Miracle-dz/UniFAR-FTUs huggingface dataset:
Aligning and Clustering Patterns to Reveal the Protein Functionality of Sequences

Discovering sequence patterns with variations unveils significant functions of a protein family. Existing combinatorial methods of discovering patterns with variations are computationally expensive, and probabilistic methods require more elaborate probabilistic representation of the amino acid associations. To overcome these shortcomings, this paper presents a new computationally efficient method for representing patterns with variations in a compact representation called Aligned Pattern Cluster (AP Cluster). To tackle the runtime, our method discovers a shortened list of non-redundant statistically significant sequence associations based on our previous work. To address the representation of protein functional regions, our pattern alignment and clustering step, presented in this paper captures the conservations and variations of the aligned patterns. We further refine our solution to allow more coverage of sequences via extending the AP Clusters containing only statistically significant patterns to Weak and Conserved AP Clusters. When applied to the cytochrome c, the ubiquitin, and the triosephosphate isomerase protein families, our algorithm identifies the binding segments as well as the binding residues. When compared to other methods, ours discovers all binding sites in the AP Clusters with superior entropy and coverage. The identification of patterns with variations help biologists to avoid time-consuming simulations and experimentations. (Software available upon request).
OPTIMIZING CHEMOTHERAPY IN AN HIV MODEL

We examine an ordinary dierential system modeling the interaction of the HIV virus and the immune system of the human body. The optimal control representsapercentageeect thechemotherapyhasontheinteractionoftheCD4 + T cells withthevirus. WemaximizethebenetbasedontheTcell countandminimize the systemic cost based on the percentage of chemotherapy given. Existence of an optimal control is proven, and the optimal control is uniquely characterized in terms of the solution of the optimality system, which is the state system coupled with the adjoint system. In addition, numerical examples are given for illustration.
Noise Induced DNA Damage Within the Auditory Nerve

An understanding of the molecular pathology that underlies noise induced neurotoxicity is a prerequisite to the design of targeted therapies. The objective of the current experiment was to determine whether or not DNA damage is part of the pathophysiologic sequela of noise induced neurotoxicity. The experiment consisted of 41 hooded Long‐Evans rats (2 month old males) that were randomized into control and noise exposed groups. Both the control and the noise group followed the same time schedule and therefore started and ended the experiment together. The noise dose consisted of a 6000 Hz noise band at 105 dB SPL. Temporal bones from both groups were harvested, and immunohistochemistry was used to identify neurons with DNA damage. Quantitative morphometric analyses was then employed to determine the level of DNA damage. Neural action potentials were recorded to assess the functional impact of noise induced DNA damage. Immunohistochemical reactions revealed that the noise exposure precipitated DNA damage within the nucleus of auditory neurons. Quantitative morphometry confirmed the noise induced increase in DNA damage levels and the precipitation of DNA damage was associated with a significant loss of nerve sensitivity. Therefore, DNA damage is part of the molecular pathology that drives noise induced neurotoxicity. Anat Rec, 300:520–526, 2017. © 2016 Wiley Periodicals, Inc.
An Automatic Test Case Generation Framework for Web Services

BPEL (Business Process Execution Language) as a de-facto standard for web service orchestration has drawn particularly attention from researchers and industries. BPEL is a semi-formal flow language with complex features such as concurrency and hierarchy. To test a model thoroughly, we need to cover different execution scenarios. As is well known, it is tedious, time consuming, and error prone to design test cases manually, especially for complex modelling languages. Hence, it is desirable to apply existing model-based-testing techniques in the domain of web services. We proposed WSA (Web Service Automata) to be the operational semantics for BPEL. Based on WSA, we propose a model checking based test case generation framework for BPEL. The SPIN and NuSMV model checkers are used as the test generation engine, and the conventional structural test coverage criteria are encoded into LTL and CTL temporal logic. State coverage and transition coverage are used for BPEL control flow testing, and all-du-path coverage is used for BPEL data flow testing. Two levels of test cases can be generated to test whether the implementation of web services conforms to the BPEL behaviour and WSDL interface models. The generated test cases are executed on the JUnit test execution engine.
Rapid Systematic Review of the Epley Maneuver for Treating Posterior Canal Benign Paroxysmal Positional Vertigo

Objective The aim of this study was to compare watchful waiting to the Epley maneuver as a management option for patients with posterior canal benign paroxysmal positional vertigo (p-BPPV) regarding symptom relief. Data Sources PubMed, Embase, and The Cochrane Library. Methods A systematic search was conducted. Studies reporting original study data were included. Relevance and risk of bias (RoB) of the selected articles were assessed. Studies with low relevance, high RoB, or both were excluded. Absolute risk differences and their 95% confidence intervals (CIs) were extracted for the included studies. Results A total of 1448 unique studies were retrieved. Eight of these satisfied the eligibility criteria. At 1-week follow-up, all included studies reported a clinically relevant effect in favor of the Epley maneuver regarding symptom relief (absolute risk differences ranging from 20% [95% CI, 5%-37%] to 59% [95% CI, 32%-76%]) or conversion to a negative Dix–Hallpike (absolute risk differences ranging from 17% [95% CI, –5%-37%] to 64% [95% CI, 29%-79%]). At 1-month follow-up, the results of the included studies diverged further. Absolute risk differences ranged from 6% (95% CI, –24%-35%) more symptom relief in favor of watchful waiting to 79% (95% CI, 56%-88%) in favor of the Epley maneuver. Conclusion and Recommendations All data of the selected studies show a benefit in favor of the Epley maneuver at 1-week follow-up in the management of p-BPPV. The Epley maneuver should be considered in all patients with p-BPPV.
Positive Psychology Interventions Addressing Pleasure, Engagement, Meaning, Positive Relationships, and Accomplishment Increase Well-Being and Ameliorate Depressive Symptoms: A Randomized, Placebo-Controlled Online Study

Seligman (2002) suggested three paths to well-being, the pursuit of pleasure, the pursuit of meaning, and the pursuit of engagement, later adding two more, positive relationships and accomplishment, in his 2011 version. The contribution of these new components to well-being has yet to be addressed. In an online positive psychology intervention study, we randomly assigned 1624 adults aged 18–78 (M = 46.13; 79.2% women) to seven conditions. Participants wrote down three things they related to either one of the five components of Seligman's Well-Being theory (Conditions 1–5), all of the five components (Condition 6) or early childhood memories (placebo control condition). We assessed happiness (AHI) and depression (CES-D) before and after the intervention, and 1-, 3-, and 6 months afterwards. Additionally, we considered moderation effects of well-being levels at baseline. Results confirmed that all interventions were effective in increasing happiness and most ameliorated depressive symptoms. The interventions worked best for those in the middle-range of the well-being continuum. We conclude that interventions based on pleasure, engagement, meaning, positive relationships, and accomplishment are effective strategies for increasing well-being and ameliorating depressive symptoms and that positive psychology interventions are most effective for those people in the middle range of the well-being continuum.
Electroconvulsive Therapy in Complex Regional Pain Syndromes

Three cases are presented in which electroconvulsive therapy (ECT) for depression led to the relief of comorbid complex regional pain syndrome as well as depression. In one of the cases, concomitant fibromyalgia was not relieved during 2 separate series of ECT. The literature regarding the role of ECT in the management of chronic pain is reviewed and discussed in light of recent findings about ECT and changes in neurotransmission associated with seizures.
Degradation of lindane by cell-free preparations of Clostridium sphenoides

Cell-free preparation of Clostridium sphenoides degraded the insecticide lindane, the gamma-isomer of 1,2,3,4,5,6-hexachlorocyclohexane, to the gamma-isomer of 3,4,5,6-tetrachloro-1-cyclohexene. The activity appeared to be associated with the membrane fraction and required reduced glutathione. The tetrachlorocy-clohexene intermediate was further metabolized by the membrane fraction to unknown substances.
Interpolation aided fuzzy image classification

This paper presents a novel application of interpolation in supporting fuzzy image classification. The recently introduced Deep Spatio-Temporal Inference Network (DeSTIN) is employed to carry out limited original feature extraction. A simple but effective linear interpolation is then used to artificially increase the dimensionality of the extracted feature sets for accurate classification, without incurring heavy computational cost. In particular, Fuzzy-Rough Nearest Neighbour (FRNN) and Fuzzy Ownership Nearest Neighbour (FRNN-O) are each utilised for image classification. The work is tested against the popular MNIST dataset of handwritten digits [1]. Experimental results indicate that the proposed approach is highly promising.
The Formants of Fricative Consonants

Spectral analysis of American English, Swedish and Polish fricatives shows that these sounds may be classified according to the relations between their formant frequencies and formant levels. Three binary distinctive features at the acoustic-phonetic (not necessarily phonemic) level are postulated: spread/compressed formants (F4–F2); higher/lower formants (F2+F3+F4); higher formant/lower formant emphasis (L4–L2 or L3–L2). A possibility of further classification according to the general shape of the spectral envelope is briefly reviewed.
Low extracellular potassium prolongs repolarization and evokes early afterdepolarization in human induced pluripotent stem cell-derived cardiomyocytes

ABSTRACT Long QT syndrome (LQTS) is characterized by a prolonged QT-interval on electrocardiogram and by increased risk of sudden death. One of the most common and potentially life-threatening electrolyte disturbances is hypokalemia, characterized by low concentrations of K+. Using a multielectrode array platform and current clamp technique, we investigated the effect of low extracellular K+ concentration ([K+]Ex) on the electrophysiological properties of hiPSC-derived cardiomyocytes (CMs) generated from a healthy control subject (WT) and from two symptomatic patients with type 1 of LQTS carrying G589D (LQT1A) or IVS7-2A>G mutation (LQT1B) in KCNQ1. The baseline prolongations of field potential durations (FPDs) and action potential durations (APDs) were longer in LQT1-CMs than in WT-CMs. Exposure to low [K+]Ex prolonged FPDs and APDs in a concentration-dependent fashion. LQT1-CMs were found to be more sensitive to low [K+]Ex compared to WT-CMs. At baseline, LQT1A-CMs had more prolonged APDs than LQT1B-CMs, but low [K+]Ex caused more pronounced APD prolongation in LQT1B-CMs. Early afterdepolarizations in the action potentials were observed in a subset of LQT1A-CMs with further prolonged baseline APDs and triangular phase 2 profiles. This work demonstrates that the hiPSC-derived CMs are sensitive to low [K+]Ex and provide a platform to study acquired LQTS. Summary: This is the first study showing the effects of low extracellular potassium on the electrophysiological properties of human induced pluripotent stem cell-derived long QT cardiomyocytes at single and multicellular level.
The cell survival kinase SGK1 and its targets FOXO3a and NDRG1 in aged human brain

Serum‐ and glucocorticoid‐inducible kinase 1 (SGK1) protects neuronal cells from injury stimuli in vitro, and exerts anti‐apoptotic effects via downstream targets including the forkhead‐like transcription factor FOXO3a. SGK1 is a homolog of Akt, a related survival kinase that is up‐regulated in Alzheimer's disease (AD). Here we aimed to examine the expression pattern of SGK1 and FOXO3a in aged human cerebral cortex.
The Relationship between Upper Basic Pupils’ Study Habits and Their Academic Performance in English Language

The study aimed at investigating the relationship between upper basic pupils’ study habits and their academic performance in English Language in Calabar Education Zone of Cross River State, Nigeria. In order to achieve the objective of this study, three null hypotheses were formulated based on the research questions. Ex-post facto research design was adopted for the study. A sample of two hundred (200) respondents was randomly selected from a population of 4,372 pupils in the study area. Data collection instrument was a questionnaire titled Study Habit Questionnaire (SHQ) and achievement test in English language to measure pupil’s performance. The data was further analyzed using Pearson Product Moment Correlation Analysis Technique. All the hypotheses were tested at 0.05 level of significance. The result of the analyses indicated that group reading, individual reading and note taking habit had a significant relationship with pupil’s academic performance in English Language. The null hypotheses were therefore rejected based on the findings. It was therefore recommended that teachers should encourage pupils to study individually or in groups through quiz, debates and taking of notes. Also the government on its part should provide the needed learning facilities that will create room for developing effective study habits. Original Research Article British Journal of Education, Society & Behavioural Science, 4(12): 1676-1686, 2014 1677
Barriers and facilitators of physical activity in knee and hip osteoarthritis: a systematic review of qualitative evidence

Physical activity (PA), including engagement in structured exercise, has a key role in the management of hip and knee osteoarthritis (OA). However, maintaining a physically active lifestyle is a challenge for people with OA. PA determinants in this population need to be understood better so that they can be optimised by public health or healthcare interventions and social policy changes. Objectives The primary aim of this study is to conduct a systematic review of the existing qualitative evidence on barriers and facilitators of PA for patients with hip or knee OA. Secondary objective is to explore differences in barriers and facilitators between (1) lifestyle PA and exercise and (2) PA uptake and maintenance. Methods Medline, Embase, Web of Science, Cumulative Index to Nursing and Allied Health Literature, SPORTDiscus, Scopus, Grey literature and qualitative journals were searched. Critical Appraisal Skills Programme—Qualitative checklist and Lincoln and Guba’s criteria were used for quality appraisal. Thematic synthesis was applied. Findings Ten studies were included, seven focusing on exercise regimes, three on overall PA. The findings showed a good fit with the biopsychosocial model of health. Aiming at symptom relief and mobility, positive exercise experiences and beliefs, knowledge, a ‘keep going’ attitude, adjusting and prioritising PA, having healthcare professionals’ and social support emerged as PA facilitators. Pain and physical limitations; non-positive PA experiences, beliefs and information; OA-related distress; a resigned attitude; lack of motivation, behavioural regulation, professional support and negative social comparison with coexercisers were PA barriers. All themes were supported by high and medium quality studies. Paucity of data did not allow for the secondary objectives to be explored. Conclusion Our findings reveal a complex interplay among physical, personal including psychological and social-environmental factors corresponding to the facilitation and hindrance of PA, particularly exercise, engagement. Further research on the efficacy of individualised patient education, psychological interventions or social policy change to promote exercise engagement and lifestyle PA in individuals with lower limb OA is required. Trial registration number CRD42016030024.
Privatisations as Price Reforms: Evaluating Consumers' Welfare Changes in the UK

This paper analyses the effects on consumers' welfare of the privatisation policy carried out in the UK since 1979. The approach we follow evaluates the privatisation of a State owned enterprise within the broader framework of the "policy reform" theory (Dreze and Stern [1990]). By adopting this perspective, the change in consumers' welfare "with" and "without" privatisations can be studied by appropriate welfare measures. We claim that an advantage of our approach is that of being able to provide the required welfare assessment in a simplified way by means of a limited set of information. In particular, we show that a series of welfare measures only based on aggregate information can be used where one accepts the use of first and second order approximations and a few "reasonable" assumptions on the shape of demand functions. These welfare measures are subsequently used for the evaluation of the welfare effects related to price variations in seven British privatised public utilities. We conclude that the contribution to consumers' welfare of the privatisation policy in the UK, when compared to the huge transfers involved in the process, has been rather modest.
Lightning in the eastern Alps 1993-1999, part I: Thunderstorm tracks

Abstract. Thunderstorm tracks in the eastern Alps for the summers of 1993-1999 are investigated based on lightning data. The tracking method consists of three steps. Step one filters weak storms. Step two fixes the positions of the single cells, which are then connected. The wind at 700hPa, which approximates the steering level of the thunderstorms, is used to distinguish between six weather patterns. Maps including all discovered tracks are discussed for each flow type. While locations from which thunderstorms originate are almost similar, the track patterns are distinct for each flow type. Main initiation areas are mountain ranges of moderate altitude (≈2.5km MSL) from where most of the tracks lead into flat areas.
Multiple-Component Remediation for Developmental Reading Disabilities

Results from a controlled evaluation of remedial reading interventions are reported: 279 young disabled readers were randomly assigned to a program according to a 2 × 2 × 2 factorial design (IQ, socioeconomic status [SES], and race). The effectiveness of two multiple-component intervention programs for children with reading disabilities (PHAB + RAVE-O; PHAB + WIST) was evaluated against alternate (CSS, MATH) and phonological control programs. Interventions were taught an hour daily for 70 days on a 1:4 ratio at three different sites. Multiple-component programs showed significant improvements relative to control programs on all basic reading skills after 70 hours and at 1-year follow-up. Equivalent gains were observed for different racial, SES, and IQ groups. These factors did not systematically interact with program. Differential outcomes for word identification, fluency, comprehension, and vocabulary were found between the multidimensional programs, although equivalent long-term outcomes and equal continued growth confirmed that different pathways exist to effective reading remediation.
Prevalence of prior hysterectomy in the Seattle-Tacoma area.

Hysterectomy is the most common major surgical procedure performed in the United States. The frequency of hysterectomy among women in the general population is of interest because it affects the population at risk for uterine diseases and because the procedure itself carries significant personal and socioeconomic consequences. We studied factors related to the occurrence of hysterectomy by interviewing a representative sample of women ages 35-74 (n= 1087) in two urban Washington counties during 1976-1977.One-third of the women studied had had a hysterectomy. Later birth cohorts were at higher risk. The ageadjusted prevalence of prior hysterectomy was negatively associated with education and age at first childbirth; it was positively associated with parity, history of irregular menses, and history of a variety of other health conditions. Contrary to expectation, income was negatively associated with hysterectomy rates in one county and showed no association in the other. Part of the income effect was due to confounding by age at first childbirth, which was a surprisingly strong predictive factor. WE CONCLUDE THAT: 1) despite economic predictions based on the discretionary nature of the procedure, hysterectomies are not necessarily more common among high-income women; 2) age at first childbirth may be a more important risk factor for uterine disease than previously thought; and 3) estimates of hysterectomy frequency based on clinic populations may be misleading. (Am J Public Health 70:40-47, 1980.)
Random Field Model Reveals Structure of the Protein Recombinational Landscape

We are interested in how intragenic recombination contributes to the evolution of proteins and how this mechanism complements and enhances the diversity generated by random mutation. Experiments have revealed that proteins are highly tolerant to recombination with homologous sequences (mutation by recombination is conservative); more surprisingly, they have also shown that homologous sequence fragments make largely additive contributions to biophysical properties such as stability. Here, we develop a random field model to describe the statistical features of the subset of protein space accessible by recombination, which we refer to as the recombinational landscape. This model shows quantitative agreement with experimental results compiled from eight libraries of proteins that were generated by recombining gene fragments from homologous proteins. The model reveals a recombinational landscape that is highly enriched in functional sequences, with properties dominated by a large-scale additive structure. It also quantifies the relative contributions of parent sequence identity, crossover locations, and protein fold to the tolerance of proteins to recombination. Intragenic recombination explores a unique subset of sequence space that promotes rapid molecular diversification and functional adaptation.