bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of heme binding residues from protein sequences with integrative sequence profiles
Authors: Xiong Yi , Liu Juan , Zhang Wen , Zeng Tao 
Published: June 2012

Abstract

Background
The heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression. The knowledge of heme binding residues can provide crucial clues to understand these activities and aid in functional annotation, however, insufficient work has been done on the research of heme binding residues from protein sequence information.

Methods
We propose a sequence-based approach for accurate prediction of heme binding residues by a novel integrative sequence profile coupling position specific scoring matrices with heme specific physicochemical properties. In order to select the informative physicochemical properties, we design an intuitive feature selection scheme by combining a greedy strategy with correlation analysis.

Results
Our integrative sequence profile approach for prediction of heme binding residues outperforms the conventional methods using amino acid and evolutionary information on the 5-fold cross validation and the independent tests.

Conclusions
The novel feature of an integrative sequence profile achieves good performance using a reduced set of feature vector elements.
Continued twitching of the latissimus dorsi miniflap after breast conservation therapy: a case report
Authors: Huang Du-Ping , Ye Xiao-He , Xiang You-qun , Zhang Xiao-Hua 
Published: June 2012

Abstract
We report a case of continued twitching of the latissimus dorsi muscle following breast conservation therapy, along with immediate reconstruction with a latissimus dorsi miniflap, which continued despite several attempts at control including BTX-A percutaneous local injection, and was finally cured by delayed division of the thoracodorsal nerve via a small well-tolerated axillary incision.
Synovial sarcoma of the buttocks presenting with a non-healing wound and rapid progression after local resection: a case report
Authors: Zhang Hai-Yan , Feng Ye , Zhang Zhuo , Gao Ge , Zhao Ji-Sheng 
Published: June 2012

AbstractSynovial sarcoma is a malignant mesenchymal neoplasm that is frequently misdiagnosed as a benign condition because of its small size, slow growth, and well-delineated appearance. Rapid spread and early death occur rarely. Here we report a case of synovial sarcoma of the buttocks presenting with a non-healing wound and rapid progression after local resection in a 23-year-old woman. She initially found a slightly painful subcutaneous mass in the left buttock and underwent local excision. Postoperatively, she developed a non-healing wound that did not respond to conventional antibiotic therapy and local wound care, and pitting edema of the lower extremities. A magnetic resonance imaging scan revealed a large heterogeneous, irregular mass in the buttocks with regional lymph node involvement. Histological and immunohistochemical analyses suggested the diagnosis of a poorly differentiated synovial sarcoma. Her condition deteriorated dramatically shortly thereafter; she developed systemic edema and died of respiratory failure. This case suggests that synovial sarcoma may be fatal within months of recognition if improperly managed and stresses the importance of adequate pre-surgical evaluation and postoperative pathological analysis in the management of a subcutaneous mass.
A mass conserved splitting method for the nonlinear Schrödinger equation
Authors: Hua Dong-Ying , Li Xiang-Gui , Zhu Jiang 
Published: June 2012

Abstract
A mass conserved time-splitting difference method is presented for the one-dimensional dipolar Bose-Einstein condensates (BECs) described by a nonlocal nonlinear Schrödinger equation with a convolution term. As a result of the singularity in the convolution term, it brings difficulties both in mathematical analysis and in numerical simulations. By properly using the difference scheme to deal with the convolution term, an imaginary time method is given to compute the ground states and then a time-splitting method is obtained for dynamics of dipolar BECs. This time-splitting numerical method is mass conserved everywhere, and it has second-order accuracy and is also unconditionally stable. Numerical results are given to verify the stability and energy conservation when there is no blow up.

Mathematics Subject Classification (2010) 65M06; 35Q41.
Sphingosine 1-phosphate receptor 5 mediates the immune quiescence of the human brain endothelial barrier
Authors: van Doorn Ruben , Lopes Pinheiro Melissa A , Kooij Gijs , Lakeman Kim , van het Hof Bert , van der Pol Susanne MA , Geerts Dirk , van Horssen Jack , van der Valk Paul , van der Kam Elizabeth , Ronken Eric , Reijerkerk Arie , de Vries Helga E 
Published: June 2012

Abstract

Background
The sphingosine 1-phosphate (S1P) receptor modulator FTY720P (Gilenya®) potently reduces relapse rate and lesion activity in the neuroinflammatory disorder multiple sclerosis. Although most of its efficacy has been shown to be related to immunosuppression through the induction of lymphopenia, it has been suggested that a number of its beneficial effects are related to altered endothelial and blood–brain barrier (BBB) functionality. However, to date it remains unknown whether brain endothelial S1P receptors are involved in the maintenance of the function of the BBB thereby mediating immune quiescence of the brain. Here we demonstrate that the brain endothelial receptor S1P5 largely contributes to the maintenance of brain endothelial barrier function.

Methods
We analyzed the expression of S1P5 in human post-mortem tissues using immunohistochemistry. The function of S1P5 at the BBB was assessed in cultured human brain endothelial cells (ECs) using agonists and lentivirus-mediated knockdown of S1P5. Subsequent analyses of different aspects of the brain EC barrier included the formation of a tight barrier, the expression of BBB proteins and markers of inflammation and monocyte transmigration.

Results
We show that activation of S1P5 on cultured human brain ECs by a selective agonist elicits enhanced barrier integrity and reduced transendothelial migration of monocytes in vitro. These results were corroborated by genetically silencing S1P5 in brain ECs. Interestingly, functional studies with these cells revealed that S1P5 strongly contributes to brain EC barrier function and underlies the expression of specific BBB endothelial characteristics such as tight junctions and permeability. In addition, S1P5 maintains the immunoquiescent state of brain ECs with low expression levels of leukocyte adhesion molecules and inflammatory chemokines and cytokines through lowering the activation of the transcription factor NFκB.

Conclusion
Our findings demonstrate that S1P5 in brain ECs contributes to optimal barrier formation and maintenance of immune quiescence of the barrier endothelium.
Molecular characteristics and chromatin texture features in acute promyelocytic leukemia
Authors: De Mello Mariana R. B. , Albuquerque Dulcineia M , Pereira-Cunha Fernanda Gonçalves , Albanez Krizzia B , Pagnano Katia B. B. , Costa Fernando F , Metze Konradin , Lorand-Metze Irene 
Published: June 2012

Abstract

Background
Acute promyelocytic leukemia is a cytogenetically well defined entity. Nevertheless, some features observed at diagnosis are related to a worse outcome of the patients.

Methods
In a prospective study, we analyzed peripheral (PB) leukocyte count, immunophenotype, methylation status of CDKN2B, CDKN2A and TP73; FLT3 and NPM1 mutations besides nuclear chromatin texture characteristics of the leukemic cells. We also examined the relation of these features with patient’s outcome.

Results
Among 19 cases, 4 had a microgranular morphology, 7 presented PB leukocytes >10x109/l, 2 had FLT3-ITD and 3 had FLT3-TKD (all three presenting a methylated CDKN2B). NPM1 mutation was not observed. PB leukocyte count showed an inverse relation with standard deviation of gray levels, contrast, cluster prominence, and chromatin fractal dimension (FD). Cases with FLT3-ITD presented a microgranular morphology, PB leukocytosis and expression of HLA-DR, CD34 and CD11b. Concerning nuclear chromatin texture variables, these cases had a lower entropy, contrast, cluster prominence and FD, but higher local homogeneity, and R245, in keeping with more homogeneously distributed chromatin. In the univariate Cox analysis, a higher leukocyte count, FLT3-ITD mutation, microgranular morphology, methylation of CDKN2B, besides a higher local homogeneity of nuclear chromatin, a lower chromatin entropy and FD were associated to a worse outcome. All these features lost significance when the cases were stratified for FLT3-ITD mutation. Methylation status of CDNK2A and TP73 showed no relation to patient’s survival.

Conclusion
in APL, patients with FLT3-ITD mutation show different clinical characteristics and have blasts with a more homogeneous chromatin texture. Texture analysis demonstrated that FLTD-ITD was accompanied not only by different cytoplasmic features, but also by a change in chromatin structure in routine cytologic preparations. Yet we were not able to detect chromatin changes by nuclear texture analysis of patients with the FTLD-TKD or methylation of specific genes.
Assessment of characteristics of patients with cholelithiasis from economically deprived rural Karachi, Pakistan
Authors: Naeem Muhammad , Rahimnajjad Nasir Ali , Rahimnajjad Muhammad Kazim , Khurshid Madiha , Ahmed Qazi Jalaluddin , Shahid Syed Mariam , Khawar Faiza , Najjar Molham Mustafa 
Published: June 2012

Abstract

Background
Gallstones have been regarded as one of the most expensive diseases in Gastroenterology, posing a great economic burden on developing nations. The majority of Pakistani people live in rural areas where healthcare facilities are not available or are very primitive. We aim to assess the characteristics among cholelithiasis patients from rural Karachi so that a prevention campaign can be launched in rural underprivileged settings to reduce the economic burden of this preventable disease.

Method
A total of 410 patients were included in the study after giving verbal consent as well as written consent. Variables such as age, weight, height, body mass index (BMI), blood pressure, waist circumference, number of children, monthly family income, number of siblings, and number of family members, were considered in this questionnaire. All data was analysed by SPSS ver. 16.0. Mean and standard deviation (SD) were calculated for continuous variables. Frequency and percentages were calculated for categorical variables.

Results
Nearly 85.4% of the participants were female. The mean ± S.D. for age was 43.8 ± 9.59. Nearly 61% of the patients were illiterate. All of our patients were from low socioeconomic status and their mean salary ± S.D. was 6915 ± 1992 PKR (1 US $ = 90.37PKR). 75% of them were smokers with mean consumption ± S.D. of 7.5 ± 10 cigarettes per day. Fibre in diet was not used by 83.65% of patients. 40.2% were living in combined families. 61% were living in purchased homes. A positive history of diabetes mellitus was given by 45.1%, family history of cholelithiasis by 61% and history of hypertension by 31.7% of subjects. Soft drink consumption was given by 45.1% of patients; while only 8.5% used snacked daily. Tea was consumed by 95.1% of the subjects. Daily physical activity for 30 minutes was reported by only 13.4% of participants.

Conclusion
In conclusion, rural dwellers from low socioeconomic strata are neglected patients and illiteracy further adds fuel to the fire by decreasing the contact with the health professionals. Assessment of the characteristics are very important because considering the great socio-economic burden, an intervention strategy in the form of mass media campaign as well as small group discussions in such rural areas can be formulated and applied to high risk populations to reduce the burden and complications of gallstone disease.
Trends in the use of rehabilitation services in the community by people with mental disabilities in Israel; the factors involved
Authors: Hornik-Lurie Tzipi , Zilber Nelly , Lerner Yaacov 
Published: June 2012

Abstract

Background
In 2001, the Rehabilitation of the Mentally Disabled Law was implemented, defining a basket of rehabilitation services to which people with mental disabilities are entitled.

Objectives
To describe change over time in the characteristics of applicants to rehabilitation committees, types of referral agencies, and the proportion of those referred who were admitted. To identify factors affecting implementation of decisions to admit people with mental disabilities into different rehabilitation services and predictors of the length of time they remain in the services.

Methods
The study population consisted of all applicants to rehabilitation committees during 2001-2008. Rehabilitation services included hostels, supported housing, and vocational services. Data were extracted from Ministry of Health rehabilitation and psychiatric hospitalization case registers. Findings were analyzed using descriptive statistics, Kaplan-Meier survival analyses, and Cox regressions.

Results
There was a trend over time for more patients with shorter or no psychiatric hospitalization histories to be referred to rehabilitation services. Moreover, there was an increase in the proportion of referrals from the community, although the majority of referrals still came from psychiatric hospitals. Less than half of those recommended for a rehabilitation program were admitted and remained in a rehabilitation facility for one year or more. One factor predicting participants' longer stays in rehabilitation services after hospitalization was the proximity of the committees' decisions to the hospitalization. Another factor was the patient receiving vocational services while in residential care.

Conclusion
Although over time the new law has resulted in a broader spectrum of people with mental disabilities receiving rehabilitation services, additional efforts are needed to enable them to remain in the system for a sufficient amount of time. Programs addressing specific needs should be developed accordingly.
Belief is only half the truth - or why screening for heterophilic antibody interference in certain assays makes double sense
Authors: Bjerner Johan , Bolstad Nils , Piehler Armin 
Published: June 2012

Background Interference in immunoassays may cause both false-negative and false-positive results. It may be detected using a number of affirmative tests such as reanalysis of certain samples using different assay platforms with known bias, after the addition of blocker antibodies, or assessment of linearity and parallelism following serial doubling dilutions. One should look for interference where it is likely and has high medical impact. Probabilistic Bayesian reasoning is a statistical tool to identify samples where interference is most likely. But when looking for interference where it is likely, do we find it where it has the largest population health consequences? Methods We used information theory to quantify the effect of assay interference by calculating the Shannon information content (using logarithms with base 2). We then obtained lower bounds of the population health consequences of a particular test and combined these expressions to get lower bounds of the population health consequences of interference. Results and conclusion We suggest that assays having a low frequency of true positives should be the primary target of retesting because: (i) assays with a low frequency of true positives exhibit a high likelihood of interference and (ii) the population health consequences of false-positive results are generally higher for assays with a low frequency of true positives. Finally, we give a worked example having a realistic frequency of interference and test costs. In some immunoassays (e.g., tumour markers), adding a blocker to all tests can be a more cost-efficient mean than retesting positive samples.
In vivo 3 T MR diffusion tensor imaging for detection of the fibre architecture of the human uterus: a feasibility and quantitative study
Authors: Fiocchi F , Nocetti L , Siopis E , Currà S , Costi T , Ligabue G , Torricelli P 
Published: June 2012

Objective
The aim of this study was to investigate the feasibility of depicting fibre architecture of human uteri in vivo using 3 T MR diffusion tensor imaging (MR-DTI) with a three-dimensional (3D) tractography approach. Quantitative results were provided.

Methods
In vivo 3 T MR-DTI was performed on 30 volunteers (9 Caesarean delivery). Main diffusion directions reflecting the fibre orientation were determined using sensitivity-encoding single-shot echo planar imaging with diffusion-sensitised gradients (b=600 mm2 s−1) along 32 directions. A deterministic fibre-tracking algorithm was used to show in vivo fibre architecture, compared with ex vivo histological slides of cadaveric uteri. The number of fibres, the fibre density, the fractional anisotropy (FA) and the apparent diffusion coefficient (ADC) were measured in 13 volunteers.

Results
Anisotropy was found in most regions of normal uteri and the preferential order of uterine fibres depicted, consisting of two representative fibre directions: circular and longitudinal, as in ex vivo studies. Two-thirds of uteri with a Caesarean scar did not have the same orientation of fibres in the anterior isthmus when compared with non-scarred myometrium. Quantitative data were obtained from 13 volunteers: Caesarean-scarred uteri (n=5) showed lower fibre number and density in the scarred anterior isthmus than the nulliparous uteri (n=8). No significant differences were found in FA (0.42±0.02, 0.41±0.02; p=0.25) and ADC (1.82±0.18×10−3 mm2 s−1, 1.93±0.25×10−3 mm2 s−1; p=0.20).

Conclusion
Fibre architecture of the human uterus can be depicted in vivo using 3 T MR-DTI.

Advances in knowledge
3 T MR-DTI can help to provide an in vivo insight of uterine anatomy non-invasively, especially in females with previous Caesarean surgery, in order to provide better management of subsequent deliveries.
Association of Insurance Status and Age With Cervical Cancer Stage at Diagnosis: National Cancer Database, 2000–2007
Authors: Fedewa Stacey A. , Cokkinides Vilma , Virgo Katherine S. , Bandi Priti , Saslow Debbie , Ward Elizabeth M. 
Published: June 2012

Objectives. We examined the relationship of age at diagnosis and insurance status with stage among cervical cancer patients aged 21 to 85 years. Methods. We selected data on women (n = 69 739) diagnosed with invasive cervical cancer between 2000 and 2007 from the National Cancer Database. We evaluated the association between late stage (stage III/IV) and both insurance and age, with adjustment for race/ethnicity and other sociodemographic and clinical factors. We used multivariable log binomial models to estimate risk ratios (RRs) and 95% confidence intervals (CIs). Results. The proportion of late-stage disease increased with age: from 16.53% (21–34 years) to 42.44% (≥ 70 years). The adjusted relative risk of advanced-stage disease among women aged 50 years and older was 2.2 to 2.5 times that of patients aged 21 to 34 years. Uninsured (RR = 1.44; 95% CI = 1.40, 1.49), Medicaid (RR = 1.37, 95% CI = 1.34, 1.41), younger Medicare (RR = 1.12, 95% CI = 1.06, 1.19), and older Medicare (RR = 1.20, 95% CI = 1.15, 1.26) patients had a higher risk of late-stage disease than did privately insured patients. Conclusions. Screening should be encouraged for women at high risk for advanced-stage disease.
Nonoccupational and Occupational Injuries to US Workers With Disabilities
Authors: Price James , Shi Junxin , Lu Bo , Smith Gary A. , Stallones Lorann , Wheeler Krista K. , Xiang Huiyun 
Published: June 2012

Objectives. We examined medically treated injuries among US workers with disability.Methods. Using 2006–2010 National Health Interview Survey data, we compared 3-month rates of nonoccupational and occupational injuries to workers with disability (n = 7729) and without disability (n = 175 947). We fitted multivariable logistic regression models to calculate odds ratios and 95% confidence intervals of injuries by disability status, controlling for sociodemographic variables. We also compared leading causes of injuries by disability status.Results. In the 3-month period prior to the survey, workers with disability were more likely than other workers to have nonoccupational injuries (odds ratio [OR] = 2.35; 95% confidence interval [CI] = 2.04, 2.71) and occupational injuries (OR = 2.39; 95% CI = 1.89, 3.01). For both groups, the leading cause was falls.Conclusions. Disability status was strongly associated with risk of nonoccupational and occupational injuries among US workers. The safety issues facing US workers with disability in the workplace warrant future research. Federal agencies with an interest in the employment of workers with disability and their safety in the workplace should take a lead in further assessing injury risk and in promoting a safe working environment for workers with disability.
Development of tools for ecological quality assessment in the Polish marine areas according to the Water Framework Directive. Part IV — preliminary assessment
Authors: Osowiecki Andrzej , Łysiak-Pastuszak Elżbieta , Kruk-Dowgiałło Lidia , Błeńska Magdalena , Brzeska Paulina , Kraśniewski Wojciech , Lewandowski Łukasz , Krzymiński Włodzimierz 
Published: June 2012

Abstract
A set of classification methods was developed for the Polish coastal and transitional waters regarding the biological quality elements — phytoplankton, macrophytes and macroinvertebrates as required by the EU Water Framework Directive. Mean summer chlorophyll-a and total summer biomass of phytoplankton were proposed as indicators in the phytoplankton assessment. Macrophytes were assessed by the Macrophyte Quality Assessment Index, including biomass and percent bottom coverage of the selected taxa. Macroinvertebrate assessment was based on a biotic index comprising abundance, dominance structure, taxonomical richness and species sensitivity/tolerance to eutrophication. A preliminary assessment of the ecological status revealed that the coastal and transitional waters failed to reach a ‘good’ ecological status.
Polyphasic characterization of the genus Anabaena from the Gulf of Gdańsk (Southern Baltic Sea). Application of DGGE in taxonomic studies on environmental samples
Authors: Siedlewicz Grzegorz , Forycka Karolina , Surosz Waldemar 
Published: June 2012

Abstract
The aim of this paper was a taxonomic verification of cyanobacteria of the genus Anabaena that occur in the Gulf of Gdańsk. Classical taxonomic methods were combined with modern molecular taxonomic methods (polyphasic approach). Analysis of the species diversity of cyanobacteria from the genus Anabaena was based on the microscopic analysis and on the analysis of 16S rRNA and ITS region. Comparison of the obtained results with sequences in GenBank showed 97.8–100% similarity for 16S rRNA and 98.8-100% similarity in the case of the ITS fragment. Similarity of the 16S rRNA and ITS sequence of 98.5% seems to be sufficient to determine the species.