bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rgtsp: a generalized top scoring pairs package for class prediction
Authors: Popovici Vlad , Budinská Eva , Delorenzi Mauro 
Published: April 2011

Abstract
Summary: A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance.
Availability and Implementation: Full C++ source code and R package Rgtsp are freely available from http://lausanne.isb-sib.ch/~vpopovic/research/. The implementation relies on existing OpenMP libraries.
Contact: vlad.popovici@isb-sib.ch
A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues
using circular dichroism spectroscopy
Authors: Abdul-Gader Ali , Miles Andrew John , Wallace B. A. 
Published: April 2011

Abstract
Motivation: Empirical analyses of protein secondary structures based on circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectroscopic data rely on the availability of reference datasets comprised of spectra of relevant proteins, whose crystal structures have been determined. Datasets comprised of only soluble proteins have not proven suitable for analysing the spectra of membrane proteins.
Results: A new reference dataset, MP180, has been created containing the spectra of 30 membrane proteins encompassing the secondary structure and fold space covered by all known membrane protein structures. In addition a mixed soluble and membrane protein dataset, SMP180, has been created, which includes 98 soluble protein spectra (SP) plus the MP180 spectra. Calculations of both membrane and soluble protein secondary structures using SMP180 are significantly improved with respect to those produced, using soluble protein-only datasets. The SMP180 dataset also enables determination of the percentage of transmembrane residues, thus enhancing the information previously obtainable from CD spectroscopy.
Availability and Implementation: Reference dataset online at the DichroWeb analysis server (http://dichroweb.cryst.bbk.ac.uk);individual protein spectra in the Protein Circular Dichroism Data Bank (http://pcddb.cryst.bbk.ac.uk).
Contact: b.wallace@mail.cryst.bbk.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
Authors: Niu Beifang , Zhu Zhengwei , Fu Limin , Wu Sitao , Li Weizhong 
Published: April 2011

Abstract
Summary: Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis. The available sequence alignment programs are either slow or insufficient for recruiting metagenomic reads. We implemented an efficient algorithm, FR-HIT, for fragment recruitment. We applied FR-HIT and several other tools including BLASTN, MegaBLAST, BLAT, LAST, SSAHA2, SOAP2, BWA and BWA-SW to recruit four metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, while FR-HIT is about two orders of magnitude faster than BLASTN. FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1–5 times more reads.
Availability: http://weizhongli-lab.org/frhit.
Contact: liwz@sdsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mcheza: a workbench to detect selection using dominant markers
Authors: Antao Tiago , Beaumont Mark A. 
Published: April 2011

AbstractMotivation: Dominant markers (DArTs and AFLPs) are commonly used for genetic analysis in the fields of evolutionary genetics, ecology and conservation of genetic resources. The recent prominence of these markers has coincided with renewed interest in detecting the effects of local selection and adaptation at the level of the genome.Results: We present Mcheza, an application for detecting loci under selection based on a well-evaluated FST-outlier method. The application allows robust estimates to be made of model parameters (e.g. genome-wide average, neutral FST), provides data import and export functions, iterative contour smoothing and generation of graphics in an easy to use graphical user interface with a computation engine that supports multicore processors for enhanced performance. Mcheza also provides functionality to mitigate common analytical errors when scanning for loci under selection.Availability: Mcheza is freely available under GPL version 3 from http://popgen.eu/soft/mcheza.Contact: tra@popgen.eu
A graphical interface for the FoldX forcefield
Authors: Van Durme Joost , Delgado Javier , Stricher Francois , Serrano Luis , Schymkowitz Joost , Rousseau Frederic 
Published: April 2011

Abstract
Summary: A graphical user interface for the FoldX protein design program has been developed as a plugin for the YASARA molecular graphics suite. The most prominent FoldX commands such as free energy difference upon mutagenesis and interaction energy calculations can now be run entirely via a windowed menu system and the results are immediately shown on screen.
Availability and Implementation: The plugin is written in Python and is freely available for download at http://foldxyasara.switchlab.org/ and supported on Linux, MacOSX and MS Windows.
Contact: frederic.rousseau@switch.vib-vub.be; joost.schymkowitz@switch.vib-vub.be; luis.serrano@crg.es
Cross-Sectional and Longitudinal Risk Factors for Falls, Fear of Falling, and Falls Efficacy in a Cohort of Middle-Aged African Americans
Authors: Andresen Elena M. , Wolinsky Fredric D. , Miller J. Philip , Wilson Margaret-Mary G. , Malmstrom Theodore K. , Miller Douglas K. 
Published: April 2011

Abstract
Purpose: The purpose of this study is to cross-sectionally and longitudinally identify risk factors for falls, fear of falling, and falls efficacy in late-middle-aged African Americans. Design and Methods: We performed in-home assessments on a probability sample of 998 African Americans and conducted two annual follow-up interviews. Multiple logistic regression modeled the associations with falls (any fall or injurious fall) during 2 years prior to the baseline interview, and baseline fear of falling and falls efficacy with 2-year prospective risks for falling and fear of falling. Results: The most consistent association for all outcomes was depressive symptoms. Age was associated with increased risk of prior and prospective falls. Lower-body functional limitations were associated with prior falls, baseline fear of falling, and low falls efficacy, whereas low ability with one-leg stands prospectively predicted fear of falling. The greatest prospective risk for incident falls was having had a prior fall (odds ratio = 2.51), and the greatest prospective risk for fear of falling was having been afraid of falling at baseline (odds ratio = 8.14). Implications: Falls, fear of falling, and low falls efficacy are important issues for late-middle-aged as well as older persons. Interventions should focus on younger adults and attend especially to lower-body function and depressive symptoms as well as building self-efficacy for safe exercise, dealing with falls risks, and managing falls themselves.
Transportation and Aging: A Research Agenda for Advancing Safe Mobility
Authors: Dickerson Anne E. , Molnar Lisa J. , Eby David W. , Adler Geri , Bédard Michel , Berg-Weger Marla , Classen Sherrilene , Foley Daniel , Horowitz Amy , Kerschner Helen , Page Oliver , Silverstein Nina M. , Staplin Loren , Trujillo Leonard 
Published: April 2011

AbstractPurpose:  We review what we currently know about older driver safety and mobility, and we highlight important research needs in a number of key areas that hold promise for achieving the safety and mobility goals for the aging baby boomers and future generations of older drivers. Design and Methods:Through the use of a framework for transportation and safe mobility, we describe key areas of screening and assessment, remediation and rehabilitation, vehicle design and modification, technological advancements, roadway design, transitioning to nondriving, and alternative transportation to meet the goals of crash prevention and mobility maintenance for older adults.  Results: Four cross-cutting themes emerged from this review: safe transportation for older adults is important; older adults have a variety of needs, abilities, and resources; research to help meet the transportation needs of older adults may be of benefit to persons with disabilities; and transportation issues concerning older adults are multifaceted. Implications: Safe mobility is essential to continued engagement in civic, social, and community life, and to the human interactions necessary for health, well-being, and quality of life. When safe driving is no longer possible for older adults, safe and practicable alternative transportation must be available. Furthermore, older adults are individuals; they have specific needs, abilities, and resources. Not all older adults will have difficulty meeting their transportation needs and no single transportation solution will work for all people. Research and countermeasures intended to help meet the transportation needs of older adults will likely also benefit younger users of the transportation system, particularly those with disabilities. The issues surrounding the maintenance of safe transportation for older adults will require an interdisciplinary research approach if we are to make significant progress in the next decade as the baby boomers begin to reach age 70.
Falling Through the Social Safety Net: Food Stamp Use and Nonuse Among Older Impoverished Americans
Authors: Fuller-Thomson Esme , Redmond Melissa 
Published: April 2011

Abstract
Purpose:  Older adults are less likely than any other age group to use the federal Food Stamp Program. The personal and social costs of elderly diet insufficiency include disease exacerbation, depression, and increased hospitalization. In order to improve targeting and outreach efforts, this study identifies the characteristics of eligible older Americans who are not receiving food stamps and assesses the validity of the Andersen behavioral model for predicting impoverished older adults food stamp use.  Design and Methods:  We conducted a secondary analysis of the 2003 American Community Survey, which is a nationally representative survey with a response rate of 96.7%. We restricted our study subsample to the 14,724 impoverished American citizens who were aged 65 years and older. We used bivariate and logistic regression analyses to compare the 2,796 food stamp recipients with the 11,928 nonrecipients.  Results:  One in five impoverished older American citizens had received foods stamps in the preceding year. Female respondents, renters, younger respondents, disabled individuals, and those who received Supplemental Security Income or welfare were more likely to receive food stamps. The pseudo-R-square value indicated that the Andersen Behavioral Model explained 28% of the model's variability.  Implications:  Improved targeting is needed to enhance older adults' participation rates. Mobile and satellite food stamp offices in lower income neighborhoods and other innovative outreach programs that collaborate with community partners could also improve access. With the vast majority of impoverished older adults not receiving food stamps, strategies such as these are extremely important to rectify this situation among the most vulnerable group of older Americans.
The Role of PENNYWISE and POUND-FOOLISH in the Maintenance of the Shoot Apical Meristem in Arabidopsis
Authors: Ung Nolan , Lal Shruti , Smith Harley M.S. 
Published: April 2011

AbstractGrowth of the aerial part of the plant is dependent upon the maintenance of the shoot apical meristem (SAM). A balance between the self-renewing stem cells in the central zone (CZ) and organogenesis in the peripheral zone (PZ) is essential for the integrity, function, and maintenance of the SAM. Understanding how the SAM maintains a balance between stem cell perpetuation and organogenesis is a central question in plant biology. Two related BELL1-like homeodomain proteins, PENNYWISE (PNY) and POUND-FOOLISH (PNF), act to specify floral meristems during reproductive development. However, genetic studies also show that PNY and PNF regulate the maintenance of the SAM. To understand the role of PNY and PNF in meristem maintenance, the expression patterns for genes that specifically localize to the peripheral and central regions of the SAM were examined in Arabidopsis (Arabidopsis thaliana). Results from these experiments indicate that the integrity of the CZ is impaired in pny pnf plants, which alters the balance of stem cell renewal and organogenesis. As a result, pools of CZ cells may be allocated into initiating leaf primordia. Consistent with these results, the integrity of the central region of pny pnf SAMs can be partially restored by increasing the size of the CZ. Interestingly, flower specification is also reestablished by augmenting the size of the SAM in pny pnf plants. Taken together, we propose that PNY and PNF act to restrict organogenesis to the PZ by maintaining a boundary between the CZ and PZ.
Antifungal prophylaxis during treatment for haematological malignancies: are we there yet?
Authors: Rogers Thomas R. , Slavin Monica A. , Donnelly J. Peter 
Published: April 2011

SummaryAntifungal prophylaxis during treatment for haematological malignancies has been studied for 50 years, yet it has not been wholly effective even when using antifungal drugs that exhibit potent activity in vitro against a broad range of fungal pathogens. Trials have demonstrated that it can reduce the incidence of invasive fungal diseases (IFD) and fungal deaths, but only two studies have had an impact on overall mortality. Furthermore, it has not significantly reduced the need for empirical antifungal therapy. Posaconazole was effective in preventing invasive aspergillosis in two studies of high‐risk patients, and consensus guidelines grade it as a suitable choice for antifungal prophylaxis of invasive mould disease; however, its bioavailability was compromised by vomiting or diarrhoea so that an alternative parenteral antifungal drug was required. A recent trial of voriconazole prophylaxis after allogeneic stem cell transplantation failed to show superiority over fluconazole. With more accurate definitions of IFD, that utilize fungal biomarkers, such as galactomannan, together with computerized tomographic imaging, there is growing interest in a diagnostic‐driven strategy, which could prove to be a more efficacious approach.
Disseminated superficial actinic porokeratosis treated effectively with topical imiquimod 5% cream
Authors: Arun B. , Pearson J. , Chalmers R. 
Published: April 2011

SummaryA 68-year-old man presented with a 3-year history of asymptomatic red marks on his limbs. On physical examination, he was found to have numerous circular, erythematous macules with a fine peripheral rim of scale on his upper arms and legs. A clinical diagnosis of disseminated superficial actinic porokeratosis (DSAP) was made. On histopathological examination of the lesional skin on the hands, an angulated parakeratotic tier was seen extending up through the epidermis. The patient was offered a trial of topical imiquimod 5% cream. He was instructed to apply it five times weekly for 6 weeks to the right forearm. This produced a dramatic inflammatory response with painful superficial ulceration of the affected skin after 4 weeks. At follow-up a further 4 weeks later, the treated areas were noted to have healed with slight superficial scarring and residual erythema, but no evidence of the original condition. DSAP is a disorder affecting areas exposed to sunlight, appearing mainly on the distal surfaces of the limbs. Treatment of DSAP is often difficult. Therapies such as cryotherapy with liquid nitrogen or use of topical 5-fluorouracil cream are generally either impractical or unsuccessful. Topical imiquimod 5% cream may prove to be a useful treatment option for DSAP. Our limited experience suggests that treatment should be introduced cautiously to avoid excessive inflammation. Further study is needed to confirm whether imiquimod should have a place in the management of DSAP.
Teledermatology: a tool for remote supervision of a general practitioner with special interest in dermatology
Authors: Thind C. K. , Brooker I. , Ormerod A. D. 
Published: April 2011

Summary
Background. Teledermatology (TD) has been developed as an alternative to face-to-face (FTF) dermatology care in remote areas.
Aim. To assess the feasibility of TD in remote supervision and education of a general practitioner with special interest (GPwSI), to reduce FTF consultations with the consultant dermatologist, and to provide appropriate diagnosis and care. Our secondary aim was to evaluate patient satisfaction with this mode of consultation.
Methods. A TD service in Aberdeen was set up to augment supervision of a remote rural GP training in dermatology. This service was audited over a 2-year period to assess its usefulness in the education of the remote GP.
Results. Prospective data on 230 selected referrals was analysed. Store-and-forward TD provided a high level of patient satisfaction, and was effective in remote supervision and education of a GPwSI in dermatology. FTF consultations with the consultant were avoided in 69% of consultations, and diagnostic agreement was considered high (61%). Educational feedback was given to the GP in 66% of consultations.
Conclusions. TD can supplement infrequent specialist dermatology service in remote areas, as in this case. We conclude that for selected patients, TD was a useful training tool for supervising the GPwSI, and ensuring clinical governance and quality assurance in clinics in a remote rural area. However, this model of care was limited by cost and the inherent limitations of TD.
Effects of a three‐month combined exercise programme on fibroblast growth factor 21 and fetuin‐A levels and arterial stiffness in obese women
Authors: Yang Sae Jeong , Hong Ho Cheol , Choi Hae Yoon , Yoo Hye Jin , Cho Geum Ju , Hwang Teak Geun , Baik Sei Hyun , Choi Dong Seop , Kim Seon Mi , Choi Kyung Mook 
Published: April 2011

SummaryObjective  We examined the relationship between brachial‐ankle pulse wave velocity (baPWV) reflecting arterial stiffness and the levels of novel hepatokines fibroblast growth factor 21 (FGF21) and fetuin‐A. In addition, we evaluated the effect of a 3‐month combined aerobic and resistance exercise programme on FGF21 and fetuin‐A levels as well as arterial stiffness in obese women.Methods  Forty nondiabetic, obese women (body mass index = 27·6 ± 2·4 kg/m2) were included in the study and were compared before and after a 3‐month exercise programme, which was composed of 45 min of aerobic exercise at an intensity of 60–75% of the age‐predicted maximum heart rate (300 kcal/session) and 20 min of resistance training (100 kcal/session) five times a week. All exercise sessions were supervised by a professional exercise physiologist.Results  At baseline, baPWV levels were correlated with age, body mass index (BMI), systolic blood pressure (SBP), high density lipoprotein cholesterol, fasting glucose and serum FGF21 levels. In a multiple stepwise regression analysis using baPWV as a dependent variable, baPWV levels were associated with age, BMI, SBP, FGF21 and fetuin‐A levels (R2 = 0·744). After the exercise programme, BMI, waist circumference, SBP, diastolic blood pressure and triglyceride levels were significantly decreased. Moreover, baPWV values were significantly improved (P < 0·001) along with modest decrease in FGF21 levels (P = 0·043). However, fetuin‐A levels were not changed significantly (P = 0·202).Conclusions  A 3‐month combined exercise programme decreases the FGF21 levels as well as arterial stiffness in obese Korean women.
Achievement of a median door‐to‐balloon time of less than 90 minutes by implementation of organizational changes in the ‘Emergency Department to Cath Lab’ pathway: a 5‐year analysis
Authors: Comelli Ivan , Vignali Luigi , Rolli Angelo , Lippi Giuseppe , Cervellin Gianfranco 
Published: April 2011

AbstractRationale  At present, most patients presenting directly to emergency departments (EDs) do not meet the recommended door‐to‐balloon goal of less than 90 minutes for ST‐elevation myocardial infarction (STEMI) patients. Until the year 2005, the goal of less than 90 minutes door‐to‐balloon time has been rarely achieved in our hospital (i.e. 17% of all cases).Method  Some organizational changes – including immediate involvement of the cardiologist in ED – were established to improve our performance. To evaluate the results of these changes, we have measured the intervals pain‐to‐door, door‐to‐electrocardiogram (ECG) and ECG‐to‐balloon for all the consecutive STEMI patients (n = 206) observed in our hospital during three sample months (May to July) of the years 2005 to 2009. We have then calculated the times door‐to‐balloon and pain‐to‐balloon (total ischemic time).Results  We have demonstrated that the door‐to‐balloon time has been progressively reduced to less than 90 minutes in 73% of patients. Only 4.5% of all patients still have a door‐to‐balloon time greater than 150 minutes (17% in 2005). It is also notable the 60% reduction (from 330 to 140 minutes) of the pain‐to‐door time, the so‐called ‘out of hospital avoidable delay’, was achieved by a sensitization campaign directed to the whole population of the province.Conclusion  Taken together, all these organizational changes have allowed to reduce the total ischemic time from 465 minutes in year 2005 to 232 minutes in year 2009, thereby demonstrating the effectiveness of our intervention.