Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution.

Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous non-biological models in parallel at reasonable cost, particularly with shotgun sequencing. Here we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies - swallowtails of the family Papilionidae - that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6,621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced dataset (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 million years ago (Ma) (95% credibility interval: 68.6-142.7 Ma) and Papilionidae around 71.4 Ma (49.8-103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
Intelligent Adaptive Feedback Assessment System in Learning Environment

evaluation of tutors and learning environment is a vital educational activity for the development of educational quality and enhancement of an educational institute"s improvement in terms of quality driven teaching and learning. Considering the above statement, it is mandatory to assess the learning activities and attitude of students towards learning along with changing trend from a teaching and learning perspective. In this paper an intelligent adaptive feedback-assessment (IAFA) system framework has been proposed where we provide relative feedback assessment by correlating different learning styles of students along with teacher"s resource utilization. The assessment is based on the features extracted using the techniques from the fields of computer vision and speech analysis. In audio processing the perception attitude of the students is taken into account which makes us compute relative and desirable audible features like speech rate, loudness for feedback analysis. Using video processing techniques for tracking and template matching, we compute resource utilization for teaching aids like black board, projector and student interaction and compare it with the desired values. The present algorithm has been rigorously tested with several sample classes of around 60 students with different student backgrounds i.e., non-English medium/English Medium/Native English speakers, and the performance results have been reported.
Resistance to CYP17A1 Inhibition with Abiraterone in Castration-Resistant Prostate Cancer: Induction of Steroidogenesis and Androgen Receptor Splice Variants

Purpose: Abiraterone is a potent inhibitor of the steroidogenic enzyme CYP17A1 and suppresses tumor growth in patients with castration-resistant prostate cancer (CRPC). The effectiveness of abiraterone in reducing tumor androgens is not known, nor have mechanisms contributing to abiraterone resistance been established. Experimental Design: We treated human CRPC xenografts with abiraterone and measured tumor growth, tissue androgens, androgen receptor (AR) levels, and steroidogenic gene expression versus controls. Results: Abiraterone suppressed serum PSA levels and improved survival in two distinct CRPC xenografts: median survival of LuCaP35CR improved from 17 to 39 days (HR = 3.6, P = 0.0014) and LuCaP23CR from 14 to 24 days (HR = 2.5, P = 0.0048). Abiraterone strongly suppressed tumor androgens, with testosterone (T) decreasing from 0.49 ± 0.22 to 0.03 ± 0.01 pg/mg (P < 0.0001), and from 0.69 ± 0.36 to 0.03 ± 0.01 pg/mg (P = 0.002) in abiraterone-treated 23CR and 35CR, respectively, with comparable decreases in tissue DHT. Treatment was associated with increased expression of full-length AR (ARFL) and truncated AR variants (ARFL 2.3-fold, P = 0.008 and ARdel567es 2.7-fold, P = 0.036 in 23 CR; ARFL 3.4-fold, P = 0.001 and ARV7 3.1-fold, P = 0.0003 in 35CR), and increased expression of the abiraterone target CYP17A1 (∼2.1-fold, P = 0.0001 and P = 0.028 in 23CR and 35CR, respectively) and transcript changes in other enzymes modulating steroid metabolism. Conclusions: These studies indicate that abiraterone reduces CRPC growth via suppression of intratumoral androgens and that resistance to abiraterone may occur through mechanisms that include upregulation of CYP17A1, and/or induction of AR and AR splice variants that confer ligand-independent AR transactivation. Clin Cancer Res; 17(18); 5913–25. ©2011 AACR.
Optimization method of spanning tree aggregation for hierarchical QoS routing

In hierarchical networks, the topology and QoS parameters of a domain have to be first aggregated before being propagated to other domains. However, topology aggregation may distort useful information. This paper focuses on minimizing the distortion caused by reducing a full-mesh representation to a spanning tree. An optimization method of minimizing the distortion of additive parameters caused by spanning tree aggregation is presented. Based on this new method, two approximation algorithms are proposed. Simulation results show that both algorithms perform much better than the traditional way of decoding the spanning tree with upper or lower bounds
Increased Adherence to Caco-2 Cells Caused by Disruption of the yhiE and yhiF Genes in Enterohemorrhagic Escherichia coli O157:H7

ABSTRACT Adherence of enterohemorrhagic Escherichia coli (EHEC) to intestinal epithelium is essential for initiation of infections, including diarrhea, and expression of the genes of the locus of enterocyte effacement (LEE) is thought to be crucial for adherence. To identify genes involved in modulating the adherent capacity, bacteria collected from an EHEC O157:H7 strain (O157Sakai) mutagenized by mini-Tn5Km2 were screened for their ability to increase the number of microcolonies (MC) on Caco-2 cells and eight mutants with increased adherence were isolated. Analysis of the mini-Tn5Km2-flanked DNA sequences indicated that one possessed the insertion within an O157 antigen gene cluster, another possessed the insertion within the yhiF gene, and the remaining six mutants had their insertions in the yhiE gene. yhiE and yhiF products share amino acid homology (23% identity) to each other and with members of the LuxR family, which are known as transcriptional regulatory proteins. The mutant having the insertion within the O157 antigen gene cluster did not express the O157 side chain (as determined by agglutination test and immunoblotting with polyclonal O157-specific antiserum), unlike the other seven mutants. Importantly, the other mutants showed enhanced type III secretion. Levels of the related mRNAs of genes of the LEE, but not that of ler mRNA, were also increased compared with those in the wild type. Indeed, when we introduced an in-frame deletion into the yhiE or yhiF gene in O157Sakai, the capacity of the resultant mutants to adhere to Caco-2 cells was greatly increased. When one of the yhiE insertion mutants was orally inoculated into ICR mice, the number of bacteria shed into feces by day 14 was greater than that for the wild type. These results suggest that yhiE and yhiF are involved in the adherence of O157Sakai to epithelial cells as negative regulators for the expression of the genes required for the type III secretion system.
Substituting Associative Load Queue with Simple Hash Tables in Out-of-Order Microprocessors

Buffering more in-flight instructions in an out-of-order microprocessor is a straightforward and effective method to help tolerate the long latencies generally associated with off-chip memory accesses. One of the main challenges of buffering a large number of instructions, however, is the implementation of a scalable and efficient mechanism to detect memory access order violations as a result of out-of-order scheduling of load and store instructions. Traditional CAM-based associative queues can be very slow and energy consuming. In this paper, instead of using the traditional age-based load queue to record load addresses, we explicitly record age information in address-indexed hash tables to achieve the same functionality of detecting premature loads. This alternative design eliminates associative searches and significantly reduces the energy consumption of the load queue. With simple techniques to reduce the number of false positives, performance degradation is kept at a minimum
Evaluating causes and consequences of turnover intention among IT workers: the development of a questionnaire survey

Abstract In this paper we describe the process of developing a questionnaire survey that evaluates the causes and consequences of turnover intention among information technology (IT) workers, with specific attention to issues of importance to women and minorities within the IT workforce. The questionnaire development process consisted of four steps: 1. Creation of the initial questionnaire from a literature review of existing scales 2. Pilot study using interviews to test the questionnaire 3. Modifications to the questionnaire based on feedback from the pilot study 4. Implementation of the revised questionnaire survey. The process used for the development of the questionnaire survey is systematic and addresses issues specific to the IT workforce, in particular the underrepresentation of women and minorities in the IT workforce. The questionnaire survey allows the collection of reliable and valid data on causes and effects of retention and intention to turnover, thus making it possible to better understand the reasons for the underrepresentation of women and minorities in the IT workforce.
Decrease in Trunk Muscular Response to Perturbation With Preactivation of Lumbar Spinal Musculature

Study Design. An experimental study of healthy subjects’ trunk muscle responses to force perturbations at differing angles and steady state efforts. Objectives. To determine whether increased preactivation of muscles was associated with decreased likelihood of muscular activation in response to a transient force perturbation. Summary of Background Data. Trunk stability (ability to return to equilibrium position after a perturbation) requires the stiffness of appropriately activated muscles to prevent buckling and consequent “self-injury. ” Therefore, greater trunk muscle preactivation might decrease the likelihood of reflex muscle responses to small perturbations. Methods. Each of 13 subjects stood in an apparatus with the pelvis immobilized. A harness around the thorax provided a preload and a force perturbation by a horizontal cable and a movable pulley attached to one of five anchorage points on a wall track surrounding the subject at angles of 0°, 45°, 90°, 135°, and 180° to the forward direction. Subjects first equilibrated with a preload effort of nominally 20% or 40% of their maximum extension effort. Then a single full sine-wave force perturbation pulse of nominal amplitude, 7.5% or 15% of maximum effort, duration 80 milliseconds or 300 milliseconds, was applied at a random time, with three repeated trials of each test condition. The applied force (via a load cell) and the electromyographic activity of six right and left pairs of trunk muscles were recorded. Muscle responses were detected by two methods. 1) Shewhart method: electromyographic signal greater than “baseline” values by more than three standard deviations, and 2) Mean Electromyographic Difference method: mean electromyographic signal in a time window 25 to 150 milliseconds after the force perturbation greater than that in a 25- to 150-millisecond window before the perturbation. Results. Lower preload efforts were associated with more muscle responses (overall mean response detection rate = 33% at low preload and 25% at high preload). Using the Shewhart method, there were significant differences by effort (P < 0.05) for all abdominal muscles and for all left dorsal muscles except multifidus. Using the Mean Electromyographic Difference method, there were significant differences by effort (P < 0.05) for the same dorsal muscles, but only for one of the abdominal muscles. Conclusions. Findings are consistent with the hypothesis that the spine can be stabilized by the stiffness ofactivated muscles, obviating the need for active muscle responses to perturbations.
Development and Implementation of the Standards for Evaluating and Reporting Epidemiologic Studies on Chronic Disease Incidence or Prevalence

We aimed to develop quality checklists for observational non-therapeutic studies. Based on a systematic review of current practices of quality assessment of observational studies, collaborating co-authors from Evidence-based Practice Centers and the Centers for Disease Control and Prevention developed a new checklist for studies examining incidence and prevalence of chronic conditions, evaluated face and content validity, and discrimination validity to distinguish reporting from methodological quality. This new checklist is available in text format or as a relational database to produce standardized reports with flaws in reporting quality, external (six criteria), and internal (five criteria) validity of the studies. Study and hypotheses (subgroups) level analyses are possible with predetermined in protocol templates criteria of major and minor flaws. Consensus around justified research specific methodological standards and reliability tests should precede quality evaluation of primary studies to assure confidence in quality assessment. To be effective, policy decisions should be made based on comprehensive systematic evidence reviews that include transparent, standardized quality appraisals. Implementation of the developed checklists would increase transparency and quality of research leading to effective informed decisions in health care.
Predictors for reoperation after lower limb amputation in patients with peripheral arterial disease.

Background: Major amputations in patients with peripheral arterial disease (PAD) carry a high risk for complications, including revision of the amputation, sometimes to a higher level. Determining a safe level for amputation with good wound healing potential depends largely on vascular measurements. This study evaluated potential predictive factors for revision of major lower extremity amputations in patients with PAD. Patients and methods: A retrospective chart review of all major lower extremity amputations at our institution was conducted. Amputations due to trauma or tumor and below-ankle amputations were excluded. Patient demographics, level/type of amputation, level/time of revision, comorbidities and risk factors were extracted. Results: 180 patients with PAD, mean age 66.48 (range: 31-93) years, 125 (69.4%) male were included. Most (154/180, 86.6%) underwent below-knee amputation. 71 (39.4%) patients had coronary arterial disease, 104 (57.8%) had diabetes. More than half of patients, (93/138; 51.7%) had undergone previous balloon angioplasty. 44 (30%) patients required revision surgery: 42/180 (23.3%) were revised at the same level, and in 12/180 (6.7%) a more proximal amputation was necessary. PAD stage was not associated with the level of reamputation (p = 0.4369). Significantly more patients who had previous balloon angioplasty required revision surgery (66.7% versus 45.2%, p = 0.009). 67 (37.2%) patients underwent preoperative TcPO2 measurement: 40/67 (59.7%) had TcPO2 ≥ 40 mmHg; 4/67 (6%) had TcPO2 < 10 mmHG. Three patients with TcPO2 ≥ 40 mmHg, one with 30 mmHg ≤ TcPO2 ≤ 40 mmHg and one with 10 mmHg ≤ TcPO2 ≤ 20 mmHg required re-amputation to a more proximal level. Conclusions: TcPO2 measurements are useful for determining level of lower limb amputation and predicting wound healing problems when an amputation level with TcPO2 < 40 mmHg is chosen. In transtibial amputations, TcPO2 ≥ 40 mmHg does not safely predict wound healing.
Is incident rheumatoid arthritis interstitial lung disease associated with methotrexate treatment? Results from a multivariate analysis in the ERAS and ERAN inception cohorts

Objectives To assess predictive factors for rheumatoid arthritis interstitial lung disease (RA-ILD) in two early rheumatoid arthritis (RA) inception cohorts with a focus on methotrexate (MTX) exposure. Design Multicentre prospective early RA inception cohort studies; the early RA study (ERAS) and the early RA network (ERAN). Setting Secondary care, ERAS nine centres, ERAN 23 centres in England, Wales and Ireland. Participants Patients with new diagnosis of RA, n=2701. Standardised data including demographics, drug therapies and clinical outcomes including the presence of RA-ILD were collected at baseline, within 3–6 months, at 12 months and annually thereafter. Primary and secondary outcome measures Primary outcome was the association of MTX exposure on RA-ILD diagnosis. Secondary outcomes were the association of demographic, comorbid and RA-specific factors on RA-ILD diagnosis and the association of MTX exposure on time to RA-ILD diagnosis. Results Of 92 eligible ILD cases, 39 occurred in 1578 (2.5%) MTX exposed and 53 in 1114 (4.8%) non-MTX exposed cases. The primary analysis of RA-ILD cases only developing after any conventional synthetic disease-modifying antirheumatic drug treatment (n=67) showed MTX exposure not to be associated with incident RA-ILD (OR 0.85, 95% CI 0.49 to 1.49, p=0.578) and a non-significant trend for delayed ILD diagnosis (OR 0.54, 95% CI 0.28 to 1.06, p=0.072). In an extended analysis including RA-ILD cases present at RA diagnosis (n=92), MTX exposure was associated with a significantly reduced risk of incident RA-ILD (OR 0.48, 95% CI 0.3 to 0.79, p=0.004) and longer time to ILD diagnosis (OR 0.41, 95% CI 0.23 to 0.75, p=0.004). Other independent baseline associations with incident RA-ILD were higher age of RA onset, ever smoking, male gender, rheumatoid nodules and longer time from first RA symptom to first outpatient visit. Conclusions MTX treatment was not associated with an increased risk of RA-ILD diagnosis. On the contrary, evidence suggested that MTX may delay the onset of ILD.
Quality control for functional magnetic resonance imaging using automated data analysis and Shewhart charting

A data acquisition and analysis protocol for quality control (QC) of functional magnetic resonance imaging studies is presented. Two sets of data are acquired, single‐timepoint data for measurement of signal‐to‐ghost and signal‐to‐noise ratios, and multiple‐timepoint data for measurement of short‐term drift. Since manual data analysis can be time consuming and an impediment to regular QC, an automated data processing scheme is presented. The use of automated Shewhart charting is proposed to identify significant changes in each parameter over the long term. The protocol has successfully identified system faults and deteriorations undetected by conventional QC. Magn Reson Med 41:1274–1278, 1999. © 1999 Wiley‐Liss, Inc.
Clinical Relevance of Gain-Of-Function Mutations of p53 in High-Grade Serous Ovarian Carcinoma

Purpose Inactivation of TP53, which occurs predominantly by missense mutations in exons 4–9, is a major genetic alteration in a subset of human cancer. In spite of growing evidence that gain-of-function (GOF) mutations of p53 also have oncogenic activity, little is known about the clinical relevance of these mutations. Methods The clinicopathological features of high-grade serous ovarian carcinoma (HGS-OvCa) patients with GOF p53 mutations were evaluated according to a comprehensive somatic mutation profile comprised of whole exome sequencing, mRNA expression, and protein expression profiles obtained from the Cancer Genome Atlas (TCGA). Results Patients with a mutant p53 protein (mutp53) with a GOF mutation showed higher p53 mRNA and protein expression levels than patients with p53 mutation with no evidence of GOF (NE-GOF). GOF mutations were more likely to occur within mutational hotspots, and at CpG sites, and resulted in mutp53 with higher functional severity (FS) scores. Clinically, patients with GOF mutations showed a higher frequency of platinum resistance (22/58, 37.9%) than patients with NE-GOF mutations (12/56, 21.4%) (p=0.054). Furthermore, patients with GOF mutations were more likely to develop distant metastasis (36/55, 65.5%) than local recurrence (19/55, 34.5%), whereas patients with NE-GOF mutations showed a higher frequency of locoregional recurrence (26/47, 55.3%) than distant metastasis (21/47, 44.7%) (p=0.035). There were no differences in overall or progression-free survival between patients with GOF or NE-GOF mutp53. Conclusion This study demonstrates that patient with GOF mutp53 is characterized by a greater likelihood of platinum treatment resistance and distant metastatic properties in HGS-OvCa.
Visual and Verbal Serial List Learning in Patients with Statistically-Determined Mild Cognitive Impairment

Abstract Background and Objective Prior research with patients with mild cognitive impairment (MCI) suggests that visual versus verbal episodic memory test performance may be more sensitive to emergent illness. However, little research has examined visual versus verbal episodic memory performance as related to MCI subtypes. Research Design and Methods Patients were diagnosed with non-MCI, amnestic MCI (aMCI), and combined mixed/dysexecutive MCI (mixed/dys MCI). Visual and verbal episodic memory were assessed with the Brief Visuospatial Memory Test-Revised (BVMT-R) and the 12-word Philadelphia (repeatable) Verbal Learning Test (P[r]VLT), respectively. Results BVMT-R and P(r)VLT scores yielded similar between-group patterns of performance. Non-MCI patients scored better than other groups on all parameters. aMCI and mixed/dys MCI did not differ on immediate or delayed free recall. Both delayed BVMT-R and P(r)VLT recognition test performance dissociated all three groups. Logistic regression analyses found that BVMT-R delayed free recall and delayed recognition scores correctly classified more patients with MCI (75.40%) than analogous P(r)VLT scores (66.20%). Visual versus verbal memory within-group analyses found no differences among non-MCI patients; P(r)VLT immediate free recall was worse among aMCI patients, but BVMT-R immediate free recall and delayed recognition were worse among mixed/dys MCI patients. Discussion and Implications Between-group analyses found convergent patterns of performance such that both tests identified elements of amnesia. However, logistic and within-group analyses found differing performance patterns suggesting that impaired visual episodic memory performance may be specific to emergent illness in mixed/dys MCI. Complementary but divergent neurocognitive networks may underlie visual versus verbal episodic memory performance in some patients with MCI.