Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding HIV-infected patients’ experiences with PEPFAR-associated transitions at a Centre of Excellence in KwaZulu Natal, South Africa: a qualitative study†

South Africa was the largest recipient of funding from the President's Emergency Plan for AIDS Relief (PEPFAR) for antiretroviral therapy (ART) programs from 2004 to 2012. Funding decreases have led to transfers from hospital and non-governmental organization-based care to government-funded, community-based clinics. We conducted semi-structured interviews with 36 participants to assess patient experiences related to transfer of care from a PEPFAR-funded, hospital-based clinic in Durban to either primary care clinics or hospital-based clinics. Participant narratives revealed the importance of connectedness between patients and the PEPFAR-funded clinic program staff, who were described as respectful and conscientious. Participants reported that transfer clinics were largely focused on dispensing medication and on throughput, rather than holistic care. Although participants appreciated the free treatment at transfer sites, they expressed frustration with long waiting times and low perceived quality of patient–provider communication, and felt that they were treated disrespectfully. These factors eroded confidence in the quality of the care. The transfer was described by participants as hurried with an apparent lack of preparation at transfer clinics for new patient influx. Formal (e.g., counseling) and informal (e.g., family) social supports, both within and beyond the PEPFAR-funded clinic, provided a buffer to challenges faced during and after the transition in care. These data support the importance of social support, adequate preparation for transfer, and improving the quality of care in receiving clinics, in order to optimize retention in care and long-term adherence to treatment.
Toward an argumentation-based dialogue framework for human-robot collaboration

The research on human-robot dialogue to support fluent human robot interaction is still in its early stages. Current issues in the human-robot dialogue domain could be divided into two major categories, which are described in this proposal as the "what to say" problem and the "how to say it" problem. The "what to say" problem addresses ways to determine the content of plausible dialogue during human robot interaction, whereas the "how to say it" problem addresses the best ways for a robot to deliver that content (e.g., using text, gestures, speech or different modalities). Dialogue within the robotics domain also needs to address the "when to say it" problem that considers the timing of dialogue delivery (e.g., turn taking). Human-robot collaboration may fail for many reasons. This research focuses on conflicts and robot errors during human-robot collaboration. Conflicting beliefs occur when participating collaborators have two different views of the physical world due to inaccessible or non-static information. Intuitively, collaborators need to persuade each other to agree on the same beliefs about the state of the world in order to complete collaborative tasks successfully. Robot errors may happen due to miscommunication or simply lack of communication. Moreover, lack of dialogue support for a human to query a robot makes it even more difficult for error recovery. This may lead to failure of a collaborative plan or shared goal. Dialogue is the natural way to resolve errors due to miscommunication. This research explores the notion of an argumentation-based dialogue method for human-robot interaction (HRI). The proposed research aims to design and implement a logic-based dialogue framework grounded on argumentation theory to address the "what to say" problem of human robot communication during a collaborative task.
Deterministic Authenticated-Encryption: A Provable-Security Treatment of the Key-Wrap Problem

Standards bodies have been addressing the key-wrap problem, a cryptographic goal that has never received a provable-security treatment. In response, we provide one, giving definitions, constructions, and proofs. We suggest that key-wrap’s goal is security in the sense of deterministic authenticated-encryption (DAE), a notion that we put forward. We also provide an alternative notion, a pseudorandom injection (PRI), which we prove to be equivalent. We provide a DAE construction, SIV, analyze its concrete security, develop a blockcipher-based instantiation of it, and suggest that the method makes a desirable alternative to the schemes of the X9.102 draft standard. The construction incorporates a method to turn a PRF that operates on a string into an equally efficient PRF that operates on a vector of strings, a problem of independent interest. Finally, we consider IV-based authenticated-encryption (AE) schemes that are maximally forgiving of repeated IVs, a goal we formalize as misuse-resistant AE. We show that a DAE scheme with a vector-valued header, such as SIV, directly realizes this goal.
No-reference blurred image quality assessment

In the aim to reduce blur in images, one could perform a No-Reference image quality assessment to control blur reduction. In this paper, a novel No-Reference blur image quality metric is proposed. This approach is based on a new Multiplicative Multiresolution Decomposition MMD. The blur is analyzed through MMD scales and a blur metric is deduced. We have also shown that the highlighted transform can be used to reduce blur. Some tests have been conducted on LIVE database images. The experimental results show that the proposed assessment method gives high correlation with subjective ratings.
Targeted enrichment of genomic DNA regions for next-generation sequencing

In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.
Toxicological profile for wood creosote, coal tar creosote, coal tar, coal tar pitch, and coal tar pitch volatiles

CREOSOTE ii DISCLAIMER The use of company or product name(s) is for identification only and does not imply endorsement by the Agency for Toxic Substances and Disease Registry. Toxicological profiles are revised and republished as necessary, but no less than once every three years. For information regarding the update status of previously released profiles, contact ATSDR at: V FOREWORD This toxicological profile is prepared in accordance with guidelines" developed by the Agency for Toxic Substances and Disease Registry (ATSDR) and the Environmental Protection Agency (EPA). The original guidelines were published in the Federal Register on April 17, 1987. Each profile will be revised and republished as necessary. The ATSDR toxicological profile succinctly characterizes the toxicologic and adverse health effects information for the hazardous substance described therein. Each peer-reviewed profile identifies and reviews the key literature that describes a hazardous substance's toxicologic properties. Other pertinent literature is also presented, but is described in less detail than the key studies. The profile is not intended to be an exhaustive document; however, more comprehensive sources of specialty information are referenced. The focus of the profiles is on health and toxicologic information; therefore, each toxicological profile begins with a public health statement that describes, in nontechnical language, a substance's relevant toxicological properties. Following the public health statement is information concerning levels of si,~ficant human exposure and, where known, significant health effects. The adequacy of information to determine a substance's health effects is described in a health effects summary. Data needs that are of significance to protection of public health are identified by ATSDR and EPA. Each profile includes the following: The examination, summary, and interpretation of available toxicologic information and epidemiologic evaluations on a hazardous substance to ascertain the levels of significant human exposure for the substance and the associated acute, subacute, and chronic health effects; A determination of whether adequate information on the health effects of each substance is available or in the process of development to determine levels of exposure that present a significant risk to human health of acute, subacute, and chronic health effects; and Where appropriate, identification of toxicologic testing needed to identify the types or levels of exposure that may present significant risk of adverse health effects in humans. The principal audiences for the toxicological profiles are health professionals at the federal, state, and local levels; interested private sector organizations and groups; and members of the public. This profile …
Preimage Problem in Kernel-Based Machine Learning

While the nonlinear mapping from the input space to the feature space is central in kernel methods, the reverse mapping from the feature space back to the input space is also of primary interest. This is the case in many applications, including kernel principal component analysis (PCA) for signal and image denoising. Unfortunately, it turns out that the reverse mapping generally does not exist and only a few elements in the feature space have a valid preimage in the input space. The preimage problem consists of finding an approximate solution by identifying data in the input space based on their corresponding features in the high dimensional feature space. It is essentially a dimensionality-reduction problem, and both have been intimately connected in their historical evolution, as studied in this article.
Scd1 Plays a Tumor-Suppressive Role in Survival of Leukemia Stem Cells and the Development of Chronic Myeloid Leukemia

ABSTRACT Chronic myeloid leukemia (CML) is derived from a stem cell, and it is widely accepted that the existence of leukemia stem cells (LSCs) is one of the major reasons for the relapse of CML treated with kinase inhibitors. Key to eradicating LSCs is to identify genes that play a critical role in survival regulation of these stem cells. Using BCR-ABL-induced CML mouse model, here we show that expression of the stearoyl-CoA desaturase 1 (Scd1) gene is downregulated in LSCs and that Scd1 plays a tumor-suppressive role in LSCs with no effect on the function of normal hematopoietic stem cells. Deletion of Scd1 causes acceleration of CML development and conversely overexpression of Scd1 delays CML development. In addition, using genetic approaches, we show that Pten, p53, and Bcl2 are regulated by Scd1 in LSCs. Furthermore, we find that induction of Scd1 expression by a PPARγ agonist suppresses LSCs and delays CML development. Our results demonstrate a critical role for Scd1 in functional regulation of LSCs, providing a new anti-LSC strategy through enhancing Scd1 activity.
Inhalant Abuse Detection and Evaluation in Young Tunisians

Abstract: Occupational exposure biological monitoring techniques were applied for the diagnosis of inhalation abuse and for the evaluation of the levels of exposure to benzene, toluene, ethylbenzene, xylenes, and n‐hexane, in 44 Tunisian adolescents and children suspected for volatile substance addiction. Urinary trans,trans‐muconic acid, hippuric acid (HA), mandelic acid, and methylhippuric acids determinations were performed by high performance liquid chromatography with a photodiode array detector, and urinary o‐cresol (o‐Cr) and 2,5‐hexanedione (HD) were extracted simultaneously and measured using gas chromatography with a flame ionization detector. Given the high linearity ranges, HD and o‐Cr occupational exposure monitoring techniques could be applied without modification. However, urinary sample dilution was necessary before HA analysis. Concentrations were compared with the maxima of normal values (MNVs) in the general population and to the biological exposure indices (BEIs) used in occupational toxicology. Values as high as 6610‐fold the MNV and 68 times the BEI were registered. The subjects showed high exposure to toluene and hexane. Measured metabolites HA and/or o‐Cr and HD enabled the easy detection and evaluation of exposure levels. The problem of inhalant abuse should be given more attention and treated through an effective prevention strategy.
Detecting and Labelling Wireless Community Network Structures from Eigen-spectra

Wireless and ad hoc networks often have local regions of highly intra-connected modules or communities of nodes against a backdrop of sparser longer-range intercommunity connectivities. We report on empirical observations and a prototype algorithm for correctly counting and labelling the number of dense community structures or modules within a fully connected network. We describe the eigen-spectral method applied to the Laplacian characteristic matrix. We illustrate the effect of different network characteristics on the eigenspectrum and on properties of the eigenvectors corresponding to the Nc smallest eigenvalues in networks with Nc such dense community modules.
Routine early angioplasty after fibrinolysis for acute myocardial infarction.

BACKGROUND Patients with a myocardial infarction with ST-segment elevation who present to hospitals that do not have the capability of performing percutaneous coronary intervention (PCI) often cannot undergo timely primary PCI and therefore receive fibrinolysis. The role and optimal timing of routine PCI after fibrinolysis have not been established. METHODS We randomly assigned 1059 high-risk patients who had a myocardial infarction with ST-segment elevation and who were receiving fibrinolytic therapy at centers that did not have the capability of performing PCI to either standard treatment (including rescue PCI, if required, or delayed angiography) or a strategy of immediate transfer to another hospital and PCI within 6 hours after fibrinolysis. All patients received aspirin, tenecteplase, and heparin or enoxaparin; concomitant clopidogrel was recommended. The primary end point was the composite of death, reinfarction, recurrent ischemia, new or worsening congestive heart failure, or cardiogenic shock within 30 days. RESULTS Cardiac catheterization was performed in 88.7% of the patients assigned to standard treatment a median of 32.5 hours after randomization and in 98.5% of the patients assigned to routine early PCI a median of 2.8 hours after randomization. At 30 days, the primary end point occurred in 11.0% of the patients who were assigned to routine early PCI and in 17.2% of the patients assigned to standard treatment (relative risk with early PCI, 0.64; 95% confidence interval, 0.47 to 0.87; P=0.004). There were no significant differences between the groups in the incidence of major bleeding. CONCLUSIONS Among high-risk patients who had a myocardial infarction with ST-segment elevation and who were treated with fibrinolysis, transfer for PCI within 6 hours after fibrinolysis was associated with significantly fewer ischemic complications than was standard treatment. (ClinicalTrials.gov number, NCT00164190.)
Brd 4 engagement from chromatin targeting to transcriptional regulation : selective contact with acetylated histone H 3 and H 4

Bromodomain-containing protein 4 (Brd4) contains two tandem bromodomains (BD1 and BD2) that bind preferentially to acetylated lysine residues found in histones and nonhistone proteins. This molecular recognition allows Brd4 to associate with acetylated chromatin throughout the cell cycle and regulates transcription at targeted loci. Recruitment of positive transcription elongation factor b, and possibly the general initiation cofactor Mediator as well, plays an important role in Brd4-regulated transcription. Selective contacts with acetyl-lysines in nucleosomal histones and chromatin-binding factors likely provide a molecular switch modulating the steps from chromatin targeting to transcriptional regulation, thus further expanding the ‘acetylation code’ for combinatorial regulation in eukaryotes. Introduction and context Bromodomain-containing protein 4 (Brd4), originally named MCAP (mitotic chromosome-associated protein) [1], belongs to a family of proteins with two aminoterminal tandem bromodomains (BD1 and BD2) and an extraterminal (ET) domain located either at its central region (for the longer isoform or family members) or close to the carboxyl terminus (for the shorter isoform or family members) (Figure 1). In addition to these three evolutionarily conserved domains, bromodomain-ET (BET) family proteins also contain other conserved regions [i.e., A, B, SEED (Ser/Glu/Asp-rich region), and carboxyl-terminal motif (CTM)] that are found in most but not all members and have mostly uncharacterized functions [2,3]. A unique feature of the BET proteins, which include yeast bromodomain factor 1 (Bdf1), bromodomain factor 2 (Bdf2), Drosophila female sterile homeotic (Fsh), and mammalian (e.g., human and mouse) Brd2, Brd3, Brd4, and testes/oocyte (i.e, germ cell)-specific Brdt (Figure 1), is their persistent association not only with interphase chromatin but also with mitotic chromosomes [4-7]. The association with mitotic chromosomes, also found for zebrafish and Xenopus Brd4 even before fish zygotic transcription is initiated [8], provides molecular marking for ensuing gene expression coinciding with or immediately following cell division [9-11]. Transcription-coupled mitotic control is likewise seen in viral systems. Several virus-encoded proteins, such as E2 transcription/replication factor encoded by BPV-1 (bovine papillomavirus type 1) and human papillomaviruses (HPVs), bind Brd4 directly to facilitate selective types of viral genome segregation during mitosis [12-15] and to generally regulate viral gene transcription during interphase [16-21]. Targeting cellular chromatin via direct association with a BET family protein seems to be widely used by other DNA tumor viruses for tethering viral genomes and exerting a dominant effect on viral and cellular gene expression [22-26]. Although viral genome partitioning also occurs through mitotic spindles/microtubules or specific regions of mitotic chromosomes in a Brd4-independent manner [27-29], attachment of viral genomes to cellular chromatin
Remodeling of the Streptococcus agalactiae Transcriptome in Response to Growth Temperature

Background To act as a commensal bacterium and a pathogen in humans and animals, Streptococcus agalactiae (group B streptococcus, GBS) must be able to monitor and adapt to different environmental conditions. Temperature variation is a one of the most commonly encountered variables. Methodology/Principal Findings To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30°C and 40°C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30°C in stationary phase. Conversely, genes up-regulated at 40°C relative to 30°C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40°C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40°C. Conclusion/Significance Growth of GBS in vitro at different temperatures resulted in extensive remodeling of the transcriptome, including genes encoding proven and putative virulence genes. The data provide extensive new leads for molecular pathogenesis research.
Online detection of effectively callback free objects with applications to smart contracts

Callbacks are essential in many programming environments, but drastically complicate program understanding and reasoning because they allow to mutate object's local states by external objects in unexpected fashions, thus breaking modularity. The famous DAO bug in the cryptocurrency framework Ethereum, employed callbacks to steal $150M. We define the notion of Effectively Callback Free (ECF) objects in order to allow callbacks without preventing modular reasoning. An object is ECF in a given execution trace if there exists an equivalent execution trace without callbacks to this object. An object is ECF if it is ECF in every possible execution trace. We study the decidability of dynamically checking ECF in a given execution trace and statically checking if an object is ECF. We also show that dynamically checking ECF in Ethereum is feasible and can be done online. By running the history of all execution traces in Ethereum, we were able to verify that virtually all existing contract executions, excluding these of the DAO or of contracts with similar known vulnerabilities, are ECF. Finally, we show that ECF, whether it is verified dynamically or statically, enables modular reasoning about objects with encapsulated state.
Les langages du web sémantique

La manipulation des resources du web par des machines requiert l'expression ou la description de ces resources. Plusieurs langages sont donc definis a cet effet, ils doivent permettre d'exprimer donnees et methadonnees (RDF, Cartes Topiques), de decrire les services et leur fonctionnement (UDDI, WSDL, DAML-S, etc.) et de disposer d'un modele abstrait de ce qui est decrit grace a l'expression d'ontologies (RDFS, OWL). On presente ci-dessous l'etat des travaux visant a doter le web semantique de tels langages. On evoque aussi les questions importantes qui ne sont pas reglees a l'heure actuelle et qui meritent de plus amples travaux.
Improving Shape Depiction under Arbitrary Rendering

Based on the observation that shading conveys shape information through intensity gradients, we present a new technique called Radiance Scaling that modifies the classical shading equations to offer versatile shape depiction functionalities. It works by scaling reflected light intensities depending on both surface curvature and material characteristics. As a result, diffuse shading or highlight variations become correlated with surface feature variations, enhancing concavities and convexities. The first advantage of such an approach is that it produces satisfying results with any kind of material for direct and global illumination: we demonstrate results obtained with Phong and Ashikmin-Shirley BRDFs, Cartoon shading, sub-Lambertian materials, perfectly reflective or refractive objects. Another advantage is that there is no restriction to the choice of lighting environment: it works with a single light, area lights, and interreflections. Third, it may be adapted to enhance surface shape through the use of precomputed radiance data such as Ambient Occlusion, Prefiltered Environment Maps or Lit Spheres. Finally, our approach works in real time on modern graphics hardware making it suitable for any interactive 3D visualization.
Applications of Abductive Logic Programming

We describe a system implementing a novel extension of Fung and Kowalski’s IFF abductive proof procedure which we call CIFF, and its application to realise intelligent agents that can construct (partial or complete) plans and react to changes in the environment. CIFF extends the original IFF procedure in two ways: by dealing with constraint predicates and by dealing with non-allowed abductive logic programs.