucets were more commonly contaminated withLegionellaspecies and other bacteria and were less likely to be disinfected after chlorine dioxide remediation. Electronic faucet components may provide points of concentrated bacterial growth.Infect Control Hosp Epidemiol2012;33(3):235-240
Effect of finite electrode area ratio on high-frequency Langmuir probe measurements
Authors: Shimoyama M , Oyama K-I , Abe T , Yau A W 
Published: February 2012

Abstract
Langmuir probe (LP) measurement generally requires a reference electrode with large surface area compared with that of a probe. Whereas a reference electrode with large surface area is available in laboratory experiments, surface area of the reference electrode is limited when the probe is installed on a small spacecraft such as a sounding rocket. Insufficient electrode area ratio of the reference electrode to the probe leads to distortion of the current–voltage (I–V) characteristics and therefore the derived electron temperature and density might be erroneous. In order to investigate the effect of finite electrode area ratio on LP measurements, we have carried out a laboratory simulation by setting up a model sounding rocket with whole apparatus for LP measurement in a vacuum chamber. By changing the frequency of sweep voltage applied to the probe from 0.1 Hz to 3 kHz, we have derived an equivalent resistance and capacitance of the reference electrode sheath, which was thought to be the principal cause of distortion in I–V characteristics. The result shows that when the electrode area ratio is 124, the electron temperature is unaffected by the impedance of the reference electrode while the electron density is underestimated by 50%. In addition, the high sweep frequency method introduced here turned out to be an effective approach to make measurements with LP possible even when a sufficient surface area ratio cannot be achieved.
Tunable energy filtering of ballistic electrons in graphene
Authors: Zubarev A , Dragoman D 
Published: February 2012

Abstract
We show, by employing the scattering matrix approach, that a magnetic field applied over a graphene strip can select obliquely incident ballistic electrons with definite energies, corresponding to specific Landau levels. The energy range in which filtering is possible depends on the position of the obliquely placed electrodes, which emit and collect the filtered electrons. Energy tuning is achieved by modifying the magnetic field strength.
Hadoop-BAM: directly manipulating next generation sequencing data in the cloud
Authors: Niemenmaa Matti , Kallio Aleksi , Schumacher André , Klemelä Petri , Korpelainen Eija , Heljanko Keijo 
Published: February 2012

Abstract
Summary: Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.
Availability: Available under the open-source MIT license at http://sourceforge.net/projects/hadoop-bam/
Contact: matti.niemenmaa@aalto.fi
Supplementary information: Supplementary material is available at Bioinformatics online.
Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts
Authors: He Feng , Ren Jie , Wang Wei , Ma Jun 
Published: February 2012

Abstract
Motivation: We describe a statistical model to dissect the noise in transcriptional bursts in a developmental system.
Results: We assume that, at any given moment of time, each copy of a native gene inside a cell can exist in either a bursting (active) or non-bursting (inactive) state. The experimentally measured total noise in the transcriptional states of a gene in a population of cells can be mathematically dissected into two contributing components: internal and external. While internal noise quantifies the stochastic nature of transcriptional bursts, external noise is caused by cell-to-cell differences including fluctuations in activator concentration. We use our developed methods to analyze the Drosophila Bicoid (Bcd) morphogen gradient system. For its target gene hunchback (hb), the noise properties can be recapitulated by a simplified gene regulatory model in which Bcd acts as the only input, suggesting that the external noise in hb transcription is primarily derived from fluctuations in the Bcd activator input. However, such a simplified gene regulatory model is insufficient to predict the noise properties of another Bcd target gene, orthodenticle (otd), suggesting that otd transcription is sensitive to additional external fluctuations beyond those in Bcd. Our results show that analysis of the relationship between input and output noise can reveal important insights into how a morphogen gradient system works. Our study also advances the knowledge about transcription at a fundamental level.
Contact: jun.ma@cchmc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Parental Knowledge of Fecal Incontinence in Children
Authors: van Tilburg Miranda A.L. , Squires Megan , Blois‐Martin Nanette , Williams Cathy , Benninga Marc A. , Peeters Babette , Ulshen Martin 
Published: February 2012

ABSTRACTObjectives:Fecal incontinence (FI) is a common and stressful symptom of constipation in children. Recurrent FI causes psychological and physiological changes, complicating treatment as symptom duration progresses; however, parental misconceptions about the causes of FI may delay seeking medical care. The aim of the present study was to assess parental knowledge about FI and determine how this relates to the care and treatment of FI.Methods:A questionnaire was developed from qualitative interviews and clinician input. The questionnaire was administered to 251 parents and tested for reliability and validity. Subscales were compared between parents who did and did not consult a clinician. In addition, 30 parents completed the questionnaire before and after consultation with a pediatric gastroenterologist and after 2 months of treatment.Results:Two subscales were identified with good psychometric properties: “Blame and Punish” and “Worry and Help.” Families who consulted a physician for their child's FI acknowledged the role of constipation and scored higher on Worry and Help (mean 36.4 vs mean 46.9; P < 0.0001). Trends were found for Blame and Punish to decrease after consultation with a pediatric gastroenterologist (mean 1.7 vs 1.5; P = 0.08) and after 2 months of treatment (mean 1.5; P = 0.08).Conclusions:Parental knowledge about FI changes with physician consultation. These findings can help in developing educational materials for parents to encourage early diagnosis and treatment and prevent chronic problems that are difficult to manage.
Histamine reduces susceptibility to natural killer cells via down‐regulation of NKG2D ligands on human monocytic leukaemia THP‐1 cells
Authors: Nagai Yasuhiro , Tanaka Yukinori , Kuroishi Toshinobu , Sato Ryutaro , Endo Yasuo , Sugawara Shunji 
Published: February 2012

SummaryNatural killer (NK) group 2D (NKG2D) is a key activating receptor expressed on NK cells, whose interaction with ligands on target cells plays an important role in tumorigenesis. However, the effect of histamine on NKG2D ligands on tumour cells is unclear. Here we showed that human monocytic leukaemia THP‐1 cells constitutively express MHC class I‐related chain A (MICA) and UL16‐binding protein 1 on their surface, and incubation with histamine reduced the expression in a dose‐dependent and time‐dependent manner as assessed by flow cytometry. Interferon‐γ augmented the surface expression of the NKG2D ligands, and this augmentation was significantly attenuated by histamine. The histamine H1 receptor (H1R) agonist 2‐pyridylethylamine and H2R agonist dimaprit down‐regulated the expression of NKG2D ligands, and activation of H1R and H2R signalling by A23187 and forskolin, respectively, had the same effect, indicating that the histamine‐induced down‐regulation of NKG2D ligands is mediated by H1R and H2R. Quantitative reverse transcription‐PCR showed that mRNA levels of the NKG2D ligands and relevant microRNAs were not significantly changed by histamine. Histamine down‐regulated the surface expression of endoplasmic reticulum protein 5, and inhibition of matrix metalloproteinases did not impair this down‐regulation, indicating that proteolytic shedding was not involved. Instead, pharmacological inhibition of protein transport and proteasome abrogated it, and histamine enhanced ubiquitination of MICA. Furthermore, histamine treatment significantly reduced susceptibility to NK cell‐mediated cytotoxicity. These results suggest that histamine down‐regulates NKG2D ligands through the activation of an H1R‐ and H2R‐mediated ubiquitin–proteasome pathway and consequently reduces susceptibility to NK cells.
S100A9 a new marker for monocytic human myeloid‐derived suppressor cells
Authors: Zhao Fei , Hoechst Bastian , Duffy Austin , Gamrekelashvili Jaba , Fioravanti Suzanne , Manns Michael P. , Greten Tim F. , Korangy Firouzeh 
Published: February 2012

SummaryMyeloid‐derived suppressor cells (MDSC) are a heterogeneous population of cells that negatively regulate the immune response during tumour progression, inflammation and infection. Only limited data are available on human MDSC because of the lack of specific markers. We have identified members of the S100 protein family – S100A8, S100A9 and S100A12 – specifically expressed in CD14+ HLA‐DR−/low MDSC. S100A9 staining in combination with anti‐CD14 could be used to identify MDSC in whole blood from patients with colon cancer. An increase in the population of CD14+ S100A9high MDSC was observed in the peripheral blood from colon cancer patients in comparison with healthy controls. Finally, nitric oxide synthase expression, a hallmark of MDSC, was induced in CD14+ S100A9high upon lipopolysaccharide/interferon‐γ stimulation. We propose S100 proteins as useful markers for the analysis and further characterization of human MDSC.
A national survey of the use of physical restraint in long‐term care hospitals in Japan
Authors: Chiba Yumi , Yamamoto‐Mitani Noriko , Kawasaki Maki 
Published: February 2012

Aims and objectives.  To investigate the prevalence of physical restraints in the long‐term care hospitals in Japan and to examine the factors of physical restraint use, including the specific skills/techniques that the staff use to minimise the restraints.Background.  Despite the national efforts to nullify physical restraint, it is still prevalent in long‐term care facilities in and out of Japan. More detailed information regarding what affects physical restraint is needed.Design.  Cross‐sectional mail survey.Method. A questionnaire was sent to a nursing ward manager of the random sample of long‐term care facilities in Japan.Results.  The average rate of physical restraint was 25·5%. Altogether, 81·0% of the restrained clients were under restraint for more than one month. The most prevalent method of restraint was bilateral bedrails, followed by the use of coveralls and gloves. Factors of restraint were different depending on the type of restraint, suggesting specific approaches are needed for specific type of restraint.Conclusions.  Physical restraint is still prevalent in Japanese long‐term care hospitals, and nurses need to develop effective intervention approach to redesigning practice related to physical restraints. Specialised intervention approach seems needed depending on the types of restraint.Relevance to clinical practice. Specific approach should be developed to minimise the physical restraint in long‐term care hospitals in Japan.