Miracle-dz/UniFAR-FTUs huggingface dataset:
Disulfide Bonding Pattern Prediction Server Based on Normalized Pair Distance by MODELLER

Prediction of the protein structure is one of the most important problems in the computational biology, and it remains one of the biggest challenges in the structural biology. Disulfide bonds play an import structural role in stabilizing protein conformations. For the protein-folding prediction, a correct prediction of disulfide bridges can greatly reduce the search space. The prediction of disulfide bonding pattern helps, to a certain degree, predicts the 3D structure of a protein and hence its function since disulfide bonds imposes geometrical constraints on the protein backbones. Then, the protein 3D structure related features called normalized pair distance (NPD) vector were imposed as the features for designing the classifier based on the support vector machine (SVM). The classifier was trained to compute the connectivity probabilities of cysteine pairs. In addition, a genetic algorithm was integrated with the SVM model to tune the parameters of the SVM and the window sizes for the features. The maximum weighted perfect matching algorithm was then used to find the disulfide connectivity pattern. In this study, the experimental results show that the accuracies rate reaches 91.7% for the prediction of the overall disulfide connectivity pattern (QP) and that of disulfide bridge prediction (QC) is 94.2% for dataset SP39.
Microbial Considerations in Genetically Engineered Mouse Research

Abstract Microbial infections have long been of concern to scientists using laboratory rodents because of their potential to confound and invalidate research. With the explosion of genetically engineered mice (GEM), new concerns over the impact of microbial agents have emerged because these rodents in many cases are more susceptible to disease than their inbred or outbred counterparts. Moreover, interaction between microbe and host and the resulting manifestation of disease conceivably differ between GEM and their inbred and outbred counterparts. As a result, infections may alter the GEM phenotype and confound interpretation of results and conclusions about mutated gene function. In addition, because GEM are expensive to produce and maintain, contamination by pathogens or opportunists has severe economic consequences. This review addresses how microbial infections may influence phenotype, how immunomodulation of the host as the result of induced mutations may modify host susceptibility to microbial infections, how novel host:microbe interactions have led to the development of new animal models for disease, how phenotype changes have led to the discovery of new pathogens, and new challenges associated with prevention and control of microbial infections in GEM. Although the focus is on naturally occurring infections, extensive literature on the use of GEM in studies of microbial pathogenesis also exists, and the reader is referred to this literature if microbial infection is a suspected culprit in phenotype alteration.
Stimulation of bone formation with an in situ setting tricalcium phosphate/rhBMP-2 composite in rats.

The aim of the study was to determine bone-regenerative effects of an in situ setting tricalcium phosphate (TCP) cement combined with rhBMP-2 and to compare it with autologous bone graft. A trepanation defect of 1.5 mm in the femur diaphysis of Sprague-Dawley rats was filled with an in situ setting TCP cement combined with 0, 0.25, 2.5, or 25 microg of rhBMP-2, an autologous bone graft, or left empty. The rats were euthanized after 1 and 3 weeks and examined by radiography, histology, histomorphometry, and bending tests. All TCP groups with or without BMP-2 showed a good bony ingrowth with a close bone-cement contact. Histomorphometric analysis showed no increase of new bone formation in the defect, but a dose-dependent increase in callus formation with a maximum at 25 microg of rhBMP-2. As shown with intravital fluorochrome staining, new bone formation started earlier using rhBMP-2. Bone strength, measured in a three-point bending test and expressed in percentage of the contralateral healthy femur, was 75% for TCP + 25 microg rhBMP-2, 44% for TCP + 2.5 microg rhBMP-2, and 34% for autologous bone graft. TCP particles were detectable in all groups after 3 weeks. Callus formation and bending strength of the TCP + 25 microg rhBMP-2 group was superior to autologous bone graft. So TCP/rhBMP-2 composites may prove to be an effective substitute for autologous bone grafts.
An efficient technique for aspect-based EHR access policy administration on ABAC

The adoption of electronically formatted medical records, so called Electronic Health Record (EHR), has become extremely important in healthcare systems to enable the exchange of medical information among healthcare providers. To the best of our knowledge, no approach has yet administrated the access policies on the basis of different aspects and subject types in a flexible, scalable and cost-effective manner. We have thus focused on an efficient improvement of policy administration along with the application of ABAC. To achieve this, we believe that a desirable EHR access policy should be created on the fly based on the appropriate primitive policies. In this paper, we thus propose AAS-pada - the composition-based technique for EHR access policy administration on ABAC. Given a subject's attributes and a set of primitive policies, AAS-pada (i) selects the desirable primitive policies across five aspects corresponding to a subject's attributes. (ii) instantiates these primitive policies with the attribute values; and (iii) composes these instantiated primitive policies to form a desirable access policy. Our experimental results show that AAS-pada supports the coverage of all subject types with less investment on the initially created policies. Moreover, it has less impact when the edition of an individual aspect concern is required. Essentially, AAS-pada brings few contributions: flexibility, scalability and cost-effective in administrating the EHR access policies to various subject types.
Residential density and adolescent overweight in a rapidly urbanising region of mainland China

Objective This study investigated the association of residential density with overweight among adolescents in an urban area of China. Methods Using multistage proportional sampling methods, a population-based cross-sectional study was conducted in Nanjing between September and November 2004 (n=2375; mean age=13.9±1.0 years old; 46.2% boys; survey response rate=89.3%). Body mass index was calculated from self-reported body weight and height. Overweight, the main outcome variable, was defined as a BMI ≥85 percentile value for age- and gender-specific reference data according to the recommendation for Chinese adolescents. The primary explanatory variable was the residential density of the urban districts. Mixed-effects logistic regression models were used for the analysis. Results Students in the higher and middle tertiles of residential density had a 2.17-fold (95% CI 1.41 to 3.33) and 1.89-fold (95% CI 1.22 to 2.92) higher likelihood of being overweight, respectively, compared with those in the lower tertile. The associations were slightly attenuated but still significant after adjusting for time spent in recreational physical activity and sedentary behaviour (viewing TV and sitting for academic study). Conclusions Residential density was positively associated with overweight among urban Chinese adolescents. Our findings warrant further research examining attributes of urban environments associated with adolescents' obesity in China and potential mechanisms between them.
Intimal Sarcoma Is the Most Frequent Primary Cardiac Sarcoma: Clinicopathologic and Molecular Retrospective Analysis of 100 Primary Cardiac Sarcomas

We report novel molecular and pathologic features of sarcomas involving the heart. Intimal sarcoma appears as the most frequent primary cardiac sarcoma within the largest described series of 100 primary cardiac sarcomas. Immunohistochemical analysis, fluorescence in situ hybridization, real-time polymerase chain reaction, and array-comparative genomic hybridization were performed on materials from 65 women and 35 men, aged 18 to 82 years (mean 50 y), retrieved from the French Departments of Pathology, between 1977 and early 2013. Right and left heart was involved in 44 and 56 cases, respectively. There were 42 intimal sarcomas, 26 angiosarcomas, 22 undifferentiated sarcomas, 7 synovial sarcomas, 2 leiomyosarcomas, and 1 peripheral neuroectodermal tumor. All but 1 angiosarcomas originated from the right heart, whereas 83% of the intimal sarcomas and 72% of the undifferentiated sarcomas were from the left heart. MDM2 overexpression was immunohistochemically observed in all intimal sarcomas, as well as in 10 of the 22 undifferentiated sarcomas and in 5 of the 26 angiosarcomas. MDM2 amplification was only demonstrated in intimal sarcomas. Genomic analysis showed a complex profile, with recurrent 12q13-14 amplicon involving MDM2, 4q12 amplicon involving KIT and PDGFRA, 7p12 gain involving EGFR, and 9p21 deletion targeting CDKN2A. Immunohistochemical detection of MDM2 overexpression can easily detect intimal sarcoma, provided that molecular aberration is proved. As resections are limited to the left atrium, this histologic subtype could benefit from therapies targeting PDGFRA or MDM2.
Linear and nonlinear analysis of autonomic regulation in depressed patients

To investigate the effect of depression and medication on the autonomic nervous system (ANS) we compared 25 patients suffering from depression with 72 matched control subjects (CON). From every patient three times ECG and non-invasive blood pressure were recorded in: acute non-mediated state (T1), medicated state (T2) and clinical recovered state (T3). Cardiac autonomic regulation was evaluated by linear and nonlinear analysis methods. The results show that non-medicated depressed patients differ significantly from CON (p<0.05). In the medicated state considerably high significant differences between depressed patient and CON were found (p<0.0001). After an 18 months follow-up a normalization of autonomic parameters was achieved in depressed patients. These results show that depression influences autonomic parameters significantly and that medical treated clinical recovered patients approximate to healthy controls in autonomic regulation.
Building multivariate Sato models with linear dependence

The increased trading in multi-name financial products has required the development of state-of-the-art multivariate models. These models should be computationally tractable and, at the same time, flexible enough to explain the stylized facts of asset log-returns and of their dependence structure. The popular class of multivariate Lévy models provides a variety of tractable models, but suffers from one major shortcoming: Lévy models can replicate single-name derivative prices for a given time-to-maturity, but not for the whole range of quoted strikes and maturities, especially during periods of market turmoil. Moreover, there is a significant discrepancy between the moment term structure of Lévy models and the one observed in the market. Sato processes on the other hand exhibit a moment term structure that is more in line with empirical evidence and allow for a better replication of single-name option price surfaces. In this paper, we propose a general framework for multivariate models characterized by independent and time-inhomogeneous increments, where the asset log-return processes at unit time are modeled as linear combinations of independent self-decomposable random variables, where at least one self-decomposable random variable is shared by all the assets. As examples, we consider two general subclasses within this new framework, where we assume a normal variance-mean mixture with a one-sided tempered stable mixing density or a difference of one-sided tempered stable laws for the distribution of the risk factors. Particular attention is given to the models' ability to explain the asset dependence structure. A numerical study reveals the advantages of these new types of models.
Additional Inhibitory Effect of Tea Extract on the Growth of Influenza A and B Viruses in MDCK Cells

It has been previously reported that green‐tea extract (GTE) inhibits the growth of influenza virus by preventing its adsorption. In this study, we further investigated whether GTE exerts an additional inhibitory effect on the acidification of intracellular compartments such as endosomes and lysosomes (referred to as ELS) and thereby inhibits the growth of influenza A and B viruses in Madin‐Darby canine kidney cells. The vital fluorescence microscopic study showed that GTE inhibited acidification of ELS in a concentration‐dependent manner. Moreover, the growth of influenza A and B viruses was equally inhibited when the cells were treated with GTE within as early as 5 to 15 min after infection, depending on the virus strains. The fact that (—)epigallocatechin (EGC), one of major catechin molecules in GTE, exerts the inhibitory effects on the acidification of ELS and virus growth in a manner similar to that of GTE strongly suggests that EGC is one of the active components in the extract.
“Authentic” Arts Teaching and Learning: An Investigation Into the Practices of Australian Home Educators

Research into the ways that “authentic” arts teaching and learning are conducted in Australian home education contexts has not yet been undertaken. Given that home education is experiencing rapid growth and that many current global education reforms place emphasis on the arts as vital to creative futures, the development of deeper understanding is warranted. In order to address the shortfall, this paper reports on the first phase of a qualitative study that investigated the arts practices of 14 Australian home educators for the purpose of understanding the variety of ways that arts learning and teaching are incorporated in individual home education contexts. The study sought to identify the issues that participants experience when facilitating their children’s arts education, the specific strategies they adopt, and how arts teaching and learning approaches are adapted to the fluctuating needs and dynamics of their individual contexts. The paper begins by outlining home education as a unique and alternative pedagogical practice that differs from formal institutional learning, before unpacking the concept of authentic arts education. Details are presented that reveal the research process when interaction between participant and researcher combined to consider engagement with the arts and of associated challenges.
Adjuvant aspirin therapy reduces symptoms of schizophrenia spectrum disorders: results from a randomized, double-blind, placebo-controlled trial.

OBJECTIVE Inflammatory processes may play a role in the pathophysiology of schizophrenia. The aim of this study was to determine the efficacy of adjuvant treatment with aspirin (acetylsalicylic acid) in schizophrenia spectrum disorders. METHOD This randomized, double-blind, placebo-controlled study was conducted between May 2004 and August 2007. Seventy antipsychotic-treated inpatients and outpatients from 10 psychiatric hospitals in The Netherlands with a DSM-IV-diagnosed schizophrenia spectrum disorder were included. Patients were randomized to adjuvant treatment with aspirin 1000 mg/d or placebo. During a 3-month follow-up, psychopathology was assessed with the Positive and Negative Syndrome Scale (PANSS). Other assessments included cognitive tests and immune function. The primary efficacy outcome was the change in total PANSS score. Secondary outcomes were changes in the PANSS subscales and cognitive test results. RESULTS Mixed-effect models showed a 4.86-point (95% CI, 0.91 to 8.80) and 1.57-point (95% CI, 0.06 to 3.07) larger decrease in the aspirin group compared to the placebo group on the total and positive PANSS score, respectively. Similar but not statistically significant results were observed for the other PANSS subscale scores. Treatment efficacy on total PANSS score was substantially larger in patients with the more altered immune function (P = .018). Aspirin did not significantly affect cognitive function. No substantial side effects were recorded. CONCLUSION Aspirin given as adjuvant therapy to regular antipsychotic treatment reduces the symptoms of schizophrenia spectrum disorders. The reduction is more pronounced in those with the more altered immune function. Inflammation may constitute a potential new target for antipsychotic drug development. TRIAL REGISTRATION controlled-trials.com Identifier: ISRCTN27745631.
Alterations in Global Patterns of Gene Expression in Synechocystis sp. PCC 6803 in Response to Inorganic Carbon Limitation and the Inactivation of ndhR, a LysR Family Regulator*

The cyanobacterium Synechocystis sp. PCC 6803 possesses multiple inorganic carbon (Ci) uptake systems that are regulated by Ci availability. The control mechanisms of these systems and their integration with other cell functions remain to be clarified. An analysis of the changes in global gene expression in response to Ci downshift and the inactivation of ndhR (sll1594), a LysR family regulator of Ci uptake is presented in this report. Mild Ci limitation (3% CO2 (v/v) in air to air alone) induced a dramatic up-regulation of genes encoding both inducible CO2 and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{HCO}_{3}^{-}\) \end{document} uptake systems. An induction of ndhD5/ndhD6 and other genes in a probable transcriptional unit was observed, suggesting a function in inducible Ci uptake. The expression of slr1513 and sll1735, physically clustered with sbtA and ndhF3/ndhD3/cupA, respectively, were also coordinated with upstream genes encoding the essential components for \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{HCO}_{3}^{-}\) \end{document} and CO2 uptake. Ci limitation induced the regulatory genes slr1214, sll1292, slr1594, sigD, sigG, and sigH, among which slr1214, a two-component response regulator, showed the earliest induction, implying a role for the early response to Ci limitation. Opposite regulation of genes encoding the assimilation of carbon and nitrogen demonstrated a striking coordination of expression to balance C- and N-fluxes. The analyses revealed that ndhR inactivation up-regulated the expression of sbtA/sbtB, ndhF3/ndhD3/cupA/sll1735, and slr2006-13 including ndhD5 and ndhD6, indicating a vital role of this regulatory gene in both CO2 and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{HCO}_{3}^{-}\) \end{document}acquisition of the cyanobacterium. We therefore suggest that ndhR be renamed ccmR to better represent its broader regulatory characteristics.
Prevalence of cervical human papillomavirus in Taiwanese women.

PURPOSE To define the prevalence rate of cervical human papilloma virus (HPV) using DNA oligonucleotide microarray and its correlation with risk factors in Taiwanese women in metropolitan Taipei. METHODS Thirteen hundred and twenty healthy women, aged 21 - 65 yr without history of cervical intraepithelial neoplasia (CIN) or carcinoma were included in this prospective study. Pap smear and HPV typing using oligonucleotide microarray were performed for each woman. They were given a standardized questionnaire to obtain information about the risk factors of cervical cancer in Taiwan. RESULTS The overall HPV positivity was 19.85% and multiple infections were found in 35.84% of the infected group, 7.92% of the whole study population. The younger the subject, the higher was the infection rate and multiple infection rates. The most common HPV types were 16, 18, 58, 52, 51 and 56, which is different from the western world. The sensitivity of the HPV DNA chip in detecting CIN and cervical carcinoma is 97.06%, and 100% in detecting CIN 2 or more lesions. Risk factors for HPV infection include earlier coitarche (P < 0.01), multiple sexual partners (P < 0.05), history of sexually transmitted disease (P < 0.05), two or more vaginal deliveries (P < 0.05) and infrequent use of condoms (P < 0.05). The association between oral contraception or cigarette smoking and HPV infection could not be determined because few women smoke or used oral contraception. There was no relationship between induced abortion and HPV infection. CONCLUSIONS About one-fifth of adult women in metropolitan Taipei were cervical HPV positive. The popular HPV types and the risk factors of HPV infection in metropolitan Taipei are not the same as those in the western world. The sensitivity of the HPV DNA chip in detecting cervical neoplasia is very high.
Membrane properties of an unusual intrinsically oscillating, wide‐field teleost retinal amacrine cell

In the retina, amacrine cells modulate the transfer of information from bipolar to ganglion cells. The nature of the modulation depends on the synaptic input and the membrane properties of the cells. In the retina of white bass, we identified a class of bistratified, wide‐field amacrine cell characterized by immunopositive labelling for GABA and calmodulin. In isolation, the cells presented resting membrane potentials averaging ‐69 mV although some cells settled at more depolarized values (‐30 mV). Injection of depolarizing current pulses induced oscillatory membrane responses. When elicited from depolarized cells, the oscillations were short‐lived (< 40 ms). For the most part, the oscillatory potentials of hyperpolarized cells remained unattenuated throughout the depolarizing pulse. The frequency of the oscillations increased logarithmically with mean membrane potential, ranging from 74 to 140 Hz. Cells exhibiting depolarized membrane potentials oscillated at twice that rate. When the membrane potential of these cells was hyperpolarized to ‐70 mV, the oscillations became unattenuated and slowed. We found the cells expressed voltage‐gated sodium, potassium and calcium currents and calcium‐dependent potassium currents. We demonstrate that the oscillatory potentials arose as a result of the interplay between calcium and potassium currents. The cells responded to local application of GABA and glycine, both of which modulate the oscillatory potentials. Glutamate and its analogues depolarized the cell and induced oscillatory potentials. Our results indicate that oscillatory responses of a type of wide‐field amacrine cell are an intrinsic feature of the cell and not due to circuit properties.