bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two methods of cord care in high-risk newborns
Authors: Ahn Youngmee , Sohn Min , Jun Yonghoon , Lee Eunyoung , Lee Sangmi 
Published: October 2013

This randomized clinical study explored the effects of two cord care methods on hydration, temperature, pH, and floras at the cord area in high-risk newborns. One group used the water method; and the other group used the alcohol method. Seventy-two newborns, including premature newborns, in the neonatal intensive care unit (NICU) of a university-affiliated hospital in South Korea were enrolled from August 2011 to May 2012. Hydration, temperature, pH, and floras were measured daily until the cords fell off. The results showed no difference between the groups in hydration, temperature, pH, and the colonization of floras, but cord detachment in the alcohol group took 2 days longer (12.8 [5.7] days) than in the water group (10.9 [4.1] days). Our findings suggest that the clean-and-dry method of cord care, which uses water, could be sufficient, possibly even better than alcohol in maintaining the physiologic surface milieu of the cord area with less chance of infection and manipulation in NICUs with optimal infection control.
Adsorption of ferrocyanide onto raw and acid-activated clinoptilolite and sepiolite: equilibrium modelling by error minimization
Authors: Önen V. , Yel E. 
Published: October 2013

AbstractThe experimental data on adsorption of Fe and CN of a ferrocyanide complex onto raw and acid-activated clinoptilolite/sepiolite on the basis of detention time and particle size was modelled by a linear and a non-linear approach. The linearized best-fit isotherm selection method and non-linear error minimization was applied through Freundlich, Langmuir and Temkin isotherms. ERRSQ, MPSD, HYBRID and ARE error functions were minimized by a developed MATLAB script to determine the isotherm parameters in non-linear optimization. The complex was not adsorbed as whole anions but the Fe and CN were adsorbed separately. 0.65 mg Fe/L. min and 4.84 mg CN/L. min initial adsorption rates were achieved with acid activated clinoptilolite. The Fe adsorption was not as successful as CN. The adsorption of Fe and CN was described by Freundlich and Langmuir isotherms respectively. The differences between the predicted isotherm parameter sets of linear models and minimized error function models indicated that both the best-fit isotherm selection and the isotherm constant determinations can be performed properly by error minimization as well as by conventional linear best fit modelling approach.
TRIM28 is essential for erythroblast differentiation in the mouse
Authors: Hosoya Tomonori , Clifford Mary , Losson Régine , Tanabe Osamu , Engel James Douglas 
Published: October 2013

Key PointsGenetic loss of the transcriptional corepressor TRIM28 in adult mice results in deficient adult erythropoiesis in bone marrow, and anemia. TRIM28 controls the mRNA levels of multiple erythroid transcription factors, heme biosynthetic enzymes, and the apoptotic apparatus.
Inflammation, obesity, and thrombosis
Authors: Samad Fahumiya , Ruf Wolfram 
Published: October 2013

Abstract
Clinical and epidemiological studies support a connection between obesity and thrombosis, involving elevated expression of the prothrombotic molecules plasminogen activator inhibitor-1 and tissue factor (TF) and increased platelet activation. Cardiovascular diseases and metabolic syndrome–associated disorders, including obesity, insulin resistance, type 2 diabetes, and hepatic steatosis, involve inflammation elicited by infiltration and activation of immune cells, particularly macrophages, into adipose tissue. Although TF has been clearly linked to a procoagulant state in obesity, emerging genetic and pharmacologic evidence indicate that TF signaling via G protein-coupled protease-activated receptors (PAR2, PAR1) additionally drives multiple aspects of the metabolic syndrome. TF–PAR2 signaling in adipocytes contributes to diet-induced obesity by decreasing metabolism and energy expenditure, whereas TF–PAR2 signaling in hematopoietic and myeloid cells drives adipose tissue inflammation, hepatic steatosis, and insulin resistance. TF-initiated coagulation leading to thrombin–PAR1 signaling also contributes to diet-induced hepatic steatosis and inflammation in certain models. Thus, in obese patients, clinical markers of a prothrombotic state may indicate a risk for the development of complications of the metabolic syndrome. Furthermore, TF-induced signaling could provide new therapeutic targets for drug development at the intersection between obesity, inflammation, and thrombosis.
Gender-specific influence of socioeconomic status on the prevalence of migraine and tension-type headache: the results from the Korean headache survey
Authors: Chu Min Kyung , Kim Dong-Wook , Kim Byung-Kun , Kim Jae-Moon , Jang Tae-Won , Park Jeong Wook , Lee Kwang Soo , Cho Soo-Jin 
Published: October 2013

Abstract

Background
Socioeconomic status plays an important role in pain coping strategy. Its influence on migraine and tension-type headache may differ by gender. This study aimed to evaluate how socioeconomic status affects the prevalence of migraine and tension-type headache by gender.

Methods
We used data from the Korean Headache Survey, a population-based sample of Koreans aged 19–69 years. Education level, district size, and household income were evaluated as socioeconomic variables.

Results
Among 1507 participants, the 1-year prevalence rates of migraine and tension-type headache were 8.7% [95% confidence interval (CI) 1.9-4.6%] and 29.1% (95% CI 25.7-32.5%) in women and 3.2% (95% CI 1.9-4.6%) and 32.5% (95% CI 29.1-35.9%) in men, respectively. In women, multiple regression analysis found that living in rural areas was related to higher prevalence of migraine [odds ratio (OR) 4.52, 95% CI 1.85-11.02] and lower prevalence of tension-type headache (OR 0.29, 95% CI 0.15–0.58) and college-level education was related to lower prevalence of tension-type headache (OR 0.37, 95% CI 0.18–0.74). In men, multiple regression analysis failed to reveal significant influences of any socioeconomic variable on the prevalence of migraine or tension-type headache.

Conclusions
The influence of socioeconomic status on migraine and tension-type headache differs by gender, with women being more susceptible to socioeconomic influence.
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Authors: Buggenthin Felix , Marr Carsten , Schwarzfischer Michael , Hoppe Philipp S , Hilsenbeck Oliver , Schroeder Timm , Theis Fabian J 
Published: October 2013

Abstract

Background
In recent years, high-throughput microscopy has emerged as a powerful tool to analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data that is generated, for example in long-term time-lapse microscopy experiments, requires automated methods for processing and analysis. Available software frameworks are well suited for high-throughput processing of fluorescence images, but they often do not perform well on bright field image data that varies considerably between laboratories, setups, and even single experiments.

Results
In this contribution, we present a fully automated image processing pipeline that is able to robustly segment and analyze cells with ellipsoid morphology from bright field microscopy in a high-throughput, yet time efficient manner. The pipeline comprises two steps: (i) Image acquisition is adjusted to obtain optimal bright field image quality for automatic processing. (ii) A concatenation of fast performing image processing algorithms robustly identifies single cells in each image. We applied the method to a time-lapse movie consisting of ∼315,000 images of differentiating hematopoietic stem cells over 6 days. We evaluated the accuracy of our method by comparing the number of identified cells with manual counts. Our method is able to segment images with varying cell density and different cell types without parameter adjustment and clearly outperforms a standard approach. By computing population doubling times, we were able to identify three growth phases in the stem cell population throughout the whole movie, and validated our result with cell cycle times from single cell tracking.

Conclusions
Our method allows fully automated processing and analysis of high-throughput bright field microscopy data. The robustness of cell detection and fast computation time will support the analysis of high-content screening experiments, on-line analysis of time-lapse experiments as well as development of methods to automatically track single-cell genealogies.
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis
Authors: Tucker George , Loh Po-Ru , Berger Bonnie 
Published: October 2013

Abstract

Background
Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput experimental techniques have been developed to generate PPI maps at proteome scale, first using yeast two-hybrid approaches and more recently via affinity purification combined with mass spectrometry (AP-MS). Unfortunately, data from both protocols are prone to both high false positive and false negative rates. To address these issues, many methods have been developed to post-process raw PPI data. However, with few exceptions, these methods only analyze binary experimental data (in which each potential interaction tested is deemed either observed or unobserved), neglecting quantitative information available from AP-MS such as spectral counts.

Results
We propose a novel method for incorporating quantitative information from AP-MS data into existing PPI inference methods that analyze binary interaction data. Our approach introduces a probabilistic framework that models the statistical noise inherent in observations of co-purifications. Using a sampling-based approach, we model the uncertainty of interactions with low spectral counts by generating an ensemble of possible alternative experimental outcomes. We then apply the existing method of choice to each alternative outcome and aggregate results over the ensemble. We validate our approach on three recent AP-MS data sets and demonstrate performance comparable to or better than state-of-the-art methods. Additionally, we provide an in-depth discussion comparing the theoretical bases of existing approaches and identify common aspects that may be key to their performance.

Conclusions
Our sampling framework extends the existing body of work on PPI analysis using binary interaction data to apply to the richer quantitative data now commonly available through AP-MS assays. This framework is quite general, and many enhancements are likely possible. Fruitful future directions may include investigating more sophisticated schemes for converting spectral counts to probabilities and applying the framework to direct protein complex prediction methods.
Genome-wide identification of WRKY45-regulated genes that mediate benzothiadiazole-induced defense responses in rice
Authors: Nakayama Akira , Fukushima Setsuko , Goto Shingo , Matsushita Akane , Shimono Masaki , Sugano Shoji , Jiang Chang-Jie , Akagi Aya , Yamazaki Muneo , Inoue Haruhiko , Takatsuji Hiroshi 
Published: October 2013

AbstractBackgroundThe rice transcription factor WRKY45 plays a crucial role in salicylic acid (SA)/benzothiadiazole (BTH)-induced disease resistance. Its knockdown severely reduces BTH-induced resistance to the fungal pathogenMagnaporthe oryzaeand the bacterial pathogenXanthomonas oryzaepv.oryzae(Xoo). Conversely, overexpression of WRKY45 induces extremely strong resistance to both of these pathogens. To elucidate the molecular basis of WRKY45-dependent disease resistance, we analyzed WRKY45-regulated gene expression using rice transformants and a transient gene expression system.ResultsWe conducted a microarray analysis usingWRKY45-knockdown (WRKY45-kd) rice plants, and identified WRKY45-dependent genes among the BTH-responsive genes. The BTH-responsiveness of 260 genes was dependent on WRKY45. Among these, 220 genes (85%), many of which encoded PR proteins and proteins associated with secondary metabolism, were upregulated by BTH. Only a small portion of these genes overlapped with those regulated by OsNPR1/NH1, supporting the idea that the rice SA pathway branches into WRKY45- regulated and OsNPR1/NH1-regulated subpathways. Dexamethazone-induced expression of myc-tagged WRKY45 in rice immediately upregulated transcription of endogenousWRKY45and genes encoding the transcription factors WRKY62, OsNAC4, and HSF1, all of which have been reported to have defense-related functions. This was followed by upregulation of defense genes encoding PR proteins and secondary metabolic enzymes. Many of these genes were also induced afterM.oryzaeinfection. Their temporal transcription patterns were consistent with those after dexamethazone-inducedWRKY45expression. In a transient expression system consisting of particle bombardment of rice coleoptiles, WRKY45 acted as an effector to trans-activate reporter genes in which the luciferase coding sequence was fused to upstream and intragenic sequences ofWRKY62andOsNAC4. Trans-activation of transcription occurred through a W-box-containing sequence upstream ofOsNAC4and mutations in the W-boxes abolished the trans-activation.ConclusionsThese data suggest a role of WRKY45 in BTH-induced disease resistance as a master regulator of the transcriptional cascade regulating defense responses in one of two branches in the rice SA pathway.
Management of low back pain in general practice – is it of acceptable quality: an observational study among 25 general practices in South Tyrol (Italy)
Authors: Piccoliori Giuliano , Engl Adolf , Gatterer Doris , Sessa Emiliano , in der Schmitten Jürgen , Abholz Heinz-Harald 
Published: October 2013

Abstract

Background
There are several guidelines dealing with the management of low back pain (LBP), but only few studies on the quality of care provided within General Practices as judged against those guidelines.
The objective of this study is to analyse the management of LBP in Italian General Practice and compare it with guideline recommendations.

Methods
In this observational study, all patients visiting their General Practitioners (GPs) for treatment of LBP within a 8-week period were monitored for at least four weeks with regard to symptoms and diagnostic and therapeutic interventions. Management of LBP was judged by pre-defined quality indicators based on guideline recommendations.

Results
Twenty-five of 114 eligible GPs participated in the study, representing a total of 43,012 registered patients. Of the 475 patients complaining of LBP and monitored for four weeks, 55.8% were diagnosed as having acute lumbar pain, 13.5% chronic lumbar pain, 17.1% acute sciatica, and 12.6% chronic sciatica; 76.0% underwent no technical investigations, 21.7% underwent x-rays, 5.5% MRI and 4% CT scans; 20.4% were referred to secondary care; 93.3% of all patients received some medication. In those receiving a medication, in 88.3% it was an NSAID, in 6.3% Paracetamol, in 10.4% Paracetamol combined with Codeine, and in 9% a muscle relaxants. When physiotherapy was prescribed (17,1%), it was mostly massage. Hardly more than 50% of GPs (partially) followed locally established guidelines, while the remainder seemed not to follow guidelines at all.

Conclusions
Our study reveals gross deviations of GP management of LBP from current guidelines and points to two different types of deviators: those who partially follow guidelines, and those who do not follow them at all. Further research should evaluate whether these two types of deviation are best addressed by different foci of education, i.e. on knowledge versus attitudes, respectively.
Fall incidents unraveled: a series of 26 video-based real-life fall events in three frail older persons
Authors: Vlaeyen Ellen , Deschodt Mieke , Debard Glen , Dejaeger Eddy , Boonen Steven , Goedemé Toon , Vanrumste Bart , Milisen Koen 
Published: October 2013

Abstract

Background
For prevention and detection of falls, it is essential to unravel the way in which older people fall. This study aims to provide a description of video-based real-life fall events and to examine real-life falls using the classification system by Noury and colleagues, which divides a fall into four phases (the prefall, critical, postfall and recovery phase).

Methods
Observational study of three older persons at high risk for falls, residing in assisted living or residential care facilities: a camera system was installed in each participant’s room covering all areas, using a centralized PC platform in combination with standard Internet Protocol (IP) cameras. After a fall, two independent researchers analyzed recorded images using the camera position with the clearest viewpoint.

Results
A total of 30 falls occurred of which 26 were recorded on camera over 17 months. Most falls happened in the morning or evening (62%), when no other persons were present (88%). Participants mainly fell backward (initial fall direction and landing configuration) on the pelvis or torso and none could get up unaided. In cases where a call alarm was used (54%), an average of 70 seconds (SD=64; range 15–224) was needed to call for help. Staff responded to the call after an average of eight minutes (SD=8.4; range 2–33). Mean time on the ground was 28 minutes (SD=25.4; range 2–59) without using a call alarm compared to 11 minutes (SD=9.2; range 3–38) when using a call alarm (p=0.445).
The real life falls were comparable with the prefall and recovery phase of Noury’s classification system. The critical phase, however, showed a prolonged duration in all falls. We suggest distinguishing two separate phases: a prolonged loss of balance phase and the actual descending phase after failure to recover balance, resulting in the impact of the body on the ground. In contrast to the theoretical description, the postfall phase was not typically characterized by inactivity; this depended on the individual.

Conclusions
This study contributes to a better understanding of the fall process in private areas of assisted living and residential care settings in older persons at high risk for falls.
Validation of the new classification of pauci-immune glomerulonephritis in a United States cohort and its correlation with renal outcome
Authors: Ellis Carla L , Manno Rebecca L , Havill John P , Racusen Lorraine C , Geetha Duvuru 
Published: October 2013

Abstract

Background
Renal biopsies provide important diagnostic and prognostic information in ANCA associated glomerulonephritis. A new classification for prognostication of pauci-immune glomerulonephritis (GN) based on four categories (Mixed, Crescentic, Sclerotic and Focal) was proposed by an international working group of renal pathologists (IWGRP). The goal of our study was to apply the proposed classification system to a United States cohort of vasculitis patients and determine the association of IWGRP class with estimated glomerular filtration rate (eGFR) at one year.

Methods
Seventy-six cases of pauci-immune glomerulonephritis diagnosed from 1995 to 2011 from a single center were identified for this retrospective study. Clinical data were collected by abstraction from medical records. Histology was reviewed by a pathologist and classified according to the new classification. MDRD formula was used to calculate eGFR. We correlated IWGRP class to renal function at presentation and at one year. ×2, ANOVA, and linear regression analysis were performed as appropriate.

Results
Renal biopsies were categorized as focal: n = 20, crescentic: n = 18, mixed: n = 27, sclerotic: n = 11. The baseline e-GFR was lowest in the crescentic class and highest in the focal class. In linear regression analysis investigating e-GFR at 1 year; age and baseline e-GFR were independent predictors of e-GFR at 1 year.

Conclusions
The e-GFR at diagnosis and age were predictors of e-GFR at 1 year. Pathologic class at diagnosis may also be a helpful tool in risk stratification at diagnosis.
The effects of augmented visual feedback during balance training in Parkinson’s disease: study design of a randomized clinical trial
Authors: van den Heuvel Maarten RC , van Wegen Erwin EH , de Goede Cees JT , Burgers-Bots Ingrid AL , Beek Peter J , Daffertshofer Andreas , Kwakkel Gert 
Published: October 2013

Abstract

Background
Patients with Parkinson’s disease often suffer from reduced mobility due to impaired postural control. Balance exercises form an integral part of rehabilitative therapy but the effectiveness of existing interventions is limited. Recent technological advances allow for providing enhanced visual feedback in the context of computer games, which provide an attractive alternative to conventional therapy. The objective of this randomized clinical trial is to investigate whether a training program capitalizing on virtual-reality-based visual feedback is more effective than an equally-dosed conventional training in improving standing balance performance in patients with Parkinson’s disease.

Methods/design
Patients with idiopathic Parkinson’s disease will participate in a five-week balance training program comprising ten treatment sessions of 60 minutes each. Participants will be randomly allocated to (1) an experimental group that will receive balance training using augmented visual feedback, or (2) a control group that will receive balance training in accordance with current physical therapy guidelines for Parkinson’s disease patients. Training sessions consist of task-specific exercises that are organized as a series of workstations. Assessments will take place before training, at six weeks, and at twelve weeks follow-up. The functional reach test will serve as the primary outcome measure supplemented by comprehensive assessments of functional balance, posturography, and electroencephalography.

Discussion
We hypothesize that balance training based on visual feedback will show greater improvements on standing balance performance than conventional balance training. In addition, we expect that learning new control strategies will be visible in the co-registered posturographic recordings but also through changes in functional connectivity.

Trial registration
ISRCTN: ISRCTN47046299
Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein
Authors: Munshi Parthapratim , Stanley Christopher B , Ghimire-Rijal Sudipa , Lu Xun , Myles Dean A , Cuneo Matthew J 
Published: October 2013

Abstract

Background
Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively.

Results
A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site.

Conclusions
The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.