bluuebunny/crossref_metadata_2025_split huggingface dataset:
SiTaR: a novel tool for transcription factor binding site prediction
Authors: Fazius Eugen , Shelest Vladimir , Shelest Ekaterina 
Published: September 2011

Abstract
Motivation: Prediction of transcription factor binding sites (TFBSs) is crucial for promoter modeling and network inference. Quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS search methods.
Results: We suggest a novel approach, which is alternative to widely used position weight matrices (PWMs) and Hidden Markov Models. Each motif of the input set is used as a search template to scan a query sequence. Found motifs are assigned scores depending on the non-randomness of the motif's occurrence, the number of matching searching motifs and the number of mismatches. The non-randomness is estimated by comparison of observed numbers of matching motifs with those predicted to occur by chance. The latter can be calculated given the base compositions of the motif and the query sequence. The method does not require preliminary alignment of the input motifs, hence avoiding uncertainties introduced by the alignment procedure. In comparison with PWM-based tools, our method demonstrates higher precision by the same sensitivity and specificity. It also tends to outperform methods combining pattern and PWM search. Most important, it allows reducing the number of false positive predictions significantly.
Availability: The method is implemented in a tool called SiTaR (Site Tracking and Recognition) and is available at http://sbi.hki-jena.de/sitar/index.php.
Contact: ekaterina.shelest@hki-jena.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data
Authors: Sorokin Alexei , Zumstein Emmanuelle , Azevedo Vasco , Ehrlich S. Dusko , Serror Pascale 
Published: September 2011

SummaryThree different lambda phage clones with overlapping inserts of Bacillus subtilis DNA, which cover the region from spoIIAA to serA, have been isolated. The nucleotide sequence of their inserts, starting after spoVAF and ending at serA, has been determined. A contiguous sequence of 35354 bp was established, including previously analysed overlapping adjacent regions. Within the newly determined sequence 31 open reading frames (ORFs) with putative ribosome‐binding sites have been found. Nine of them correspond to previously sequenced and characterized genes: spoVAF, lysA, sipS, ribG, ribB, ribA, ribH, ribTD and dacB. Comparison of the amino acid sequences of the products encoded by the other ORFs to known proteins allowed putative functions to be assigned to seven of these ORFs. Among these are the following: (i) the ppiB gene, encoding a cytoplasmic peptidylprolyl isomerase; (ii) two pairs of signal‐transducers, one homologous to phoR–phoP of B. subtilis, encoding regulators of phosphatase biosynthesis, and the second to the fecI–fecR of Escherichia coli, which is responsible for the regulation of the citrate‐dependent iron (III) transport system; (iii) aroC and serA genes, involved in the biosynthesis of aromatic amino acids and serine, respectively, the function of which has beer: confirmed by constructing corresponding mutants with disrupted ORFs. The organization of putative operons has been postulated on the basis of the sequences of their transcription terminators, promoters and regulatory elements.
The Cochrane Library review titles that are important to users of health care, a Cochrane Consumer Network project
Authors: Wale Janet L. , Belizán María , Nadel Jane , Jeffrey Claire , Vij Sita L. 
Published: September 2011

AbstractBackground  The Cochrane Consumer Network is an internet‐based community of international users of health care contributing to the work of The Cochrane Collaboration, whose mission is to inform healthcare decision making through development of systematic reviews of best evidence on healthcare interventions.Objective  To prioritize existing review titles listed on The Cochrane Library from a healthcare user perspective, with particular emphasis on patients, carers and health consumers.Design  An online survey was developed and after piloting was made available internationally. The broad dissemination strategy targeted Consumer Network members and Cochrane Review Group editorial staff to identify champions who notified patient support groups and participated in snowballing. The first part of the survey defined criteria that could be applied to review titles and asked survey respondents to rank them. The second part asked respondents to select a health area and prioritize review titles that were of importance to them. Each health area corresponded to a Cochrane Review Group.Results and discussion  Sufficient responses were obtained from 522 valid responses to prioritize review topics in 19 health areas. A total of 321 respondents completed the titles assessment. The types of prioritized interventions were determined by the health area. An important observation was the emphasis on lifestyle and non‐medication therapies in many of the included health areas. The clearest exception to this broad observation was where acute care is required such as antibiotics for acute respiratory tract and HIV‐associated infections and for cardiac conditions. For some cancers, advanced cancer interventions were prioritized. The most important criteria were for the title to convey a clear meaning and the title conveyed that the review would have an impact on health and well‐being. The least important criteria were that the topic was newsworthy or prioritized in the healthcare system.Conclusion  This project was able to identify priority Cochrane review topics for users of health care in 19 of the 50 areas of health care covered by The Cochrane Collaboration. Reviews addressing lifestyle and non‐medical interventions were strongly represented in the prioritized review titles. These findings highlight the importance of developing readable, informative lay summaries to support evidence‐based decision making by healthcare users.
Evaluating the clinical efficacy of a primary care‐focused, nurse‐led, consultation liaison model for perinatal mental health
Authors: Harvey Simone T. , Fisher Lisa J. , Green Vicki M. 
Published: September 2011

ABSTRACTIn Australia, perinatal mental illness is common, although poorly identified and treated. Improved perinatal mental health depends on service provision models that reflect a focus on promotion, prevention, and early intervention, while facilitating improved referral pathways between primary health and specialist mental health services. In 2008, a contemporary community‐based model of mental health service provision was developed as an alternative to the pre‐existing hospital‐based service model. The model is delivered primarily by mental health nurses using a consultation liaison framework. It provides for specialist mental health assessment and brief intervention in collaboration with the general practitioner, who remains the primary health provider. It also aims to raise community awareness and build capacity for the management of perinatal disorders in the primary care sector. Evaluation of the clinical effectiveness of the model, and the improvement in access for primary health providers and women, was conducted at 2 years from its implementation. Clinical effectiveness was evaluated by using comparative data from the Edinburgh Depression Scale and Depression Anxiety and Stress Scale, and the results demonstrated clinical efficacy. Improved attendance rates indicated that women preferred this community‐based service model as an alternative to the pre‐existing service model.
Microbial diversity and stratification of South Pacific abyssal marine sediments
Authors: Durbin Alan M. , Teske Andreas 
Published: September 2011

SummaryAbyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group IArchaeain the aerobic and nitrate‐reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate‐depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community ofAlpha‐,Gamma‐ andDeltaproteobacteria,ActinobacteriaandGemmatimonadetesin oxic surface sediments towards unculturedChloroflexiandPlanctomycetesin the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate‐reducing marine sediment column provides initial constraints for their microbial habitat preferences.
Regenerative medicine in urology
Authors: Wezel Felix , Southgate Jennifer , Thomas David F.M. 
Published: September 2011

What's known on the subject? and What does the study add?Urology was one of the first specialties to report the introduction of regenerative medicine into clinical practice and has been at the forefront of scientific innovation. Despite the scale of investment and research effort, the promise of regenerative medicine remains largely unfulfilled. We review recent developments underpinning the emerging science of regenerative medicine and evaluate critically both the potential for novel regenerative therapies to transform urological practice and the outstanding challenges that remain to be addressed.The term ‘regenerative medicine’ encompasses strategies for restoring or renewing tissue or organ function by: (i) in vivo tissue repair by in‐growth of host cells into an acellular natural or synthetic biomaterial, (ii) implantation of tissue ‘engineered’in vitro by seeding cultured cells into a biomaterial scaffold, and (iii) therapeutic cloning and stem cell‐based tissue regeneration. In this article, we review recent developments underpinning the emerging science of regenerative medicine and critically assess where successful implementation of novel regenerative medicine approaches into urology practice might genuinely transform the quality of life of affected individuals. We advocate the need for an evidence‐based approach supported by strong science and clinical objectivity.
Forecasting Heavy‐Tailed Densities with Positive Edgeworth and Gram‐Charlier Expansions*
Authors: Ñíguez Trino‐Manuel , Perote Javier 
Published: September 2011

AbstractThis article presents a new semi‐nonparametric (SNP) density function, named Positive Edgeworth‐Sargan (PES). We show that this distribution belongs to the family of (positive) Gram‐Charlier (GC) densities and thus it preserves all the good properties of this type of SNP distributions but with a much simpler structure. The in‐ and out‐of‐sample performance of the PES is compared with symmetric and skewed GC distributions and other widely used densities in economics and finance. The results confirm the PES as a good alternative to approximate financial returns distribution, specially when skewness is not severe.
The role of intima‐media‐thickness, ankle‐brachial‐index and inflammatory biochemical parameters for stroke risk prediction: a systematic review
Authors: Sander D. , Poppert H. , Sander K. , Etgen T. 
Published: September 2011

Background:  Despite important advances in therapeutic approaches in stroke, the options of acute treatment are still limited. Primary prevention represents another potentially highly efficient strategy. For effective prevention the early detection of subjects at risk is of utmost importance. Coinciding with a change in current understanding of atherosclerosis as an inflammatory, cross‐organ disease, new parameters to assess the individual risk are emerging.Methods:  Systematic review of the potential of selected parameters for prediction of cerebrovascular events beyond detection of traditional risk factors that might expand the repertoire of primary prevention programs in stroke.Results:  An absolute carotid intima‐media thickness difference of 0.1 mm increases the future risk of stroke by 13–18%. An ankle‐brachial index <0.9 was associated with a relative risk of 2.33 (95% CI 2.02–2.68) for stroke. In patients with acute stroke and ABI values < 0.9 the risk for a new vascular event is significantly increased (HR 2.1; 95% CI 1.6–2.8). Measurements of several molecular biomarkers may be used to predict future vascular events independently of traditional risk factors.Conclusions:  Based on the data presented, there is clear evidence that measurement of the ankle‐brachial index identifies subjects of increased stroke risk in primary and secondary care settings as well as of stroke recurrence in acute stroke.
Electrocortical reactivity to emotional faces in young children and associations with maternal and paternal depression
Authors: Kujawa Autumn , Hajcak Greg , Torpey Dana , Kim Jiyon , Klein Daniel N. 
Published: September 2011

Background:  The late positive potential (LPP) is an event‐related potential component that indexes selective attention toward motivationally salient information and is sensitive to emotional stimuli. Few studies have examined the LPP in children. Depression has been associated with reduced reactivity to negative and positive emotional stimuli, including reduced LPPs in response to emotional faces. The current study sought to identify the time course and scalp distribution of the LPP in response to emotional faces in young children and to determine whether reduced reactivity is observed among children at risk for depression.Methods:  Electrocortical reactivity to emotional faces was examined in a large sample of young children and as a function of maternal and paternal depression.Results:  In the overall sample, emotional faces were associated with increased positivities compared to neutral faces at occipital sites 200–600 ms after stimulus onset and at parietal sites 600–1,000 ms after stimulus onset. Children of mothers with a history of depressive disorders exhibited reduced differentiation in the early occipital LPP for emotional compared to neutral faces.Conclusions:  Results suggest that children as young as 6 years exhibit LPPs to emotional faces, and patterns of electrocortical reactivity to emotional stimuli may be associated with vulnerability to depressive disorders.
β‐Lactotensin derived from bovine β‐lactoglobulin exhibits anxiolytic‐like activity as an agonist for neurotensin NTS2 receptor via activation of dopamine D1 receptor in mice
Authors: Hou I‐Ching , Suzuki Chihiro , Kanegawa Norimasa , Oda Ayako , Yamada Ayako , Yoshikawa Masaaki , Yamada Daisuke , Sekiguchi Masayuki , Wada Etsuko , Wada Keiji , Ohinata Kousaku 
Published: September 2011

J. Neurochem. (2011) 119, 785–790.Abstractβ‐Lactotensin (His‐Ile‐Arg‐Leu) is a bioactive peptide derived from bovine milk β‐lactoglobulin, acting as a natural agonist for neurotensin receptors. We found that β‐lactotensin exhibited anxiolytic‐like activity in an elevated plus‐maze test after its intraperitoneal (i.p.) administration in mice. β‐Lactotensin was also orally active. The anxiolytic‐like activity of β‐lactotensin after i.p. administration was blocked by levocabastine, an antagonist for the neurotensin NTS2 receptor. β‐Lactotensin had anxiolytic‐like activity in wild‐type but not Ntsr2‐knockout mice. β‐Lactotensin increased intracellular Ca2+ flux in glial cells derived from wild‐type mice but not Ntsr2 knockout mice. These results suggest that β‐lactotensin acts as an NTS2 receptor agonist having anxiolytic‐like activity. The anxiolytic‐like activity of β‐lactotensin was also blocked by SCH23390 and SKF83566, antagonists for dopamine D1 receptor, but not by raclopride, an antagonist for D2 receptor. Taken together, β‐lactotensin may exhibit anxiolytic‐like activity via NTS2 receptor followed by D1 receptor.
Ethanol‐Induced Loss‐of‐Righting Response During Ethanol Withdrawal in Male and Female Rats: Associations with Alterations in Arc Labeling
Authors: Walls Shawn A. , Macklin Zachary L. , Devaud Leslie L. 
Published: September 2011

Background:  There is increasing evidence for relevant sex differences in responses to ethanol. Several investigations have found differences in expression and recovery from ethanol withdrawal (EW) in people and across various animal models. We have found that female rats recover more quickly than male rats and show differential responses to various behavioral assessments and pharmacological challenges during withdrawal. The purpose of this study was to determine whether sex differences in EW behaviors extend to the hypnotic effects of acute ethanol administration.
Methods:  We used a repeated measures design to assess duration and latency for loss‐of‐righting reflex following an acute injection of ethanol (4.2 g/kg; 20% w/v) to pair‐fed control or ethanol‐withdrawn animals at 1 and 3 days EW in male, female, and ovariectomized female (OVX) rats. We determined protein levels of the activity‐regulated cytoskeletal protein (Arc), used as a marker for synaptic activity in glutamatergic synapses, in the motor cortex and prefrontal cortex across these same treatment conditions.
Results:  Ethanol‐withdrawn animals had a reduced ethanol‐induced sleep time compared to controls at 1 day EW. Sleep time remained shortened at 3 days EW for males and OVX, but not females. Arc protein levels in motor cortex and preoptic nuclei significantly increased at 1 day EW across all sex conditions, suggestive of an association with the reduced ethanol‐induced sleep times during EW. Arc levels increased further for males and OVX, but not females, at the 3 days EW time point.
Conclusions:  These findings add further support to sex differences in effects of and responses to ethanol. They suggest that the more rapid recovery from EW for females than males also includes expression of tolerance to the hypnotic effects of ethanol. These sex differences may involve some differential neuroadaptations in glutamatergic signaling.
Legitimating Inequality: Fooling Most of the People All of the Time
Authors: WISMAN JON D. , SMITH JAMES F. 
Published: September 2011

AbstractOver the three decades leading up to the crisis of 2008, inequality dramatically increased in the United States and Great Britain. What stands out, but is seldom noted, is that this occurred within democracies where the relative losers—the overwhelming majority—could in principle have used the political system to block or reverse rising inequality. Why did they not do so? A glance at history reveals that peoples have only very infrequently contested inequality because they were led to believe that their inferior status in terms of income, wealth, and privilege was just, that it was not really so bad, or that it was necessary for their future well‐being. Ideological systems legitimated a status quo of inequality, or in more modern times even increasing inequality. This article surveys the manner in which inequality has been historically legitimated, first predominantly by religion, then predominately by economic thought. Attention is then focused on the manner in which contemporary economic science and its popular interpretations in the media have served to legitimate inequality in the U.S. since the mid‐1970s. The article concludes with a reflection on the unique conditions that enable the legitimation of inequality to be delegitimated.
Open Source Software Production, Spontaneous Input, and Organizational Learning
Authors: GARZARELLI GIAMPAOLO , FONTANELLA RICCARDO 
Published: September 2011

AbstractThis work shows that the modular organization of voluntary open source software (OSS) production, whereby programmers supply effort of their accord, capitalizes more on division than on specialization of labor. This is so because voluntary OSS production is characterized by an organizational learning process that dominates the individual one. Organizational learning reveals production choices that would otherwise remain unknown, thereby increasing productivity and indirectly reinforcing incentives to undertake collective problem solving.
Aortic aneurysm in a Cebus apella monkey with experimentally induced atherosclerosis
Authors: Borda Juan T. , Ruiz Julio C. , Sánchez‐Negrette Marcial 
Published: September 2011

The sudden death of a Cebus apella female (>19 years old) on an experimental hyperlipidic diet during three years is described. The gross lesions were hemothorax, atherosclerotic plaques in the aortic curve, and an aneurysm in the ascending aorta.Histologically, an enlargement of the intima in the ascending aorta with hyalinization and a thrombus were observed. The media was thinned and showed sclerosis and hemorrhage extending to the tunica adventicia.
Generation of monoclonal antibodies to Macaca mulatta (rhesus) IgA
Authors: Ward Dawn C. , Jackson Susan , Eldridge John H. , Radl Jiri , Michalek Suzanne M. 
Published: September 2011

One IgG1 and five IgM murine monoclonal antibodies (mAb) specific for rhesus (Rh) IgA were generated. These mAbs bound to Rh IgA but not IgG or IgM when tested by enzyme‐linked immunosorbent assay.Immunoblotting revealed that the mAbs reacted with the alpha heavy chain of Rh but not human IgA. The IgG1 anti‐Rh IgA mAb detected IgA‐producing cells in sections of monkey gut examined by immunofluorescent staining. These mAbs should be useful for characterizing IgA responses in the Rh monkey.
Noninvasive markers of bone metabolism in the rhesus monkey: Normal effects of age and gender
Authors: Cahoon Scott , Boden Scott D. , Gould Kenneth G. , Vailas Arthur C. 
Published: September 2011

Abstract: Measurement of bone turnover in conditions such as osteoporosis has been limited by the need for invasive iliac bone biopsy to reliably determine parameters of bone metabolism. Recent advances in the area of serum and urinary markers of bone metabolism have raised the possibility for noninvasive measurements; however, little nonhuman primate data exist for these parameters. The purpose of this experiment was to define the normal range and variability of several of the newer noninvasive bone markers which are currently under investigation in humans. The primary intent was to determine age and gender variability, as well as provide some normative data for future experiments in nonhuman primates.Twenty‐four rhesus macaques were divided into equal groups of male and female according to the following age groupings: 3 years, 5–10 years, 15–20 years, and > 25 years. Urine was collected three times daily for a four‐day period and measured for several markers of bone turnoverm including pyridinoline (PYD), deoxypyrodinoline (DPD), hydroxyproline, and creatinine. Bone mineral density measurements of the lumbar spine were performed at the beginning and end of the study period. Serum was also obtained at the time of bone densitometry for measurement of osteocalcin levels by radioimmunoassay.There were no significant differences in bone mineral density, urine PYD, or urine DPD based on gender. Bone density was lowest in the youngest animals, peaked in the 15–20‐year group, but again decreased in the oldest animals. The osteocalcin, PYD, and DPD levels followed an inversely related pattern to bone density. The most important result was the relative age insensitivity of the ratio of PYD:DPD in monkeys up to age 20 years. Since bone density changes take months or years to become measurable and iliac biopsies are invasive, the PYD/DPD marker ratio may have important implications for rapid noninvasive measurement of the effects of potential treatments for osteoporosis in the non‐human primate model.