LLukas22/scidocs huggingface dataset:
An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging

BACKGROUND
In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization.


RESULTS
After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI) T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data.


CONCLUSIONS
MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.
Knowledge, Attitudes, and Beliefs Regarding Cardiovascular Disease in Women: The Women's Heart Alliance.

BACKGROUND
Cardiovascular disease (CVD) is the number 1 killer of women in the United States, yet few younger women are aware of this fact. CVD campaigns focus little attention on physicians and their roles in assessing risk.


OBJECTIVES
In 2014, the Women's Heart Alliance (WHA) conducted a nationwide survey to determine barriers and opportunities for women and physicians with regard to CVD.


METHODS
From September 18 to 26, 2014, a total of 1,011 U.S. women (age 25 to 60 years) were interviewed using the GfK ("Gesellschaft für Konsumforschung" Knowledge Panel). From May 6 to 12, 2014, the e-Rewards Inc. Physician and Healthcare Professional Panel surveyed 200 primary care physicians (PCPs) and 100 cardiologists.


RESULTS
Overall, 45% of women were unaware that CVD is the number 1 killer of women; only 11% knew a woman who died from CVD. Overall, 45% of women reported it was common to cancel or postpone a physician appointment until losing weight. CVD was rated as the top concern by only 39% of PCPs, after weight and breast health. Only 22% of PCPs and 42% of cardiologists (p = 0.0477) felt extremely well prepared to assess CVD risk in women, while 42% and 40% felt well-prepared (p = NS), respectively. Few comprehensively implemented guidelines.


CONCLUSIONS
CVD was rated as the top concern less frequently than weight issues by both women and physicians. Social stigma particularly regarding body weight appeared to be a barrier. Physicians reported limited training and use of guideline assessment, whereas most supported a campaign and improved physician education. Campaigns should make CVD "real" to U.S. women, countering stereotypes with facts and validated assessments. Both community women and physicians endorsed investment in women's CVD research and physician education.
The role of urine prostate cancer antigen 3 mRNA levels in the diagnosis of prostate cancer among Hong Kong Chinese patients.

OBJECTIVE
To establish and verify the utility of measuring urine prostate cancer antigen 3 (PCA3) mRNA levels in the diagnosis of prostate cancer among Hong Kong Chinese patients.


DESIGN
Cross-sectional study.


SETTING
Urology Unit of a regional hospital in Hong Kong.


PATIENTS
This study was carried out in two parts. In the first part, 102 post-prostatic massage urine samples were collected from patients with known prostate cancer (38 patients) and controls (64 patients, with normal digital rectal examination and serum prostate-specific antigen <4 ng/mL). The urine levels of PCA3 and prostate-specific antigen mRNA were measured and the best cut-off point for differentiating cancer was determined. In the second part of the study, post-prostatic massage urine samples from 47 patients with clinically suspected prostate cancer were collected prior to prostate biopsy. The performance of PCA3 as a diagnostic aid for cancer was then assessed using the aforementioned cut-off value.


RESULTS
In the first part of the study, the best cut-off for the PCA3 ratio (defined as the ratio of the Ct value of PCA3/PSA mRNA) was 1.127. Applying this cut-off to the 47 patients with clinically suspected prostate cancer and no history of previous prostate biopsy, the sensitivity and specificity of PCA3 for diagnosing prostate cancer were 71% and 92%, respectively.


CONCLUSION
The post-prostatic massage urine PCA3 level shows utility for diagnosing prostate cancer in patients with elevated prostate-specific antigen levels that could facilitate decisions to undertake prostate biopsy and avoid unnecessary biopsies.
Randomized clinical effectiveness trial of nurse-administered small-group cognitive behavior therapy for persistent insomnia in general practice.

STUDY OBJECTIVES
Persistent insomnia, although very common in general practice, often proves problematic to manage. This study investigates the clinical effectiveness and the feasibility of applying cognitive behavior therapy (CBT) methods for insomnia in primary care.


DESIGN
Pragmatic randomized controlled trial of CBT versus treatment as usual.


SETTING
General medical practice.


PARTICIPANTS
Two hundred one adults (mean age, 54 years) randomly assigned to receive CBT (n = 107; 72 women) or treatment as usual (n = 94; 65 women).


INTERVENTION
CBT comprised 5 sessions delivered in small groups by primary care nurses. Treatment as usual comprised usual care from general practitioners.


MEASUREMENTS AND RESULTS
Assessments were completed at baseline, after treatment, and at 6-month follow-up visits. Sleep outcomes were appraised by sleep diary, actigraphy, and clinical endpoint. CBT was associated with improvements in self-reported sleep latency, wakefulness after sleep onset, and sleep efficiency. Improvements were partly sustained at follow-up. Effect sizes were moderate for the index variable of sleep efficiency. Participants receiving treatment as usual did not improve. Actigraphically estimated sleep improved modestly after CBT, relative to no change in treatment as usual. CBT was also associated with significant positive changes in mental health and energy/vitality. Comorbid physical and mental health difficulties did not impair sleep improvement following CBT.


CONCLUSION
This study suggests that trained and supervised nurses can effectively deliver CBT for insomnia in routine general medical practice. Treatment response to small-group service delivery was encouraging, although effect sizes were smaller than those obtained in efficacy studies. Further research is required to consider the possibility that CBT could become the treatment of first choice for persistent insomnia in primary healthcare.
Conflict and Cooperation in Wild Chimpanzees

The twin themes of competition and cooperation have been the focus of many studies in animal behavior (Alcock, 2001; Dugatkin, 2004; Krebs and Davies, 1997). Competition receives prominent attention because it forms the basis for the unifying, organizing principle of biology. Darwin’s (1859) theory of natural selection furnishes a powerful framework to understand the origin and maintenance of organic and behavioral diversity. Because the process of natural selection depends on reproductive competition, aggression, dominance, and competition for mates serve as important foci of ethological research. In contrast, cooperation in animals is less easily explained within a Darwinian framework. Why do animals cooperate and behave in ways that benefit others? Supplements to the theory of natural selection in the form of kin selection, reciprocal altruism, and mutualism provide mechanisms that transform the study of cooperative behavior in animals into a mode of inquiry compatible with our current understanding of the evolutionary process (Clutton‐Brock, 2002; Hamilton, 1964; Trivers, 1971). If cooperation can be analyzed via natural selection operating on individuals, a new way to conceptualize the process emerges. Instead of viewing cooperation as distinct from competition, it becomes productive to regard them together. Students of animal behavior have long recognized that an artificial dichotomy may exist insofar as animals frequently cooperate to compete with conspecifics. In taxa as diverse as insects, birds, andmammals, animals cooperate to obtain immediate or deferred fitness benefits.
Open resection of osteoid osteoma guided by a gamma-probe

Osteoid osteoma is the third most common type of bone tumour. Radiofrequency ablation and other percutaneous procedures are the treatment of choice. However, in some sites these methods are difficult or dangerous. Our objective of this study was to evaluate whether open resection and intraoperative nidus detection with a hand-held gamma probe is an efficient method for treating this type of tumour. Fifty-three patients with osteoid osteomas were submitted to surgical treatment. The first group (gamma group) consisted of 34 patients submitted to open nidus resection guided by a hand-held gamma probe. The control group consisted of 19 patients operated on by conventional technique. In the postoperative period, histopathology, imaging studies, and clinical outcome were evaluated. The gamma group patients were followed up for an average 26.2 months; the control group patients were followed up for an average 38 months. There was no difference with regard to pain relief and histopathology findings between the two groups. However, in the postoperative imaging studies, there was significantly less nidus present in the gamma group (p = 0.01).The gamma probe helped to locate the osteoid osteoma nidus more precisely, as demonstrated by the postoperative imaging studies. L’ostéome ostéoïde est la troisième tumeur osseuse par ordre de fréquence. L’ablation par radio fréquence et les autres procédés d’éxérèse percutanée, représentent le traitement de choix de ces tumeurs, cependant, pour quelques sites, ces méthodes sont difficiles voire dangereuses. Notre objectif est d’évaluer la possibilité d’une résection à foyer ouvert avec détection per-opératoire du nidus à l’aide d’une sonde à rayonnements gamma. Matériel et méthode: 53 patients présentant une ostéome ostéoïde ont bénéficié de ce traitement chirurgical. Le premier groupe (gamma groupe) représentait 34 patients avec une résection à foyer ouvert guidé par sonde manuelle gamma. Le groupe contrôle, 19 patients étaient opérés selon la technique conventionnelle avec, dans la période post-opératoire, examen histopathologique et évaluation clinique. Le groupe par détection sonde gamma a été suivi, en moyenne, 26,2 mois et le groupe contrôle 38 mois. Résultats: il n’y a pas de différences concernant la récidive des douleurs et les constatations histopathologiques parmi les deux groupes. Cependant, il y a de façon significative moins de nidus présents dans le groupe gamma en post-opératoire. En conclusion: la sonde avec rayonnement gamma permet de localiser le nidus de l’ostéome ostéoïde de façon plus précise comme l’a démontré notre évaluation post-opératoire.
3D Bounding Box Estimation Using Deep Learning and Geometry

We present a method for 3D object detection and pose estimation from a single image. In contrast to current techniques that only regress the 3D orientation of an object, our method first regresses relatively stable 3D object properties using a deep convolutional neural network and then combines these estimates with geometric constraints provided by a 2D object bounding box to produce a complete 3D bounding box. The first network output estimates the 3D object orientation using a novel hybrid discrete-continuous loss, which significantly outperforms the L2 loss. The second output regresses the 3D object dimensions, which have relatively little variance compared to alternatives and can often be predicted for many object types. These estimates, combined with the geometric constraints on translation imposed by the 2D bounding box, enable us to recover a stable and accurate 3D object pose. We evaluate our method on the challenging KITTI object detection benchmark [2] both on the official metric of 3D orientation estimation and also on the accuracy of the obtained 3D bounding boxes. Although conceptually simple, our method outperforms more complex and computationally expensive approaches that leverage semantic segmentation, instance level segmentation and flat ground priors [4] and sub-category detection [23][24]. Our discrete-continuous loss also produces state of the art results for 3D viewpoint estimation on the Pascal 3D+ dataset[26].
Analogical Learning and Reasoning

Analogy is a kind of similarity in which the same system of relations holds across different objects. Analogies thus capture parallels across different situations. When such a common structure is found, then what is known about one situation can be used to infer new information about the other. This chapter describes the processes involved in analogical reasoning, reviews foundational research and recent developments in the field, and proposes new avenues of investigation.
Improving the discrimination of hand motor imagery via virtual reality based visual guidance

While research on the brain-computer interface (BCI) has been active in recent years, how to get high-quality electrical brain signals to accurately recognize human intentions for reliable communication and interaction is still a challenging task. The evidence has shown that visually guided motor imagery (MI) can modulate sensorimotor electroencephalographic (EEG) rhythms in humans, but how to design and implement efficient visual guidance during MI in order to produce better event-related desynchronization (ERD) patterns is still unclear. The aim of this paper is to investigate the effect of using object-oriented movements in a virtual environment as visual guidance on the modulation of sensorimotor EEG rhythms generated by hand MI. To improve the classification accuracy on MI, we further propose an algorithm to automatically extract subject-specific optimal frequency and time bands for the discrimination of ERD patterns produced by left and right hand MI. The experimental results show that the average classification accuracy of object-directed scenarios is much better than that of non-object-directed scenarios (76.87% vs. 69.66%). The result of the t-test measuring the difference between them is statistically significant (p = 0.0207). When compared to algorithms based on fixed frequency and time bands, contralateral dominant ERD patterns can be enhanced by using the subject-specific optimal frequency and the time bands obtained by our proposed algorithm. These findings have the potential to improve the efficacy and robustness of MI-based BCI applications.
Relationship between peer victimization, cyberbullying, and suicide in children and adolescents: a meta-analysis.

IMPORTANCE
Peer victimization is related to an increased chance of suicidal ideation and suicide attempts among children and adolescents. OBJECTIVE To examine the relationship between peer victimization and suicidal ideation or suicide attempts using meta-analysis. DATA SOURCES Ovid MEDLINE, PsycINFO, and Web of Science were searched for articles from 1910 to 2013. The search terms were bully*, teas*, victim*, mobbing, ragging, and harassment in combination with the term suic*. Of the 491 studies identified, 34 reported on the relationship between peer victimization and suicidal ideation, with a total of 284,375 participants. Nine studies reported on the relationship between peer victimization and suicide attempts, with a total of 70,102 participants. STUDY SELECTION Studies were eligible for inclusion if they reported an effect size on the relationship between peer victimization and suicidal ideation or suicide attempt in children or adolescents.


DATA EXTRACTION AND SYNTHESIS
Two observers independently coded the effect sizes from the articles. Data were pooled using a random effects model. MAIN OUTCOMES AND MEASURES This study focused on suicidal ideation and suicide attempts. Peer victimization was hypothesized to be related to suicidal ideation and suicide attempts. RESULTS Peer victimization was found to be related to both suicidal ideation (odds ratio, 2.23 [95% CI, 2.10-2.37]) and suicide attempts (2.55 [1.95 -3.34]) among children and adolescents. Analyses indicated that these results were not attributable to publication bias. Results were not moderated by sex, age, or study quality. Cyberbullying was more strongly related to suicidal ideation compared with traditional bullying. CONCLUSIONS AND RELEVANCE Peer victimization is a risk factor for child and adolescent suicidal ideation and attempts. Schools should use evidence-based practices to reduce bullying.
Risky sexual behaviours of high-school pupils in an era of HIV and AIDS.

OBJECTIVE
To identify risky sexual behaviours and demographic factors that place high-school pupils at risk of HIV and AIDS.


METHODS
A cross-sectional study was undertaken to explore factors influencing the sexual behaviour of high-school pupils (mean age 15.4 years; SD 1.11). Structured self-reported questionnaires were completed by all grade 10 pupils (N = 805) at all the Wentworth, Durban, public high schools.


RESULTS
Significant gender differences in sexual practices were reported, such as males being more likely to engage in sexual activity than females (OR 4.92; p < 0.001). More males (24.8%) initiated sex before age 12, compared with more females (30%) who initiated sex between 16 to 20 years of age (p < 0.001). Significantly more males preferred older partners than females (p = 0.002), more females were forced to have sex than males (p = 0.009), and more males used alcohol on the last occasion of sex than females (p = 0.04). Religious affiliation and parental supervision were found to have a significant effect on sexual activity among pupils.


CONCLUSIONS
High-school pupils are at high risk of HIV and AIDS, yet they continue to engage in risky sexual behaviours. Preventive efforts therefore need to be aggressively up-scaled and redirected towards specific risky practices, taking gender differences into account. Contextual factors such as religious norms and parental supervision also require greater attention. Risky sexual behaviours are reflective of a broader crisis in society.
Comparison of three methods for quantifying brown algal polyphenolic compounds

Three methods of quantifying total phenolic compounds in marine brown algae were compared for their ability to measure accurately known concentrations of phloroglucinol in the presence of a protein, bovine serum albumin (BSA). These methods were: (1) a Folin-Ciocalteu assay for compounds dissolved in 80% methanol, (2) a Folin-Ciocalteu assay for compounds dissolved in 75% methanol-25% trichloroacetic acid, and (3) an assay in which polyvinylpolypyrrolidone (PVPP) was used to remove phenolic compounds in order to quantify nonphenolic, Folin-Ciocalteu-reactive materials. The Folin-Ciocalteu assay used with compounds dissolved in 80% methanol was the method that produced the most consistent results. It was also the assay in which the presence of proteins interfered least with the measurements of phloroglucinol and the assay that was easiest to conduct. The presence of TCA decreased the pH of the extracting solution and increased the amounts of proteins in solution. These proteins later interfered with the Folin-Ciocalteu reaction. TCA effectively bound proteins when protein concentrations were low but not when protein concentrations were high. The amount of phloroglucinol removed by PVPP varied widely and was dependent on phloroglucinol concentration, making this an unreliable method for quantifying phenolic concentrations. The Folin-Ciocalteu assay will measure some nonphenolic substances when brown algae are extracted in 80% methanol; however, inFucus gardneri, nonphenolic substances were at most 5% of the material quantified by the assay.
Evidence for the Flipped Classroom in STEM

The flipped classroom (or flipping) [4] is a new educational technique which seeks to invert the traditional model of in-classroom lectures and out-of-class homework. Instead, it advocates in-class interactive group learning, and out-of-class instruction via videos or podcasts. Intuitively, this approach moves classroom time away from mere dissemination of information, and allows teachers to focus on solving student problems and enabling learning. This connects with the increasing evidence that problem-based learning is an effective teaching technique (see e.g. the meta-analysis in [9]). The intuition for flipping seems compelling, reflected in attention in the non-academic media (e.g. [11, 18]). However, flipping is not trivial to apply. Applying it means restructuring the entire course to focus on group learning, while also recording supporting instructional material. Given the up-front costs, it is important to know whether flipping is truly effective before applying it in practice. In this study, I investigate the evidence that flipping is effective in improving student learning outcomes in STEM subjects, and I also examine some of the pitfalls and opportunities flipping presents. My aim is to understand better how these ideas can be applied to teaching in my home department, Computer Science.
One-year outcomes after a strategy using enoxaparin vs. unfractionated heparin in patients undergoing fibrinolysis for ST-segment elevation myocardial infarction: 1-year results of the ExTRACT-TIMI 25 trial.

AIMS
To determine the impact of a strategy using enoxaparin for up to 8 days compared with unfractionated heparin (UFH) for 48 h as an adjunct to fibrinolysis for ST-segment elevation myocardial infarction (STEMI) on 1-year clinical outcomes.


METHODS AND RESULTS
Follow-up at 1 year (n = 20 275) was conducted by telephone in the ExTRACT-TIMI 25 trial to ascertain the endpoints of death, MI, and disabling stroke. The primary endpoint of death or non-fatal MI occurred in 1614 (15.8%) and 1732 (17.0%) of patients allocated to enoxaparin and UFH, respectively [hazard ratio (HR) 0.92, 95% confidence interval (CI) 0.86-0.98, P = 0.01]. The enoxaparin strategy significantly reduced non-fatal MI at 1 year (5.7 vs. 6.8%, HR 0.82, 95% CI 0.73-0.92, P < 0.001). The risks of death (10.5 vs. 10.6%, HR 0.98, 95% CI 0.91-1.07) and disabling stroke (1.1 vs. 1.2%, HR 0.97, 95% CI 0.75-1.26) were not reduced. The composite of death, MI, or disabling stroke favoured enoxaparin (HR 0.91, 95% CI 0.85-0.98, P = 0.007).


CONCLUSION
Compared with UFH for 48 h, a strategy using enoxaparin as an adjunct to fibrinolysis resulted in a sustained reduction in death or MI at 1 year with no additional benefit after 30 days. Mortality was not reduced at 1 year with the enoxaparin strategy. The study was registered at ClinicalTrials.gov, NCT00077792.