Miracle-dz/UniFAR-FTUs huggingface dataset:
Adenosine triphosphate promotes locomotor recovery after spinal cord injury by activating mammalian target of rapamycin pathway in rats

The mammalian target of rapamycin (mTOR) pathway plays an important role in neuronal growth, proliferation and differentiation. To better understand the role of mTOR pathway involved in the induction of spinal cord injury, rat models of spinal cord injury were established by modified Allen's stall method and interfered for 7 days by intraperitoneal administration of mTOR activator adenosine triphosphate and mTOR kinase inhibitor rapamycin. At 1–4 weeks after spinal cord injury induction, the Basso, Beattie and Bresnahan locomotor rating scale was used to evaluate rat locomotor function, and immunohistochemical staining and western blot analysis were used to detect the expression of nestin (neural stem cell marker), neuronal nuclei (neuronal marker), neuron specific enolase, neurofilament protein 200 (axonal marker), glial fibrillary acidic protein (astrocyte marker), Akt, mTOR and signal transduction and activator of transcription 3 (STAT3). Results showed th+at adenosine triphosphate-mediated Akt/mTOR/STAT3 pathway increased endogenous neural stem cells, induced neurogenesis and axonal growth, inhibited excessive astrogliosis and improved the locomotor function of rats with spinal cord injury.
A randomized controlled trial of cognitive behavioral therapy (CBT) for adjusting to multiple sclerosis (the saMS trial): does CBT work and for whom does it work?

OBJECTIVE The aims were (a) to test the effectiveness of a nurse-led cognitive behavioral therapy (CBT) program to assist adjustment in the early stages of multiple sclerosis (MS) and (b) to determine moderators of treatment including baseline distress, social support (SS), and treatment preference. METHOD Ninety-four ambulatory people with MS within 10 years of diagnosis were randomized to receive 8 individual sessions of CBT (n = 48) or supportive listening (n = 46), most delivered on the telephone, in a multicenter randomized controlled trial. The primary outcomes were distress and functional impairment. Secondary outcomes included global improvement, acceptance of illness, and dysfunctional cognitions. Assessments were completed at home and were coordinated by a blind assessor. Data were analyzed by intention-to-treat using multilevel models. RESULTS The CBT group was significantly less distressed at the end of treatment (estimated General Health Questionnaire group difference = 3.2 points, 95\% CI 1.1 to 5.4 points) and at the 12-month follow-up (estimated group difference = 2.2 points, 95\% CI 0.01 to 4.4 points). There were no differences between the groups on functional impairment. The CBT group also demonstrated significantly greater improvements on secondary outcomes at the end of treatment but not at the 12-month follow-up. CBT participants with poor SS and/or clinically defined levels of distress at baseline showed significantly greater gains on both primary outcomes. Treatment preference did not moderate treatment effects. CONCLUSION CBT is more effective than supportive listening in reducing distress in people with MS. CBT appears most effective for patients with poor SS and high levels of distress. The loss of gains in the secondary outcomes by 12 months suggests further follow-up sessions may be warranted.
Recovery of speech following total glossectomy: An acoustic and perceptual appraisal

Abstract This study involved an acoustic and perceptual analysis of the speech produced by a 31-year-old female following total glossectomy. Speech samples were collected on three occasions within the first 3 months following glossectomy. Vowel articulation was examined acoustically as a function of vowel space and the Euclidean distance separating corner vowels. Perceptual analyses involved presentation of the participant's CV productions to 30 healthy adult listeners who made forced-choice identifications of consonant type. Acoustic analysis revealed improvements in vowel space area and an increase in the Euclidean distances. The perceptual results revealed a statistically significant deterioration in consonants over the 3-month period with anterior sounds being perceived more correctly than medial and posterior sounds. The current study highlights the variable nature of speech following glossectomy, with greater improvements in vowel articulation compared to consonant articulation during the earliest stages of surgical recovery.
The effect of different training modes on skeletal muscle microvascular density and endothelial enzymes controlling NO availability

It is becoming increasingly apparent that a high vasodilator response of the skeletal muscle microvasculature to insulin and exercise is of critical importance for adequate muscle perfusion and long‐term microvascular and muscle metabolic health. Previous research has shown that a sedentary lifestyle, obesity and ageing lead to impairments in the vasodilator response, while a physically active lifestyle keeps both microvascular density and vasodilator response high. To investigate the molecular mechanisms behind these impairments and the benefits of exercise training interventions, our laboratory has recently developed quantitative immunofluorescence microscopy methods to measure protein content of eNOS and NAD(P)Hoxidase specifically in the endothelial layer of capillaries and arterioles of human skeletal muscle. As eNOS produces nitric oxide (NO) and NAD(P)Hoxidase produces superoxide anions (O2−, quenching NO) we propose that the eNOS/NAD(P)Hoxidase protein ratio is a marker of vasodilator capacity. The novel methods show that endurance training (ET) and high intensity interval training (HIT), generally regarded as a time‐efficient alternative to ET, increase eNOS protein content and the eNOS/NADP(H)oxidase protein ratio in previously sedentary lean and obese young men. Resistance exercise training had smaller but qualitatively similar effects. Western blot data of other laboratories suggest that endurance exercise training leads to similar changes in sedentary elderly men. Future research will be required to investigate the relative importance of other sources and tissues in the balance between NO and O2− production seen by the vascular smooth muscle layer of terminal arterioles.
Mathematical Computations for Linked Data Applications with OpenMath

Linked data can be used to connect information stemming from usually disparate sources. The Semantic Web combines various kinds of logical reasoning for the inference of additional knowledge from existing data and for consistency checking of data sets. Although mathematics is crucial for most areas where Semantic Web technologies can be applied, support for them is lacking from related standards and tools. This paper presents an approach for integrating OpenMath with RDF data for the representation of mathematical relationships and the integration of mathematical computations into reasoning systems.
The RIAD peptidomimetic inhibits HIV‐1 replication in humanized NSG mice

Increased intracellular concentration of cyclic AMP (cAMP) in T cells is associated with various immunodeficiency conditions including human immunodeficiency virus (HIV) infection. Several reports indicate a critical role of activated protein kinase A (PKA) in the susceptibility of cells to HIV infection. We have used a cell permeable, stable peptidomimetic version (P3) of the RI‐anchoring disruptor (RIAD), which prevents PKA interaction with A‐kinase‐anchoring proteins (AKAPs). It is known that RIAD peptide abrogates effects of localized cAMP signalling through anchored type I PKA in lymphocytes and prevents murine AIDS (MAIDS) infection when expressed as a transgene in mice.
A shared task involving multi-label classification of clinical free text

This paper reports on a shared task involving the assignment of ICD-9-CM codes to radiology reports. Two features distinguished this task from previous shared tasks in the biomedical domain. One is that it resulted in the first freely distributable corpus of fully anonymized clinical text. This resource is permanently available and will (we hope) facilitate future research. The other key feature of the task is that it required categorization with respect to a large and commercially significant set of labels. The number of participants was larger than in any previous biomedical challenge task. We describe the data production process and the evaluation measures, and give a preliminary analysis of the results. Many systems performed at levels approaching the inter-coder agreement, suggesting that human-like performance on this task is within the reach of currently available technologies.
Role of intraseptal anesthesia for pain-free dental treatment

Pain control during the dental procedure is essentials and challenging. A complete efficacious pulp anesthesia has not been attained yet. The regional anesthesia such as inferior alveolar nerve block (IANB) only does not guarantee the effective anesthesia with patients suffering from irreversible pulpitis. This main aim of this review was to discuss various aspects of intraseptal dental anesthesia and its role significance in pain-free treatment in the dental office. In addition, reasons of failure and limitations of this technique have been highlighted. Literature search was conducted for peer-reviewed articles published in English language in last 30 years. Search words such as dental anesthesia, pain control, intraseptal, and nerve block were entered using a web of knowledge and Google scholar databases. Various dental local anesthesia techniques were reviewed. A combination of block anesthesia, buccal infiltration and intraligamentary injection resulted in deep anesthesia (P = 0.003), and higher success rate compared to IANB. For pain-free management of conditions such as irreversible pulpitis, buccal infiltration (4% articaine), and intraosseous injection (2% lidocaine) are better than intraligamentary and IANB injections. Similarly, nerve block is not always effective for pain-free root canal treatment hence, needing supplemental anesthesia. Intraseptal anesthesia is an efficient and effective technique that can be used in maxillary and mandibular adult dentition. This technique is also beneficial when used in conjunction to the regional block or local dental anesthesia.
ECONOMIC EVALUATION OF DIAGNOSTIC LOCALIZATION FOLLOWING BIOCHEMICAL PROSTATE CANCER RECURRENCE

Objectives: The aim of this study was to assess potential cost-effectiveness of using a prostate cancer specific functional imaging technology capable of identifying residual localized disease versus small volume metastatic disease for asymptomatic men with low but detectable prostate specific antigen (PSA) elevation following radical prostatectomy. Methods: Markov modeling was used to estimate the incremental impact on healthcare system costs (2012 USD) and quality-adjusted life-years (QALYs) of two alternative strategies: (i) using the new diagnostic to guide therapy versus (ii) current usual care—using a combination of computed tomography, magnetic resonance imaging, and bone scan to guide therapy. Costs were based on estimates from literature and Medicare reimbursement. Prostate cancer progression, survival, utilities, and background risk of all-cause mortality were obtained from literature. Base-case diagnostic sensitivity (75 percent), specificity (90 percent), and cost (USD 2,500) were provided by our industry partner GE Healthcare. Results: The new diagnostic strategy provided an average gain of 1.83 (95 percent uncertainty interval [UI]: 1.24–2.64) QALYs with added costs of USD 15,595 (95 percent UI: USD -6,330–44,402) over 35 years. The resulting incremental cost-effectiveness ratio was USD 8,516/QALY (95 percent UI: USD -2,947–22,372). Results were most influenced by the utility discounting rate and test performance characteristics; however, the new diagnostic provided clinical benefits over a wide range of sensitivity and specificity. Conclusion: This analysis suggests a diagnostic technology capable of identifying whether men with biochemical recurrence after radical prostatectomy have localized versus metastatic disease would be a cost-effective alternative to current standard work-up. The results support additional investment in development and validation of such a diagnostic.
Open-Label Pilot Study of Modafinil for Methamphetamine Dependence

Methamphetamine has become a major public health issue globally, particularly in the United States. Despite this, no effective pharmacotherapy for methamphetamine abuse has been developed to date. This 6-week, open-label pilot clinical trial examined the safety and tolerability of modafinil up to 400 mg/d in 8 methamphetamine-dependent individuals. Subjects were inducted onto modafinil at 400 mg/d for more than 3 days and remained on 400 mg/d for 4.5 weeks. Participants received weekly blister packs and underwent weekly individual cognitive behavioral therapy. Adjunctive contingency management procedures were used to enhance retention. Vital signs and supervised urine samples were obtained thrice weekly, and self-reported drug use and Hamilton anxiety and depression ratings were completed once weekly. Eight subjects (50% female, 100% white, aged 35-52 years) were enrolled. Four completed the 6-week study, 3 completed a portion, and 1 withdrew consent before completing intake. Results showed that systolic blood pressure (t = 1.09, P = 0.28), diastolic blood pressure, (t = 1.18, P = 0.24), and heart rate (t = 1.55, P = 0.13) did not change over time. Scores on the modafinil side effects checklist (t = −2.63, P = 0.01), Hamilton anxiety scale (t = −2.50, P = 0.018), and Hamilton depression scale (t = −3.25, P = 0.003) all decreased over time. The proportion of urine positive for amphetamines did not change over time (t = −0.52, P = 0.61), whereas self-reported methamphetamine use did (t = −2.86, P < 0.005). These results suggest that modafinil at 400 mg/d is safe and tolerable for methamphetamine-dependent individuals.
Risk factors associated with adverse reactions to antituberculosis drugs

This review sought to identify the available scientific evidence on risk factors associated with adverse reactions to antituberculosis drugs. We performed a systematic review of studies published in the 1965-2012 period and indexed in the MEDLINE and LILACS databases. A total of 1,389 articles were initially selected. After reading their abstracts, we selected 85 studies. Of those 85 studies, 16 were included in the review. Risk factors for adverse reactions to antituberculosis drugs included age > 60 years, treatment regimens, alcoholism, anemia, and HIV co-infection, as well as sodium, iron, and albumin deficiency. Protective factors against hepatic adverse effects of antituberculosis drugs included being male (combined OR = 0.38; 95% CI: 0.20-0.72) and showing a rapid/intermediate N-acetyltransferase 2 acetylator phenotype (combined OR = 0.41; 95% CI: 0.18-0.90). There is evidence to support the need for management of adverse reactions to antituberculosis drugs at public health care facilities.
Handling Data Skew in MapReduce

MapReduce systems have become popular for processing large data sets and are increasingly being used in e-science applications. In contrast to simple application scenarios like word count, e-science applications involve complex computations which pose new challenges to MapReduce systems. In particular, (a) the runtime complexity of the reducer task is typically high, and (b) scientific data is often skewed. This leads to highly varying execution times for the reducers. Varying execution times result in low resource utilisation and high overall execution time since the next MapReduce cycle can only start after all reducers are done. In this paper we address the problem of efficiently processing MapReduce jobs with complex reducer tasks over skewed data. We define a new cost model that takes into account non-linear reducer tasks and we provide an algorithm to estimate the cost in a distributed environment. We propose two load balancing approaches, fine partitioning and dynamic fragmentation, that are based on our cost model and can deal with both skewed data and complex reduce tasks. Fine partitioning produces a fixed number of data partitions, dynamic fragmentation dynamically splits large partitions into smaller portions and replicates data if necessary. Our approaches can be seamlessly integrated into existing MapReduce systems like Hadoop. We empirically evaluate our solution on both synthetic data and real data from an e-science application.
CYP1A1 and GSTM1 Polymorphisms and Oral Cancer Risk: Association Studies Via Evidence-Based Meta-Analyses

Previous studies have implicated CYP1A1 and GSTM1 polymorphisms as risk factors for various cancers. A number of studies have been devoted to the association of CYP1A1 or GSTM1 polymorphism with susceptibility to oral carcinoma and have yielded conflicting results. The aim of the present study was to assess the possible associations of oral cancer risk with CYP1A1 genetic variation and GSTM1 null genotype respectively via systematic meta-analyses. The data suggest that variant genotypes of CYP1A1 might not be risk factors for oral cancer, whereas GSTM1 null genotype significantly increases susceptibility to oral cancer in Asians but not Caucasians.
Differential mRNA Expression of Antimicrobial Peptides and Proteins in Atopic Dermatitis as Compared to Psoriasis Vulgaris and Healthy Skin

Background: Patients with atopic dermatitis (AD) are prone to have skin infections. We aimed to investigate mRNA expression levels of various antimicrobial peptides and proteins (AMPs) in AD patients, and compare it with psoriasis vulgaris (PV) patients and healthy subjects. Methods: Skin biopsies were obtained from healthy subjects and patients with AD and PV. Quantitative real-time RT-PCR was used to determine the mRNA levels of human β-defensin (hBD)-1, hBD-2, hBD-3, LL-37, psoriasin, RNase 7, interferon-γ, and interleukin-10 (IL-10). Results: Except for LL-37, mRNA of hBDs, psoriasin, and RNase 7 was significantly higher expressed in AD (n = 42) and/or PV (n = 35) patients when compared to controls (n = 18). While PV lesions showed significantly higher mRNA hBD-2 levels than lesions of AD, the latter was associated with significantly higher mRNA levels of RNase 7 when compared to PV. A significant positive correlation of hBD expression was observed both in AD patients and PV patients. hBD mRNA levels of AD skin correlated with psoriasin and RNase 7 levels. hBD-1 mRNA expression correlated with AD activity and IL-10 mRNA expression. Conclusions: Most AMPs investigated in this study proved to be overexpressed in AD as well as PV when compared to controls. However, a statistically significant difference in AMP mRNA expression between AD and PV was only found for hBD-2 and RNase 7. A moderate-to-strong linear relationship between the mRNA expression of particular AMPs appears to exist in AD, and to a lesser extent in PV as well.
High-Intensity Inspiratory Protocol Increases Heart Rate Variability in Myocardial Revascularization Patients

Objective: To evaluate heart rate variability during an inspiratory muscle endurance protocol at three different load levels [30%, 60% and 80% of maximal inspiratory pressure], in patients who had previously undergone coronary artery bypass grafting. Methods: Nineteen late postoperative myocardial revascularization patients participating in a cardiovascular rehabilitation program were studied. Maximal inspiratory pressure maneuvers were performed. An inspiratory muscle endurance protocol at 30%, 60% and 80% of maximal inspiratory pressure was applied for four minutes each, in random order. Heart rate and RR intervals were recorded and heart rate variability was analyzed by time (RMSSD-the mean of the standard deviations for all R-R intervals, and RMSM-root-mean square differences of successive R-R intervals) and frequency domains indices (high and low frequency) in normalized units. ANOVA for repeated measurements was used to compare heart rate variability indices and Student t-test was used to compare the maximal inspiratory pressure and maximal expiratory pressure values. Results: Heart rate increased during performance of maximal respiratory pressures maneuvers, and the maximal inspiratory pressure and maximal expiratory pressure mean values were significantly lower than predicted values (P<0.05). RMSSD increased significantly at 80% in relation to rest and 30% of maximal inspiratory pressure and RMSM decreased at 30% and 60% of maximal inspiratory pressure in relation to rest (P<0.05). Additionally, there was significant and progressive decrease in low frequency and increase in high frequency at 30%, 60% and 80% of maximal inspiratory pressure in relation to the resting condition. Conclusion: These results suggest that respiratory muscle training at high intensities can promote greater parasympathetic activity and it may confer important benefits during a rehabilitation program in post-coronary artery bypass grafting.
Cell line profiling to improve monoclonal antibody production

Mammalian cell culture performance is influenced by both intrinsic (genetic) and extrinsic (media and process) factors. In this study, intrinsic capacity of various monoclonal antibody‐producing Chinese Hamster Ovary (CHO) cell lines was compared by exposing them to the same culture condition. Microarray‐based transcriptomics and LC–MS/MS shotgun proteomics technologies were utilized to obtain expression landscape of different cell lines. Specific transcripts and proteins correlating with productivity, growth rate and cell size have been identified. The proteomics analysis results showed a strong correlation between the intracellular protein expression levels of the recombinant DHFR and productivity. In contrast, neither the light chain nor the heavy chain of the recombinant monoclonal antibody showed correlation to productivity. Other top ranked proteins which demonstrated positive correlation to productivity included the adaptor protein complex subunits AP3D1and AP2B2, DNA repair protein DDB1 and the ER translocation complex component, SRPR. The subunits of molecular chaperone T‐complex protein 1 and the regulator of mitochondrial one‐carbon metabolism MTHFD2 showed negative correlation to productivity. The transcriptomics analysis has identified the regulators of calcium signaling, Tmem20 and Rcan1, as the top ranked genes displaying positive and negative correlation to productivity, respectively. For the second part of the study, the principal component analysis (PCA) was generated to view the underlying global structure of the expression data. A clear division and expression polarity was observed between the two distinct clusters of cell lines, independent of link to productivity or any other traits examined. The primary component of the PCA generated from either transcriptomics or proteomics data displayed a strong correlation to cell size and doubling time, while none of the main principal components showed correlation to productivity. Our findings suggest that productivity is rather a minor feature in the context of global transcriptional or protein expression space. Biotechnol. Bioeng. 2014;111: 748–760. © 2013 Wiley Periodicals, Inc.