LLukas22/scidocs huggingface dataset:
Temporal reasoning over clinical text: the state of the art

OBJECTIVES
To provide an overview of the problem of temporal reasoning over clinical text and to summarize the state of the art in clinical natural language processing for this task.


TARGET AUDIENCE
This overview targets medical informatics researchers who are unfamiliar with the problems and applications of temporal reasoning over clinical text.


SCOPE
We review the major applications of text-based temporal reasoning, describe the challenges for software systems handling temporal information in clinical text, and give an overview of the state of the art. Finally, we present some perspectives on future research directions that emerged during the recent community-wide challenge on text-based temporal reasoning in the clinical domain.
C-reactive protein, carotid intima-media thickness, and incidence of ischemic stroke in the elderly: the Cardiovascular Health Study.

BACKGROUND
Increased carotid artery intima-media thickness (IMT) and elevated C-reactive protein (CRP) are both associated with the occurrence of stroke. We investigated whether elevated CRP is a risk factor for ischemic stroke independent of carotid IMT and studied the interaction between CRP and IMT.


METHODS AND RESULTS
We studied 5417 participants aged 65 years or older without preexisting stroke or chronic atrial fibrillation who were participants in the Cardiovascular Health Study. The hazard ratio of incident ischemic stroke was estimated by Cox proportional hazards regression. During 10.2 years of follow-up, 469 incident ischemic strokes occurred. The adjusted hazard ratios for ischemic stroke in the 2nd to 4th quartiles of baseline CRP, relative to the 1st quartile, were 1.19 (95% CI 0.92 to 1.53), 1.05 (95% CI 0.81 to 1.37), and 1.60 (95% CI 1.23 to 2.08), respectively. With additional adjustment for carotid IMT, there was little confounding. The association of CRP with stroke was significantly different depending on IMT (P<0.02), with no association of CRP with stroke among those in the lowest IMT tertile and a significant association among those with higher levels of IMT.


CONCLUSIONS
We conclude that elevated CRP is a risk factor for ischemic stroke, independent of atherosclerosis severity as measured by carotid IMT. The association of CRP with stroke is more apparent in the presence of a higher carotid IMT. CRP and carotid IMT may each be independent integrals in determining the risk of ischemic stroke.
Development and Evaluation of Anti-Acne Products from Terminalia arjuna Bark

Propionibacterium acnes and Staphylococcus epidermidis have been recognized as pus-forming bacteria triggering an inflammation in acne. The present study was conducted to evaluate antimicrobial activities of Terminalia arjuna bark against these etiologic agents of acne vulgaris. Topical formulations (cream) have been developed containing flavonoid (FF-I to III) and tannin fraction (TF-I to III) of Terminalia arjuna bark at different concentrations i.e. 0.5%, 1% and 2% (w/w). These topical formulations were tested for pH, viscosity, spreadability, stability, drug contents uniformity and in vitro diffusion. The drug content uniformity of creams were found within the range of 97.31% to 98.80% (FF-I to III) and 96.84% to 98.66% (TF-I to III) respectively. The formulations of FF -III and TF –III showed maximum drug release of 83% and 78% over a period of 8h. All the formulations were evaluated for its acute skin irritancy activity in Swiss Albino rats. These formulations did not produce any skin irritation for about a week when applied over the skin. Comparative studies showed that the viscosity of the formulations increases, spreadability decreases and vice versa. From the stability studies, creams showed no changes in pH, viscosity, spreadability and drug contents, after keeping at different temperatures for 90 days. In vitro antibacterial activity was performed against Propionibacterium acnes (P. acnes) and Staphylococcus epidermidis, a causative organism for Acne vulgar for the developed formulations using agar well diffusion method. The measured zones of inhibitions of the formulations were compared with standard marketed topical herbal preparation for acne. Results of the investigation showed that formulation FF-III ( cream containing 2% flavonoid fraction) has greater antibacterial activity against Propionibacterium acnes (zones of inhibition >17 mm) and Staphylococcus epidermidis (zones of inhibition >20 mm) than other formulations and which is comparable to that of standard marketed topical herbal preparation. Therefore, this plant would possibly for an alternative treatment for acne.
Energy-optimal trajectory planning for robot manipulators with holonomic constraints

In this paper, we study two different trajectory planning problems for robotmanipulators. In the first case, the end-effector of the robot is constrained to move along a prescribed path in the workspace, whereas in the second case, the trajectory of the end-effector has to be determined in the presence of obstacles. Constraints of this type are called holonomic constraints. Both problems have been solved as optimal control problems. Given the dynamicmodel of the robotmanipulator, the initial state of the system, some specifications about the final state and a set of holonomic constraints, one has to find the trajectory and the actuator torques that minimize the energy consumption during the motion. The presence of holonomic constraints makes the optimal control problem particularly difficult to solve. Our method involves a numerical resolution of a reformulation of the constrained optimal control problem into an unconstrained calculus of variations problem in which the state space constraints and the dynamic equations, also regarded as constraints, are treated by means of special derivative multipliers. We solve the resulting calculus of variations problem using a numerical approach based on the Euler–Lagrange necessary condition in the integral form in which time is discretized and admissible variations for each variable are approximated using a linear combination of piecewise continuous basis functions of time. The use of the Euler–Lagrange necessary condition in integral form avoids the need for numerical corner conditions and thenecessity of patching together solutions between corners. In thisway, a generalmethod for the solution of constrained optimal control problems is obtained inwhich holonomic constraints can be easily treated. Numerical results of the application of thismethod to trajectory planning of planar horizontal robot manipulators with two revolute joints are reported. © 2011 Elsevier B.V. All rights reserved.
The longevity of amalgam versus compomer/composite restorations in posterior primary and permanent teeth: findings From the New England Children's Amalgam Trial.

BACKGROUND
Limited information is available from randomized clinical trials comparing the longevity of amalgam and resin-based compomer/composite restorations. The authors compared replacement rates of these types of restorations in posterior teeth during the five-year follow-up of the New England Children's Amalgam Trial.


METHODS
The authors randomized children aged 6 to 10 years who had two or more posterior occlusal carious lesions into groups that received amalgam (n=267) or compomer (primary teeth)/composite (permanent teeth) (n=267) restorations and followed them up semiannually. They compared the longevity of restorations placed on all posterior surfaces using random effects survival analysis.


RESULTS
The average+/-standard deviation follow-up was 2.8+/-1.4 years for primary tooth restorations and 3.4+/-1.9 years for permanent tooth restorations. In primary teeth, the replacement rate was 5.8 percent of compomers versus 4.0 percent of amalgams (P=.10), with 3.0 percent versus 0.5 percent (P=.002), respectively, due to recurrent caries. In permanent teeth, the replacement rate was 14.9 percent of composites versus 10.8 percent of amalgams (P=.45), and the repair rate was 2.8 percent of composites versus 0.4 percent of amalgams (P=.02).


CONCLUSION
Although the overall difference in longevity was not statistically significant, compomer was replaced significantly more frequently owing to recurrent caries, and composite restorations required seven times as many repairs as did amalgam restorations.


CLINICAL IMPLICATIONS
Compomer/composite restorations on posterior tooth surfaces in children may require replacement or repair at higher rates than amalgam restorations, even within five years of placement.
Are rheumatologists' treatment decisions influenced by patients' age?

OBJECTIVES
The objective of this study was to determine whether physicians' treatment preferences are influenced by patients' age.


METHODS
We mailed a survey to a random sample of rheumatologists practicing in the US. The survey included a scenario describing a hypothetical patient with rheumatoid arthritis (RA) on hydroxychloroquine, sulfasalazine and low-dose prednisolone, who presents with active disease during a follow-up appointment. The scenario was formulated in two versions that were identical except for the age of the patient. After reading the scenario, respondents were asked to rate (on a 10 cm numerical rating scale) their recommendations for each of the three options: (i) increasing the dose of prednisolone, (ii) adding a new disease-modifying anti-rheumatic drug (DMARD) and (iii) switching DMARDs. Rheumatologists who rated either adding a new DMARD or switching DMARDs higher than increasing the dose of prednisolone were classified as 'preferring aggressive treatment with DMARDs', while the others were classified as 'NOT preferring aggressive treatment with DMARDs'.


RESULTS
A total of 480 rheumatologists were mailed a questionnaire; 204 responded, giving a response rate of 42.5%. Overall 163 (80%) respondents were classified as preferring aggressive treatment with DMARDs. Rheumatologists responding to this survey were more likely to prefer aggressive DMARD treatment for the young RA patient vs the older RA patient (87 vs 71%, P= 0.007).


CONCLUSIONS
Our findings suggest that rheumatologists' treatment recommendations may be influenced by age. Future educational efforts should increase physician awareness of this possible bias in order to ensure equal service delivery across ages.
Use of ultrasound guidance and contrast enhancement: a study of continuous infraclavicular brachial plexus approach.

PURPOSE
We describe our experience of combining the use of ultrasound (US) guidance with contrast enhancement and peripheral nerve stimulation for the insertion of infraclavicular brachial plexus catheters.


METHODS
Thirty patients scheduled to have upper limb surgery under regional block were studied. Under US guidance and peripheral nerve stimulation assistance, continuous peripheral nerve block needle and stimulating catheter were placed in the infraclavicular area. Needle and catheter tip location was confirmed with agitated 5% dextrose and seen under colour Doppler with US before injecting local anaesthetic (LA). Patients were evaluated in terms of onset times and efficacy of block. Post-operatively, on block recession a catheter was stimulated and visualization of spread of LA during injection through the catheter was done. Secondary block (subsequent to re-injection of LA) was assessed. Patients were followed-up for a week.


RESULTS
Mean time to onset of block was 19.7 (+/- 4.9) min. There were no incomplete blocks and all components of the plexus were blocked completely. Post-operatively, in 95.7% of patients, the spread of hand-agitated LA via the catheter could be seen by color Doppler with ultrasonography. All patients had excellent post-operative analgesia and high degree of satisfaction. There were no complications.


CONCLUSION
Contrast enhancement with US guidance during infraclavicular brachial plexus block enables direct visualization of needle and catheter tip location. Our early experience suggests that this leads to successful initial and subsequent post-operative block. Further controlled studies are needed to compare this technique with more prevalent and conventional techniques of catheter insertion.
sonSchema: A Conceptual Schema for Social Networks

sonSQL is a MySQL variant that aims to be the default database system for social network data. It uses a conceptual schema called sonSchema to translate a social network design into logical tables. This paper introduces sonSchema, shows how it can be instantiated, and illustrates social network analysis for sonSchema datasets. Experiments show such SQL-based analysis brings insight into community evolution, cluster discovery and action propagation.
Development of 'rural week' for medical students: impact and quality report.

INTRODUCTION
The Rural Undergraduate Support and Coordination program funds medical schools to provide all medical students some time in rural Australia throughout their course. The University of Adelaide has developed a rural week program for both first and second year students to fulfill part of this objective.


METHODS
First year students' rural week is an introduction to a range of rural health issues, Indigenous culture and rural lifestyle issues. Second year students choose either a clinical rural week with a general practitioner or a week of Indigenous cultural learning with the Adnyamathanha people in the Flinders ranges, South Australia. Evaluation data were collected from students, practitioners and university staff during rural weeks in 2003 and 2004 using quantitative and qualitative methods.


RESULTS
First year students increased their knowledge of and interest in rural medicine and enjoyed their (limited) clinical interaction with patients. Second year students appreciated the clinical experience and valued the welcome they received from doctors and practice staff. Those who chose Indigenous cultural programs appreciated the opportunity to interact with and learn from Indigenous people. General practitioners valued contributing to student knowledge and skills and the opportunity to promote rural practice. Volunteer community members were very enthusiastic about meeting the students and their generosity had a significant impact on the students' ideas about rural lifestyle. University academic and administrative staff found rural week very intensive work but experience and thorough preparation now ensures that few problems occur.


CONCLUSION
Rural weeks are now an established part of the first year and second year curriculum at the University of Adelaide Medical School. The ability to provide small groups of students with an intense introduction to rural practice and/or Indigenous culture results in a positive change in opinion about this aspect of medical education. Students now have first-hand experience to positively influence their choice of rural education or Indigenous health options in the medical course. Problems do occur with students being away from the traditional classroom, and protocols have been put in place for behaviour of all parties. Despite the rural weeks program being very demanding on staff energy, financial resources, general practices and rural communities, we feel that this program is valuable and sustainable. Further experience will determine if rural weeks function effectively as a recruitment strategy for the long rural placements offered by the Rural Clinical School.
Conjugated equine estrogens and coronary heart disease: the Women's Health Initiative.

BACKGROUND
In recent randomized trials, conjugated equine estrogens (CEE) with continuous medroxyprogesterone acetate provided no protection against coronary heart disease in postmenopausal women and may have increased cardiac risk. These trials did not address the role of unopposed estrogen for coronary protection.


METHODS
A total of 10 739 women aged 50 to 79 years at baseline (mean age, 63.6 years) who had previously undergone hysterectomy were randomized to receive CEE, 0.625 mg/d, or placebo at 40 US clinical centers beginning in 1993. The trial was terminated early after 6.8 years of follow-up (planned duration, 8.5 years). This report includes final, centrally adjudicated results for the primary efficacy outcome (myocardial infarction or coronary death), secondary coronary outcomes, and subgroup analyses.


RESULTS
During the active intervention period, 201 coronary events were confirmed among women assigned to receive CEE compared with 217 events among women assigned to receive placebo (hazard ratio, 0.95; nominal 95% confidence interval, 0.79-1.16). Among women aged 50 to 59 years at baseline, the hazard ratio for the primary outcome was 0.63 (nominal 95% confidence interval, 0.36-1.08). In that age group, coronary revascularization was less frequent among women assigned to receive CEE (hazard ratio, 0.55; nominal 95% confidence interval, 0.35-0.86), as were several composite outcomes, which included the primary outcome and coronary revascularization (hazard ratio, 0.66; nominal 95% confidence interval, 0.44-0.97).


CONCLUSIONS
Conjugated equine estrogens provided no overall protection against myocardial infarction or coronary death in generally healthy postmenopausal women during a 7-year period of use. There was a suggestion of lower coronary heart disease risk with CEE among women 50 to 59 years of age at baseline.
Mental workload and driving

The aim of this review is to identify the most representative measures of subjective and objective mental workload in driving, and to understand how the subjective and objective levels of mental workload influence the performance as a function of situation complexity and driving experience, i.e., to verify whether the increase of situation complexity and the lack of experience increase the subjective and physiological levels of mental workload and lead to driving performance impairments. This review will be useful to both researchers designing an experimental study of mental workload and to designers of drivers' training content. In the first part, we will broach the theoretical approach with two factors of mental workload and performance, i.e., situation complexity and driving experience. Indeed, a low complex situation (e.g., highways), or conversely a high complex situation (e.g., town) can provoke an overload. Additionally, performing the driving tasks implies producing a high effort for novice drivers who have not totally automated the driving activity. In the second part, we will focus on subjective measures of mental workload. A comparison of questionnaires usually used in driving will allow identifying the most appropriate ones as a function of different criteria. Moreover, we will review the empirical studies to verify if the subjective level of mental workload is high in simple and very complex situations, especially for novice drivers compared to the experienced ones. In the third part, we will focus on physiological measures. A comparison of physiological indicators will be realized in order to identify the most correlated to mental workload. An empirical review will also take the effect of situation complexity and experience on these physiological indicators into consideration. Finally, a more nuanced comparison between subjective and physiological measures will be established from the impact on situation complexity and experience.
Generation of OAM radio waves with three polarizations using circular horn antenna array

An effective solution of generating OAM-carrying radio beams with three polarizations is provided. Through the reasonable configuration of phased antenna array using elements with three polarizations, the OAM radio waves with three polarizations for different states can be generated. The vectors of electric fields with different OAM states for linear, as well as left or right circular polarizations are presented and analyzed in detail.
Translation of Use Case Scenarios to Java Code

Use cases are usually treated as second class citizens in the software development chain based on models. Their textual descriptions (scenarios) are treated as informal input to more formal design models that can then be (semi)automatically transformed down to code. In this paper we will show that use case scenarios can gain precise metamodel-based notation and semantics enabling automatic processing. What is more, we will show transformation algorithms that can transform use case scenarios directly to dynamic code in Java. The presented transformation can generate the full structure of the system following the MVP architectural pattern, including complete method contents for the application logic (Presenter) and presentation (View) layers. It also provides a code skeleton for the domain logic (Model) layer. The use case notation and the transformation were implemented within a sophisticated tool suite. Based on this, the paper discusses the evaluation efforts based on a case study.
Role of Brassinosteroids, Ethylene, Abscisic Acid, and Indole-3-Acetic Acid in Mango Fruit Ripening

Rapid ripening of mango fruit limits its distribution to distant markets. To better understand and perhaps manipulate this process, we investigated the role of plant hormones in modulating climacteric ripening of ‘Kensington Pride’ mango fruits. Changes in endogenous levels of brassinosteroids (BRs), abscisic acid (ABA), indole-3-acetic acid (IAA), and ethylene and the respiration rate, pulp firmness, and skin color were determined at 2-day intervals during an 8-day ripening period at ambient temperature (21 ± 1°C). We also investigated the effects of exogenously applied epibrassinolide (Epi-BL), (+)-cis, trans-abscisic acid (ABA), and an inhibitor of ABA biosynthesis, nordihydroguaiaretic acid (NDGA), on fruit-ripening parameters such as respiration, ethylene production, fruit softening, and color. Climacteric ethylene production and the respiration peak occurred on the fourth day of ripening. Castasterone and brassinolide were present in only trace amounts in fruit pulp throughout the ripening period. However, the exogenous application of Epi-BL (45 and 60 ng g−1 FW) advanced the onset of the climacteric peaks of ethylene production and respiration rate by 2 and 1 day, respectively, and accelerated fruit color development and softening during the fruit-ripening period. The endogenous level of ABA rose during the climacteric rise stage on the second day of ripening and peaked on the fourth day of ripening. Exogenous ABA promoted fruit color development and softening during ripening compared with the control and the trend was reversed in NDGA-treated fruit. The endogenous IAA level in the fruit pulp was higher during the preclimacteric minimum stage and declined during the climacteric and postclimacteric stages. We speculate that higher levels of endogenous IAA in fruit pulp during the preclimacteric stage and the accumulation of ABA prior to the climacteric stage might switch on ethylene production that triggers fruit ripening. Whilst exogenous Epi-BL promoted fruit ripening, endogenous measurements suggest that changes in BRs levels are unlikely to modulate mango fruit ripening.