LLukas22/scidocs huggingface dataset:
An ensemble method for extracting adverse drug events from social media

OBJECTIVE
Because adverse drug events (ADEs) are a serious health problem and a leading cause of death, it is of vital importance to identify them correctly and in a timely manner. With the development of Web 2.0, social media has become a large data source for information on ADEs. The objective of this study is to develop a relation extraction system that uses natural language processing techniques to effectively distinguish between ADEs and non-ADEs in informal text on social media.


METHODS AND MATERIALS
We develop a feature-based approach that utilizes various lexical, syntactic, and semantic features. Information-gain-based feature selection is performed to address high-dimensional features. Then, we evaluate the effectiveness of four well-known kernel-based approaches (i.e., subset tree kernel, tree kernel, shortest dependency path kernel, and all-paths graph kernel) and several ensembles that are generated by adopting different combination methods (i.e., majority voting, weighted averaging, and stacked generalization). All of the approaches are tested using three data sets: two health-related discussion forums and one general social networking site (i.e., Twitter).


RESULTS
When investigating the contribution of each feature subset, the feature-based approach attains the best area under the receiver operating characteristics curve (AUC) values, which are 78.6%, 72.2%, and 79.2% on the three data sets. When individual methods are used, we attain the best AUC values of 82.1%, 73.2%, and 77.0% using the subset tree kernel, shortest dependency path kernel, and feature-based approach on the three data sets, respectively. When using classifier ensembles, we achieve the best AUC values of 84.5%, 77.3%, and 84.5% on the three data sets, outperforming the baselines.


CONCLUSIONS
Our experimental results indicate that ADE extraction from social media can benefit from feature selection. With respect to the effectiveness of different feature subsets, lexical features and semantic features can enhance the ADE extraction capability. Kernel-based approaches, which can stay away from the feature sparsity issue, are qualified to address the ADE extraction problem. Combining different individual classifiers using suitable combination methods can further enhance the ADE extraction effectiveness.
Regionally localized thinning of the cerebral cortex in schizophrenia

BACKGROUND
Schizophrenia is characterized by small reductions in cortical gray matter volume, particularly in the temporal and prefrontal cortices. The question of whether cortical thickness is reduced in schizophrenia has not been addressed using magnetic resonance imaging (MRI) techniques. Our objectives were to test the hypothesis that cortical thinning in patients with schizophrenia (relative to control subjects) is greater in temporal and prefrontal regions of interest (ROIs) than in control ROIs (superior parietal, calcarine, postcentral, central, and precentral cortices), and to obtain an unbiased estimate of the distribution of cortical thinning in patients (relative to controls) by constructing mean and statistical cortical thickness difference maps.


METHODS
Participants included 33 right-handed outpatients receiving medication and meeting DSM-IV criteria for schizophrenia and 32 healthy volunteers, matched on age and parental socioeconomic status. After high-resolution MRI scans, models of the gray-white and pial surfaces were generated for each individual's cortex, and the distance between these 2 surfaces was used to compute cortical thickness. A surface-based averaging technique that aligned the main cortical folds across individuals allowed between-group comparisons of thickness within ROIs, and at multiple, uniformly sampled loci across the cortical ribbon.


RESULTS
Relative to controls, patients showed greater cortical thinning in temporal-prefrontal ROIs than in control ROIs, as revealed by a significant (P<.009) interaction between group and region type. Cortical thickness difference maps revealed significant (at P<.05, corrected) thinning within the orbitofrontal cortices bilaterally; the inferior frontal, inferior temporal, and occipitotemporal cortices on the left; and within the medial temporal and medial frontal cortices on the right. Superior parietal and primary somatosensory and motor cortices were relatively spared, even at subthreshold significance levels.


CONCLUSIONS
Patients with chronic schizophrenia showed widespread cortical thinning that particularly affected the prefrontal and temporal cortices. This thinning might reflect underlying neuropathological abnormalities in cortical structure.
Novel detector technology for clinical PET

Positron emission tomography (PET) is the most sensitive of all medical imaging modalities for quantitatively probing biologic processes at the molecular level. However, spatial resolution in PET is significantly inferior to that of other imaging modalities that can provide exquisite images of the anatomy, such as X-ray computed tomography (CT) or magnetic resonance (MR) imaging. It has been one of the outstanding challenges of the last decade to combine PET with these complementary imaging modalities in order to synergistically exploit the benefits of each modality and to enhance the role of PET in pre-clinical research as well as in clinical routine and research. The simple juxtaposition of tomographs around a common axial bed, such as with current PET/CT technology, is very successful in allowing sequential acquisition of PET and anatomical data. However, novel imaging combinations are being considered that would enable simultaneous, or at least concurrent, dual-modality imaging through combined PET/MR or PET/CT. The development of these new integrated instruments creates new bewildering challenges for PET detection systems, which, in addition to the ability to measure annihilation radiation in PET, must satisfy several other critical requirements.
Effects of diet cycling during training on weight loss and resting energy expenditure: a preliminary analysis

Background Long-term dieting has been reported to reduce resting energy expenditure (REE) leading to weight regain once the diet has been curtailed. Diets are also difficult to follow for a significant length of time. The purpose of this preliminary proof of concept study was to examine the effects of short-term intermittent dieting during exercise training on REE and weight loss in overweight women.
Guidelines for facilitating the development of learning communities in online courses

Online learning has grown exponentially in recent years; however, dropout problem remains challenging for some online programmes. The dropout problem can be attributed to a number of reasons, with a lack of interaction between learners and the instructor constituting one of the main reasons. The lack of interaction also leads to learners’ feeling of isolation. Learning communities can provide learners with an environment conducive to increased interactions and alleviate their feeling of isolation. Unfortunately, there are no clear rules that instructors can follow to help learners create learning communities. In this paper, we propose guidelines for online instructors to facilitate the development of learning communities in online courses. We first review the definition of a learning community, importance of a learning community and factors affecting the development of a learning community. Afterwards, based on a review of the existing guidelines and other relevant literature, we propose guidelines for facilitating the development of learning communities in online courses.
On the algebraic K-theory of model categories

Abstract Waldhausen defined the algebraic K-theory of categories with cofibrations and weak equivalences. In many examples, these categories arise as full subcategories of model categories in the sense of Quillen. We use parts of the additional structure coming from model categories to compare the algebraic K-theory of different categories. The main tool for this is a generalization of Waldhausen's Approximation Theorem.
A Distributed Access Control Architecture for Cloud Computing

The large-scale, dynamic, and heterogeneous nature of cloud computing poses numerous security challenges. But the cloud's main challenge is to provide a robust authorization mechanism that incorporates multitenancy and virtualization aspects of resources. The authors present a distributed architecture that incorporates principles from security management and software engineering and propose key requirements and a design model for the architecture.
Anatomic reconstruction of chronic symptomatic anterolateral proximal tibiofibular joint instability

Symptomatic chronic proximal tibiofibular joint subluxation is a pathology which is difficult to diagnose and treat. Surgical treatment has not been well defined. A report of two patients successfully treated with an anatomic reconstruction of the posterior aspect of the proximal tibiofibular joint is presented.
Patient's global assessment of disease activity and patient's assessment of general health for rheumatoid arthritis activity assessment: are they equivalent?

OBJECTIVES
To assess (A) determinants of patient's global assessment of disease activity (PTGL) and patient's assessment of general health (GH) scores of rheumatoid arthritis (RA) patients; (B) whether they are equivalent as individual variables; and (C) whether they may be used interchangeably in calculating common RA activity assessment composite indices.


METHODS
Data of 7023 patients from 30 countries in the Quantitative Standard Monitoring of Patients with RA (QUEST-RA) was analysed. PTGL and GH determinants were assessed by mixed-effects analyses of covariance models. PTGL and GH equivalence was determined by Bland-Altman 95% limits of agreement (BALOA) and Lin's coefficient of concordance (LCC). Concordance between PTGL and GH based Disease Activity Score 28 (DAS28), Clinical Disease Activity Index (CDAI) and Routine Assessment of Patient Index Data 3 (RAPID3) indices were calculated using LCC, and the level of agreement in classifying RA activity in four states (remission, low, moderate, high) using κ statistics.


RESULTS
Significant differences in relative and absolute contribution of RA and non-RA related variables in PTGL and GH ratings were noted. LCC of 0.64 and BALOA of -4.41 to 4.54 showed that PTGL and GH are not equivalent. There was excellent concordance (LCC 0.95-0.99) for PTGL and GH based DAS28, CDAI and RAPID3 indices, and >80% absolute agreement (κ statistics 0.75-0.84) in RA activity state classification for all three indices.


CONCLUSIONS
PTGL and GH ratings differ in their determinants. Although they are individually not equivalent, they may be used interchangeably for calculating composite indices for RA activity assessment.
Consensus for dry needling for plantar heel pain (plantar fasciitis): a modified Delphi study.

HYPOTHESIS
Plantar heel pain (plantar fasciitis) is a common and disabling condition. A variety of treatment options are available to patients with plantar heel, however the evidence for these treatments is generally weak and the best way to manage plantar heel pain remains unclear. Trigger point dry needling is increasingly used as an adjunct therapy for musculoskeletal pain. In patients with plantar heel pain this technique is thought to improve muscle activation patterns, increase joint range of motion and alleviate pain. However, there have been no randomised controlled trials that have evaluated the effectiveness of dry needling for plantar heel pain.


METHODS
In order to develop a treatment protocol to evaluate the effectiveness of dry needling for plantar heel pain we conducted a three stage modified Delphi process using a web-based survey technique. Over a series of three iterations, 30 experts (participants) worldwide indicated their level of agreement on specific issues relating to the use of dry needling for plantar heel pain including their treatment rationale, needling details and treatment regimen. Consensus for a dry needling protocol for plantar heel pain was achieved when >60% of participants (IQR ≤ 1.0 category on 5-point Likert scale) agreed the protocol was adequate.


RESULTS
The response rate was 75% (n=30), 100% (n=30) and 93% (n=28) in the first, second and third rounds respectively. Round 1 helped generate a list of 10 items that were deemed important for developing a dry needling protocol for plantar heel pain. These 10 items were subsequently presented in Round 2. Of these, 5 of the 10 items met the criteria to be included in a dry needling protocol for plantar heel pain that was presented in the final round, Round 3. Items that did not meet the criteria were either removed or amended and then presented in Round 3. In the final round, 93% of participants (IQR range = 1) agreed the proposed dry needling protocol for plantar heel pain was adequate. The protocol can now be used in future research projects designed to evaluate the effectiveness of dry needling for plantar heel pain.
A randomized trial of deep-brain stimulation for Parkinson's disease.

BACKGROUND
Neurostimulation of the subthalamic nucleus reduces levodopa-related motor complications in advanced Parkinson's disease. We compared this treatment plus medication with medical management.


METHODS
In this randomized-pairs trial, we enrolled 156 patients with advanced Parkinson's disease and severe motor symptoms. The primary end points were the changes from baseline to six months in the quality of life, as assessed by the Parkinson's Disease Questionnaire (PDQ-39), and the severity of symptoms without medication, according to the Unified Parkinson's Disease Rating Scale, part III (UPDRS-III).


RESULTS
Pairwise comparisons showed that neurostimulation, as compared with medication alone, caused greater improvements from baseline to six months in the PDQ-39 (50 of 78 pairs, P=0.02) and the UPDRS-III (55 of 78, P<0.001), with mean improvements of 9.5 and 19.6 points, respectively. Neurostimulation resulted in improvements of 24 to 38 percent in the PDQ-39 subscales for mobility, activities of daily living, emotional well-being, stigma, and bodily discomfort. Serious adverse events were more common with neurostimulation than with medication alone (13 percent vs. 4 percent, P<0.04) and included a fatal intracerebral hemorrhage. The overall frequency of adverse events was higher in the medication group (64 percent vs. 50 percent, P=0.08).


CONCLUSIONS
In this six-month study of patients under 75 years of age with severe motor complications of Parkinson's disease, neurostimulation of the subthalamic nucleus was more effective than medical management alone. (ClinicalTrials.gov number, NCT00196911 [ClinicalTrials.gov].).
M2M remote telemetry and cloud IoT big data processing in viticulture

Current M2M communication platforms are being integrated in cloud IoT applications for providing remote sensing and actuating. Nevertheless, requirements for energy efficiency and resilience in severe operating environments are driving the development of new algorithms and infrastructures. This paper presents a survey of the measurement results for the winegrowing season 2014, as it was seen by an M2M remote telemetry station in cooperation with a big data processing platform and several sensors. We demonstrate the use of recent technologies such as Cloud IoT systems and Big Data processing in order to implement disease prediction and alerting application for viticulture. Finally, the extension of the proposed system for other agriculture applications is discussed.
Patient and professional delay in the referral trajectory of patients with diabetic foot ulcers.

AIMS
A cohort study investigated referral and treatment trajectories of patients with diabetic foot ulceration consulting podiatrists. The study aims were to quantify patient, professional and treatment (=total) delay and to identify relationships between patient- or professional-related characteristics, delays or ulcer healing time.


METHODS
Ten podiatrists specialising in diabetes care included 54 consecutive adults with diabetic foot ulceration. Assessments were performed retrospectively (e.g. delays) and prospectively (12 weeks).


RESULTS
Median (SD; range) patient delay was 3.0 days (50.6; 0-243), professional delay 7.0 days (63.4; 0-279) and treatment delay 20.5 days (97.3; 0-522). 57% of patients took >2 weeks before visiting a podiatrist. Ulcers healed in 67% of patients in 49.0 days (90.2; 4-408). The number of health care professionals in the referral trajectory was positively related to treatment delay (p<0.01) and to ulcer healing time (p<0.01). Professional delay and treatment delay was positively correlated with the duration of the podiatric treatment (p<0.05). Patient awareness of ulceration risk tended to decrease the healing time.


CONCLUSIONS
Patients with diabetic foot ulcers presented small median delays in the referral trajectory to podiatrists specialising in diabetes. The study results suggest that reducing the number of health care professionals in the referral trajectory might decrease treatment delay and ulcer healing time. Also improving patient awareness of ulceration risk might be beneficial for the healing time.
The economics of Everglades restoration

The restoration of the Florida Everglades, the largest ecosystem restoration project in the world, is now underway. Missing from the original plan, however, is a study of the region’s cities and farms and the economic impact their growth will make on this already endangered ecosystem. This book provides that analysis.
Breaking bad habits by improving executive function in individuals with obesity

BACKGROUND
Two primary factors that contribute to obesity are unhealthy eating and sedentary behavior. These behaviors are particularly difficult to change in the long-term because they are often enacted habitually. Cognitive Remediation Therapy has been modified and applied to the treatment of obesity (CRT-O) with preliminary results of a randomized controlled trial demonstrating significant weight loss and improvements in executive function. The objective of this study was to conduct a secondary data analysis of the CRT-O trial to evaluate whether CRT-O reduces unhealthy habits that contribute to obesity via improvements in executive function.


METHOD
Eighty participants with obesity were randomized to CRT-O or control. Measures of executive function (Wisconsin Card Sort Task and Trail Making Task) and unhealthy eating and sedentary behavior habits were administered at baseline, post-intervention and at 3 month follow-up.


RESULTS
Participants receiving CRT-O demonstrated improvements in both measures of executive function and reductions in both unhealthy habit outcomes compared to control. Mediation analyses revealed that change in one element of executive function performance (Wisconsin Card Sort Task perseverance errors) mediated the effect of CRT-O on changes in both habit outcomes.


CONCLUSION
These results suggest that the effectiveness of CRT-O may result from the disruption of unhealthy habits made possible by improvements in executive function. In particular, it appears that cognitive flexibility, as measured by the Wisconsin Card Sort task, is a key mechanism in this process. Improving cognitive flexibility may enable individuals to capitalise on interruptions in unhealthy habits by adjusting their behavior in line with their weight loss goals rather than persisting with an unhealthy choice.


TRIAL REGISTRATION
The RCT was registered with the Australian New Zealand Registry of Clinical Trials (trial id: ACTRN12613000537752 ).
Direct leaf trajectory optimization for volumetric modulated arc therapy planning with sliding window delivery.

PURPOSE
The authors propose a novel optimization model for volumetric modulated arc therapy (VMAT) planning that directly optimizes deliverable leaf trajectories in the treatment plan optimization problem, and eliminates the need for a separate arc-sequencing step.


METHODS
In this model, a 360° arc is divided into a given number of arc segments in which the leaves move unidirectionally. This facilitates an algorithm that determines the optimal piecewise linear leaf trajectories for each arc segment, which are deliverable in a given treatment time. Multileaf collimator constraints, including maximum leaf speed and interdigitation, are accounted for explicitly. The algorithm is customized to allow for VMAT delivery using constant gantry speed and dose rate, however, the algorithm generalizes to variable gantry speed if beneficial.


RESULTS
The authors demonstrate the method for three different tumor sites: a head-and-neck case, a prostate case, and a paraspinal case. The authors first obtain a reference plan for intensity modulated radiotherapy (IMRT) using fluence map optimization and 20 intensity-modulated fields in equally spaced beam directions, which is beyond the standard of care. Modeling the typical clinical setup for the treatment sites considered, IMRT plans using seven or nine beams are also computed. Subsequently, VMAT plans are optimized by dividing the 360° arc into 20 corresponding arc segments. Assuming typical machine parameters (a dose rate of 600 MU/min, and a maximum leaf speed of 3 cm/s), it is demonstrated that the optimized VMAT plans with 2-3 min delivery time are of noticeably better quality than the 7-9 beam IMRT plans. The VMAT plan quality approaches the quality of the 20-beam IMRT benchmark plan for delivery times between 3 and 4 min.


CONCLUSIONS
The results indicate that high quality treatments can be delivered in a single arc with 20 arc segments if sufficient time is allowed for modulation in each segment.
Irritable Bowel Syndrome Patients’ Ideal Expectations and Recent Experiences with Healthcare Providers: A National Survey

The purpose of this paper is to identify patients’ ideal expectations from their healthcare providers. The IBS-Patient Education Questionnaire was developed using focus groups, and was administered to a national sample of IBS patients. Frequencies of item endorsements were obtained. Subgroup analysis was done comparing the responses for patients’ ideal expectations of their healthcare providers vs. their experiences with their last provider. Among the 1,242 patients who completed the survey, the mean age was 39.3 years, educational attainment 15 years, 85% female, IBS duration 6.9 years, 1,028 (83%) had seen a physician for IBS in the past, and 92.6% have used the Internet to obtain health information. Among the subjects who have seen a physician for IBS, the most desired qualities of providers were to give comprehensive information (96%), to refer to a source for additional information (95.8%), to answer questions (95.9%), to listen (94.4%), to provide information about IBS studies and medications (94%), and to provide support (88.6%) and hope (82.1%). Importantly, patients’ prior experiences with their last healthcare provider differed from their ideal expectations: “provide information” (38.3%); answer questions during the visit (68%), “to listen” (63.8%), and support (47.1%). Patients’ ideal expectations from healthcare providers (what patients ideally would like to experience) relate to obtaining information and relationship needs of receiving support and hope. Notably, their prior experiences with recent healthcare providers (what patients perceived actually occurred) were different from their ideal expectations. A better understanding of different types of expectations is necessary in order to construct an effective therapeutic relationship, which is critical for the management of IBS. Practice implications: Practice guidelines for IBS should emphasize a better understanding of a patient’s expectations and the therapeutic value of patient–provider communication.