LLukas22/scidocs huggingface dataset:
Clustering and Classification of Software Component for Efficient Component Retrieval and Building Component Reuse Libraries

A Software Repository is a collection of library files and function codes. Programmers and Engineers design develop and build software libraries in a continuous process. Selecting suitable function code from one among many in the repository is quite challenging and cumbersome as we need to analyze semantic issues in function codes or components. Clustering and Mining Software Components for efficient reuse is the current topic of interest among researchers in Software Reuse Engineering and Information Retrieval. A relatively less research work is contributed in this field and has a good scope in the future. In this paper, the main idea is to cluster the software components and form a subset of libraries from the available repository. These clusters thus help in choosing the required component with high cohesion and low coupling quickly and efficiently. We define a similarity function and use the same for the process of clustering the software components and for estimating the cost of new project. The approach carried out is a feature vector based approach. © 2014 The Authors. Published by Elsevier B.V. Selection and/or peer-review under responsibility of the organizers of ITQM 2014
Significance of Circulating Tumor Cells in Metastatic Triple-Negative Breast Cancer Patients within a Randomized, Phase II Trial: TBCRC 019.

PURPOSE
Circulating tumor cells (CTC) are prognostic in metastatic breast cancer (MBC). We tested whether EpCAM-based capture system (CellSearch) is effective in patients with triple-negative (TN) MBC, and whether CTC apoptosis and clustering enhances the prognostic role of CTC.


EXPERIMENTAL DESIGN
CTC enumeration and apoptosis were determined using the CXC CellSearch kit at baseline and days 15 and 29 in blood drawn from TN MBC patients who participated in a prospective randomized phase II trial of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) with or without tigatuzumab. Association between levels of CTC and patient outcomes was assessed using logistic regression, Kaplan-Meier curves, and Cox proportional hazards modeling.


RESULTS
Nineteen of 52 (36.5%), 14 of 52 (26.9%), and 13 of 49 (26.5%) patients who were evaluable had elevated CTC (≥5 CTC/7.5 mL whole blood) at baseline and at days 15 and 29, respectively. Patients with elevated versus not elevated CTC at each time point had worse progression-free survival (PFS; P = 0.005, 0.0003, 0.0002, respectively). The odds of clinical benefit response for those who had elevated versus low CTC at baseline and days 15 and 29 were 0.25 (95% CI: 0.08-0.84; P = 0.024), 0.19 (95% CI: 0.05-0.17; P = 0.014), and 0.06 (95% CI: 0.01-0.33; P = 0.001), respectively. There was no apparent prognostic effect comparing CTC apoptosis versus non-apoptosis. Presence of CTC cluster at day 15 and day 29 was associated with shorter PFS.


CONCLUSIONS
CTC were detected using CellSearch assay in approximately one-third of TN MBC patients. Elevated CTC at baseline and days 15 and 29 were prognostic, and reductions in CTC levels reflected response.
Patients' experiences of disruptions associated with post-stroke dysarthria.

BACKGROUND
Post-stroke dysarthria rehabilitation should consider social participation for people with dysarthria, but before this approach can be adopted, an understanding of the psychosocial impact of dysarthria is required. Despite the prevalence of dysarthria as a result of stroke, there is a paucity of research into this communication disorder, particularly studies that address the experiences of individuals. The available literature focuses mainly on the perceptions of others or includes groups of mixed aetiologies.


AIMS
To investigate the beliefs and experiences of people with dysarthria as a result of stroke in relation to their speech disorder, and to explore the perceived physical, personal and psychosocial impacts of living with dysarthria.


METHODS & PROCEDURES
Participants for this qualitative study were recruited from twelve hospitals in Scotland that served both rural and urban populations and afforded opportunity for comparison. Semi-structured, in-depth interviews were carried out over a 12-month period with 24 individuals with varying severity of dysarthria following stroke. The interviews were orthographically transcribed and coded using the NVivo package, which also facilitated identification of patterns using the constant comparative method.


OUTCOMES & RESULTS
The results of the study indicate that the effects of dysarthria following stroke extend beyond the physiological characteristics of the impairment. In turn, the resulting communication difficulties lead to changes in self-identity, relationships, social and emotional disruptions, and feelings of stigmatization or perceived stigmatization. The impact of dysarthria was found to be disproportionate to the physiological severity, with participants continually striving to get their speech back to 'normal'.


CONCLUSIONS & IMPLICATIONS
The findings provide insight into the psychosocial impact of dysarthria following stroke. Speech and language therapy interventions need to go beyond the speech impairment to address and promote psychosocial well being, reduce the likelihood of feelings of stigmatization and changes in self-identity, irrespective of the severity of dysarthria.
Impact of Response Shift on Time to Deterioration in Quality of Life Scores in Breast Cancer Patients

BACKGROUND
This prospective multicenter study aimed to study the impact of the recalibration component of response-shift (RS) on time to deterioration (TTD) in health related quality of life (QoL) scores in breast cancer (BC) patients and the influence of baseline QoL expectations on TTD.


METHODS
The EORTC-QLQ-C30 and BR-23 questionnaires were used to assess the QoL in a prospective multicenter study at inclusion (T0), at the end of the first hospitalization (T1) and, three (T2) and 6 months after the first hospitalization (T3). Recalibration was investigated by the then-test method. QoL expectancy was assessed at diagnosis. Deterioration was defined as a 5-point decrease in QoL scores, considered a minimal clinically important difference (MCID). TTD was estimated using the Kaplan-Meier method. Cox regression analyses were used to identify factors influencing TTD.


RESULTS
From February 2006 to February 2008, 381 women were included. Recalibration of breast cancer patients' internal standards in the assessment of their QoL had an impact on TTD. Median TTD were significantly shorter when recalibration was not taken into account than when recalibration was taken into account for global health, role-functioning, social-functioning, body-image and side effects of systemic therapy. Cox multivariate analyses showed that for body image, when recalibration was taken into account, radiotherapy was associated with a shorter TTD (HR: 0.60[0.38-0.94], whereas, no significant impact of surgery type on TTD was observed. For global health, cognitive and social functioning dimensions, patients expecting a deterioration in their QoL at baseline had a significantly shorter TTD.


CONCLUSIONS
Our results showed that RS and baseline QoL expectations were associated with time to deterioration in breast cancer patients.
Generic naming in generative, constraint-based design

In generative, collstraint;..based design, users graphically select shape elements of design instances in order to specify shape operations that have generic intent. We discuss techniques for naming algorithmically and generically the identified geometric instance, and report on our experience with implementing these techniques. In a. companion paper, we give algorithms for matching the names when editing designs.
Metabolic engineering of strains: from industrial-scale to lab-scale chemical production

A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5–50 g/L), and lab-scale (0–5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.
Worlds of dying children and their well siblings

Abstract This paper examines the place of illness and death in the lives of healthy children and their ill siblings at the end stages of life. The behaviors that the children exhibit provide important insights into the children's views of their lives as well as their views of death.
THE PRIMES CONTAIN ARBITRARILY LONG ARITHMETIC PROGRESSIONS

We prove that there are arbitrarily long arithmetic progressions of primes. There are three major ingredients. [. . . ] [. . . ] for all x ∈ ZN (here (m0, t0, L0) = (3, 2, 1)) and E ( ν((x− y)/2)ν((x− y + h2)/2)ν(−y)ν(−y − h1)× × ν((x− y′)/2)ν((x− y′ + h2)/2)ν(−y)ν(−y − h1)× × ν(x)ν(x + h1)ν(x + h2)ν(x + h1 + h2) ∣∣∣∣ x, h1, h2, y, y′ ∈ ZN) = 1 + o(1) (0.1) (here (m0, t0, L0) = (12, 5, 2)). [. . . ] Proposition 0.1 (Generalised von Neumann). Suppose that ν is k-pseudorandom. Let f0, . . . , fk−1 ∈ L(ZN) be functions which are pointwise bounded by ν+νconst, or in other words |fj(x)| 6 ν(x) + 1 for all x ∈ ZN , 0 6 j 6 k − 1. (0.2) Let c0, . . . , ck−1 be a permutation of {0, 1, . . . , k − 1} (in practice we will take cj := j). Then E ( k−1 ∏ j=0 fj(x + cjr) ∣∣∣∣ x, r ∈ ZN) = O( inf 06j6k−1 ‖fj‖Uk−1) + o(1).
A phase II study on the role of gemcitabine plus romidepsin (GEMRO regimen) in the treatment of relapsed/refractory peripheral T-cell lymphoma patients

BACKGROUND
There is no consensus regarding optimal treatment for peripheral T-cell lymphomas (PTCL), especially in relapsed or refractory cases, which have very poor prognosis and a dismal outcome, with 5-year overall survival of 30 %.


METHODS
A multicenter prospective phase II trial was conducted to investigate the role of the combination of gemcitabine plus romidepsin (GEMRO regimen) in relapsed/refractory PTCL, looking for a potential synergistic effect of the two drugs. GEMRO regimen contemplates an induction with romidepsin plus gemcitabine for six 28-day cycles followed by maintenance with romidepsin for patients in at least partial remission. The primary endpoint was the overall response rate (ORR); secondary endpoints were survival, duration of response, and safety of the regimen.


RESULTS
The ORR was 30 % (6/20) with 15 % (3) complete response (CR) rate. Two-year overall survival was 50 % and progression-free survival 11.2 %. Grade ≥3 adverse events were represented by thrombocytopenia (60 %), neutropenia (50 %), and anemia (20 %). Two patients are still in CR with median response duration of 18 months. The majority of non-hematological toxicities were mild and transient. No treatment-related death occurred and no toxicity led to treatment interruption.


CONCLUSIONS
GEMRO combination regimen shows efficacy data similar to those of single-agent romidepsin with additional hematologic toxicities. Synergy observed in preclinical phase did not turn into ability to improve clinical outcomes.


TRIAL REGISTRATION
The trial was registered under EudraCT 2012-001404-38; ClinicalTrials.gov number, NCT01822886 .
Prospective, randomized, controlled trial comparing lightweight versus heavyweight mesh in chronic pain incidence after TEP repair of bilateral inguinal hernia

This prospective, clinical, randomized, controlled study was performed to define the incidence of chronic pain after total extraperitoneal (TEP) repair with a light-weighted mesh compared with heavyweight mesh in patients with bilateral inguinal hernias. Consecutive patients with bilateral inguinal hernias were recruited for TEP inguinal hernia repair under general anesthesia. Heavyweight mesh was randomly assigned to one side of the groin and lightweight mesh to the other. Patients were followed up regularly for up to 1 year by an independent surgeon who was unaware of the mesh assignment. The postoperative pain score by means of a visual analogue scale (VAS) and other data were recorded. Fifty bilateral TEP hernia repairs were performed between September 2007 and February 2009. Six patients (12%) complained of chronic pain 3 months after the operation. A higher average pain score was observed for the side of hernia repaired by heavyweight mesh compared with lightweight mesh, but the difference was not statistically significant. More patients complained about foreign body sensation on the side repaired with heavyweight mesh (24%) compared with the side with lightweight mesh (8%; P < 0.05). There was no recurrence or need for reintervention for either type of mesh. Lightweight polypropylene mesh may be preferable to heavyweight mesh for TEP inguinal hernia repair because it provides less postoperative foreign body sensation; however, there was no significant difference in the incidence of chronic pain.
Pyrometamorphism of limestones and the temperature of basaltic magmas

Abstract Calc-silicate rocks which have been subjected to thermal metamorphism (sanidinite or spurrite-merwinite facies) are described from three localities on the Siberian Platform. All have formed in the aureoles of subvolcanic basaltic intrusions. The temperature of metamorphism, as estimated from the earlier published experimental data, is about 800–1000°C, whilst the temperature of the basaltic magma is believed to have been not less than 1200°C.
Engineered Endolysin-Based “Artilysins” To Combat Multidrug-Resistant Gram-Negative Pathogens

The global threat to public health posed by emerging multidrug-resistant bacteria in the past few years necessitates the development of novel approaches to combat bacterial infections. Endolysins encoded by bacterial viruses (or phages) represent one promising avenue of investigation. These enzyme-based antibacterials efficiently kill Gram-positive bacteria upon contact by specific cell wall hydrolysis. However, a major hurdle in their exploitation as antibacterials against Gram-negative pathogens is the impermeable lipopolysaccharide layer surrounding their cell wall. Therefore, we developed and optimized an approach to engineer these enzymes as outer membrane-penetrating endolysins (Artilysins), rendering them highly bactericidal against Gram-negative pathogens, including Pseudomonas aeruginosa and Acinetobacter baumannii. Artilysins combining a polycationic nonapeptide and a modular endolysin are able to kill these (multidrug-resistant) strains in vitro with a 4 to 5 log reduction within 30 min. We show that the activity of Artilysins can be further enhanced by the presence of a linker of increasing length between the peptide and endolysin or by a combination of both polycationic and hydrophobic/amphipathic peptides. Time-lapse microscopy confirmed the mode of action of polycationic Artilysins, showing that they pass the outer membrane to degrade the peptidoglycan with subsequent cell lysis. Artilysins are effective in vitro (human keratinocytes) and in vivo (Caenorhabditis elegans). Importance: Bacterial resistance to most commonly used antibiotics is a major challenge of the 21st century. Infections that cannot be treated by first-line antibiotics lead to increasing morbidity and mortality, while millions of dollars are spent each year by health care systems in trying to control antibiotic-resistant bacteria and to prevent cross-transmission of resistance. Endolysins--enzymes derived from bacterial viruses--represent a completely novel, promising class of antibacterials based on cell wall hydrolysis. Specifically, they are active against Gram-positive species, which lack a protective outer membrane and which have a low probability of resistance development. We modified endolysins by protein engineering to create Artilysins that are able to pass the outer membrane and become active against Pseudomonas aeruginosa and Acinetobacter baumannii, two of the most hazardous drug-resistant Gram-negative pathogens.
Open-field arena boundary is a primary object of exploration for Drosophila

Drosophila adults, when placed into a novel open-field arena, initially exhibit an elevated level of activity followed by a reduced stable level of spontaneous activity and spend a majority of time near the arena edge, executing motions along the walls. In order to determine the environmental features that are responsible for the initial high activity and wall-following behavior exhibited during exploration, we examined wild-type and visually impaired mutants in arenas with different vertical surfaces. These experiments support the conclusion that the wall-following behavior of Drosophila is best characterized by a preference for the arena boundary, and not thigmotaxis or centrophobicity. In circular arenas, Drosophila mostly move in trajectories with low turn angles. Since the boundary preference could derive from highly linear trajectories, we further developed a simulation program to model the effects of turn angle on the boundary preference. In an hourglass-shaped arena with convex-angled walls that forced a straight versus wall-following choice, the simulation with constrained turn angles predicted general movement across a central gap, whereas Drosophila tend to follow the wall. Hence, low turn angled movement does not drive the boundary preference. Lastly, visually impaired Drosophila demonstrate a defect in attenuation of the elevated initial activity. Interestingly, the visually impaired w(1118) activity decay defect can be rescued by increasing the contrast of the arena's edge, suggesting that the activity decay relies on visual detection of the boundary. The arena boundary is, therefore, a primary object of exploration for Drosophila.
Preventing dog bites in children: randomised controlled trial of an educational intervention.

haemorrhage (÷ = 2.64, P > 0.05). The inpatients remained in hospital longer after stroke (median 31 (interquartile range 13-59) days) than the admitted patients (16 (6-43) days). Twenty four (24%) inpatients returned to their previous residence, compared with 799 (63%) admitted patients (odds ratio 0.19, 95% confidence interval 0.11 to 0.31). Sixteen (16%) inpatients were newly discharged to an institution, compared with 124 (10%) admitted patients (1.77, 95% confidence interval 0.93 to 3.16), which may partly account for the longer stay for inpatients. Sixty (60%) inpatients died in hospital, compared with 351 (28%) admitted patients (3.94, 95% confidence interval 2.55 to 6.15); stroke was the primary or secondary cause of death for 51 (85%) inpatients and 301 (86%) admitted patients.
Developmental brain trajectories in children with ADHD and controls: a longitudinal neuroimaging study

BACKGROUND
The symptom profile and neuropsychological functioning of individuals with Attention Deficit/Hyperactivity Disorder (ADHD), change as they enter adolescence. It is unclear whether variation in brain structure and function parallels these changes, and also whether deviations from typical brain development trajectories are associated with differential outcomes. This paper describes the Neuroimaging of the Children's Attention Project (NICAP), a comprehensive longitudinal multimodal neuroimaging study. Primary aims are to determine how brain structure and function change with age in ADHD, and whether different trajectories of brain development are associated with variations in outcomes including diagnostic persistence, and academic, cognitive, social and mental health outcomes.


METHODS/DESIGN
NICAP is a multimodal neuroimaging study in a community-based cohort of children with and without ADHD. Approximately 100 children with ADHD and 100 typically developing controls will be scanned at a mean age of 10 years (range; 9-11years) and will be re-scanned at two 18-month intervals (ages 11.5 and 13 years respectively). Assessments include a structured diagnostic interview, parent and teacher questionnaires, direct child cognitive/executive functioning assessment and magnetic resonance imaging (MRI). MRI acquisition techniques, collected at a single site, have been selected to provide optimized information concerning structural and functional brain development.


DISCUSSION
This study will allow us to address the primary aims by describing the neurobiological development of ADHD and elucidating brain features associated with differential clinical/behavioral outcomes. NICAP data will also be explored to assess the impact of sex, ADHD presentation, ADHD severity, comorbidities and medication use on brain development trajectories. Establishing which brain regions are associated with differential clinical outcomes, may allow us to improve predictions about the course of ADHD.
Factors associated with viral rebound in HIV-1-infected individuals enrolled in a therapeutic HIV-1 gag vaccine trial.

BACKGROUND
Human immunodeficiency virus type 1 (HIV-1) vaccines directed to the cell-mediated immune system could have a role in lowering the plasma HIV-1 RNA set point, which may reduce infectivity and delay disease progression.


METHODS
Randomized, placebo-controlled trial involving HIV-1-infected participants who received a recombinant adenovirus serotype 5 (rAd5) HIV-1 gag vaccine or placebo. Sequence-based HLA typing was performed for all 110 participants who initiated analytic treatment interruption (ATI) to assess the role of HLA types previously associated with HIV prognosis. Plasma HIV-1 gag and pol RNA sequences were obtained during the ATI. Virologic endpoints and HLA groups were compared between treatment arms using the 2-sample rank sum test. A linear regression model was fitted to derive independent correlates of ATI week 16 plasma viral load (w16 PVL).


RESULTS
Vaccinated participants with neutral HLA alleles had lower median w16 PVLs than did vaccinated participants with protective HLA alleles (P = .01) or placebo participants with neutral HLA alleles (P = .02). Factors independently associated with lower w16 PVL included lower pre-antiretroviral therapy PVL, greater Gag sequence divergence from the vaccine sequence, decreased proportion of HLA-associated polymorphisms in Gag, and randomization to the vaccine arm.


CONCLUSIONS
Therapeutic vaccination with a rAd5-HIV gag vaccine was associated with lower ATI week 16 PVL even after controlling for viral and host genetic factors.


CLINICAL TRIALS REGISTRATION
NCT00080106.
Detection of obestatin in seminal plasma and its relationship with ghrelin and semen parameters.

OBJECTIVE
To investigate the occurrence of ghrelin and obestatin in human semen.


DESIGN
Prospective study.


SETTING
University, center for research and therapy of male infertility.


PATIENT(S)
112 consecutively selected men.


INTERVENTION(S)
Family history, clinical and physical examination, radioimmunoassay for ghrelin and obestatin determinations, semen analysis, annexinV/propidium iodide assay.


MAIN OUTCOME MEASURE(S)
Ghrelin and obestatin detected in the semen and relationships with semen parameters and conditions influencing semen quality (smoking, varicocele, ex varicocele, leukocytospermia).


RESULT(S)
The levels of both peptides in semen were higher versus serum. Linear correlations between ghrelin and obestatin levels in serum and in semen were observed. Serum ghrelin levels were negatively correlated with the men's ages. Semen obestatin levels were positively correlated with sperm concentration and motility. Obestatin levels were decreased in the semen of smokers and in the presence of leukocytospermia.


CONCLUSION(S)
This is the first study on the presence of obestatin in human semen and its relationship with sperm concentration and motility, suggesting a possible role of the peptide in controlling cell proliferation and survival. Further investigations are required to explore the exact role of obestatin and ghrelin in human semen.