LLukas22/scidocs huggingface dataset:
Using the UML for Architectural Description

There is much interest in using the Unified Modeling Language (UML) for architectural description – those techniques by which architects sketch, capture, model, document and analyze architectural knowledge and decisions about software-intensive systems. IEEE P1471, the Recommended Practice for Architectural Description, represents an emerging consensus for specifying the content of an architectural description for a software-intensive system. Like the UML, IEEE P1471 does not prescribe a particular architectural method or life cycle, but may be used within a variety of such processes. In this paper, I provide an overview of IEEE P1471, describe its conceptual framework, and investigate the issues of applying the UML to meet the requirements of IEEE P1471.
Smoking among premenopausal women is associated with increased risk of low bone status: the JPOS Study

The impact of smoking on peak bone density has not been conclusively established. We examined how smoking exposure influences bone mineral density (BMD) or the risk of low bone status in premenopausal women. We conducted a baseline survey with a representative sample of Japanese women in 1996. The effect of current and former smokers (ever-smoker) was investigated with 789 premenopausal women aged 20–40 years. The multiple regression with stepwise method was used to identify significant determinants for BMD or the risk of low bone status (T-score < −1) with age, height, weight, calcium intake, coffee consumption, exercise habits, level of daily activity, parity ≥ 1, and smoking as explanatory variables. The smoking effect was determined after adjusting for age, height, weight, and significant variables in the multiple regression with stepwise method. Ever-smoker was significantly associated with decreased lumbar BMD adjusted for age, height, and weight. The odds ratio of an ever-smoker for low bone status at the lumbar spine was 2.03 (95% CI 1.12, 5.82) adjusted for age, height, weight, and parity. The odds ratio for low bone status at the lumbar spine was 1.59 (95% CI 0.65, 3.91) and 2.55 (95% CI 1.12, 5.82) in those with less than 3 pack-years of tobacco use and in those with 3 or more pack-years of tobacco use, respectively. These values were adjusted for age, height, weight, and parity using a never-smoker as a reference. Cumulative smoking exposure may be associated with increased risk of low bone status among premenopausal women.
A Systematic Review of Topical Finasteride in the Treatment of Androgenetic Alopecia in Men and Women.

INTRODUCTION
Currently, only topical minoxidil (MNX) and oral finasteride (FNS) are approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) for the treatment of androgenetic alopecia. Although FNS is efficacious for hair regrowth, its systemic use is associated with side effects limiting long-term utilization. Exploring topical FNS as an alternative treatment regimen may prove promising.


METHODS
A search was conducted to identify studies regarding human in vivo topical FNS treatment efficacy including clinically relevant case reports, randomized controlled trials (RCTs), and prospective studies.


RESULTS
Seven articles were included in this systematic review. In all studies, there was significant decrease in the rate of hair loss, increase in total and terminal hair counts, and positive hair growth assessment with topical FNS. Both scalp and plasma DHT significantly decreased with application of topical FNS; no changes in serum testosterone were noted.


CONCLUSION
Preliminary results on the use of topical FNS are limited, but safe and promising. Continued research into drug-delivery, ideal topical concentration and application frequency, side effects, and use for other alopecias will help to elucidate the full extent of topical FNS' use. J Drugs Dermatol. 2018;17(4):457-463..
Perceived challenges and opportunities arising from integration of mental health into primary care: a cross-sectional survey of primary health care workers in south-west Ethiopia

BACKGROUND
The WHO's mental health Gap Action Programme seeks to narrow the treatment gap for mental disorders by advocating integration of mental health into primary health care (PHC). This study aimed to assess the challenges and opportunities of this approach from the perspective of PHC workers in a sub-Saharan African country.


METHODS
A facility-based cross-sectional survey of 151 PHC workers was conducted from 1st to 30th November 2011 in Jimma zone, south-west Ethiopia. A structured questionnaire was used to ask about past training and mental health experience, knowledge and attitudes towards mental disorders and provision of mental health care in PHC. Semi-structured interviews were carried out with 12 heads of health facilities for more in-depth understanding.


RESULTS
Almost all PHC workers (96.0%) reported that mental health care was important in Ethiopia and the majority (66.9%) expressed interest in actually delivering mental health care. Higher levels of general health training (degree vs. diploma) and pre-service clinical exposure to mental health care were associated with more favourable attitudes. Knowledge about mental disorder diagnoses, symptoms and treatments was low. Almost half (45.0%) of PHC workers reported that supernatural factors were important causes of mental disorders. Health system and structural issues, such as poor medication supply, lack of rooms, time constraints, absence of specialist supervision and lack of treatment guidelines, were identified as challenges. Almost all PHC workers (96.7%) reported a need for more training, including a clinical attachment, in order to be able to deliver mental health care competently.


CONCLUSIONS
Despite acceptability to PHC workers, the feasibility of integrating mental health into PHC in this sub-Saharan African setting is limited by important gaps in PHC worker knowledge and expectations regarding mental health care, coupled with health system constraints. In addition to clinically-based refresher mental health training, expansion of the specialist mental health workforce may be needed to support integration in practice.
Stress may add bite to appetite in women: a laboratory study of stress-induced cortisol and eating behavior

To date, there are few known predictors of stress-induced eating. The purpose of this study was to identify whether physiological and psychological variables are related to eating after stress. Specifically, we hypothesized that high cortisol reactivity in response to stress may lead to eating after stress, given the relations between cortisol with both psychological stress and mechanisms affecting hunger. To test this, we exposed fifty-nine healthy pre-menopausal women to both a stress session and a control session on different days. High cortisol reactors consumed more calories on the stress day compared to low reactors, but ate similar amounts on the control day. In terms of taste preferences, high reactors ate significantly more sweet food across days. Increases in negative mood in response to the stressors were also significantly related to greater food consumption. These results suggest that psychophysiological response to stress may influence subsequent eating behavior. Over time, these alterations could impact both weight and health.
The Structure of the Relational Database Model

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A test of static and dynamic balance function in children with cochlear implants: the vestibular olympics.

OBJECTIVES
To determine the incidence of static and dynamic balance dysfunction in a group of children with profound sensorineural hearing loss receiving a cochlear implant and to assess the impact of cochlear implant activation on equilibrium.


DESIGN
Observational cross-sectional study of children with single-sided implants, tested under 2 conditions: (1) implant on and (2) implant off in a random order.


SETTING
Ambulatory setting within an academic, tertiary care children's hospital.


PARTICIPANTS
Forty-one children (ages 4-17 years) with cochlear implants comprised the study group. Fourteen children with normal hearing served as controls.


INTERVENTION
All participants performed a standardized test of static and dynamic balance function (Bruininks-Oseretsky Test of Motor Proficiency 2 [BOT2], balance subset). Children with implants performed the BOT2 under the 2 randomized conditions.


MAIN OUTCOME MEASURES
Overall performance on the balance subset of the BOT2 and the influence of implant activation on performance.


RESULTS
The mean (SD) age-adjusted scale score for our control group was 17 (5) points (95% confidence interval [CI], 14-20), which was not significantly different (P = .15) from the published age-adjusted mean for the BOT2 balance subset (15 [5] points). The group that had undergone implantation, however, performed significantly more poorly (12 [ 6] points; 95% CI, 10-14) than either the control group or the published test mean (P = .004). Children with implants performed better with their implants on than with their implants off (mean [SD] difference, 1.3 [2.7] points; 95% CI, 0.3-2.3; P = .01).


CONCLUSIONS
Large differences exist in the balance ability of children with sensorineural hearing loss requiring cochlear implantation compared with age-matched controls. Implant activation, however, conferred a slight advantage in accomplishing balance-related tasks. These results substantiate the need to further quantify the baseline vestibular dysfunction of our study population of children with cochlear implants, as well as the impact of implant activation on the input and output of the vestibular system.
Confidence intervals construction for difference of two means with incomplete correlated data.

BACKGROUND
Incomplete data often arise in various clinical trials such as crossover trials, equivalence trials, and pre and post-test comparative studies. Various methods have been developed to construct confidence interval (CI) of risk difference or risk ratio for incomplete paired binary data. But, there is little works done on incomplete continuous correlated data. To this end, this manuscript aims to develop several approaches to construct CI of the difference of two means for incomplete continuous correlated data.


METHODS
Large sample method, hybrid method, simple Bootstrap-resampling method based on the maximum likelihood estimates (B 1) and Ekbohm's unbiased estimator (B 2), and percentile Bootstrap-resampling method based on the maximum likelihood estimates (B 3) and Ekbohm's unbiased estimator (B 4) are presented to construct CI of the difference of two means for incomplete continuous correlated data. Simulation studies are conducted to evaluate the performance of the proposed CIs in terms of empirical coverage probability, expected interval width, and mesial and distal non-coverage probabilities.


RESULTS
Empirical results show that the Bootstrap-resampling-based CIs B 1, B 2, B 4 behave satisfactorily for small to moderate sample sizes in the sense that their coverage probabilities could be well controlled around the pre-specified nominal confidence level and the ratio of their mesial non-coverage probabilities to the non-coverage probabilities could be well controlled in the interval [0.4, 0.6].


CONCLUSIONS
If one would like a CI with the shortest interval width, the Bootstrap-resampling-based CIs B 1 is the optimal choice.
FudanNLP: A Toolkit for Chinese Natural Language Processing

The growing need for Chinese natural language processing (NLP) is largely in a range of research and commercial applications. However, most of the currently Chinese NLP tools or components still have a wide range of issues need to be further improved and developed. FudanNLP is an open source toolkit for Chinese natural language processing (NLP), which uses statistics-based and rule-based methods to deal with Chinese NLP tasks, such as word segmentation, part-ofspeech tagging, named entity recognition, dependency parsing, time phrase recognition, anaphora resolution and so on.
A randomized controlled trial of simulation-based teaching versus traditional instruction in medicine: a pilot study among clinical medical students.

OBJECTIVE
To compare simulator-based teaching with traditional instruction among clinical medical students.


METHODS
Randomized controlled trial with written pre-post testing. Third-year medical students (n = 38) received either a myocardial infarction (MI) simulation followed by a reactive airways disease (RAD) lecture, or a RAD simulation followed by an MI lecture.


RESULTS
Mean pre-post test score improvement was seen across teaching modalities (overall change score [simulation] = 8.8 [95% CI = 2.3-15.3], pretest [62.7]; change score [lecture] = 11.3 [95% CI = 5.7-16.9], pretest [59.7]). However, no significant differences were observed between simulator-based teaching and lecture, in either subject domain.


CONCLUSIONS
After a single instructional session for clinical medical students, differences between simulator-based teaching and lecture could not be established by the written test protocols used in this pilot. Future studies should consider the effects of iterative exposure assessed by clinical performance measures across multiple centers.
A case study for scientific I/O: improving the FLASH astrophysics code

The FLASH code is a computational science tool for simulating and studying thermonuclear reactions. The program periodically outputs large checkpoint files (to resume a calculation from a particular point in time) and smaller plot files (for visualization and analysis). Initial experiments on BlueGene/P spent excessive time in input/output (I/O), making it difficult to do actual science. Our investigation of time spent in I/O revealed several locations in the I/O software stack where we could make improvements. Fixing data corruption in the MPI-IO library allowed us to use collective I/O, yielding an order of magnitude improvement. Restructuring the data layout provided a more efficient I/O access pattern and yielded another doubling of performance, but broke format assumptions made by other tools in the application workflow. Using new nonblocking APIs in the ParallelNetCDF library allowed us to keep high performance and maintain backward compatibility. The I/O research community has studied a host of optimizations and strategies. Sometimes the challenge for applications is knowing how to apply these new techniques to production codes. In this case study, we offer a demonstration of how computational scientists, with a detailed understanding of their application, and the I/O community, with a wide array of approaches from which to choose, can magnify each other’s efforts and achieve tremendous application productivity gains. Computational Science & Discovery 5 (2012) 015001 www.iop.org/journals/csd © 2012 IOP Publishing Ltd 1749-4699/12/015001+16$33.00 Computational Science & Discovery 5 (2012) 015001 R Latham et al
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments

MOTIVATION
The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but also their potential secondary structures. Sankoff's algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required.


RESULTS
We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable with the much slower existing algorithms.


AVAILABILITY
The web server of SCARNA with graphical structural alignment viewer is available at http://www.scarna.org/.
Digital image processing techniques for detecting, quantifying and classifying plant diseases

ABSTRACT
This paper presents a survey on methods that use digital image processing techniques to detect, quantify and classify plant diseases from digital images in the visible spectrum. Although disease symptoms can manifest in any part of the plant, only methods that explore visible symptoms in leaves and stems were considered. This was done for two main reasons: to limit the length of the paper and because methods dealing with roots, seeds and fruits have some peculiarities that would warrant a specific survey. The selected proposals are divided into three classes according to their objective: detection, severity quantification, and classification. Each of those classes, in turn, are subdivided according to the main technical solution used in the algorithm. This paper is expected to be useful to researchers working both on vegetable pathology and pattern recognition, providing a comprehensive and accessible overview of this important field of research.
The Worst-Case Running Time of the Random Simplex Algorithm is Exponential in the Height

The random simplex algorithm for linear programming proceeds as follows: at each step, it moves from a vertex v of the polytope to a randomly chosen neighbor of v, the random choice being made from those neighbors of v that improve the objective function. We exhibit a polytope deened by n constraints in three dimensions with height O(log n), for which the expected running time of the random simplex algorithm is (n= log n). We consider linear programming problems deened by n constraints involving d variables. The constraints deene a polytope in d dimensions; we seek a point of the polytope that maximizes an objective function that is linear in the variables. It is known that the optimum, if bounded, occurs at a vertex of this polytope. The classic simplex algorithm begins at a vertex of the polytope and, at each step proceeds to a neighboring vertex that improves the objective function. The simplex algorithm uses a deterministic rule to choose among the neighbors with improving objective function at each step. For virtually all such known rules, there are polytopes for which the simplex algorithm requires time exponential in d 5]. The random simplex algorithm 1, 2] is the following: at each step, go to a neighbor chosen uniformly at random from all neighbors that improve the objective function. It is not known whether the expected number of steps for the random simplex algorithm is sub-exponential in d.
Massage therapy for essential hypertension: a systematic review

Massage, an ancient Chinese healing art, is widely practiced for symptom relief in hypertensive patients with anxiety, depression, headache, vertigo, chronic pain in neck, shoulder and back. A large number of case series and clinical trials have been published. However, it is still unclear whether massage can be recommended as an effective therapy for essential hypertension (EH). We estimated the current clinical evidence of massage for EH. Articles published before 10 December 2013 were searched using Cochrane Library, PubMed, EMBASE, Chinese Scientific Journal Database (VIP), Chinese Biomedical Literature Database, Wanfang data and Chinese National Knowledge Infrastructure. Randomized controlled trials comparing massage with any type of control intervention were included. Trials testing massage combined with antihypertensive drugs versus antihypertensive drugs were included as well. Meta-analysis was performed on the effects on blood pressure (BP). Twenty-four articles involving 1962 patients with EH were selected. Methodological quality of most trials was evaluated as generally low. Meta-analyses demonstrated that massage combined with antihypertensive drugs may be more effective than antihypertensive drugs alone in lowering both systolic BP (SBP; mean difference (MD): −6.92 (−10.05, −3.80); P<0.0001) and diastolic BP (MD: −3.63 (−6.18, −1.09); P=0.005); massage appears beneficial for reducing SBP (MD: −3.47 (−5.39, −1.56); P=0.0004) for hypertensive patients as compared with antihypertensive drugs. Safety of massage is still unclear. There is some encouraging evidence of massage for EH. However, because of poor methodological quality, the evidence remains weak. Rigorously designed trials are needed to validate the use of massage in future.
Genetic variation of CYP2C19 affects both pharmacokinetic and pharmacodynamic responses to clopidogrel but not prasugrel in aspirin-treated patients with coronary artery disease

AIMS
The metabolic pathways leading to the formation of prasugrel and clopidogrel active metabolites differ. We hypothesized that decreased CYP2C19 activity affects the pharmacokinetic and pharmacodynamic response to clopidogrel but not prasugrel.


METHODS AND RESULTS
Ninety-eight patients with coronary artery disease (CAD) taking either clopidogrel 600 mg loading dose (LD)/75 mg maintenance dose (MD) or prasugrel 60 mg LD/10 mg MD were genotyped for variation in six CYP genes. Based on CYP genotype, patients were segregated into two groups: normal function (extensive) metabolizers (EM) and reduced function metabolizers (RM). Plasma active metabolite concentrations were measured at 30 min, 1, 2, 4, and 6 h post-LD and during the MD period on Day 2, Day 14, and Day 29 at 30 min, 1, 2, and 4 h. Vasodilator-stimulated phosphoprotein (VASP) and VerifyNow P2Y12 were measured predose, 2, and 24 +/- 4 h post-LD and predose during the MD period on Day 14 +/- 3 and Day 29 +/- 3. For clopidogrel, active metabolite exposure was significantly lower (P = 0.0015) and VASP platelet reactivity index (PRI, %) and VerifyNow P2Y(12) reaction unit (PRU) values were significantly higher (P < 0.05) in the CYP2C19 RM compared with the EM group. For prasugrel, there was no statistically significant difference in active metabolite exposure or pharmacodynamic response between CYP2C19 EM and RM. Variation in the other five genes demonstrated no statistically significant differences in pharmacokinetic or pharmacodynamic responses.


CONCLUSION
Variation in the gene encoding CYP2C19 in patients with stable CAD contributes to reduced exposure to clopidogrel's active metabolite and a corresponding reduction in P2Y(12) inhibition, but has no significant influence on the response to prasugrel.