Miracle-dz/UniFAR-FTUs huggingface dataset:
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform

Historically, in computational biology the fast Fourier transform (FFT) has been used almost exclusively to count the number of exact letter matches between two biosequences. This paper presents an FFT algorithm that can compute the match score of a sequence against a position-specific scoring matrix (PSSM). Our algorithm finds the PSSM score simultaneously over all offsets of the PSSM with the sequence, although like all previous FFT algorithms, it still disallows gaps. Although our algorithm is presented in the context of global matching, it can be adapted to local matching without gaps. As a benchmark, our PSSM-modified FFT algorithm computed pairwise match scores. In timing experiments, our most efficient FFT implementation for pairwise scoring appeared to be 10 to 26 times faster than a traditional FFT implementation, with only a factor of 2 in the acceleration attributable to a previously known compression scheme. Many important algorithms for detecting biosequence similarities, e.g., gapped BLAST or PSIBLAST, have a heuristic screening phase that disallows gaps. This paper demonstrates that FFT algorithms merit reconsideration in these screening applications.
Attitudes, access and anguish: a qualitative interview study of staff and patients’ experiences of diabetic retinopathy screening

Objective To examine the experiences of patients, health professionals and screeners; their interactions with and understandings of diabetic retinopathy screening (DRS); and how these influence uptake. Design Purposive, qualitative design using multiperspectival, semistructured interviews and thematic analysis. Setting Three UK Screening Programme regions with different service-delivery modes, minority ethnic and deprivation levels across rural, urban and inner-city areas, in general practitioner practices and patients’ homes. Participants 62 including 38 patients (22 regular-screening attenders, 16 non-regular attenders) and 24 professionals (15 primary care professionals and 9 screeners). Results Antecedents to attendance included knowledge about diabetic retinopathy and screening; antecedents to non-attendance included psychological, pragmatic and social factors. Confusion between photographs taken at routine eye tests and DRS photographs was identified. The differing regional invitation methods and screening locations were discussed, with convenience and transport safety being over-riding considerations for patients. Some patients mentioned significant pain and visual disturbance from mydriasis drops as a deterrent to attendance. Conclusions In this, the first study to consider multiperspectival experiential accounts, we identified that proactive coordination of care involving patients, primary care and screening programmes, prior to, during and after screening is required. Multiple factors, prior to, during and after screening, are involved in the attendance and non-attendance for DRS. Further research is needed to establish whether patient self-management educational interventions and the pharmacological reformulation of shorter acting mydriasis drops, may improve uptake of DRS. This might, in turn, reduce preventable vision loss and its associated costs to individuals and their families, and to health and social care providers, reducing current inequalities.
Sleep and Everyday Functioning in Older Adulthood

As individuals age they report increasing numbers of sleep problems (e.g., increased nighttime wakings) and this poorer sleep quality has been associated with increased risk for various medical conditions; however limited research has focused on the implications of sleep quality on everyday functioning in older adulthood. We compared three methods of sleep data collection (wrist actigraphy, self-report questionnaires, and sleep diary) and evaluated their relationships with three approaches to assessing everyday functioning (direct observation, self-report, and paper-and-pencil-based problem-solving tasks) in cognitively healthy older adults. Consistent with previous research, subjective sleep measures correlated significantly with each other but did not correlate with objective sleep measures. Multiple regression analyses revealed neither objective nor subjective sleep measures predicted everyday functioning. Individual variability in sleep may affect prediction of everyday functioning using a cross-sectional sample. Future research should investigate the combined influence of sleep and cognitive factors on everyday functioning in older adults.
Recognizing Relevant Code Elements during Change Task Navigation

Developers spend a significant amount of their time exploring source code. Yet, little is known about the way developers break down their code exploration or the fine-grained navigation for change tasks within methods. The objective of our research is to address this gap and learn more about developers' code navigation for change tasks to devise better tool support. For our research, we perform exploratory studies also taking advantage of eye-tracking technology and interaction monitoring to gather detailed data on developers' code navigation down to the line-level. Based on the findings, we devise a model and approach that capture developers' code navigation and allow to automatically determine code elements that are relevant in the near future as well as to determine and summarize the elements that are currently relevant and might, for instance, be helpful for task resumption after interruptions. We plan to evaluate our model and approach in a multiple cases study on navigation recommendation and work resumption.
Dysfunction of Simian Immunodeficiency Virus/Simian Human Immunodeficiency Virus-Induced IL-2 Expression by Central Memory CD4+ T Lymphocytes1

Production of IL-2 and IFN-γ by CD4+ T lymphocytes is important for the maintenance of a functional immune system in infected individuals. In the present study, we assessed the cytokine production profiles of functionally distinct subsets of CD4+ T lymphocytes in rhesus monkeys infected with pathogenic or attenuated SIV/simian human immunodeficiency virus (SHIV) isolates, and these responses were compared with those in vaccinated monkeys that were protected from immunodeficiency following pathogenic SHIV challenge. We observed that preserved central memory CD4+ T lymphocyte production of SIV/SHIV-induced IL-2 was associated with disease protection following primate lentivirus infection. Persisting clinical protection in vaccinated and challenged monkeys is thus correlated with a preserved capacity of the peripheral blood central memory CD4+ T cells to express this important immunomodulatory cytokine.
Blood Pressure Treatment Slows the Progression of Carotid Stenosis in Patients With Isolated Systolic Hypertension

Background and Purpose The Systolic Hypertension in the Elderly Program (SHEP) was a randomized trial testing the efficacy of treating systolic hypertension in older adults. A significant reduction in stroke risk was observed among participants assigned to active treatment. Serial carotid duplex scans were performed on 129 participants at the University of Pittsburgh center, and rates of progression and regression of carotid stenosis were observed. Methods Changes in blood flow velocity ratios were used to detect progression because they can be reliably measured and their relation to degree of residual lumen is known. Progression required the development of a 40% to 50% diameter stenosis when stenosis was not initially present or, if already present, further reduction in the lumen diameter. Regression required the absence of a 40% to 50% diameter stenosis when stenosis was initially present or a stenosis significantly less severe than that initially seen. Results Progression occurred in 22% (28/129) of participants and regression in 16% (8/49). Progression of carotid stenosis occurred more often among participants randomized to placebo as compared with active treatment (31% versus 14%, P=.020). All eight patients exhibiting regression were randomized to active treatment. In multivariate analysis, participants assigned to placebo had 4.3 times greater odds of progressing than participants assigned to active treatment. Other factors significantly related to progression were higher degree of plaque at baseline, low high-density lipoprotein-3, high lipoprotein(a), and younger age. Conclusions Treating systolic hypertension appears to slow progression of carotid stenosis. Similar effects occurring in the intracranial vessels may be one reason for the substantial decrease in stroke among SHEP participants assigned to active treatment.
Head injury (moderate to severe).

INTRODUCTION Head injury in young adults is often associated with motor vehicle accidents, violence, and sports injuries. In older adults it is often associated with falls. Severe head injury can lead to secondary brain damage from cerebral ischaemia resulting from hypotension, hypercapnia, and raised intracranial pressure. Severity of brain injury is assessed using the GCS. While about a quarter of people with severe brain injury (GCS score less than 8) will make a good recovery, about a third will die, and a fifth will have severe disability or be in a vegetative state. METHODS AND OUTCOMES We conducted a systematic review and aimed to answer the following clinical question: What are the effects of interventions to reduce complications of moderate to severe head injury as defined by Glasgow Coma Scale? We searched: Medline, Embase, The Cochrane Library and other important databases up to April 2007 (Clinical Evidence reviews are updated periodically, please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). RESULTS We found 17 systematic reviews, RCTs, or observational studies that met our inclusion criteria. CONCLUSIONS In this systematic review we present information relating to the effectiveness and safety of the following interventions: antibiotics, anticonvulsants, corticosteroids, hyperventilation, hypothermia, and mannitol.
Pricing and Resource Allocation via Game Theory for a Small-Cell Video Caching System

Evidence indicates that downloading on-demand videos accounts for a dramatic increase in data traffic over cellular networks. Caching popular videos in the storage of small-cell base stations (SBS), namely, small-cell caching, is an efficient technology for reducing the transmission latency while mitigating the redundant transmissions of popular videos over back-haul channels. In this paper, we consider a commercialized small-cell caching system consisting of a network service provider (NSP), several video retailers (VRs), and mobile users (MUs). The NSP leases its SBSs to the VRs for the purpose of making profits, and the VRs, after storing popular videos in the rented SBSs, can provide faster local video transmissions to the MUs, thereby gaining more profits. We conceive this system within the framework of Stackelberg game by treating the SBSs as specific types of resources. We first model the MUs and SBSs as two independent Poisson point processes, and develop, via stochastic geometry theory, the probability of the specific event that an MU obtains the video of its choice directly from the memory of an SBS. Then, based on the probability derived, we formulate a Stackelberg game to jointly maximize the average profit of both the NSP and the VRs. In addition, we investigate the Stackelberg equilibrium by solving a non-convex optimization problem. With the aid of this game theoretic framework, we shed light on the relationship between four important factors: the optimal pricing of leasing an SBS, the SBSs allocation among the VRs, the storage size of the SBSs, and the popularity distribution of the VRs. Monte Carlo simulations show that our stochastic geometry-based analytical results closely match the empirical ones. Numerical results are also provided for quantifying the proposed game-theoretic framework by showing its efficiency on pricing and resource allocation.
The Aspergillus fumigatus Dihydroxyacid Dehydratase Ilv3A/IlvC Is Required for Full Virulence

Dihydroxyacid dehydratase (DHAD) is a key enzyme in the branched-chain amino acid biosynthetic pathway that exists in a variety of organisms, including fungi, plants and bacteria, but not humans. In this study we identified four putative DHAD genes from the filamentous fungus Aspergillus fumigatus by homology to Saccharomyces cerevisiae ILV3. Two of these genes, AFUA_2G14210 and AFUA_1G03550, initially designated AfIlv3A and AfIlv3B for this study, clustered in the same group as S. cerevisiae ILV3 following phylogenetic analysis. To investigate the functions of these genes, AfIlv3A and AfIlv3B were knocked out in A. fumigatus. Deletion of AfIlv3B gave no apparent phenotype whereas the Δilv3A strain required supplementation with isoleucine and valine for growth. Thus, AfIlv3A is required for branched-chain amino acid synthesis in A. fumigatus. A recombinant AfIlv3A protein derived from AFUA_2G14210 was shown to have DHAD activity in an in vitro assay, confirming that AfIlv3A is a DHAD. In addition we show that mutants lacking AfIlv3A and ilv3B exhibit reduced levels of virulence in murine infection models, emphasising the importance of branched-chain amino acid biosynthesis in fungal infections, and hence the potential of targeting this pathway with antifungal agents. Here we propose that AfIlv3A/AFUA_2G2410 be named ilvC.
Acupuncture as analgesia for non-emergent acute non-specific neck pain, ankle sprain and primary headache in an emergency department setting: a protocol for a parallel group, randomised, controlled pilot trial

Introduction This study aims to assess the feasibility of acupuncture as an add-on intervention for patients with non-emergent acute musculoskeletal pain and primary headache in an emergency department (ED) setting. Methods and analysis A total of 40 patients who present to the ED and are diagnosed to have acute non-specific neck pain, ankle sprain or primary headache will be recruited by ED physicians. An intravenous or intramuscular injection of analgesics will be provided as the initial standard pain control intervention for all patients. Patients who still have moderate to severe pain after the 30 min of initial standard ED management will be considered eligible. These patients will be allocated in equal proportions to acupuncture plus standard ED management or to standard ED management alone based on computer-generated random numbers concealed in opaque, sealed, sequentially numbered envelopes. A 30 min session of acupuncture treatment with manual and/or electrical stimulation will be provided by qualified Korean medicine doctors. All patients will receive additional ED management at the ED physician's discretion and based on each patient's response to the allocated intervention. The primary outcome will be pain reduction measured at discharge from the ED by an unblinded assessor. Adverse events in both groups will be documented. Other outcomes will include the patient-reported overall improvement, disability due to neck pain (only for neck-pain patients), the treatment response rate, the use of other healthcare resources and the patients’ perceived effectiveness of the acupuncture treatment. A follow-up telephone interview will be conducted by a blinded assessor 72±12 h after ED discharge. Ethics and dissemination Written informed consent will be obtained from all participants. The study has been approved by the Institutional Review Boards (IRBs). The results of this study will guide a full-scale randomised trial of acupuncture in an ED context. Trial registration number ClinicalTrials.gov: NCT02013908.
Belief in Superstition and Intolerance in Conditions of Uncertainty

The condition of intolerance to uncertainty in individuals arises when there is a possibility of a bad situation or having a risky future. Therefore, many individuals try to reduce these adverse effects that may occur in the future by believing in superstitions. This research will reveal whether there is a superstitious belief in intolerance in uncertain conditions. Data will be analyzed using Pearson Product Moment involving 395 subjects selected through quota sampling. The results showed that there was a relationship between superstitious beliefs and intolerance of uncertainty with a correlation strength of 0.423. This means that when an individual is in an uncertain situation, it can trigger the presence of intolerance of uncertainty. On the other hand, the presence of superstitious belief is believed to have existed in the individual and tends to be used as a protector in making decisions.
Epidemiology of congenital idiopathic talipes equinovarus in Iowa, 1997–2005

Congenital idiopathic talipes equinovarus (ITEV), also known as clubfoot, is a well‐recognized foot deformity. To date, prevalence estimates and descriptive data reported for ITEV have varied due to differences in study methodology. Using population‐based surveillance data collected by the Iowa Registry for Congenital and Inherited Disorders, we examined isolated ITEV births delivered from 1997 through 2005 and compared to live births in Iowa during the same time period. An overall prevalence was calculated for live, singleton full‐term births only. Prevalence odds ratios (POR)s and 95% confidence intervals (CI)s were examined for selected infant and parental characteristics. The prevalence of isolated ITEV was 11.4 per 10,000 live, singleton full‐term births (95% CI = 10.3, 12.6), with no significant variation in prevalence during the study period. Increased PORs were found for males (POR 1.8; 95% CI = 1.5, 2.3) and maternal smoking during pregnancy (POR = 1.5, 95% CI = 1.2, 1.9); low birth weight (<2,500 g) showed an increase among females (POR = 3.2, 95% CI = 1.5, 6.9) but not males (POR = 0.9, 95% CI = 0.3, 2.8). Elevated, but non‐significant, PORs were found for season of birth, maternal education, and trimester prenatal care was initiated; decreased PORs were found for fetal presentation, maternal race/ethnicity, parity, area of residence, and parental age at delivery. Our study of a well‐defined, homogenous sample suggested that prevalence of isolated ITEV in Iowa was similar to that reported in other population‐based studies and provided support for some, but not all, previously reported associations with infant and parental characteristics. More detailed, longitudinal studies of isolated ITEV are recommended. © 2010 Wiley‐Liss, Inc.
Proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective

Bacterial colonization of biotic or abiotic surfaces results from two quite distinct physiological processes, namely bacterial adhesion and biofilm formation. Broadly speaking, a biofilm is defined as the sessile development of microbial cells. Biofilm formation arises following bacterial adhesion but not all single bacterial cells adhering reversibly or irreversibly engage inexorably into a sessile mode of growth. Among molecular determinants promoting bacterial colonization, surface proteins are the most functionally diverse active components. To be present on the bacterial cell surface, though, a protein must be secreted in the first place. Considering the close association of secreted proteins with their cognate secretion systems, the secretome (which refers both to the secretion systems and their protein substrates) is a key concept to apprehend the protein secretion and related physiological functions. The protein secretion systems are here considered in light of the differences in the cell-envelope architecture between diderm-LPS (archetypal Gram-negative), monoderm (archetypal Gram-positive) and diderm-mycolate (archetypal acid-fast) bacteria. Besides, their cognate secreted proteins engaged in the bacterial colonization process are regarded from single protein to supramolecular protein structure as well as the non-classical protein secretion. This state-of-the-art on the complement of the secretome (the secretion systems and their cognate effectors) involved in the surface colonization process in diderm-LPS and monoderm bacteria paves the way for future research directions in the field.
Spectrin redistributes to the cytosol and is phosphorylated during mitosis in cultured cells

Dramatic changes in morphology and extensive reorganization of membrane- associated actin filaments take place during mitosis in cultured cells, including rounding up; appearance of numerous actin filament-containing microvilli and filopodia on the cell surface; and disassembly of intercellular and cell-substratum adhesions. We have examined the distribution and solubility of the membrane-associated actin-binding protein, spectrin, during interphase and mitosis in cultured CHO and HeLa cells. Immunofluorescence staining of substrate-attached, well- spread interphase CHO cells reveals that spectrin is predominantly associated with both the dorsal and ventral plasma membranes and is also concentrated at the lateral margins of cells at regions of cell- cell contacts. In mitotic cells, staining for spectrin is predominantly in the cytoplasm with only faint staining at the plasma membrane on the cell body, and no discernible staining on the membranes of the microvilli and filopodia (retraction fibers) which protrude from the cell body. Biochemical analysis of spectrin solubility in Triton X-100 extracts indicates that only 10-15% of the spectrin is soluble in interphase CHO or HeLa cells growing attached to tissue culture plastic. In contrast, 60% of the spectrin is soluble in mitotic CHO and HeLa cells isolated by mechanical "shake-off" from nocodazole-arrested synchronized cultures, which represents a four- to sixfold increase in the proportion of soluble spectrin. This increase in soluble spectrin may be partly due to cell rounding and detachment during mitosis, since the amount of soluble spectrin in CHO or HeLa interphase cells detached from the culture dish by trypsin-EDTA or by growth in spinner culture is 30-38%. Furthermore, mitotic cells isolated from synchronized spinner cultures of HeLa S3 cells have only 2.5 times as much soluble spectrin (60%) as do synchronous interphase cells from these spinner cultures (25%). The beta subunit of spectrin is phosphorylated exclusively on serine residues both in interphase and mitosis. Comparison of steady-state phosphorylation levels of spectrin in mitotic and interphase cells demonstrates that solubilization of spectrin in mitosis is correlated with a modest increase in the level of phosphorylation of the spectrin beta subunit in CHO and HeLa cells (a 40% and 70% increase, respectively). Two-dimensional phosphopeptide mapping of CHO cell spectrin indicates that this is due to mitosis- specific phosphorylation of beta-spectrin at several new sites. This is independent of cell rounding and dissociation from other cells and the substratum, since no changes in spectrin phosphorylation take place when cells are detached from culture dishes with trypsin-EDTA. (ABSTRACT TRUNCATED AT 400 WORDS)