LLukas22/scidocs huggingface dataset:
Chronic low back pain clinical outcomes present higher associations with the STarT Back Screening Tool than with physiologic measures: a 12-month cohort study

BACKGROUND
Stratification strategies based on identifying patient's prognosis in order to guide patient care constitute one of the most prominent and recent approach in low back pain research. The STarT Back Screening Tool (SBST) although promising, has not been studied in patients with chronic low back pain (cLBP). Considering how challenging it is to translate research into practice, the value of integrating a new tool should be thoroughly assessed. The purpose was therefore to assess associations between the short- and long-terms clinical status and two types of variables, physiologic measures and the SBST, in participants with cLBP. The ability of both types of variables to discriminate between participants with and without higher levels of disability, pain, fear of movement and patient's global impression of change was also investigated.


METHODS
Fifty-three volunteers with cLBP participated in an initial evaluation and follow-ups at 2-, 4-, 6- and 12-month. Physiologic measures (maximal voluntary contraction, maximal endurance and muscle activity evaluated during prone and lateral isometric tasks) and the SBST were assessed at baseline. Disability (Oswestry Disability Index, ODI), pain intensity (101-point Numerical Rating Scale, NRS), fear of movement (Tampa Scale for Kinesiophobia, TSK) and patient's global impression of change (7-point scale, PGIC) were evaluated at baseline and at each follow-up. Aside the use of correlation analyses to assess potential associations; ROC curves were performed to evaluate the discriminative ability of physiologic measures and the SBST.


RESULTS
The SBST allowed for the identification of participants presenting higher levels of disability (ODI ≥24 %), pain (NRS ≥37 %) or fear of movement (TSK ≥41/68) over a 12-month period (AUC = 0.71 to 0.84, ps < 0.05). The SBST score was also correlated with disability at each follow-up (τ = 0.22 to 0.33, ps < 0.05) and with pain intensity and fear of movement at follow-ups. Among physiologic measures, only maximal voluntary contraction was correlated to disability, pain intensity or fear of movement during the follow-up (|τ| = 0.26 to 0.32, ps < 0.05) and none was able to identify participants presenting higher levels of outcomes (AUC ps > 0.05).


CONCLUSION
Physiologic measures obtained during prone and lateral tests have limited associations with the clinical status over a 12-month period in patients with nonspecific chronic low back pain. On the other hand, the STarT Back Screening Tool is useful for the identification of patients who will present higher levels of disability, pain intensity and fear of movement over a year.


TRIAL REGISTRATION
Clinicaltrials.gov NCT02226692.
Concept annotation in the CRAFT corpus

Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml .
Impact of S-1 in patients with gemcitabine-refractory pancreatic cancer in Japan.

OBJECTIVE
We investigated the impact of S-1 on the prognosis of patients with gemcitabine-refractory pancreatic cancer.


METHODS
A total of 108 patients with gemcitabine-refractory pancreatic cancer were divided by the time of S-1 introduction in our institution: 47 patients who experienced progressive disease before February 2005 (pre-S-1 group) and 61 patients showed progressive disease after February 2005 (post-S-1 group). Introduction rates of second-line chemotherapy and survival were compared. Prognostic factors for residual survival were analyzed using the Cox proportional hazards model.


RESULTS
Introduction rates of second-line chemotherapy were 12.8% in the pre-S-1 group and 45.9% in the post-S-1 group. Second-line chemotherapy was administered to 34 patients: 29 using S-1, 4 using 5-fluorouracil-based chemoradiation and 1 using 5-fluorouracil. The objective response rate, progression-free survival and overall survival for second-line chemotherapy with S-1 were 17.2%, 2.5 and 7.7 months, respectively. By the introduction of S-1 in our institution, residual survival was prolonged from 3.1 months in the pre-S-1 group to 6.7 months in the post-S-1 group (P < 0.001). Overall survival from the initiation of gemcitabine was 8.8 months in the pre-S-1 group and 11.3 months in the post-S-1 group (P = 0.013). Multivariate analysis identified the post-S-1 group (hazard ratio, 0.43; P = 0.001), gender, performance status, liver metastasis, and lactate dehydrogenase and C-reactive protein levels at progressive disease for gemcitabine to be prognostic factors for residual survival.


CONCLUSIONS
The introduction of S-1 might improve the prognosis of patients with gemcitabine-refractory pancreatic cancer.
A REACTIVE DRIVING AGENT FOR MICROSCOPIC TRAFFIC SIMULATION

Computer traffic simulation is important for making new traffic-control strategies. Microscopic traffic simulators can model traffic flow in a realistic manner and are ideal for agent-based vehicle control. In this paper we describe a model of a reactive agent that is used to control a simulated vehicle. The agent is capable of tactical-level driving and has different driving styles. To ensure fast reaction times, the agent’s driving task is divided in several competing and reactive behaviour rules. The agent is implemented and tested in a prototype traffic simulator. The simulator consists of an urban environment with multi-lane roads, intersections, traffic lights, and vehicles. Every vehicle is controlled by a separate driving agent and all agents have individual behaviour settings. Preliminary experiments have shown that the agents exhibit human-like behaviour ranging from slow and careful to fast and aggressive driving behaviour.
Psychosocial outcomes in patients with recurrent major depressive disorder during 2 years of maintenance treatment with venlafaxine extended release.

BACKGROUND
Psychosocial outcomes from the Prevention of Recurrent Episodes of Depression with Venlafaxine ER for Two Years (PREVENT) study were evaluated.


METHODS
Adult outpatients with recurrent major depressive disorder (MDD) and response or remission following 6-month continuation treatment with venlafaxine extended release (ER) were randomized to receive venlafaxine ER or placebo for 1 year. Patients without recurrence on venlafaxine ER during year 1 were randomized to venlafaxine ER or placebo for year 2. Psychosocial functioning was assessed using the Quality of Life Enjoyment and Satisfaction Questionnaire-Short Form (Q-LES-Q), Life Enjoyment Scale-Short Version (LES-S), Social Adjustment Scale-Self-Report (SAS-SR) total and individual factors, Short Form Health Survey (SF-36) (vitality, social functioning, and role function-emotional items), and Longitudinal Interval Follow-up Evaluation (LIFE).


RESULTS
At year 1 end, better overall psychosocial functioning was seen among patients randomly assigned to venlafaxine ER (n=129) vs placebo (n=129), with significant differences at end point on SF-36 role function-emotional, Q-LES-Q, and SAS-SR total, and work, house work, social/leisure, and extended-family factor scores (p≤0.05). At year 2 end, significant differences favored venlafaxine ER (n=43) vs placebo (n=40) on SF-36 vitality and role function-emotional, Q-LES-Q, LES-S, LIFE, and SAS-SR total, social/leisure, and extended-family factor scores (p≤0.05).


LIMITATIONS
Patients with chronic MDD or treatment resistance were excluded and long-term specialist care was a financial incentive for treatment compliance. Discontinuation-related adverse events may have compromised the integrity of the treatment blind.


CONCLUSIONS
For patients with recurrent MDD, 2 years' maintenance therapy with venlafaxine ER may improve psychosocial functioning vs placebo.
An extremal problem for Graham-Rothschild parameter words

This paper exposes connections between the theory of Möbius functions and extremal problems, extending ideas of Frankl and Pach [8]. Extremal results concerning the trace of objects in geometric lattices and Graham—Rothschild parameter posets are proved, covering previous results due to Sauer [16] and Perles and Shelah [17].
[Treatment duration of extra-pulmonary tuberculosis: 6 months or more? TB-INFO database analysis].

PURPOSE
The recommended duration of pulmonary tuberculosis therapy is 6 months. For extrapulmonary tuberculosis, treatment duration depends on tuberculosis involvement and HIV status. The objective of this study was to describe the main characteristics of a cohort of extrapulmonary tuberculosis patients, to compare patients with a 6-month treatment to those with more than a 6-month treatment, and to analyze the compliance of medical centres with recommended duration of treatment.


METHODS
A retrospective cohort study of 210 patients with extrapulmonary tuberculosis was carried from January 1999 to December 2006 in two hospitals in the north-east of Paris. These patients were treated with quadruple therapy during two months, followed by dual therapy during 4 months (n=77) or more (n=66). The characteristics of each group were compared by uni- and multivariate analysis. The primary endpoint was the rate of relapse or treatment failure at 24-month follow-up after treatment completion.


RESULTS
No relapse was observed after 24 months of follow-up after the end of treatment in the two groups. In univariate analysis, patients with lymph node tuberculosis were more often treated for 6 months than at other sites of tuberculosis (respectively 61% versus 40.9%; P=0.02); the decision of treatment duration was related to medical practices (79.2% treated 6 months in one hospital versus 20.7% in the other, P<0.001); patients living in private residence were more often treated during 6 months than patients living in residence (24.2% versus 10.3%, P=0.042). In multivariate analysis, only hospital (P=0.046), sex (P=0.007) and private residence were significantly different in each group.


CONCLUSION
A period of 6 months seems to be sufficient to treat extrapulmonary tuberculosis (except for neuromeningeal localization).
Text Input on a Smart Watch

Smart watches provide users with access to many applications directly from their wrists, without the need to touch their smartphones. While applications such as email, messaging, calendar, and social networking provide views on the watch, there is normally no text-entry method, so users cannot reply on the same device. Here, the authors introduce their interaction design and an optimized alphabetic layout for smart-watch text entry, and present a lab evaluation of an implemented prototype using the OpenAdaptxt engine on a Sony SmartWatch 2. While raising some problems, the feedback from study participants indicates that reasonable quality and speed is achievable on a smart watch and encourages future work in this area. This article is part of a special issue on wearable computing.
Gradual changes in the age distribution of excess deaths in the years following the 1918 influenza pandemic in Copenhagen: using epidemiological evidence to detect antigenic drift.

BACKGROUND
The 1918 influenza pandemic was associated with an unusual age pattern of mortality, with most deaths occurring among young adults. Few studies have addressed changes in the age distribution for influenza-related mortality in the pre-pandemic and post-pandemic period, which has implications for pandemic preparedness. In the present paper, we analyse the age patterns of influenza-related excess mortality in the decades before and after the 1918 pandemic, using detailed historic surveillance data from Copenhagen.


METHODS
Weekly age-specific rates of respiratory mortality and influenza-like-illnesses were compiled for 1904-1937. Seasonal excess rates of morbidity and mortality attributable to influenza were calculated using a seasonal regression approach. To characterize the age patterns of influenza-related deaths in individual seasons, we used two rate ratio (RR) measures representing ratios of excess mortality rates between age groups and influenza seasons.


RESULTS
Individuals aged 15-64 years experienced sharply elevated excess respiratory mortality rates in the 1918-1919 and 1919-1920 pandemic periods, compared to pre-pandemic seasons (RR for excess mortality in the fall of 1918 = 67 relative to inter-pandemic seasons). Of all excess respiratory deaths occurring during 1918-1919, 84% were reported in individuals 15-64 years. By contrast, seniors over 65 years of age experienced no measurable excess mortality during 1918-1919 and moderate excess mortality in the recrudescent pandemic wave of 1919-1920. The first post-pandemic season associated with high excess mortality rates in individuals over 65 years was 1928-1929, with 73% of excess deaths occurring among seniors. We estimate that the age patterns of influenza-related mortality returned to pre-pandemic levels after 1925, based on trends in the rate ratio of excess respiratory mortality in people under and over 65 years.


CONCLUSIONS
The unusual elevation of excess respiratory mortality rates in young and middle-aged adults was confined to the first three years of A/H1N1 virus circulation 1918-1920; the rapid return to "epidemic" mortality pattern in this age group was probably due to high attack rates and build-up of immunity. In contrast, seniors were completely spared from pandemic mortality during 1918-1919, likely due to childhood exposure to an A/H1-like influenza virus. The rise in excess mortality rates in seniors in the recrudescent pandemic wave of 1919-1920 may suggest the emergence of an early influenza A/H1N1 drift variant. Subsequent drift events may have been associated with the particularly severe 1928-1929 epidemic in Denmark and elsewhere.
1|A Kalman filter-based algorithm for IMU-camera calibration

Vision-aided Inertial Navigation Systems (V-INS) can provide precise state estimates for the 3D motion of a vehicle when no external references (e.g., GPS) are available. This is achieved by combining inertial measurements from an IMU with visual observations from a camera under the assumption that the rigid transformation between the two sensors is known. Errors in the IMU-camera calibration process causes biases that reduce the accuracy of the estimation process and can even lead to divergence. In this paper, we present a Kalman filter-based algorithm for precisely determining the unknown transformation between a camera and an IMU. Contrary to previous approaches, we explicitly account for the time correlations of the IMU measurements and provide a figure of merit (covariance) for the estimated transformation. The proposed method does not require any special hardware (such as spin table or 3D laser scanner) except a calibration target. Simulation and experimental results are presented that validate the proposed method and quantify its accuracy.
Randomized, placebo-controlled study of cetirizine and loratadine in children with seasonal allergic rhinitis.

BACKGROUND
Pharmacologic treatment is a mainstay of allergy therapy and many caregivers use over-the-counter antihistamines for the treatment of seasonal allergic rhinitis (SAR) symptoms in children.


OBJECTIVE
To assess the efficacy and safety of cetirizine 10 mg syrup versus loratadine 10 mg syrup versus placebo syrup in a randomized double-blind study of children, ages 6-11 years, with SAR.


METHODS
This randomized, double-blind, parallel-group, placebo-controlled study was conducted at 71 U.S. centers during the spring tree and grass pollen season. After a 1-week placebo run-in period, qualified subjects were randomized to once-daily cetirizine 10 mg (n = 231), loratadine 10 mg (n = 221), and placebo (n = 231) for 2 weeks. The primary efficacy end point was change from baseline in the subject's mean reflective total symptom severity complex (TSSC) score over 14 days.


RESULTS
Children treated with cetirizine experienced significantly greater TSSC score reductions versus children treated with placebo over 14 days (least square mean change, -2.1 versus -1.6; p = 0.006). The differences in TSSC score improvement over 14 days between the cetirizine versus loratadine groups (-2.1 versus -1.8; p = 0.124) and between the loratadine versus placebo groups (-1.8 versus -1.6; p = 0.230) were not statistically significant. Predominant adverse events in the cetirizine, loratadine, and placebo groups were headache (3.5, 3.6, and 3.1%, respectively) and pharyngitis (3.5, 2.7, and 3.5%, respectively). Somnolence was reported in three subjects (1.3%) treated with cetirizine and in none of the other subjects.


CONCLUSION
Cetirizine 10 mg was statistically significantly more efficacious than placebo in the treatment of SAR symptoms in children ages 6-11 years. Symptom improvement was not significantly different between the loratadine 10 mg and placebo groups.
Forecasting the onset and course of mental illness with Twitter data

We developed computational models to predict the emergence of depression and Post-Traumatic Stress Disorder in Twitter users. Twitter data and details of depression history were collected from 204 individuals (105 depressed, 99 healthy). We extracted predictive features measuring affect, linguistic style, and context from participant tweets (N = 279,951) and built models using these features with supervised learning algorithms. Resulting models successfully discriminated between depressed and healthy content, and compared favorably to general practitioners’ average success rates in diagnosing depression, albeit in a separate population. Results held even when the analysis was restricted to content posted before first depression diagnosis. State-space temporal analysis suggests that onset of depression may be detectable from Twitter data several months prior to diagnosis. Predictive results were replicated with a separate sample of individuals diagnosed with PTSD (Nusers = 174, Ntweets = 243,775). A state-space time series model revealed indicators of PTSD almost immediately post-trauma, often many months prior to clinical diagnosis. These methods suggest a data-driven, predictive approach for early screening and detection of mental illness.
Advanced metering infrastructure for smart grid applications

The existing power grid may not support future growing electric demand. Advanced technologies can be used to improve efficiencies and moderate electric usage by avoiding the need for new generation, transmission and distribution plants. To meet the needs of the future and to fix the problems of the past, smart grid technology harnesses the most advanced digital computing technologies to monitor and adjust the usage. Smart grid also aids in optimizing the amount of energy generated. This technology assures better usage of resources and accurate billing to customers based on actual consumption rather than estimates. Smart grid implementation demands developments in the technologies like Advanced Metering Infrastructure, Two-Way communications , Smart meters / Smart sensors, Load control , interoperability, security, Information Technology, web connectivity and Renewable Energy & Storage Systems. This paper details the Advanced Metering Infrastructure development particularly the Power Quality Analysis. The paper also briefs National scenario of Advanced Metering Infrastructure to meet smart grid applications and its development.
A systematic literature review on the barriers faced by newcomers to open source software projects

Context: Numerous open source software projects are based on volunteers’ collaboration and require a continuous influx of newcomers for their continuity. Newcomers face barriers that can lead them to give up. These barriers hinder both developers willing to make a single contribution and those willing to become a project member. Objective: This study aims to identify and classify the barriers that newcomers face when contributing to Open Source Software projects. Method: We conducted a systematic literature review of papers reporting empirical evidence regarding the barriers that newcomers face when contributing to Open Source Software (OSS) projects. We retrieved 291 studies *Corresponding author [Address: Rua das Cerejeiras, 60 CEP 87301-350 Campo Mourao–PR–Brazil – Phone +55(44)88383380 ] Email addresses: igorfs@utfpr.edu.br (Igor Steinmacher), magsilva@utfpr.edu.br (Marco Aurelio Graciotto Silva), gerosa@ime.usp.br (Marco Aurelio Gerosa), redmiles@ics.uci.edu (David F. Redmiles) Preprint submitted to Information and Software Technology November 5, 2014 by querying 4 digital libraries. Twenty studies were identified as primary. We performed a backward snowballing approach, and searched for other papers published by the authors of the selected papers to identify potential studies. Then, we used a coding approach inspired by open coding and axial coding procedures from Grounded Theory to categorize the barriers reported by the selected studies. Results: We identified 20 studies providing empirical evidence of barriers faced by newcomers to OSS projects while making a contribution. From the analysis, we identified 15 different barriers, which we grouped into five categories: social interaction, newcomers’ previous knowledge, finding a way to start, documentation, and technical hurdles. We also classified the problems with regard to their origin: newcomers, community, or product. Conclusion: The results are useful to researchers and OSS practitioners willing to investigate or to implement tools to support newcomers. We mapped technical and non-technical barriers that hinder newcomers’ first contributions. The most evidenced barriers are related to socialization, appearing in 75% (15 out of 20) of the studies analyzed, with a high focus on interactions in mailing lists (receiving answers and socialization with other members). There is a lack of in-depth studies on technical issues, such as code issues. We also noticed that the majority of the studies relied on historical data gathered from software repositories and that there was a lack of experiments and qualitative studies in this area.