Miracle-dz/UniFAR-FTUs huggingface dataset:
Cervicovaginal HIV-1 and herpes simplex virus type 2 shedding during genital ulcer disease episodes

Objective:To investigate correlates of herpes simplex virus type 2 (HSV-2) DNA and HIV-1 RNA among women with genital ulcer disease (GUD). Design:Baseline data from a randomized placebo-controlled trial of episodic herpes treatment in Ghana and the Central African Republic. Methods:GUD aetiology was determined by polymerase chain reaction (PCR) from a lesional swab. Real-time PCR was used to quantify HIV-1 RNA, and HSV-2 DNA in cervicovaginal lavages (CVL) and HIV-1 RNA in plasma. Genital infection was defined as the presence of virus in the lesion or CVL. Results:Of 441 women enrolled, 79.0% were HSV-2 seropositive, 46.6% were HIV-1 seropositive, and 50.0% had an HSV-2 ulcer. Among 180 HSV-2/HIV-1 co-infected women, cervicovaginal HIV-1 RNA was detected more frequently in women with HSV-2 ulcers (67.9%) or cervicovaginal HSV-2 DNA only (72.3%) compared with women without genital HSV-2 infection (42.4%) (P = 0.004). Women with genital HSV-2 infection had higher median cervicovaginal HIV-1-RNA loads (3.14 log10 copies/mL versus 2.10 log10 copies/mL; P = 0.003), higher plasma HIV-1-RNA loads (median 5.10 versus 4.65 log10 copies/mL; P = 0.07), and lower median CD4 cell counts) (198 versus 409 cells/mm3, P = 0.03). Cervicovaginal HIV-1 RNA and HSV-2 DNA were significantly correlated after adjusting for plasma HIV-1 RNA and CD4 cell counts (P < 0.001) and a 10-fold increase in cervicovaginal HSV-2 DNA was associated with a 1.7-fold increase in plasma HIV-1 RNA (P = 0.003). Conclusion:Genital HSV-2 infection is associated with increased cervicovaginal and plasma HIV-1 RNA among co-infected women with genital ulcers, independently of the level of immunodeficiency, highlighting the close interaction between these two viruses and the role of HSV-2 as a co-factor for the sexual transmission of HIV-1.
VISUAL RECOGNITION OF EVENTS AND ACTIVITIES BASED ON MOMENTUM OF MOTION ENERGY MASS

We propose a new activity-based event recognition system that is based on the construction of a novel Momentum Template combining the apparent moving areas and the velocity of the associated movement. Consideration is also given to movement that is not taking place in parallel to the projection plane of the camera. The construction of the momentum template is followed by the application of an angular transform. Linear discriminant analysis is applied to angular coefficients for dimensionality reduction. Recognition is performed by comparing Euclidean distances in the resulting subspace. Experimental evaluation in comparison to other recent methods shows the efficiency of the proposed method.
New deep-water cnidarian sites in the southern Adriatic Sea

Recent ROV (Remotely Operated Vehicle) exploration and bottom sampling in the southern Adriatic Sea (Apulian and Montenegrin margins) resulted in the discovery of cnidarian-rich deep-sea habitats in the depth range of ca. 400-700 m. In particular, ROV inspection of Montenegrin canyons reveals the existence of megabenthic communities dominated by a variety of cnidarians, including scleractinians ( Madrepora oculata, Lophelia pertusa, Dendrophyllia cornigera ), antipatharians ( Leiopathes glaberrima ) and gorgonians ( Callogorgia verticillata ) as major habitat forming taxa, often in association with sponges and, subordinately, serpulids. All such cnidarians are new records for the southeastern side of the Adriatic Sea. Our investigation indicates that an almost continuous belt of patchy cold water coral sites occurs along the entire southwestern margin (Apulian), basically connecting the Adriatic populations with those inhabiting the Ionian margin (Santa Maria di Leuca coral province).
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering ≈94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.
A Stage Model of Blood Donor Behaviour: Assessing Volunteer Behaviour

Are there valid stages to explain blood donor behaviour? Three studies (event contingent diary, interview and psychometric) are reported that address this question. Stage and process constructs from the transtheoretical model (TTM), past behaviour and intentions are measured. The qualitative studies demonstrated that blood donors describe their behaviour using TTM constructs. The psychometric study identified: (1) groupings of blood donors consistent with Ferguson’s (1996) stage predictions; (2) TTM constructs varied meaningfully as a function of these groupings; (3) associations within clusters indicated qualitatively distinct stages; and (4) TTM constructs showed incremental validity over intentions with respect to past behaviour.
An Argument for Vitamin E Supplementation in the Management of Systemic Inflammatory Response Syndrome

The systemic inflammatory response syndrome results from an uncontrolled, overexpression of the normal host inflammatory response, leading to destruction of host tissue and subsequent organ failure. Oxidant stress has been implicated in this process both as a mechanism for direct cellular injury, as well as activation of intracellular signaling cascades within inflammatory cells resulting in progression of the inflammatory response. Vitamin E is an inexpensive, nontoxic, chain-breaking antioxidant that has therapeutic potential in regulating this process. This review seeks to evaluate the current literature regarding the use of Vitamin E in controlling the excessive inflammation seen in systemic inflammatory response syndrome and argues for further study of its therapeutic potential for these critically ill patients.
Atrazine Exposure Impacts Behavior and Survivorship of Neonatal Turtles

Abstract: Atrazine (2-chloro-4-ethythlamino-6-isopropylamine-1,3,5-tiazine) is a widely used preemergent herbicide for controlling broadleaf plants. Because atrazine (a known endocrine-disrupting chemical) is applied in the late spring and early summer, its incidental effects on species exposed to runoff from terrestrial sources in this time period are of special interest. To examine the possible secondary impact of atrazine, we obtained eggs from 10 nests of two map turtle species, Graptemys ouachitensis and G. pseudogeographica, that nest on riverine sandbars. We incubated two eggs from each nest in sand containing one of four initial concentrations of atrazine (control and 0.1, 10, and 100 µg/L) based on levels measured in the river at the site where eggs were collected. We recorded hatching success, incubation time, external morphological abnormalities, gonadal sex, three measures of body size, righting time, and swimming time for all turtles. We reared a subset of the original neonates individually for 11 mo, during which time nest escape behavior, time to first foraging event, time to capture prey, growth, and survival were evaluated. None of the variables recorded at hatching was significantly affected by atrazine treatment, although abnormalities declined as atrazine levels increased. However, turtles deriving from the lowest atrazine-treated eggs had inhibited nest escape behavior and reduced posthatching survival. These findings reveal persistent fitness-reducing impacts on neonatal turtles resulting from atrazine exposure during embryonic development.
Helicobacter pylori—Associated Dyspepsia in Paediatrics

Helicobacter pylori ubiquitously infects the human gastric mucosa since time immemorial, predictably before the man’s diaspora out of East Africa around 58,000 years ago [1]. Colonization may have been somehow beneficial for human carriers, allowing the coevolution of this gram-negative bacterium and its host over the centuries. Yet, at least nowadays [2], this may not be a peaceful association, with infection almost invariably causing an acute host immune response. However, in a fully adapted manner, H. pylori avoids recognition and, thus, clearance, by the host immune system, with both infection and the consequent gastritis persisting throughout the patients’ life. The clinical outcome of this persistence is dependent on a sophisticated crosstalk between the host and the pathogen. If often asymptomatic, the H. pylori-associated non-ulcer dyspepsia is clearly the strongest aetiological factor for severe gastric diseases that will develop late in adult life in a minority of infected patients, i.e., peptic ulcer disease, both gastric and duodenal ulcers, and gastric cancer, namely, adenocarcinoma and mucosa associated lymphoid tissue (MALT) lymphoma (reviewed in [3]). Peptic ulcer disease rarely occurs soon after H. pylori infection [4-8] that generally starts in childhood; this presumably reflects marked differen‐ ces in the virulence [9-16] and/or in the susceptibility of young patients [17-19].
Capacidade erro-zero de canais quânticos e estados puros

Resumo— Neste trabalho e mostrado que a capacidade errozero para a transmissao de informacao classica atraves de canais quânticos e calculada considerando somente estados puros na entrada do canal. Este resultado e usado para calcular a capacidade classica de erro-zero de alguns canais quânticos. Por fim, sao apresentados alguns resultados preliminares no calculo da capacidade quando o canal quântico e usado n vezes para a transmissao de um unico estado quântico de entrada. Palavras-Chave— Canais quânticos, Capacidade erro-zero, Estados puros.
Assistance au fraisage par comanipulation en chirurgie orthopédique

Le fraisage de volumes osseux au cours de certaine chirurgie orthopedique comme la laminectomie est une etape delicate devant etre realisee avec une grande precision. En chirurgie conventionnelle, seuls les cliches radiographiques du patient permettent d'identifier les regions a retirer et les regions a proteger. Dans cette these, nous proposons plusieurs modes de commande d'un robot de comanipulation pour assister et securiser ce type de fraisage. L'apport du dispositif, en terme de precision, est evalue experimentalement par le fraisage de formes a geometrie donnee. Une premiere solution propose d'utiliser le robot pour imposer des contraintes virtuelles, definies suivant un profil d'effort particulier, sur l'environnement de travail de l'utilisateur afin de separer l'espace de travail en une region libre et une region interdite. Cette modalite ne fournit cependant pas une separation assez fine de ces deux regions pour l'utilisateur. Une seconde modalite est alors proposee pour ameliorer la precision : un retour visuel, constitue d'un barre-graphe unidimensionnel a LED , est positionne sur l'outil de fraisage. Placee dans le champ de vision de l'utilisateur lors de la tâche, l'information transmise est relative a la position de l'outil vis-a-vis de la frontiere entre les deux regions. Dans la derniere partie de ces travaux, nous proposons une solution pour compenser les mouvements physiologiques du patient et recaler les modeles geometriques en temps reel. Un capteur a lumiere structuree, implemente directement sur le poignet du robot, permet de mesurer les mouvements relatifs de l'environnement vis-a-vis de l'outil comanipule.
Microwave Imaging for Breast Cancer

Microwaves and millimeter waves have been used extensively to image dielectric bodies. The application of microwaves in biomedical imaging and diagnostics, however, remains a field with many uncharted territories. This article is an overview on medical imaging using microwave imaging for breast cancer and its challenges, hopes, and outlook.
Deep Learning for Facial Keypoints Detection

A new area of machine learning research called deep learning has moved machine learning closer to one of its original goals: artificial intelligence and feature learning. Originally the key idea of training deep networks was to pretrain models in completely unsupervised way and then fine-tune the parameters for the task at hand using supervised learning. In this study, deep learning is applied to a facial keypoints detection. The task is to predict the positions of 15 keypoints on grayscale face images. Each predicted keypoint is specified by a realvalued pair in the space of pixel coordinates. In the experiments, we pretrained a Deep Belief Network (DBN) and finally performed discriminative fine-tuning. We varied the depth and size of the network. We tested both deterministic and sampled hidden activations, and the effect of additional unlabeled data on pretraining. The experimental results show that our model provides better results than the publicly available benchmarks for
Falls and Fall Injuries Among Adults Aged ≥65 Years - United States, 2014.

Falls are the leading cause of fatal and nonfatal injuries among adults aged ≥65 years (older adults). During 2014, approximately 27,000 older adults died because of falls; 2.8 million were treated in emergency departments for fall-related injuries, and approximately 800,000 of these patients were subsequently hospitalized. * To estimate the numbers, percentages, and rates of falls and fall injuries among older adults by selected characteristics and state, CDC analyzed data from the 2014 Behavioral Risk Factor Surveillance System (BRFSS) survey. In 2014, 28.7% of older adults reported falling; the estimated 29.0 million falls resulted in 7.0 million injuries. Known effective strategies for reducing the number of older adult falls include a multifactorial clinical approach (e.g., gait and balance assessment, strength and balance exercises, and medication review). Health care providers can play an important role in fall prevention by screening older adults for fall risk, reviewing and managing medications linked to falls, and recommending vitamin D supplements to improve bone, muscle, and nerve health and reduce the risk for falls.
Clinical utility of multiple stool ova and parasite examinations in low-prevalence patient populations.

algorithm (shown in figure 1 in our article [2]) if they are serving a population with low or moderate prevalence (as defined in our article). We agree with Suputtamongkol et al. [6] that our approach may not be applicable in all settings. First, the most frequently detected pathogenic parasites (i.e., Srongyloides stercoralis, Cryptosporidium species, and Opisthorchis viverrini) listed in their report differ considerably from those reported in our study. Secondly, their stool ova and parasite procedure differs importantly from ours in that it does not include a general-purpose, permanently stained smear (e.g., GomoriWheatley trichrome, iron hematoxylin, or chlorazol black E stain), which aids in the detection of intestinal protozoa [7] and is a significant component of the comprehensive examination on which our findings and recommendations are based.
Shape analysis of molecular surfaces

The description of molecular shape is important in the analysis of protein–protein and protein–ligand interactions. We describe volumetric and surface‐based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface‐based approach, the matrix is the approximate gradient of the surface normal. Derivatives 4 are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu‐Zu superoxide dismutase. © 1993 John Wiley & Sons, Inc.
A Multilevel NER Framework for Automatic Clinical Name Entity Recognition

In this paper, we propose a novel multilevel NER framework, for addressing the challenges of clinical name entity recognition, based on different machine learning and text mining algorithms. The proposed framework, with multiple levels, allows models for increasingly complex NER tasks to be built. The experimental evaluation on two different publicly available datasets, corresponding to different application contexts - the CLEF 2016 challenge shared task 1A for nursing handover context, and the BIONLP/NLPBPA 2004 challenge shared task on GENIA corpus for recognizing entities in microbiology, has validated the proposed framework.
Turbo equalization for single-carrier underwater acoustic communications

Recent research in underwater acoustic communications has taken advantage of MIMO technologies to achieve reliable communication with 10-100 times increase of data rate in comparison to traditional systems. The powerful turbo equalization and FEC coding techniques enable both single-carrier modulation and OFDM systems to combat triply selective UWA channels. This article reviews the time-domain and frequency-domain turbo equalizer schemes for MIMO SCM systems. Low-complexity techniques are presented with both turbo linear equalizers and turbo soft decision feedback equalizers in both the time and frequency domains. Although results are shown specifically for UWA channels, these turbo equalizer techniques are also suitable for terrestrial RF communication systems.
Experience with executing shared memory programs using fine-grain communication and multithreading in EM-4

We present our experience and results obtained from executing shared memory application programs using fine-grain remote memory access communication and multithreading in the EM-4 multiprocessor. The EM-4 is a distributed memory multiprocessor which has a dataflow mechanism. The dataflow mechanism enables a fine-grain communication packet through the network to invoke the thread of control dynamically with very small overhead and is extended to access remote memory in different processors. We hide the remote memory access latencies with multithreading. The benchmark results show that shared memory applications achieve reasonable speedup with four to eight threads in the EM-4 prototype. We found that aggressive multithreading can negatively affect its network interface and increase the network contention. We also describe the EM-4 parallel programming language called EM-C, which provides the notion of a global address space and parallel constructs for exploiting medium-grain parallelism to tolerate several remote operation latencies. <<ETX>>
Evaluation of the Response Bias Scale and Improbable Failure Scale in Assessing Feigned Cognitive Impairment

The present study evaluated the Response Bias scale (RBS), a symptom validity test embedded within the Minnesota Multiphasic Personality Inventory (MMPI)-2 Restructured Form (MMPI-2-RF) that assesses for feigned neurocognitive complaints, in a sample of pretrial incompetent to stand trial (IST) criminal defendants. Additionally, we examined the Improbable Failure (IF) scale, a performance validity test embedded within the Structured Interview of Reported Symptoms, Second Edition (SIRS-2), which similarly assesses for feigned cognitive impairment (FCI). Results indicated that both the RBS (area under the curve [AUC] = .76) and IF scale (AUC = .72) achieved moderate classification accuracy using the Test of Memory Malingering (TOMM) as the criterion. Further, the RBS and IF scale appeared to be most useful for screening out those defendants who presented as genuine (specificity = 99% and 88%, respectively), and less effective at classifying those defendants suspected of feigning according to the TOMM (sensitivity = 29% and 46%, respectively). In order to identify a significant proportion of IST defendants who may be feigning impairment, considerably lower cutoff scores than those recommended in each measure’s manual were evaluated. An RBS T score of 63 (sensitivity = 86%; specificity = 37%), and IF scale raw score of 2 (sensitivity = 80%; specificity = 43%), was required to achieve ≥80% sensitivity; these alternate cutoff scores may therefore be useful when screening inpatient forensic psychiatric IST defendants. Further, the 2 scales effectively predicted TOMM classification in combination, although only the RBS significantly contributed to the model. Implications for the assessment of FCI in forensic psychiatric settings are discussed.
Ensemble Learning and Optimizing KNN Method for Speaker Recognition

Ensemble with K Nearest Neighbor (KNN) learner is a novel approach to speaker recognition. It has many advantages over other conversational methods such as simplicity and good generalization ability. At the same time, the generalization ability of an ensemble could be significantly better than that of a single learner. In this paper, we intend to improve the performance of the speaker recognition system by introducing a novel method combining optimizing annular region-weighted distance k nearest neighbor with BagWithProb ensemble learning schemes. Experiments studied in this paper indicate that the proposed method can effectively improve the accuracy of speaker identification system.
Information Processing and Management

, thus contributing to improve the effectiveness of the ranked results across different types of queries. Our approach relies on a novel temporal similarity measure that is capable of determining the most important dates for a query, while ﬁltering out the non-relevant ones. Through extensive experimental evaluation over web corpora, we show that our model offers promising results compared to baseline approaches. As a result of our investigation, we publicly provide a set of web services and a web search interface so that the system can be graphically explored by the research community. © 2015 Elsevier Ltd. All rights reserved.