Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Serendipitous Drug Usages in Patient Forum Data - A Feasibility Study

Drug repositioning reduces safety risk and development cost, compared to developing new drugs. Computational approaches have examined biological, chemical, literature, and electronic health record data for systematic drug repositioning. In this work, we built an entire computational pipeline to investigate the feasibility of mining a new data source – the fast-growing online patient forum data for identifying and verifying drug-repositioning hypotheses. We curated a gold-standard dataset based on filtered drug reviews from WebMD. Among 15,714 sentences, 447 mentioned novel desirable drug usages that were not listed as known drug indications by WebMD and thus were defined as serendipitous drug usages. We then constructed 347 features using text-mining methods and drug knowledge. Finally we built SVM, random forest and AdaBoost.M1 classifiers and evaluated their classification performance. Our best model achieved an AUC score of 0.937 on the independent test dataset, with precision equal to 0.811 and recall equal to 0.476. It successfully predicted serendipitous drug usages, including metformin and bupropion for obesity, tramadol for depression and ondansetron for irritable bowel syndrome with diarrhea. Machine learning methods make this new data source feasible for studying drug repositioning. Our future efforts include constructing more informative features, developing more effective methods to handle imbalance data, and verifying prediction results using other existing methods.
Classification and Evaluation the Privacy Preserving Data Mining Techniques by using a Data Modification-based Framework

In recent years, the data mining techniques have met a serious challenge due to the increased concerning and worries of the privacy, that is, protecting the privacy of the critical and sensitive data. Different techniques and algorithms have been already presented for Privacy Preserving data mining, which could be classified in three common approaches: Data modification approach, Data sanitization approach and Secure Multi-party Computation approach. This paper presents a Data modification- based Framework for classification and evaluation of the privacy preserving data mining techniques. Based on our framework the techniques are divided into two major groups, namely perturbation approach and anonymization approach. Also in proposed framework, eight functional criteria will be used to analyze and analogically assessment of the techniques in these two major groups. The proposed framework provides a good basis for more accurate comparison of the given techniques to privacy preserving data mining. In addition, this framework allows recognizing the overlapping amount for different approaches and identifying modern approaches in this field.
Autologous chondrocyte implantation: a systematic review.

BACKGROUND The purpose of the present study was to determine (1) whether the current literature supports the choice of using autologous chondrocyte implantation over other cartilage procedures with regard to clinical outcome, magnetic resonance imaging, arthroscopic assessment, and durability of treatment, (2) whether the current literature supports the use of a specific generation of autologous chondrocyte implantation, and (3) whether there are patient-specific and defect-specific factors that influence outcomes after autologous chondrocyte implantation in comparison with other cartilage repair or restoration procedures. METHODS We conducted a systematic review of multiple databases in which we evaluated Level-I and II studies comparing autologous chondrocyte implantation with another cartilage repair or restoration technique as well as comparative intergenerational studies of autologous chondrocyte implantation. The methodological quality of studies was evaluated with use of Delphi list and modified Coleman methodology scores. Effect size analysis was performed for all outcome measures. RESULTS Thirteen studies (917 subjects) were included. Study methodological quality improved with later publication dates. The mean modified Coleman methodology score was 54 (of 100). Patients underwent autologous chondrocyte implantation (n = 604), microfracture (n = 271), or osteochondral autograft (n = 42). All surgical techniques demonstrated improvement in comparison with the preoperative status. Three of seven studies showed better clinical outcomes after autologous chondrocyte implantation in comparison with microfracture after one to three years of follow-up, whereas one study showed better outcomes two years after microfracture and three other studies showed no difference in these treatments after one to five years. Clinical outcomes after microfracture deteriorated after eighteen to twenty-four months (in three of seven studies). Autologous chondrocyte implantation and osteochondral autograft demonstrated equivalent short-term clinical outcomes, although there was more rapid improvement after osteochondral autograft (two studies). Although outcomes were equivalent between first and second-generation autologous chondrocyte implantation and between open and arthroscopic autologous chondrocyte implantation, complication rates were higher with open, periosteal-cover, first-generation autologous chondrocyte implantation (four studies). Younger patients with a shorter preoperative duration of symptoms and fewer prior surgical procedures had the best outcomes after both autologous chondrocyte implantation and microfracture. A defect size of >4 cm(2) was the only factor predictive of better outcomes when autologous chondrocyte implantation was compared with a non-autologous chondrocyte implantation surgical technique. CONCLUSIONS Cartilage repair or restoration in the knee provides short-term success with microfracture, autologous chondrocyte implantation, or osteochondral autograft. There are patient-specific and defect-specific factors that influence clinical outcomes.
Germline chimeric chickens from dispersed donor blastodermal cells and compromised recipient embryos.

Stage-X blastoderms, within intact eggs from White Leghorn hens, were exposed to 500-700 rads of gamma radiation from a 60Co source prior to injection, into the subgerminal cavity, of approximately 100 or 200-400 dispersed cells from stage-X blastoderms isolated from eggs laid by Barred Plymouth Rock hens. Embryos developing past day 14 of incubation and hatched chicks were assessed for donor and recipient cell contribution to the melanocyte population through examination of black and yellow down pigmentation, respectively (Barred Plymouth Rocks have a recessive allele at the I locus while the White Leghorns have a dominant allele at the I locus). Of the 809 embryos injected with approximately 100 cells, 192 developed past day 14 and black pigmentation, indicating somatic chimerism, was observed on 118 of the 192 (58%) embryos and chicks. Of the 296 embryos injected with 200-400 donor cells, 86 developed past day 14 of incubation. Somatic chimerism was observed on 55 of the 86 (64%) embryos and chicks. To test for germline chimerism, birds surviving to maturity were mated to Barred Plymouth Rocks. Five somatically chimeric females were produced when approximately 100 cells were injected, and one was a germline chimera. Six somatic female chimeras were produced following the injection of 200-400 cells, three of which proved to be germline chimeras by the presence of Barred Rock chicks among their offspring. Two of the nine males produced by injecting approximately 100 cells were germline chimeras. (ABSTRACT TRUNCATED AT 250 WORDS)
How About the New Antiepileptic Drugs?

Abstract: No new antiepileptic drugs (AEDs) were licensed in the United States from 1978 to 1992. In late 1992, felbamate and gabapentin were recommended for approval, and in early 1993, lamotrigine. In July 1993, felbamate was licensed, and gabapentin and lamotrigine may soon follow. Lamotrigine, vigabatrin and clobazam are in use outside the US. Tiagabine, oxcarbazepine, fosphenytoin, topiramate, vigabatrin and zonisamide are in Phase II clinical testing in the US. All of the new AEDs are effective against partial and tonic-clonic seizures. Few controlled clinical trials have been done in patients with absence and myoclonic seizures. Mechanisms of action of the new drugs have not been clearly defined. The new AEDs will provide an opportunity to improve the care of epileptic patients. Even with optimal management with currently available drugs, some 30% of patients remain refractory to medical management.
[Multiprofessional care and mental health in pregnant women].

OBJECTIVE To identify non-psychotic affective disorders in pregnant women, to intervene by means of psychoprophylactic groups, and to evaluate possible alterations following intervention. METHODS One-hundred and three pregnant women (71 adults and 32 adolescents) were seen at a community program in the Paraisópolis neighborhood in the city of Sao Paulo, southeastern Brazil. We used the following instruments: Self Reporting Questionnaire and Beck Depression Inventory. Ten weekly two-hour meetings were held, addressing the link between mother and fetus and subjects related to mother and child, and answering mother's doubts. We used the chi-squared test (chi2) to compare mental health before and after the intervention, with a significance level of p<0.05. RESULTS Affective disorders were found in 45 pregnant women (43.7%) before the intervention and in 23 (22.3%) after the intervention. The impact of the intervention on affective disorders was statistically significant (p=0.001). Twenty-one women (20.4%) showed depression before the intervention, and 13 (12.6%) after the intervention, a non-significant difference (p=0.133). CONCLUSIONS Multiprofessional care can prevent, detect, and treat affective disorders during pregnancy in both adults and adolescents.
Early childhood otitis media in relation to children's attention-related behavior in the first six years of life.

OBJECTIVE This study examined whether otitis media with effusion (OME) and associated hearing loss during the first 4 years of life were related to the ratings of parents, teachers, and clinicians of children's attention and behavior in the first 6 years of life. METHODS In a prospective study, 85 black children were recruited from community-based child care programs when they were between 6 and 12 months old. OME and hearing status were monitored repeatedly from 6 months to 4 years old. Measures of attention and behavior were collected from parents, teachers, and clinicians when the children were infants, preschoolers, and first graders. RESULTS On average, children experienced either bilateral or unilateral OME 30% of the time and hearing loss 19.9% of the time between 6 months and 4 years old. Descriptive and inferential analyses revealed no significant associations between OME or hearing loss and the measures of attention or behavior completed by parents, teachers, and clinicians. CONCLUSIONS In this sample of children, there was no relationship between amount of early childhood OME or hearing loss and measures of attention or behavior in the first 6 years of life as reported by parents, teachers, and clinicians.otitis media, hearing, attention, behavior.
Antipsychotics in dementia: prevalence and quality of antipsychotic drug prescribing in UK mental health services

Background Up to a quarter of people in the UK with a diagnosis of dementia are prescribed an antipsychotic in any year. The potential risks of such treatment are becoming clearer, but the benefits remain uncertain. Concern about the frequency and quality of such prescribing was expressed in the National Dementia Strategy for England in 2009. Aims To provide an estimate of the prevalence of antipsychotic use for dementia in secondary mental health services in the UK and to collect data relevant to quality improvement initiatives for such prescribing practice. Method In the context of a UK quality improvement programme, relevant clinical audit data were collected for patients with dementia under the care of specialist older people's mental health services. Results Fifty-four mental health National Health Service (NHS) trusts submitted data on 10 199 patients. Of those patients without comorbid psychotic illness, 1620 (16%) were prescribed an antipsychotic; the common clinical indications for such medication were agitation, psychotic symptoms, aggression and distress. Multivariable regression found younger age, care home or in-patient setting, vascular or Parkinson's disease dementia and greater severity of dementia to be all significantly associated with being prescribed antipsychotic medication. Of the 1001 (62%) patients prescribed treatment for more than 6 months, only three-quarters had a documented review of therapeutic response in the previous 6 months. Conclusions The data reveal areas of relatively good current practice, including consideration of alternatives to antipsychotic medication and clear documentation of target symptoms. They also suggest areas for improvement, such as the frequency and quality of review of long-term medication. Strategies to reduce antipsychotic use should take account of the demographic and clinical variables predicting increased likelihood of antipsychotic prescription.
Patient information needs: pre- and post-consultation

This paper presents findings from a study of information seeking behaviour by National Health Service patients which explored motivational triggers for infor- mation needs. Previous research has highlighted the importance of contextual elements in users' changing information needs. This paper highlights how those needs may centre on specific events: in particular, a patient's consultation with their doctor. Patients initiate information seeking to assess whether they need clinical intervention, in preparation for the patient–doctor consultation and to verify the diagnosis or treatment stemming from that consultation. The study has revealed that having confidence in health practitioners is one key motiva- tion for information seeking. Another is a desire to use health service resources judiciously, efficiently and effectively.
Current Challenges in the Bioinformatics of Single Cell Genomics

Single cell genomics is a rapidly growing field with many new techniques emerging in the past few years. However, few bioinformatics tools specific for single cell genomics analysis are available. Single cell DNA/RNA sequencing data usually have low genome coverage and high amplification bias, which makes bioinformatics analysis challenging. Many current bioinformatics tools developed for bulk cell sequencing do not work well with single cell sequencing data. Here, we summarize current challenges in the bioinformatics analysis of single cell genomic DNA sequencing and single cell transcriptomes. These challenges include calling copy number variations, identifying mutated genes in tumor samples, reconstructing cell lineages, recovering low abundant transcripts, and improving the accuracy of quantitative analysis of transcripts. Development in single cell genomics bioinformatics analysis will promote the application of this technology to basic biology and medical research.
Prediction of Protein Secondary Structure using Artificial Neural Network

: Structural information can provide insight into protein function, and therefore, high-accuracy prediction of protein structure from its sequence is highly desirable. We predicted the secondary structure of query protein sequence using Artificial Neural Network available in Neurosolutions. The structure is described in terms of Alpha Helix (H), Extended Strand (E) and Random Coil (C). The results are displayed in tabular forms. By proper training of the network on the data related to structure we tested and predicted the secondary structure of the query protein.
The highly conserved aspartic acid residue between hypervariable regions 1 and 2 of human immunodeficiency virus type 1 gp120 is important for early stages of virus replication

Between hypervariable regions V1 and V2 of human immunodeficiency virus type 1 (HIV-1) gp120 lies a cluster of relatively conserved residues. The contribution of nine charged residues in this region to virus infectivity was evaluated by single-amino-acid substitutions in an infectious provirus clone. Three of the HIV-1 mutants studied had slower growth kinetics than the wild-type virus. The delay was most pronounced in a mutant with an alanine substituted for an aspartic acid residue at position 180. This aspartic acid is conserved by all HIV-1 isolates with known nucleotide sequences. Substitutions with three other residues at this position, including a negatively charged glutamic acid, all affected virus infectivity. The defect identified in these mutants suggests that this aspartic acid residue is involved in the early stages of HIV-1 replication.
Comparing the Effectiveness of Regulation and Pro‐Social Emotions to Enhance Cooperation: Experimental Evidence from Fishing Communities in Colombia

This paper presents the results from a series of framed field experiments conducted in fishing communities off the Caribbean coast of Colombia. The goal is to investigate the relative effectiveness of exogenous regulatory pressure and pro-social emotions in promoting cooperative behavior in a public goods context. The random public revelation of an individual’s contribution and its consequences for the rest of the group leads to significantly higher public good contributions and social welfare than regulatory pressure, even under regulations that are designed to motivate fully efficient contributions.
Issues arising when crossing a border to give birth: an exploratory study on the French-Belgian border

Background: Anecdotal evidence suggests that many organised initiatives for cross-border collaboration in healthcare in border regions originate from the need for women to give birth close to home. Despite this, there is remarkably little research on these practices and the specific modes of collaboration between providers and experiences and needs of these women. In this paper we describe the experiences of French women who choose to give birth in Belgium. Study design: We conducted semi-structured interviews with 14 key informants and captured the experiences of 14 French mothers using a 40-item questionnaire. Results: The chief motivations for French mothers to cross the border to deliver a baby in Belgium were geographical proximity as well as perceived better quality of care. Several procedural differences between France and Belgium were highlighted as possibly affecting the quality of follow-up care, including the absence, in some cases, of a contact person in France, and communication problems between providers. Conclusion: There is a tension between the testimony of patients who are clearly satisfied and evidence of problems in communication and weak collaboration between providers on either side of this cross border collaboration. This paradox requires more research efforts to generate clear evidence of the added value of these cross-border collaborations for patients.
A High-Temperature, High-Voltage SOI Gate Driver IC with High Output Current and On-Chip Low-Power Temperature Sensor

High-temperature power conversion modules (DC-DC converters, inverters, etc.) have enormous potential in extreme environment applications, including automotive, aerospace, geothermal, nuclear, and well logging. Power-to-volume and power-to-weight ratios of these modules can be significantly improved by employing Silicon Carbide (SiC) based power switches (MOSFET or JFET). Wide bandgap material such as SiC is capable of much higher temperature operation than conventional Silicon based power devices. For successful realization of such high temperature power conversion modules, associated control electronics also need to perform at high temperature. This paper presents a Silicon-on-Insulator (SOI) based high-temperature, high-voltage gate driver integrated circuit (IC) with improved peak output current drive over previous work as well as an on-chip low-power temperature sensor. This driver IC has been primarily designed for automotive applications where the under hood temperature can reach 200°C. This new gate driver prototype has been designed and implemented in a 0.8-micron, 2-poly, and 3metal Bipolar-CMOS-DMOS (BCD) on SOI process and has been successfully tested up to 200oC ambient temperature driving a SiC MOSFET or a SiC normally-ON JFET. In this design, the peak output current capability of the driver is 5 A and is thus capable of driving several power switches connected in parallel. An ultra low-power on-chip temperature supervisory circuit has also been integrated into the die to safeguard the driver circuit against excessive die temperature (≥ 220°C). This approach utilizes the increased diode leakage current at higher temperature to monitor the die temperature. Up to 200°C, the power consumption of the proposed temperature sensor circuit is below 10 μW.
eRing: multiple finger gesture recognition with one ring using an electric field

Since gestures are one of the natural interaction modalities between humans they also represent a promising interaction modality for human computer interaction. Finger rings provide an unobtrusive way to detect hand and finger gestures if they are able to detect a large variety of gestures involving hands and multiple fingers. One method that could be used to detect such gestures with a single ring is electric field sensing. In this paper we present an early prototype, called eRing, which uses this method and evaluate its capability to detect different finger- and hand-gestures via user study.
Preparation and Characterization of Bis-GMA/TEGDMA/Clay Nanocomposites at Low Filler Content Regimes

Photo-curable polymer/clay nanocomposites have been prepared using Bis-GMA/TEGDMA (50/50 wt%) and modified as well as unmodified clays at different loading levels <10 wt%. The dispersion state of the clay layers has been studied using wide-angle X-ray diffraction and transmission electron microscopy as the key factor affecting the properties of the final cured nanocomposites. Photopolymerization induced volume shrinkage and double bond conversion percent was determined using density measurement techniques and Fourier transform infrared spectroscopy in order to verify the opacity of the clay filler on polymerization characteristics. Mechanical properties (flexural strength, flexural modulus, and diametral tensile strength) of the photo-cured nanocomposites were also evaluated according to standard test methods provided for materials with dental application. The results showed that the exfoliation or intercalation of the layers play to be the key factor on polymerization features and the mechanical properties of the final nanocomposites. The dispersion state is determined, first, to be dependent to the compatibilization level of the clay and secondly to its content in the composition. Experiments carried out by thermogravimetric analysis revealed also the thermal property dependence to relative abundance of exfoliated/intercalated layers.