Miracle-dz/UniFAR-FTUs huggingface dataset:
What sort of bioethical values are the evidence-based medicine and the GRADE approaches willing to deal with?

The concept of evidence-based medicine (EBM) has been invented by physicians mostly from English Canada, mostly from McMaster University, Ontario, Canada. The term EBM first appeared in the biomedical literature in 1991 in an article written by a prominent member of this group—Gordon Guyatt from McMaster University. The inventors of EBM have also created the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) working group, which is a prominent international organisation whose main purpose is to develop evidence-based clinical practice guidelines (CPGs). CPGs that are based on the GRADE approach are becoming increasingly adopted worldwide, in particular by many professional or governmental organisations. This group of thinkers being thus identified, we have retrieved and read many of their publications in order to try and understand how they intend to incorporate bioethical values into their concept. The author of this little essay did also spend a few years on the internet as an active member of the GRADE group discussion list. The observations thus gathered suggest that although some of the inventors of EBM, at least Gordon Guyatt, wish to incorporate core principles of biomedical ethics into their concept (ie, non-malevolence, beneficence and maybe to a lesser extent respect for autonomy, and justice), some clarifications are still necessary in order to better understand how they intend to more explicitly incorporate bioethical values into their concept and, perhaps more importantly, into evidence-based CPGs.
Serum lysozyme in pulmonary tuberculosis

Serum lysozyme was related to tuberculosis disease activity in 67 patients with proven active pulmonary tuberculosis. A strong relationship was established between serum lysozyme activity and the clinical classification of disease. Relationships were poor between serum lysozyme and the presence or absence of tubercle bacilli in the sputum. The only two patients with lysozymuria died. Elderly patients with tuberculosis had significantly higher serum lysozyme activity than did younger subjects with comparable amounts of pulmonary tuberculosis. The clinical usefulness of serum lysozyme determinations in patients with pulmonary tuberculosis, however, must await further investigation. Evidence is presented to show that chronic tissue inflammation is the most likely source of the increased serum lysozyme activity in patients with active pulmonary tuberculosis.
Changes in inhibitory control and drug salience in response to stress: differences between opiate users, ex-users and non-users.

Rationale: Whilst relapse to drug taking, even after a substantial period of abstinence, is common, laboratory-based research documenting precursors to relapse in humans is limited. ;Objectives: The purpose of this literature review is to evaluate evidence from both animal and human studies on the effect of acute stressors on drug craving and relapse. ;Method: Attempts at conceptualizing the definition of stress have been unsuccessful (Chrousos & Gold, 1992). For the purposes of this review, stress was broadly defined in line with Piazza & Le Moal (1998) as coerced exposure to environmental conditions or events that would normally be considered aversive enough to motivate avoidance. This review considered both physical and psychological stressors and is limited to opiate (specifically heroin and morphine) and psychostimulant drugs (e.g. cocaine, amphetamine) in animals, and alcohol, opiates, nicotine, and cocaine in humans. ;Conclusions: Results from animal studies of acute stress and relapse are inconsistent. Human studies, despite providing more consistent findings, have a range of methodological limitations. A greater understanding of how stress precipitates relapse is likely to have a significant impact on the way clinical interventions are offered to substance misusing individuals.
Ultraviolet‐B radiation stimulates shikimate pathway‐dependent accumulation of mycosporine‐like amino acids in the coral Stylophora pistillata despite decreases in its population of symbiotic dinoflagellates

Colonies of Stylophora pistillata maintained for four years in indoor aquaria in the near absence of ultraviolet radiation (UVR) contained only small amounts (<5 nmol mg−1 protein) of 10 identified mycosporine‐like amino acids (MAAs, which act as UV sunscreens), the largest number reported in any organism. The concentrations of most MAAs increased linearly or exponentially when colonies were exposed to ultraviolet‐A (UVA) and ultraviolet‐B (UVB) for 8 h d−1 in the presence of photosynthetically active radiation (PAR). Total MAA concentration reached 174 nmol mg−1 protein after 30 d, with palythine and mycosporine−2 glycine constituting more than half of the final total. UVB specifically stimulated MAA accumulation: after 15 d, MAA levels in colonies exposed to PAR alone and to PAR and UVA did not differ (7 and 5 nmol MAA mg−1 protein, respectively), while those in colonies exposed to PAR and UVA + UVB were significantly higher (28 nmol mg−1 protein). Glyphosate, an inhibitor of the shikimate pathway, eliminated or reduced the UV‐induced accumulation of most MAAs during 7 d of exposure, providing the first experimental evidence of their synthesis via this pathway in a coral symbiosis. Densities of zooxanthellae in colonies of S. pistillata, Acropora sp. , and Seriatopora hystrix exposed to UVR for 15 d were only one‐third of those in control colonies unexposed to UVR. This net decrease in the number of zooxanthellae in the corals (bleaching) occurred despite UV stimulated increases in algal cytokinesis and in the host cell‐specific density of zooxanthellae in hospite, increases that apparently destabilized the symbiosis and caused expulsion of the zooxanthellae.
Enrichment of transcriptional regulatory sites in non-coding genomic region

MOTIVATION Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment. RESULTS To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions.
Spatial elongation of population receptive field profiles revealed by model‐free fMRI back‐projection

Estimates of visual field topographies in human visual cortex obtained through fMRI traveling wave techniques usually provide the parameters of population receptive field (pRF) location (polar angle, eccentricity) and receptive field size. These parameters are obtained by fitting the recorded data to a standard model population receptive field. In this work, pRF profiles are measured directly by back‐projecting preprocessed fMRI time‐series to sweeps of a bar across the visual field in different angles. The current data suggest that the model‐free pRF profiles contain information not only about receptive field location and size but also about the pRF shape characteristics. The elongation (ellipticity) of pRFs decreases along the early visual hierarchy to a different degree for the ventral and the dorsal stream. Furthermore, ellipticity changes as a function of eccentricity. pRF orientation shows a high degree of collinearity with its angular position within the visual field. Using model‐free pRF measurements, the traveling wave technique provides additional characteristics of pRF topographies that are not restricted to size and provide robust measures within the single subject.
Empathy, Target Distress, and Neurohormone Genes Interact to Predict Aggression for Others–Even Without Provocation

Can empathy for others motivate aggression on their behalf? This research examined potential predictors of empathy-linked aggression including the emotional state of empathy, an empathy target’s distress state, and the function of the social anxiety-modulating neuropeptides oxytocin and vasopressin. In Study 1 (N = 69), self-reported empathy combined with threat to a close other and individual differences in genes for the vasopressin receptor (AVPR1a rs3) and oxytocin receptor (OXTR rs53576) to predict self-reported aggression against a person who threatened a close other. In Study 2 (N = 162), induced empathy for a person combined with OXTR variation or with that person’s distress and AVPR1a variation led to increased amount of hot sauce assigned to that person’s competitor. Empathy uniquely predicts aggression and may do so by way of aspects of the human caregiving system in the form of oxytocin and vasopressin.
Distributed mining of the Internet for novel news: evolutionary community of news foragers

We populated a huge scale-free portion of Internet environment with news foragers. They evolved by a simple internal selective algorithm: selection concerned the memory components, being finite in size and containing the list of most promising supplies. Foragers received reward for locating not yet found news and used value estimation. Foragers were allowed to multiply if they passed a given productivity threshold. A particular property of this community is that there is no direct interaction (here, communication) amongst foragers. It is found that, still, fast compartmentalization, i.e., fast division of work can be achieved.
CIRQuL - Complex Information Retrieval Query Language

In this paper we will present a new framework for the retrieval of XML documents. We will describe the extension for existing query languages (XPath and XQuery) geared toward ranked information retrieval and full-text search in XML documents. Furthermore we will present language models for ranked information retrieval applied to the XML and describe the ultimate goal of our research.
Low voltage, low power (5:2) compressor cell for fast arithmetic circuits

This paper presents a new (5:2) compressor circuit capable of operating at ultra-low voltages. Its power efficacy is derived from the novel design of composite XOR-XNOR gate at transistor level. The new circuit eliminates the weak logic and threshold voltage drop problems, which are the main factors limiting the performance of pass transistor based circuits at low supply voltages. The proposed (5:2) compressor has been designed with special consideration on output drivability to ensure that it can function reliably at low voltages when these cells are employed in the tree structured multiplier and multiply-accumulator. Simulation results show that the proposed (5:2) compressor is able to function at supply voltage as low as 0.7 V, and. outperforms other (5:2) compressors constructed with various combinations of recently reported superior low-power logic cells.
CiteSeerX data: semanticizing scholarly papers

Scholarly big data is, for many, an important instance of Big Data. Digital library search engines have been built to acquire, extract, and ingest large volumes of scholarly papers. This paper provides an overview of the scholarly big data released by CiteSeerX, as of the end of 2015, and discusses various aspects such as how the data is acquired, its size, general quality, data management, and accessibility. Preliminary results on extracting semantic entities from body text of scholarly papers with Wikifier show biases towards general terms appearing in Wikipedia and against domain specific terms. We argue that the latter will play a more important role in extracting important facts from scholarly papers.
Intraoperative Visualization of Fiber Tracking Based Reconstruction of Language Pathways in Glioma Surgery

BACKGROUND: For neuroepithelial tumors, the surgical goal is maximum resection with preservation of neurological function. This is contributed to by intraoperative magnetic resonance imaging (iMRI) combined with multimodal navigation. OBJECTIVE: We evaluated the contribution of diffusion tensor imaging (DTI)-based fiber tracking of language pathways with 2 different algorithms (tensor deflection, connectivity analysis [CA]) integrated in the navigation on the surgical outcome. METHODS: We evaluated 32 patients with neuroepithelial tumors who underwent surgery with DTI-based fiber tracking of language pathways integrated in neuronavigation. The tensor deflection algorithm was routinely used and its results intraoperatively displayed in all cases. The CA algorithm was furthermore evaluated in 23 cases. Volumetric assessment was performed in pre- and intraoperative MR images. To evaluate the benefit of fiber tractography, language deficits were evaluated pre- and postoperatively and compared with the volumetric analysis. RESULTS: Final gross-total resection was performed in 40.6% of patients. Absolute tumor volume was reduced from 55.33 ± 63.77 cm3 to 20.61 ± 21.67 cm3 in first iMRI resection control, to finally 11.56 ± 21.92 cm3 (P < .01). Fiber tracking of the 2 algorithms showed a deviation of the displayed 3D objects by <5 mm. In long-term follow-up only 1 patient (3.1%) had a persistent language deficit. CONCLUSION: Intraoperative visualization of language-related cortical areas and the connecting pathways with DTI-based fiber tracking can be successfully performed and integrated in the navigation system. In a setting of intraoperative high-field MRI this contributes to maximum tumor resection with low postoperative morbidity.
Conceptualizing the Commons-Based Peerproduction of Software: an Activity Theoretic Analysis

Commons-based peer-production (CBPP), as exemplified by community-based open source software (OSS) development, has been posited by Yochai Benkler as an alternative to hierarchies and markets for organizing the production of information goods. This study seeks to conceptualize viable CBPP through an Activity Theoretic analysis of 524 peer-reviewed OSS research artifacts. The analysis reveals the reliance of peer-production communities on complex systems of interrelated tools, rules, and roles as mediating components enabling communities to (i) exploit the two theorized advantages of CBPP (resource allocation and information processing) and (ii) overcome the two theorized challenges associated with this mode of production (motivation and organization). The study clarifies and extends extant understanding of CBPP in several significant ways, and concludes that in order for CBPP to be viable, participants must operate in a sustainable fashion that both enhances the commons and leaves the community intact.
Rejuvenating, Reconstituting, and Transforming Physical Education to Meet the Needs of Vulnerable Children, Youth, and Families

The U.S. has a children’s crisis. A crisis also looms for physical education. Physical education is becoming a plowed out, decimated, and disappearing field because of its design flaws, selectivity, and silences. The children’s crisis provides opportunities for physical education to rejuvenate, reconstitute, and transform itself. New visions, missions, and conceptions of competent practice can be developed in response to the multiple, interdependent needs of poor and vulnerable children, youth, families, and their local neighborhood communities. Opportunities are emerging to develop new change theories and design models in conjunction with emergent complex change initiatives in school communities. Different kinds of change theories are identified. Possibilities for new design models are sketched. Together, these change theories and design models provide new directions for research and practice. They signal a change in paradigms.
Semi-automatic player detection for real-time broadcasting systems

Computer vision technology such as object detection and tracking has been widely applied to sports video analysis. This technology analyzes the physical activity and performance of sports players. With this technology, it is also necessary to perform video analysis immediately after important events. In this paper, we focus on cutting out regions of full-screen images according to the movement of an important player in the image. In our system, an operator only assists by means of a simple input for a key player position in the sports game and our semi-automatic detection scheme accurately estimates the region of interest related to the key player. According to our experimental results, the proposed method can extract regions of interest more accurately and rapidly than conventional pedestrian detectors.
New insights into SILC-based life time extraction

The breakdown (TDDB/SILC) characteristics of nMOS transistors with hafnium-based gate dielectric stacks of various zirconium content were investigated. It is found that the gate stack composition affects the SILC-voltage dependency while the voltage value chosen for SILC monitoring impacts significantly the SILC-based lifetime projection. For the worst case lifetime evaluation, SILC should be monitored at its maximum value rather than at any pre-defined, fixed voltage.
Motif-based protein ranking by network propagation

MOTIVATION Sequence similarity often suggests evolutionary relationships between protein sequences that can be important for inferring similarity of structure or function. The most widely-used pairwise sequence comparison algorithms for homology detection, such as BLAST and PSI-BLAST, often fail to detect less conserved remotely-related targets. RESULTS In this paper, we propose a new general graph-based propagation algorithm called MotifProp to detect more subtle similarity relationships than pairwise comparison methods. MotifProp is based on a protein-motif network, in which edges connect proteins and the k-mer based motif features that they contain. We show that our new motif-based propagation algorithm can improve the ranking results over a base algorithm, such as PSI-BLAST, that is used to initialize the ranking. Despite the complex structure of the protein-motif network, MotifProp can be easily interpreted using the top-ranked motifs and motif-rich regions induced by the propagation, both of which are helpful for discovering conserved structural components in remote homologies.
A Model-Based Method for Information Alignment: A Case Study on Educational Standards

We propose a model-based method for information alignment using educational standards as a case study. Discrepancies and inconsistencies in educational standards across different states/cities hinder the retrieval and sharing of educational resources. Unlike existing educational standards alignment systems that only give binary judgments (either “aligned” or “not-aligned”), our proposed system classifies each pair of educational standard statements in one of seven levels of alignments: Strongly Fully-aligned, Weakly Fully-aligned, Partially-aligned***, Partially-aligned**, Partially-aligned*, Poorly-aligned, and Not-aligned. Such a 7-level categorization extends the notion of binary alignment and provides a finer-grained system for comparing educational standards that can broaden categories of resource discovery and retrieval. This study continues our previous use of mathematics education as a domain, because of its generally unambiguous concepts. We adopt a materialization pattern (MP) model developed in our earlier work to represent each standard statement as a verb-phrase graph and a noun-phrase graph; we align a pair of statements using graph matching based on Bloom’s Taxonomy, WordNet, and taxonomy of mathematics concepts. Our experiments on data sets of mathematics educational standards show that our proposed system can provide alignment results with a high degree of agreement with domain expert’s judgments.
Local infusion of the nitric oxide donor sin-1 after angioplasty: Effects on intimal hyperplasia in porcine coronary arteries

Purpose: To investigate the development of intimal hyperplasia in response to percutaneous transluminal coronary angioplasty (PTCA) followed by local delivery of the nitric oxide (NO) donor 3-morpholino-sydnonimine (SIN-1). Material and Methods: Overdilation PTCA was performed in coronary arteries in 20 healthy pigs. One of the dilated segments was additionally treated with local delivery of SIN-1 for 10 min. Segments distal to the treated part of the arteries served as controls. Arteries were radiographically depicted and analyzed after 1 and 8 weeks for actin, myosin and intermediate filaments (IF), nitric oxide synthetase (NOS) and histological evaluation. Results: Segments treated with PTCA+SIN-1 showed a significantly (p = 0.03) larger luminal diameter compared with PTCA only treated segments. The luminal loss after SIN-1 was not significant compared with the diameter prior to treatment. Endothelial NOS content was significantly lower in the PTCA+SIN-1 group compared with the PTCA group after 1 (p = 0.03) and 8 weeks (p = 0.013). IF/actin ratio after 1 week was significantly increased in PTCA-treated segments compared with untreated controls (p = 0.004), and compared with PTCA+SIN-1-treated segments (p = 0.004). Conclusion: PTCA-induced intimal hyperplasia was potently inhibited by local delivery of the NO donor SIN-1. Momentary events at the time of injury play a significant role in the development of intimal hyperplasia and long-lasting down-regulation of the endothelial NOS expression after SIN-1 exposure is suggested. The IF/actin ratio can be useful as an early marker of intimal hyperplasia.