LLukas22/scidocs huggingface dataset:
Best Practices for Automated Traceability

Automated traceability applies information-retrieval techniques to generate candidate links, sharply reducing the effort of manual approaches to build and maintain a requirements trace matrix as well as providing after-the-fact traceability in legacy documents.The authors describe nine best practices for implementing effective automated traceability.
Moderate alcohol consumption is associated with reduced long-term cardiovascular risk in patients following a complicated acute myocardial infarction.

BACKGROUND
The impact on prognosis of alcohol use in patients with coronary artery disease remains uncertain. We related alcohol use to all-cause mortality, cardiovascular (CV)-mortality and hospitalization in patients following a complicated myocardial infarction (MI).


METHODS
In the OPTIMAAL trial, 5477 patients from 7 Western European countries with heart failure and/or evidence of left ventricular dysfunction following MI were recruited. Following randomization median 3 days, patients were asked to assess their average alcohol consumption prior to the index infarction. Patients were stratified by the frequency of the use of alcohol into either non-users (n = 2160), moderate users (1-7 drinks/week, n = 2753) and heavy users (> 7 drinks/week, n = 545) and related to prespecified clinical outcomes in the groups.


RESULTS
A total of 5477 patients were included in the trial. During the follow-up period of 2.7 years 946 deaths were reported. Adjusted for age and smoking status, patients with moderate use of alcohol had 24% lower risk of all-cause death (p < 0.001), 26% lower risk of CV-death (p < 0.000) and 8% lower risk for hospitalization (p = 0.030) than abstainers. There was no significant difference between non-drinkers and heavy drinkers with regard to survival following adjustment for age and smoking status.


CONCLUSION
Our results demonstrate a strong positive association between moderate alcohol use and survival in a cohort of patients following complicated MI. Both heavy drinkers and abstainers had poorer prognosis, with no significance difference between those 2 groups.
Calcium and 1,25-dihydroxyvitamin D3 regulation of adipokine expression.

OBJECTIVE
Obesity is associated with elevated oxidative stress and low-grade systemic inflammation. We have demonstrated recently that 1alpha,25-(OH)(2)-D(3) promotes reactive oxygen species production in cultured adipocytes, whereas suppression of 1alpha,25-(OH)(2)-D(3) by increasing dietary calcium down-regulates diet-induced oxidative stress in aP2-agouti transgenic mice. However, whether the anti-obesity effect of dietary calcium plays a role in regulation of obesity-associated inflammation is not clear.


RESEARCH METHODS AND PROCEDURES
We investigated the role of dietary calcium in the regulation of inflammatory cytokine production in aP2-agouti transgenic mice fed low- and high-calcium obesigenic diets and in the modulation of cytokine production by 1alpha,25-(OH)(2)-D(3) in cultured murine and human adipocytes.


RESULTS
The high-calcium diet inhibited the expression of pro-inflammatory factors tumor necrosis factor alpha and interleukin (IL)-6 by 64% and 51%, respectively (p < 0.001), in visceral fat, stimulated the expression of the anti-inflammatory factors IL-15 and adiponectin by 52% (p = 0.001) and 54% (p = 0.025), respectively, in visceral fat, and induced a 2-fold increase in IL-15 expression in soleus muscle (p = 0.01) compared with litter mate controls on a low-calcium diet. 1alpha,25-(OH)(2)-D(3) also markedly stimulated the expression of tumor necrosis factor alpha (p < 0.001) and IL-6 (p = 0.016) in differentiated 3T3-L1 adipocytes and increased IL-6 (p = 0.004) and IL-8 (p < 0.001) production in differentiated human adipocytes. These effects were blocked by calcium channel antagonism with nifedipine.


DISCUSSION
These data demonstrate that 1alpha,25-(OH)(2)-D(3) favors inflammatory cytokine expression and inhibits anti-inflammatory cytokine expression; accordingly, suppression of 1alpha,25-(OH)(2)-D(3) by dietary calcium inhibits adipocyte-derived inflammation associated with obesity.
Disease-specific outcomes of Radical Prostatectomies in Northern Norway; a case for the impact of perineural infiltration and postoperative PSA-doubling time

BACKGROUND
Prostate cancer is the most common male malignancy and a mayor cause of mortality in the western world. The impact of clinicopathological variables on disease related outcomes have mainly been reported from a few large US series, most of them not reporting on perineural infiltration. We therefore wanted to investigate relevant cancer outcomes in patients undergoing radical prostatectomy in two Norwegian health regions with an emphasis on the impact of perineural infiltration (PNI) and prostate specific antigen- doubling time (PSA-DT).


METHODS
We conducted a retrospective analysis of 535 prostatectomy patients at three hospitals between 1995 and 2005 estimating biochemical failure- (BFFS), clinical failure- (CFFS) and prostate cancer death-free survival (PCDFS) with the Kaplan-Meier method. We investigated clinicopathological factors influencing risk of events using cox proportional hazard regression.


RESULTS
After a median follow-up of 89 months, 170 patients (32%) experienced biochemical failure (BF), 36 (7%) experienced clinical failure and 15 (3%) had died of prostate cancer. pT-Stage (p = 0.001), preoperative PSA (p = 0.047), Gleason Score (p = 0.032), non-apical positive surgical margins (PSM) (p = 0.003) and apical PSM (p = 0.031) were all independently associated to BFFS. Gleason score (p = 0.019), PNI (p = 0.012) and non-apical PSM (p = 0.002) were all independently associated to CFFS while only PNI (P = 0.047) and subgroups of Gleason score were independently associated to PCDFS. After BF, patients with a shorter PSA-DT had independent and significant worse event-free survivals than patients with PSA-DT > 15 months (PSA-DT = 3-9 months, CFFS HR = 6.44, p < 0.001, PCDFS HR = 13.7, p = 0.020; PSA-DT < 3 months, CFFS HR = 11.2, p < 0.001, PCDFS HR = 27.5, p = 0.006).


CONCLUSIONS
After prostatectomy, CFFS and PCDFS are variable, but both are strongly associated to Gleason score and PNI. In patients with BF, PSA-DT was most strongly associated to CF and PCD. Our study adds weight to the importance of PSA-DT and re-launches PNI as a strong prognosticator for clinically relevant endpoints.
A simplified purification protocol for recombinant adeno-associated virus vectors

We describe a new rapid, low cost, and scalable method for purification of various recombinant adeno-associated viruses (rAAVs) from the lysates of producer cells of either mammalian or insect origin. The method takes advantage of two general biochemical properties of all characterized AAV serotypes: (i) low isoelectric point of a capsid and (ii) relative biological stability of the viral particle in the acidic environment. A simple and rapid clarification of cell lysate toremove the bulk of proteins and DNA is accomplished by utilizing inexpensive off-the-shelf reagents such as sodium citrate and citric acid. After the low-speed centrifugation step, the supernatant is subjected to cation exchange chromatography via sulfopropyl (SP) column. The eluted virus may then be further concentrated by either centrifugal spin devices or tangential flow filtration yielding material of high titer and Good Manufacturing Practice (GMP) grade biochemical purity. The protocol is validated for rAAV serotypes 2, 8, and 9. The described method makes rAAV vector technology readily available for the low budget research laboratories and could be easily adapted for a large scale GMP production format.
Prevention of restenosis by a novel drug-eluting stent system with a dose-adjustable, polymer-free, on-site stent coating.

AIMS
Drug-eluting stents (DES) represent a major advance in interventional cardiology. Along with the success shown, current DES also present limitations related to the presence of polymer-coating, fixed drug, and dose used. With the ISAR (Individualized Drug-Eluting Stent System to Abrogate Restenosis) project, a DES system has been developed that permits individualized choice of the drug and dose to use for the given patient. The objective of this prospective dose finding study was to assess the feasibility, safety, and efficacy of a polymer-free on-site stent coating with increasing rapamycin doses.


METHODS AND RESULTS
In this dose finding study, 602 patients were sequentially enrolled in four groups: microporous bare metal stent (BMS), DES stents coated with a 0.5, 1.0, and 2.0% rapamycin solution. The angiographic in-segment restenosis rate at follow-up angiography was the primary study endpoint. In-segment restenosis was significantly reduced from 25.9% with BMS to 18.9, 17.2, and 14.7% with 0.5, 1.0, and 2.0% rapamycin-eluting stents, respectively (P=0.024). Similarly, the need for target lesion revascularization at 1 year follow-up was reduced from 21.5% with BMS to 16.4, 12.6, and 8.8% with 0.5, 1.0, and 2.0% rapamycin-eluting stents, respectively (P=0.006).


CONCLUSION
The placement of polymer-free stents coated on-site with rapamycin is feasible and safe. Furthermore, a dose-dependent efficacy in restenosis prevention is achievable with this new DES concept.
Is Small Prostate Volume a Predictor of Gleason Score Upgrading after Radical Prostatectomy?

PURPOSE
We aimed to analyze the relationship between prostate volume and Gleason score (GS) upgrading [higher GS category in the radical prostatectomy (RP) specimen than in the prostate biopsy] in Korean men.


MATERIALS AND METHODS
We retrospectively analyzed the medical records of 247 men who underwent RP between May 2006 and April 2011 at our institution. Transrectal ultrasound (TRUS) volume was categorized as 25 cm³ or less (n=61), 25 to 40 cm³ (n=121) and greater than 40 cm³ (n=65). GS was examined as a categorical variable of 6 or less, 3+4 and 4+3 or greater. The relationship between TRUS volume and upgrading of GS was analyzed using multivariate logistic regression.


RESULTS
Overall, 87 patients (35.2%) were upgraded, 20 (8.1%) were downgraded, and 140 (56.7%) had identical biopsy and pathological Gleason sum groups. Smaller TRUS volume was significantly associated with increased likelihood of upgrading (p trend=0.022). Men with prostates 25 cm³ or less had more than 2.7 times the risk of disease being upgraded relative to men with TRUS volumes more than 40 cm³ (OR 2.718, 95% CI 1.403-8.126).


CONCLUSION
In our study, smaller prostate volumes were at increased risk for GS upgrading after RP. This finding should be kept in mind when making treatment decisions for men with prostate cancer that appears to be of a low grade on biopsy, especially in Asian urologic fields.
Papaya preparation (Caricol®) in digestive disorders.

OBJECTIVE
Papaya (Carica papaya L.) is used as a natural remedy in abnormal digestion in tropical and industrialized countries. Besides this wide distribution little evidence has been produced with reference to its physiological effect in humans and the proof of efficacy. Former clinical observations had revealed positive effects for patients with constipation, heartburn, and symptoms of irritable bowel syndrome (IBS) after eating papaya preparations. In line with these former positive clinical observations, we studied the clinical effects of the papaya preparation Caricol® in a double blind placebo controlled study design.


METHODS
In this study the participants were volunteers, with chronic (prevailing) indigestions and dysfunctions in the gastrointestinal tract. During the trial the intake of the substance of intent and placebo was 20 ml daily for 40 days. The endpoints were the frequency of 22 symptoms recorded before and after the documented intake recorded by questionnaire.


RESULTS
The symptoms "Constipation", "Bloating", and "Heartburn" were defined as primary and frequency of "painful (straining) bowel movements" as secondary endpoint. The participation ended after the intake period within two days ("early returnees"). Wash out effects were observed in "late returnees", who returned with a delay of 8.6 (±5.95 days). In the verum group early returnees revealed statistically significant improvements of the symptoms "constipation" and "bloating". The analysis of "heartburn" felt short of significant improvement because of the small number of included cases with this criteria (N=13, p=0.114). None of the significant benefits were observed after the washout phase.


CONCLUSION
We conclude from these results, that the papaya preparation (Caricol®) contributes to the maintenance of digestive tract physiology. It ameliorates various functional disturbances, like symptoms of IBS. The mechanism of this digestive tract physiology support is discussed.
Game Data Mining

1. The data revolution in games – and everywhere else – calls for analysis methods that scale to with dataset size. The solution: game data mining. 2. Game data mining deals with the challenges of acquiring actionable insights from game telemetry. 3. Read the chapter for an introduction to game data mining, an overview of methods commonly and not so commonly used, examples, case studies and a substantial amount of practical advice on how to employ game data mining effectively.
Voice recognition and touch screen control based wheel chair for paraplegic persons

The wide spread prevalence of lost limbs and sensing system is of major concern in present day due to accident, age and health problems. To assist people with such defects, the proposed intelligent wheelchair system uses dual control for navigation in familiar environments. The two modes of input control to the wheelchair are voice recognition and touch screen. When one want to change the direction, the touch screen sensor is modelled by pressing finger against the various quadrants on the touch screen, which has different values programmed for different direction. This can also be controlled through simple voice commands using voice controller. By storing a single letter in voice recognition kit for each direction control, the recognition time is reduced drastically and thus quick reach to destination is obtained. The wheelchair consists of DC brushless motors at the rear end and it is controlled by using PWM technique. A brake control mechanism is included to control the wheelchair. From previous literature surveys observed, the accuracy of the touch screen was found to be 50%. In this proposed system achievement of wheelchair movement in all direction is obtained with an accuracy of 94.6%. Voice recognition has accuracy of 80.8% which is 30% higher than the study done by Prathyusha et al. This device helps the disabled to have automatic advancement to their destination through predefined paths in the indoor system.
Mechanisms for Geographical Transmission of Economic Fluctuations

ABSTRACT Geographers have made considerable descriptive progress in studies of business cycles, but the ways in which economic impulses are transmitted, known as “the transmission mechanism,'’remain inadequately analyzed. After reviewing several transmission mechanisms proposed in previous studies, the paper suggests that interregional commodity trade, with limited mobility of factors of production such as labor, is an obvious candidate for transmitting economic fluctuations among regions. Three models are constructed to analyze transmission mechanisms involved in interregional commodity trade in a monetary setting. Increases in wages or unemployment in one region could induce increases or decreases in wages or unemployment in another region. The directions of transmitted changes depend crucially on the cause of the change and the economic structures of the regions involved.
Ptolemy's map of Ireland: a modern decoding

Abstract Claudius Ptolemy (roughly AD 90–168) presents us the oldest surviving account of Ireland in the form of a set of coordinates showing different geographical features or a ‘virtual map’. While Ptolemy's map looks roughly like today's Ireland there are a number of discrepancies. Likewise, while some locations are obvious, others are disputed or obscure. After reviewing earlier attempts at reconciling Ptolemy's map with modern ones we adjust Ptolemy's coordinates to modern references with two equations. We find Ptolemy's map is consistent with some intimate Mediterranean knowledge of Ireland, its peoples, coastal features and principal places with their respective locations. We correct some of the modern locations attributed to Ptolemy, offer possible explanations for certain disputed or uncertain locations and offer some external validation to the prehistoric division of Ireland passed down from pre-Patrician sources.
Relation between quantum tunneling times for relativistic particles

A general relation between the phase time (group delay) and the dwell time is derived for relativistic tunneling particles described by the Dirac equation. It is shown that the phase time equals the dwell time plus a self-interference delay which is a relativistic generalization of previous results.
Tuning in to kids: an emotion‐focused parenting program—initial findings from a community trial

This study evaluated a new group parenting program, Tuning in to Kids, which taught emotion coaching skills to parents of preschool children. In a randomized control trial, 218 primary caregiver parents of children aged 4.0–5.11 years completed questionnaires assessing parent emotion socialization (emotion coaching vs. emotion dismissing), parent emotional competence, parent wellbeing and child behavior. Assessment occurred at preintervention and 10 weeks later. Parents randomized to the intervention condition (n 5 107) attended a 6-session parenting program. Results showed parents in the intervention condition reported significant increases in emotion coaching and significant reductions in emotion dismissing with their children. Child behavior was also reported to improve. Of those with clinical levels of behavior difficulties, more than half were no longer at clinical level postprogram. These findings suggest that an emotion-focused parenting intervention may assist parents to
School finance reform, the distribution of school spending, and the distribution of student test scores

This paper studies the effect of school finance reforms on the distribution of school spending across richer and poorer districts, and the consequences of spending equalization for the relative test performance of students from different family backgrounds. We find that states where the school finance system was declared unconstitutional in the 1980s increased the relative funding of low-income districts. Increases in the amount of state aid available to poorer districts led to increases in the spending of these districts, narrowing the spending gap between richer and poorer districts. Using micro samples of SAT scores from this same period, we then test whether changes in spending inequality affect the gap in achievement between different family background groups. We find evidence that equalization of spending leads to a narrowing of test score outcomes across family background groups.  2002 Elsevier Science B.V. All rights reserved.
Stress Detection Using Wearable Physiological and Sociometric Sensors

Stress remains a significant social problem for individuals in modern societies. This paper presents a machine learning approach for the automatic detection of stress of people in a social situation by combining two sensor systems that capture physiological and social responses. We compare the performance using different classifiers including support vector machine, AdaBoost, and [Formula: see text]-nearest neighbor. Our experimental results show that by combining the measurements from both sensor systems, we could accurately discriminate between stressful and neutral situations during a controlled Trier social stress test (TSST). Moreover, this paper assesses the discriminative ability of each sensor modality individually and considers their suitability for real-time stress detection. Finally, we present an study of the most discriminative features for stress detection.
XPONENTIALLY VANISHING SUB-OPTIMAL LOCAL MINIMA IN MULTILAYER NEURAL NETWORKS

Background: Statistical mechanics results (Dauphin et al. (2014); Choromanska et al. (2015)) suggest that local minima with high error are exponentially rare in high dimensions. However, to prove low error guarantees for Multilayer Neural Networks (MNNs), previous works so far required either a heavily modified MNN model or training method, strong assumptions on the labels (e.g., “near” linear separability), or an unrealistically wide hidden layer with Ω (N) units. Results: We examine a MNN with one hidden layer of piecewise linear units, a single output, and a quadratic loss. We prove that, with high probability in the limit of N → ∞ datapoints, the volume of differentiable regions of the empiric loss containing sub-optimal differentiable local minima is exponentially vanishing in comparison with the same volume of global minima, given standard normal input of dimension d0 = Ω̃ (√ N ) , and a more realistic number of d1 = Ω̃ (N/d0) hidden units. We demonstrate our results numerically: for example, 0% binary classification training error on CIFAR with only N/d0 ≈ 16 hidden neurons.
Caring for Aged Dementia Care Resident Study (CADRES) of person-centred care, dementia-care mapping, and usual care in dementia: a cluster-randomised trial

BACKGROUND
Evidence for improved outcomes for people with dementia through provision of person-centred care and dementia-care mapping is largely observational. We aimed to do a large, randomised comparison of person-centred care, dementia-care mapping, and usual care.


METHODS
In a cluster randomised controlled trial, urban residential sites were randomly assigned to person-centred care, dementia-care mapping, or usual care. Carers received training and support in either intervention or continued usual care. Treatment allocation was masked to assessors. The primary outcome was agitation measured with the Cohen-Mansfield agitation inventory (CMAI). Secondary outcomes included psychiatric symptoms including hallucinations, neuropsychological status, quality of life, falls, and cost of treatment. Outcome measures were assessed before and directly after 4 months of intervention, and at 4 months of follow-up. Hierarchical linear models were used to test treatment and time effects. Analysis was by intention to treat. This trial is registered with the Australia and New Zealand Clinical Trials Registry, number ACTRN12608000084381.


FINDINGS
15 care sites with 289 residents were randomly assigned. Pairwise contrasts revealed that at follow-up, and relative to usual care, CMAI score was lower in sites providing mapping (mean difference 10.9, 95% CI 0.7-21.1; p=0.04) and person-centred care (13.6, 3.3-23.9; p=0.01). Compared with usual care, fewer falls were recorded in sites that used mapping (0.24, 0.08-0.40; p=0.02) but there were more falls with person-centred care (0.15, 0.02-0.28; p=0.03). There were no other significant effects.


INTERPRETATION
Person-centred care and dementia-care mapping both seem to reduce agitation in people with dementia in residential care.