Miracle-dz/UniFAR-FTUs huggingface dataset:
Darwin: A Hardware-acceleration Framework for Genomic Sequence Alignment

Genomics is set to transform medicine and our understanding of life in fundamental ways. But the growth in genomics data has been overwhelming - far outpacing Moore’s Law. The advent of third generation sequencing technologies is providing new insights into genomic contribution to diseases with complex mutation events, but have prohibitively high computational costs. Over 1,300 CPU hours are required to align reads from a 54× coverage of the human genome to a reference (estimated using [1]), and over 15,600 CPU hours to assemble the reads de novo [2]. This paper proposes “Darwin” - a hardware-accelerated framework for genomic sequence alignment that, without sacrificing sensitivity, provides 125× and 15.6× speedup over the state-of-the-art software counterparts for reference-guided and de novo assembly of third generation sequencing reads, respectively. For pairwise alignment of sequences, Darwin is over 39,000× more energy-efficient than software. Darwin uses (i) a novel filtration strategy, called D-SOFT, to reduce the search space for sequence alignment at high speed, and (ii) a hardware-accelerated version of GACT, a novel algorithm to generate near-optimal alignments of arbitrarily long genomic sequences using constant memory for trace-back. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.
An evaluation of components manufactured from a range of materials, fabricated using PolyJet technology

Abstract With advances in additive manufacturing, particularly in the area of three dimensional (3D) printing, it is becoming possible to generate small quantities of functional components. As with all manufacturing technologies, the ability to reproducibly generate parts with defined dimensional accuracy and surface finish is of key importance. This work characterises the ability of one such technology, PolyJet 3D printing, to produce such parts. In order to characterise the output from the manufacturing technique, a test part was designed and manufactured in three alternative materials representative of alternative grades across a commercial range. The designed test part consisted of positive and negative feature types printed both in the direction of, and normal to, the print head traverse direction. The test parts were characterised in terms of dimensional accuracy in three dimensions and also in terms of surface finish. Differences in dimensional accuracy and surface profile were observed depending on the orientation of the feature relative to the print head travel direction.
AOL: A logic of Acting, Sensing, Knowing, and Only Knowing

This work is motivated by the existence of two useful but quite different knowledge representation formalisms, the situation calculus due to McCarthy, and the logic of only knowing due to Levesque. In this paper, we propose the logic , which combines both approaches in a clean and natural way. We present a semantics for which generalizes the semantics of to account for actions, and a sound and complete set of axioms for which generalizes the Lin and Reiter foundational axioms of the situation calculus to account for only knowing. The logic is compatible with earlier work on knowledge and action in that the solution to the frame problem for knowledge proposed by Scherl and Levesque becomes now a theorem of . We also demonstrate that the logic avoids certain anomalies present in related work by Lakemeyer. Finally we provide a mapping from into such that a sentence of is valid iff its mapping is a theorem of , thus providing, for the first time, a complete axiomatic characterization of .
Framework for internet-supported inter-organizational product development collaboration

Purpose – The purpose of this article is to introduce a framework for internet supported inter‐organizational product development, which enables companies to efficiently configure their development processes according to their needs.Design/methodology/approach – Three ideal types of partner integration are identified and specific design guidelines for each type are proposed. Current approaches for product development collaboration are analysed. Based on their shortcomings the main approach of this paper evolves. Additionally the main results of interviews with experts are used to develop and introduce a framework which has been tested partially in the shipbuilding industry.Findings – The paper identifies three types of partner integration and proposes specific design guidelines.Research limitations/implications – The framework introduced in this paper provides guidance for future research in the area of product development collaboration.Practical implications – The framework further supports managers in d.
Lexicon adaptation for LVCSR: speaker idiosyncracies, non-native speakers, and pronunciation choice

We report on our preliminary experiments on building dynamic lexicons for native-speaker conversational speech and for foreign-accented conversational speech. Our goal is to build a lexicon with a set of pronunciations for each word, in which the probability distribution over pronunciation is dynamically computed. The set of pronunciations are derived from hand-written rules (for foreign accent) or clustering (for phonetically-transcribed Switchboard data). The dynamic pronunciation-probability will take into account specific characteristics of the speaker as well as factors such as language-model probability, disfluencies, sentence position, and phonetic context. This work is still in progress; we hope to be further along by the time of the workshop.
Plasma 8-iso-prostaglandin F2α, a marker of oxidative stress, is increased in patients with acute myocardial infarction

Background: Oxidative stress has been implicated in the pathogenesis of atherogenesis. The aim of our study is to examine whether the plasma 8-iso-prostaglandin F2α level, a marker of oxidative stress, is elevated in patients with acute myocardial infarction. Methods: Three groups of patients were enrolled: (1) patients with no or minimal coronary artery disease (CAD) (n = 15); (2) patients with stable CAD (n = 31); (3) patients with acute myocardial infarction (n = 13). Results: Plasma 8-iso-prostaglandin F2α levels were significantly elevated (p < 0.001) in patients with acute myocardial infarction (290.7 ± 73.9 pg/ml) as compared to patients with stable CAD (182.0+75.7 pg/ml) and patients with no significant CAD (118.9 ± 85.5 pg/ml). This remained significant after correcting for coronary atherosclerosis risk factors, age, extent of atherosclerosis, and C-reactive protein (CRP) level. Conclusion: Plasma 8-iso-prostaglandin F2α levels are elevated in patients with acute myocardial infarction. Endogenous oxidative stress may contribute to the pathogenesis of atherosclerosis and its complications, namely myocardial infarction.
In Vitro Antioxidative Activity of (−)-Epicatechin Glucuronide Metabolites Present in Human and Rat Plasma

Recently we identified four conjugated glucuronide metabolites of epicatechin, (−)-epicatechin-3′-O-glucuronide (E3′G), 4′-O-methyl-(−)-epicatechin-3′-O-glucuronide (4′ME3′G), (−)-epicatechin-7-O-glucuronide (E7G) and 3′-O-methyl-(−)-epicatechin-7-O-glucuronide (3′ME7G) from plasma and urine. E3′G and 4′ME3′G were isolated from human urine, while E7G and 3′ME7G were isolated from rats that had received oral administration of (−)-epicatechin (Natsume et al. (2003), Free Radic. Biol. Med. 34, 840–849). It has been suggested that these metabolites possess considerable in vivo activity, and therefore we carried out a study to compare the antioxidant activities of the metabolites with that of the parent compound. This was achieved by measuring superoxide scavenging activity, reduction of plasma TBARS production and reduced susceptibility of low-density-lipoprotein (LDL) to oxidation. (−)-Epicatechin was found to have more potent antioxidant activity than the conjugated glucuronide metabolites. Both (−)-epicatechin and E7G had marked antioxidative properties with respect to superoxide radical scavenging activity, plasma oxidation induced by 2,2′-azobis-(2-aminopropane) dihydrochloride (AAPH) and LDL oxidation induced by copper ions or 2,2′-azobis(4-methoxy-2,4-dimethylvaleronitrile) (MeO-AMVN). In contrast, the other metabolites had light antioxidative activities over the range of physiological concentrations found in plasma.
Preprocedure and Postprocedure Predictive Values of Serum &bgr;2-Microglobulin for Contrast-Induced Nephropathy in Patients Undergoing Coronary Computed Tomography Angiography: A Comparison With Creatinine-Based Parameters and Cystatin C

Objective This study aimed to investigate the values of serum &bgr;2-microglobulin to predict contrast-induced nephropathy (CIN) before and early after coronary computed tomography angiography (CCTA), comparing with creatinine-based parameters and cystatin C. Methods A total of 424 patients were enrolled. Serum &bgr;2-microglobulin, cystatin C, and creatinine were measured at 0, 24, and 48 hours of CCTA. Contrast-induced nephropathy was defined as an elevation of serum creatinine level by 25% or higher or 0.5 mg/dL or greater from baseline within 48 hours. The estimated glomerular filtration rate (eGFR) was calculated by the Modification of Diet in Renal Disease study equation. Receiver operating characteristic curves and multivariate logistic regression analysis were used to detect the efficiency of biomarkers in predicting CIN. Results Fifty-two subjects (12.26%) developed CIN. Before CCTA, CIN was predicted by both baseline &bgr;2-microglobulin (area under the receiver operating characteristic curve [AUC], 0.791; P < 0.001) and cystatin C (AUC, 0.781; P < 0.001), whereas creatinine and eGFR were not predictive. After CCTA, CIN was predicted by both the absolute post-CCTA levels of &bgr;2-microglobulin, cystatin C, creatinine, and eGFR (AUC, 0.842 vs 0.961 vs 0.691 vs 0.688 at 24 hours, P < 0.001; and 0.937 vs 1.000 vs 0.908 vs 0.898 at 48 hours, P < 0.001) and their relative changes (&Dgr;) to baseline (AUC, 0.677 vs 0.846 vs 0.850 vs 0.844 at 24 hours, P < 0.001; and 0.731 vs 0.968 vs 0.984 vs 0.966 at 48 hours, P < 0.001). Multivariate regression analysis confirmed that baseline &bgr;2-microglobulin (odds ratio, 2.137; 95% confidence interval, 1.805–3.109; P < 0.001) and cystatin C (odds ratio, 1.873; 95% confidence interval, 1.667–2.341; P = 0.003) were independent predictors for CIN. Conclusions Serum &bgr;2-microglobulin, with values superior to creatinine-based parameters and similar with cystatin C, was a useful biomarker for the prediction of CIN at pre-CCTA and early post-CCTA.
[Fiability Study of Diabetes Empowerment Scale: Short Version].

PURPOSE To compare the final score of the scale to the levels of HbA1c. MATERIAL AND METHODS Cross-sectional observational study by applying the Diabetes Empowerment Scale-Short Form to diabetics at three primary care units in the central region of Portugal. The test-retest (in writing first and, five minutes later, orally) was performed to access Cronbach's alpha in 20 patients not studied in the next phase. Then, the scale was applied to diabetic patients after nursing consultation and prior to entering the medical consultation. Descriptive and inferential statistics after checking for the normality of the data were performed. RESULTS In the first phase Cronbach's alpha was 0.90 to 1.00 in all of eight scale items. The average result obtained in the written phase was 3.78 ± 0.71 and in the oral 3.79 ± 0.64, p = 0.629. The sample of the second stage was of 81 diabetic patients, 55.6% male. Sample's mean age was 68.5 ± 1.1 years, mean HbA1c of 6.8 ± 0.2 and mean time from diagnosis of 9.2 ± 0.9 years. The average final score of the scale was 4.1± 0.8. There was significant correlation between the final score and HbA1c levels (p= -0.114; p = 0.312). CONCLUSION The Portuguese version of the Diabetes Empowerment Scale-Short Form proved to be a reliable scale to measure empowerment in diabetic patients in Portugal. It was evident the presence of a statistically significant correlation between the results obtained at the end of the scale and HbA1c.
Sports reporters in the Twittersphere: Challenging and breaking down traditional conceptualizations of genderlect

Purpose The purpose of this paper is to investigate the impact of a dual medium/content context – the one offered by the online Twitter communication (medium-context) of reporting on elite sports (content-context) – on traditional conceptualizations of genderlect. Design/methodology/approach A quantitative content analysis, coding for a variety of traditional gendered language markers – was conducted on the tweets of male and female reporters who covered the men’s and women’s NCAA final four basketball tournaments. Findings Consistent with tenets of social role theory, the duel medium/content context of Twitter and sports produces several language patterns that frustrate attempts to categorize language markers according to traditional conceptualizations of genderlect and thus provides support for a redefinition of genderlect. Research limitations/implications This paper’s findings suggest that people adapt their communication patterns to match the context in which they communicate. Whether adaptation takes place with conscious effort or as a natural byproduct of moving from one context to another remains to be discovered. Advice to female sports journalists on being vigilant against unwittingly undermining their credibility and perceived expertise is offered. This inquiry allows researchers to study sociology through sport. Practical implications This paper demonstrates that online environments can allow for traditional gender roles and expectations to be challenged and broken down, but some genderlect features appear tenacious and could undermine attempts to break down gender barriers. Social implications If sport mirrors society, then the same communication adaptations that appear in the online environmental context of reporters’ tweets about sport should appear in other societal contexts. Originality/value Few studies have investigated differences in reporting by gender, and fewer have investigated differences in sports reporting by gender. Fewer, if any, have investigated differences in sports reporting by gender through Twitter.
FFAS server: novel features and applications

The Fold and Function Assignment System (FFAS) server [Jaroszewski et al. (2005) FFAS03: a server for profile–profile sequence alignments. Nucleic Acids Research, 33, W284–W288] implements the algorithm for protein profile–profile alignment introduced originally in [Rychlewski et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science: a Publication of the Protein Society, 9, 232–241]. Here, we present updates, changes and novel functionality added to the server since 2005 and discuss its new applications. The sequence database used to calculate sequence profiles was enriched by adding sets of publicly available metagenomic sequences. The profile of a user’s protein can now be compared with ∼20 additional profile databases, including several complete proteomes, human proteins involved in genetic diseases and a database of microbial virulence factors. A newly developed interface uses a system of tabs, allowing the user to navigate multiple results pages, and also includes novel functionality, such as a dotplot graph viewer, modeling tools, an improved 3D alignment viewer and links to the database of structural similarities. The FFAS server was also optimized for speed: running times were reduced by an order of magnitude. The FFAS server, http://ffas.godziklab. org, has no log-in requirement, albeit there is an option to register and store results in individual, password-protected directories. Source code and Linux executables for the FFAS program are available for download from the FFAS server.
Could Cord Blood Cell Therapy Reduce Preterm Brain Injury?

Major advances in neonatal care have led to significant improvements in survival rates for preterm infants, but this occurs at a cost, with a strong causal link between preterm birth and neurological deficits, including cerebral palsy (CP). Indeed, in high-income countries, up to 50% of children with CP were born preterm. The pathways that link preterm birth and brain injury are complex and multifactorial, but it is clear that preterm birth is strongly associated with damage to the white matter of the developing brain. Nearly 90% of preterm infants who later develop spastic CP have evidence of periventricular white matter injury. There are currently no treatments targeted at protecting the immature preterm brain. Umbilical cord blood (UCB) contains a diverse mix of stem and progenitor cells, and is a particularly promising source of cells for clinical applications, due to ethical and practical advantages over other potential therapeutic cell types. Recent studies have documented the potential benefits of UCB cells in reducing brain injury, particularly in rodent models of term neonatal hypoxia–ischemia. These studies indicate that UCB cells act via anti-inflammatory and immuno-modulatory effects, and release neurotrophic growth factors to support the damaged and surrounding brain tissue. The etiology of brain injury in preterm-born infants is less well understood than in term infants, but likely results from episodes of hypoperfusion, hypoxia–ischemia, and/or inflammation over a developmental period of white matter vulnerability. This review will explore current knowledge about the neuroprotective actions of UCB cells and their potential to ameliorate preterm brain injury through neonatal cell administration. We will also discuss the characteristics of UCB-derived from preterm and term infants for use in clinical applications.
Weighted Approximations of Tail Copula Processes with Application to Testing the Multivariate Extreme Value Condition

Consider n i.i. d. random vectors on R2, with unknown, common distribution function F.Under a sharpening of the extreme value condition on F, we derive a weighted approximation of the corresponding tail copula process.Then we construct a test to check whether the extreme value condition holds by comparing two estimators of the limiting extreme value distribution, one obtained from the tail copula process and the other obtained by first estimating the spectral measure which is then used as a building block for the limiting extreme value distribution.We derive the limiting distribution of the test statistic from the aforementioned weighted approximation.This limiting distribution contains unknown functional parameters.Therefore we show that a version with estimated parameters converges weakly to the true limiting distribution.Based on this result, the finite sample properties of our testing procedure are investigated through a simulation study.A real data application is also presented.
THE EVOLUTION OF SEXUAL SIZE DIMORPHISM IN THE HOUSE FINCH. V. MATERNAL EFFECTS

Abstract The phenotype of a mother and the environment that she provides might differentially affect the phenotypes of her sons and daughters, leading to change in sexual size dimorphism. Whereas these maternal effects should evolve to accommodate the adaptations of both the maternal and offspring generations, the mechanisms by which this is accomplished are rarely known. In birds, females adjust the onset of incubation (coincident with the first egg or after all eggs are laid) in response to the environment during breeding, and thus, indirectly, determine the duration of offspring growth. In the two house finch (Carpodacus mexicanus) populations that breed at the extremes of the species' distribution (Montana and Alabama), females experience highly distinct climatic conditions during nesting. We show that in close association with these conditions, females adjusted jointly the onset of incubation and the sequence in which they produced male and female eggs and consequently modified the growth of sons and daughters. The onset of incubation in newly breeding females closely tracked ambient temperature in a pattern consistent with the maintenance of egg viability. Because of the very different climates in Montana and Alabama, females in these populations showed the opposite patterns of seasonal change in incubation onset and the opposite sex bias in egg-laying order. In females with breeding experience, incubation onset and sex bias in laying order were closely linked regardless of the climatic variation. In nests in which incubation began with the onset of egg laying, the first-laid eggs were mostly females in Montana, but mostly males in Alabama. Because in both populations, male, but not female, embryos grew faster when exposed to longer incubation, the sex-bias produced highly divergent sizes of male and female juveniles between the populations. Overall, the compensatory interaction between the onset of incubation and the sex-biased laying order achieved a compromise between maternal and offspring adaptations and contributed to rapid morphological divergence in sexual dimorphism between populations of the house finch breeding at the climatic extremes of the species range.
Enhanced listen-before-talk scheme for frequency reuse of licensed-assisted access using LTE

Licensed-Assisted Access (LAA) using Long Term Evolution (LTE) is a promising solution to alleviate the problem of scarce spectrum resources by extending to the unlicensed band. However, co-existence mechanisms should be carefully taken into consideration to provide fair co-existence to other LAA and 802.11 based Wi-Fi networks that operate on the same unlicensed carrier. In this paper, we focus on the design of listen-before-talk (LBT) for the LAA system and provide insights into the impact of LAA clear channel assessment (CCA) threshold on the trade-off between frequency reuse and interference avoidance. Moreover, an enhanced LBT scheme is proposed by adaptively adjusting the LAA CCA threshold to exploit the benefits of frequency reuse for LAA while guaranteeing the fair co-existence with Wi-Fi at the same time. System-level simulation is performed to analyze the CCA threshold among LAA networks and evaluate the effectiveness of the proposed LBT scheme compared to that with fixed CCA threshold. It is shown that significant performance gains can be achieved for LAA by using the proposed LBT scheme under efficient protection of Wi-Fi performance.