bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planning combinatorial disulfide cross-links for protein fold determination
Authors: Xiong Fei , Friedman Alan M , Bailey-Kellogg Chris 
Published: November 2011

AbstractBackgroundFold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the absence of sufficient sequence identity, it remains difficult for fold recognition methods to always select the correct model. While a native-like model is often among a pool of highly ranked models, it is not necessarily the highest-ranked one, and the model rankings depend sensitively on the scoring function used.Structure elucidationmethods can then be employed to decide among the models based on relatively rapid biochemical/biophysical experiments.ResultsThis paper presents an integrated computational-experimental method to determine the fold of a target protein by probing it with a set of planned disulfide cross-links. We start with predicted structural models obtained by standard fold recognition techniques. In a first stage, we characterize the fold-level differences between the models in terms of topological (contact) patterns of secondary structure elements (SSEs), and select a small set of SSE pairs that differentiate the folds. In a second stage, we determine a set of residue-level cross-links to probe the selected SSE pairs. Each stage employs an information-theoretic planning algorithm to maximize information gain while minimizing experimental complexity, along with a Bayes error plan assessment framework to characterize the probability of making a correct decision once data for the plan are collected. By focusing on overall topological differences and planning cross-linking experiments to probe them, ourfold determinationapproach is robust to noise and uncertainty in the models (e.g., threading misalignment) and in the actual structure (e.g., flexibility). We demonstrate the effectiveness of our approach in case studies for a number of CASP targets, showing that the optimized plans have low risk of error while testing only a small portion of the quadratic number of possible cross-link candidates. Simulation studies with these plans further show that they do a very good job of selecting the correct model, according to cross-links simulated from the actual crystal structures.ConclusionsFold determination can overcome scoring limitations in purely computational fold recognition methods, while requiring less experimental effort than traditional protein structure determination approaches.
Prevalence and clinical management of cytomegalovirus retinitis in AIDS patients in shanghai, china
Authors: Shi Ying , Lu Hongzhou , He Taiwen , Yang Yalin , Liu Li , Zhang Renfang , Zheng Yufang , Shen Yinzhong , Zhang Yunzhi , Zhang Zhiyong 
Published: November 2011

Abstract

Background
Cytomegalovirus retinitis is a common AIDS-associated illness, leading to blindness in up to 30% of patients. This study was to investigate the prevalence and clinical management of the cytomegalovirus retinitis associated with AIDS in a large municipality of China.

Methods
Clinical and laboratory data from 23 cytomegalovirus retinitis patients (35 eyes) out of 303 hospitalized AIDS individuals in a single medical center were analyzed retrospectively. Two of 23 patients were diagnosed cytomegalovirus retinitis just before hospitalization without anti-CMV therapy. Ganciclovir combined with the high active anti-retroviral therapy was installed for treatment of cytomegalovirus retinitis after diagnosis was confirmed. The data were analyzed by specialists and statistics was also applied.

Results
The prevalence of cytomegalovirus retinitis in hospitalized AIDS patients was 7.6% in this study. The level of CD4
+ T lymphocytes was correlated well with the occurrence of cytomegalovirus retinitis, showing 16.8% (19/113) (95% confidence interval: 10.4,25.0), 5.4% (3/56) (95% confidence interval: 1.1,14.9), and 1.4% (1/69) (95% confidence interval: 0.0,7.8) occurrence in the patients with CD4
+ T lymphocyte counts < 50, 50~99, and 100~199 cells/μl, respectively. The mean CD4
+ T lymphocyte counts was 31.7 ± 38.6 cells/μl in 23 AIDS patients with cytomegalovirus retinitis. Median CD4
+ T lymphocyte count is 20 cells/μl with inter-quartile range as (5, 36). Seven patients died (11 eyes) and 16 patients (24 eyes) survived. The proportion of blindness and low vision in eyes infected with cytomegalovirus retinitis respectively was 20.8% (5/24) and 29.2% (7/24) when they were diagnosed in survivors. The ganciclovir therapy was effective in 16 patients (24 eyes). Clinical recovery of cytomegalovirus retinitis was 41.7% (10/24) and clinical improvement 58.3% (14/24). After anti-CMV treatment, the proportion of blindness or low vision was 16.7% (4/24).

Conclusions
The AIDS patients with CD4
+ T lymphocyte < 50 cells/μl had increased susceptibility to cytomegalovirus associated retinitis. Cytomegalovirus retinitis is a serious disease causing blindness. The cytomegalovirus retinitis in the AIDS patients was response well to ganciclovir therapy. We should check their eyes routinely such as dilated fundus examination with an indirect ophthalmoscope in the AIDS patients with CD4
+ T lymphocyte counts < 50 cells/μl.
Association between chronic viral hepatitis infection and breast cancer risk: a nationwide population-based case-control study
Authors: Su Fu-Hsiung , Chang Shih-Ni , Chen Pei-Chun , Sung Fung-Chang , Su Chien-Tien , Yeh Chih-Ching 
Published: November 2011

AbstractBackgroundIn Taiwan, there is a high incidence of breast cancer and a high prevalence of viral hepatitis. In this case-control study, we used a population-based insurance dataset to evaluate whether breast cancer in women is associated with chronic viral hepatitis infection.MethodsFrom the claims data, we identified 1,958 patients with newly diagnosed breast cancer during the period 2000-2008. A randomly selected, age-matched cohort of 7,832 subjects without cancer was selected for comparison. Multivariable logistic regression models were constructed to calculate odds ratios of breast cancer associated with viral hepatitis after adjustment for age, residential area, occupation, urbanization, and income. The age-specific (<50 years and ≥50 years) risk of breast cancer was also evaluated.ResultsThere were no significant differences in the prevalence of hepatitis C virus (HCV) infection, hepatitis B virus (HBV), or the prevalence of combined HBC/HBV infection between breast cancer patients and control subjects (p= 0.48). Multivariable logistic regression analysis, however, revealed that age <50 years was associated with a 2-fold greater risk of developing breast cancer (OR = 2.03, 95% CI = 1.23-3.34).ConclusionsHCV infection, but not HBV infection, appears to be associated with early onset risk of breast cancer in areas endemic for HCV and HBV. This finding needs to be replicated in further studies.
Impact of meteorological variation on hospital visits of patients with tree pollen allergy
Authors: Kim Si-Heon , Park Hae-Sim , Jang Jae-Yeon 
Published: November 2011

Abstract

Background
Climate change could affect allergic diseases, especially due to pollen. However, there has been no epidemiologic study to demonstrate the relationship between meteorological factors, pollen, and allergic patients. We aimed to investigate the association between meteorological variations and hospital visits of patients with tree pollen allergy.

Methods
The study subjects were adult patients who received skin prick tests between April and July from 1999 to 2008. We reviewed the medical records for the test results of 4,715 patients. Patients with tree pollen allergy were defined as those sensitized to more than 1 of 12 tree pollen allergens. We used monthly means of airborne tree pollen counts and meteorological factors: maximum/average/minimum temperature, relative humidity, and precipitation. We analyzed the correlations between meteorological variations, tree pollen counts, and the patient numbers. Multivariable logistic regression analyses were used to investigate the associations between meteorological factors and hospital visits of patients.

Results
The minimum temperature in March was significantly and positively correlated with tree pollen counts in March/April and patient numbers from April through July. Pollen counts in March/April were also correlated with patient numbers from April through July. After adjusting for confounders, including air pollutants, there was a positive association between the minimum temperature in March and hospital visits of patients with tree pollen allergy from April to July(odds ratio, 1.14; 95% CI 1.03 to 1.25).

Conclusions
Higher temperatures could increase tree pollen counts, affecting the symptoms of patients with tree pollen allergy, thereby increasing the number of patients visiting hospitals.
Isolation and functional characterization of a cotton ubiquitination-related promoter and 5'UTR that drives high levels of expression in root and flower tissues
Authors: Viana Antonio AB , Fragoso Rodrigo R , Guimarães Luciane M , Pontes Naiara , Oliveira-Neto Osmundo B , Artico Sinara , Nardeli Sarah M , Alves-Ferreira Marcio , Batista João AN , Silva Maria CM , Grossi-de-Sa Maria F 
Published: November 2011

Abstract

Background
Cotton (Gossypium spp.) is an important crop worldwide that provides raw material to 40% of the textile fiber industry. Important traits have been studied aiming the development of genetically modified crops including resistance to insect and diseases, and tolerance to drought, cold and herbicide. Therefore, the characterization of promoters and regulatory regions is also important to achieve high gene expression and/or a specific expression pattern. Commonly, genes involved in ubiquitination pathways are highly and differentially expressed. In this study, we analyzed the expression of a cotton ubiquitin-conjugating enzyme (E2) family member with no previous characterization.

Results
Nucleotide analysis revealed high identity with cotton E2 homologues. Multiple alignment showed a premature stop codon, which prevents the encoding of the conserved cysteine residue at the E2 active site, and an intron that is spliced in E2 homologues, but not in GhGDRP85. The GhGDRP85 gene is highly expressed in different organs of cotton plants, and has high transcript levels in roots. Its promoter (uceApro2) and the 5'UTR compose a regulatory region named uceA1.7, and were isolated from cotton and studied in Arabidopsis thaliana. uceA1.7 shows strong expression levels, equaling or surpassing the expression levels of CaMV35S. The uceA1.7 regulatory sequence drives GUS expression 7-fold higher in flowers, 2-fold in roots and at similar levels in leaves and stems. GUS expression levels are decreased 7- to 15-fold when its 5'UTR is absent in uceApro2.

Conclusions
uceA1.7 is a strong constitutive regulatory sequence composed of a promoter (uceApro2) and its 5'UTR that will be useful in genetic transformation of dicots, having high potential to drive high levels of transgene expression in crops, particularly for traits desirable in flower and root tissues.
Factors associated with self-reported number of teeth in a large national cohort of Thai adults
Authors: Yiengprugsawan Vasoontara , Somkotra Tewarit , Kelly Matthew , Seubsman Sam-ang , Sleigh Adrian C ,   the Thai Cohort Study Team
Published: November 2011

Abstract

Background
Oral health in later life results from individual's lifelong accumulation of experiences at the personal, community and societal levels. There is little information relating the oral health outcomes to risk factors in Asian middle-income settings such as Thailand today.

Methods
Data derived from a cohort of 87,134 adults enrolled in Sukhothai Thammathirat Open University who completed self-administered questionnaires in 2005. Cohort members are aged between 15 and 87 years and resided throughout Thailand. This is a large study of self-reported number of teeth among Thai adults. Bivariate and multivariate logistic regressions were used to analyse factors associated with self-reported number of teeth.

Results
After adjusting for covariates, being female (OR = 1.28), older age (OR = 10.6), having low income (OR = 1.45), having lower education (OR = 1.33), and being a lifetime urban resident (OR = 1.37) were statistically associated (p < 0.0001) with having less than 20 teeth. In addition, daily soft drink consumptions (OR = 1.41), current regular smoking (OR = 1.39), a history of not being breastfed as a child (OR = 1.34), and mother's lack of education (OR = 1.20) contributed significantly to self-reported number of teeth in fully adjusted analyses.

Conclusions
This study addresses the gap in knowledge on factors associated with self-reported number of teeth. The promotion of healthy childhoods and adult lifestyles are important public health interventions to increase tooth retention in middle and older age.
Mortality associated with timing of admission to and discharge from ICU: a retrospective cohort study
Authors: Laupland Kevin B , Misset Benoit , Souweine Bertrand , Tabah Alexis , Azoulay Elie , Goldgran-Toledano Dany , Dumenil Anne-Sylvie , Vésin Aurélien , Jamali Samir , Kallel Hatem , Clec'h Christophe , Darmon Michael , Schwebel Carole , Timsit Jean-Francois 
Published: November 2011

Abstract

Background
Although the association between mortality and admission to intensive care units (ICU) in the "after hours" (weekends and nights) has been the topic of extensive investigation, the timing of discharge from ICU and outcome has been less well investigated. The objective of this study was to assess effect of timing of admission to and discharge from ICUs and subsequent risk for death.

Methods
Adults (≥18 years) admitted to French ICUs participating in Outcomerea between January 2006 and November 2010 were included.

Results
Among the 7,380 patients included, 61% (4,481) were male, the median age was 62 (IQR, 49-75) years, and the median SAPS II score was 40 (IQR, 28-56). Admissions to ICU occurred during weekends (Saturday and Sunday) in 1,708 (23%) cases, during the night (18:00-07:59) in 3,855 (52%), and on nights and/or weekends in 4,659 (63%) cases. Among 5,992 survivors to ICU discharge, 903 (15%) were discharged on weekends, 659 (11%) at night, and 1,434 (24%) on nights and/or weekends. After controlling for a number of co-variates using logistic regression analysis, admission during the after hours was not associated with an increased risk for death. However, patients discharged from ICU on nights were at higher adjusted risk (odds ratio, 1.54; 95% confidence interval, 1.12-2.11) for death.

Conclusions
In this study, ICU discharge at night but not admission was associated with a significant increased risk for death. Further studies are needed to examine whether minimizing night time discharges from ICU may improve outcome.
Noxious gas detection using carbon nanotubes with Pd nanoparticles
Authors: Choi Hyang Hee , Lee Junmin , Dong Ki-Young , Ju Byeong-Kwon , Lee Wooyoung 
Published: November 2011

Abstract
Noxious gas sensors were fabricated using carbon nanotubes [CNTs] with palladium nanoparticles [Pd NPs]. An increase in the resistance was observed under ammonia for both CNTs and CNT-Pd sensors. Under carbon monoxide [CO], the two sensors exhibited different behaviors: for CNT sensors, their resistance decreased slightly with CO exposure, whereas CNT-Pd sensors showed an increase in resistance. The sensing properties and effect of Pd NPs were demonstrated, and CNT-Pd sensors with good repeatability and fast responses over a range of concentrations may be used as a simple and effective noxious gas sensor at room temperature.
Perfusion MRI (dynamic susceptibility contrast imaging) with different measurement approaches for the evaluation of blood flow and blood volume in human gliomas
Authors: Thomsen H , Steffensen E , Larsson E-M 
Published: November 2011

Background Perfusion magnetic resonance imaging (MRI) is increasingly used in the evaluation of brain tumors. Relative cerebral blood volume (rCBV) is usually obtained by dynamic susceptibility contrast (DSC) MRI using normal appearing white matter as reference region. The emerging perfusion technique arterial spin labelling (ASL) presently provides measurement only of cerebral blood flow (CBF), which has not been widely used in human brain tumor studies. Purpose To assess if measurement of blood flow is comparable with measurement of blood volume in human biopsy-proven gliomas obtained by DSC-MRI using two different regions for normalization and two different measurement approaches. Material and Methods Retrospective study of 61 patients with different types of gliomas examined with DSC perfusion MRI. Regions of interest (ROIs) were placed in tumor portions with maximum perfusion on rCBF and rCBV maps, with contralateral normal appearing white matter and cerebellum as reference regions. Larger ROIs were drawn for histogram analyses. The type and grade of the gliomas were obtained by histopathology. Statistical comparison was made between diffuse astrocytomas, anaplastic astrocytomas, and glioblastomas. Results rCBF and rCBV measurements obtained with the maximum perfusion method were correlated when normalized to white matter (r = 0.60) and to the cerebellum (r = 0.49). Histogram analyses of rCBF and rCBV showed that mean and median values as well as skewness and peak position were correlated (0.61 < r < 0.93), whereas for kurtosis and peak height, the correlation coefficient was about 0.3 when comparing rCBF and rCBV values for the same reference region. Neither rCBF nor rCBV quantification provided a statistically significant difference between the three types of gliomas. However, both rCBF and rCBV tended to increase with tumor grade and to be lower in patients who had undergone resection/treatment. Conclusion rCBF measurements normalized to white matter or cerebellum are comparable with the established rCBV measurements used for the clinical evaluation of cerebral gliomas.
Low agreement of visual rating for detailed quantification of pulmonary emphysema in whole-lung CT
Authors: Mascalchi Mario , Diciotti Stefano , Sverzellati Nicola , Camiciottoli Gianna , Ciccotosto Cesareo , Falaschi Fabio , Zompatori Maurizio 
Published: November 2011

Background Multidetector spiral computed tomography (CT) has opened the possibility of quantitative evaluation of emphysema extent in the whole lung. Visual assessment can be used for such a purpose, but its reproducibility has not been established. Purpose To assess agreement of detailed assessment of pulmonary emphysema on whole-lung CT using a visual scale. Material and Methods Thirty patients with chronic obstructive pulmonary disease underwent whole-lung inspiratory CT. Four chest radiologists rated the same 22 ± 2 thin sections using a visual scale which defines a range of emphysema extent between 0 and 100. Two of them repeated the rating two months later. Inter- and intra-operator agreement was evaluated with the Bland and Altman method. In addition, the percentage of emphysema at –950 Hounsfield units in the whole lung was determined using fully automated commercially available software for 3D densitometry. Results In three of six operator pairs and in one of two intra-operator pairs the Kendall τ test showed a significant correlation between the difference and the average magnitude of visual scores. Among different operators the half-width of 95% limits of agreement (95% LoA) was wide ranging between a score of 14.2–27.7 for an average visual score of 20 and between 18.5–36.8 for an average visual score of 80. Within the same operator the half-width of 95% LoA ranged between a score of 10.9–21.0 for an average visual score of 20 and between 25.1–30.1 for an average visual score of 80. The visual scores of the four radiologists were correlated with the results of densitometry ( P < 0.001; r = 0.65–0.81). Conclusion The inter- and intra-operator agreement of detailed assessment of emphysema in the whole lung using a visual scale is low and decreases with increasing emphysema extent.
Development of 29 microsatellite markers for Osmanthus fragrans (Oleaceae), a traditional fragrant flowering tree of China
Authors: Zhang Zhi‐Rong , Fan Deng‐Mei , Guo Shi‐Quan , Li De‐Zhu , Zhang Zhi‐Yong 
Published: November 2011

• Premise of the study: Microsatellite markers were developed for a traditional fragrant flowering tree of China, Osmanthus fragrans, to investigate the genetic diversity of its wild populations and to facilitate the classification and identification of O. fragrans cultivars.• Methods and Results: Using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol, 29 primer sets were identified in two wild populations. All primer pairs displayed polymorphism. The number of alleles per locus ranged from two to eight, with a mean of 3.9. The expected and observed heterozygosities ranged from 0.125 to 0.932 and from 0.083 to 0.917, respectively. The transferability of the 29 primer pairs was tested on O. serrulatus, O. delavayi, and O. yunnanensis (three individuals for each species). Eighteen (62.1%), 16 (55.2%), and 21 (72.4%) of them were successfully amplified in O. serrulatus, O. delavayi, and O. yunnanensis, respectively.• Conclusions: These markers will facilitate further studies on the population genetics of O. fragrans and the classification and identification of O. fragrans cultivars.
Soins psychiatriques : le retour de la contrainte et de la stigmatisation
Authors: Durand Bernard 
Published: November 2011

Résumé La loi du 5 juillet 2011, fortement contestée par les professionnels et les usagers de la psychiatrie, a modifié le paysage psychiatrique. Après une évolution quasiment continue qui a permis de remplacer la pratique asilaire de l’enfermement par des soins acceptés par le patient, on assiste à un retour des pratiques d’enfermement. Après des années d’engagement des professionnels et des familles pour redonner leur dignité aux personnes dont le psychisme est altéré, on constate que l’on a réactivé, à partir de quelques faits divers aussi exceptionnels que dramatiques, des représentations du fou et plus spécifiquement du schizophrène comme quelqu’un de potentiellement dangereux. La nouvelle loi, qui prétend garantir la continuité des soins, est en fait une loi de continuité de la contrainte. Elle est le résultat d’une volonté de reprise en main de la gestion de la folie par le ministère de l’intérieur depuis 2003, au détriment de celui de la santé. Pourtant, on y trouve des dispositions qui auraient pu faire l’objet d’un consensus dans une autre logique que l’obsession des troubles à l’ordre public.
L'assurance maladie dans la tourmente économique et politique (2007-2011)
Authors: Tabuteau Didier 
Published: November 2011

Résumé Les années 2007-2011 ont été placées pour l’assurance maladie sous le signe des crises économiques et financières mais aussi de réformes menées le plus souvent dans la discrétion de législations techniques. Elles auront ainsi été marquées par l’absence de véritable débat public sur le financement de la protection sociale, malgré la succession de déficits historiques, mais aussi par la priorité donnée au thème de la « responsabilisation » des assurés sociaux et par l’affirmation d’une logique de concurrence dans le système de santé et d’assurance maladie.