Miracle-dz/UniFAR-FTUs huggingface dataset:
Discussion and revision of the mathematical modeling tool described in the previously published article “Modeling HIV Transmission risk among Mozambicans prior to their initiating highly active antiretroviral therapy”

Abstract Mathematical models are increasingly used in social and behavioral studies of HIV transmission; however, model structures must be chosen carefully to best answer the question at hand and conclusions must be interpreted cautiously. In Pearson et al. (2007), we presented a simple analytically tractable deterministic model to estimate the number of secondary HIV infections stemming from a population of HIV-positive Mozambicans and to evaluate how the estimate would change under different treatment and behavioral scenarios. In a subsequent application of the model with a different data set, we observed that the model produced an unduly conservative estimate of the number of new HIV-1 infections. In this brief report, our first aim is to describe a revision of the model to correct for this underestimation. Specifically, we recommend adjusting the population-level sexually transmitted infection (STI) parameters to be applicable to the individual-level model specification by accounting for the proportion of individuals uninfected with an STI. In applying the revised model to the original data, we noted an estimated 40 infections/1000 HIV-positive persons per year (versus the original 23 infections/1000 HIV-positive persons per year). In addition, the revised model estimated that highly active antiretroviral therapy (HAART) along with syphilis and herpes simplex virus type 2 (HSV-2) treatments combined could reduce HIV-1 transmission by 72% (versus 86% according to the original model). The second aim of this report is to discuss the advantages and disadvantages of mathematical models in the field and the implications of model interpretation. We caution that simple models should be used for heuristic purposes only. Since these models do not account for heterogeneity in the population and significantly simplify HIV transmission dynamics, they should be used to describe general characteristics of the epidemic and demonstrate the importance or sensitivity of parameters in the model.
Deep Matrix Factorization Models for Recommender Systems

Recommender systems usually make personalized recommendation with user-item interaction ratings, implicit feedback and auxiliary information. Matrix factorization is the basic idea to predict a personalized ranking over a set of items for an individual user with the similarities among users and items. In this paper, we propose a novel matrix factorization model with neural network architecture. Firstly, we construct a user-item matrix with explicit ratings and non-preference implicit feedback. With this matrix as the input, we present a deep structure learning architecture to learn a common low dimensional space for the representations of users and items. Secondly, we design a new loss function based on binary cross entropy, in which we consider both explicit ratings and implicit feedback for a better optimization. The experimental results show the effectiveness of both our proposed model and the loss function. On several benchmark datasets, our model outperformed other state-of-the-art methods. We also conduct extensive experiments to evaluate the performance within different experimental settings.
Rising Levels of Human Cytomegalovirus (HCMV) Antigenemia during Initial Antiviral Treatment of Solid-Organ Transplant Recipients with Primary HCMV Infection

ABSTRACT In 7 of 18 solid-organ transplant recipients with primary human cytomegalovirus (HCMV) infection, HCMV antigenemia levels were unexpectedly found to rise significantly (P = 0.018) during a mean time of 7.3 ± 3.2 days after initiation of specific antiviral treatment, whereas corresponding levels of viremia dropped significantly (P = 0.043). Thus, shifting to an alternative antiviral drug based solely on increasing antigenemia levels is not justified in this group of patients.
FIVE YEARS OF ALCOHOL DE-ADDICTION SERVICES IN A TERTIARY CARE GENERAL HOSPITAL

This paper highlights the characteristics of 800 alcohol-dependent patients treated at a drug de-addiction centre, over a period of 5 years. The mean score on SADD (severity of alcohol dependence data) questionnaire was 23.95, which indicates a severe level of dependence. Followup analysis of 607 cases showed that 379 (62.4%) patients had not utilised the follow-up services beyond one month. Discussion focuses on retaining patients in follow-up.
Biologia reprodutiva e conservação do estrato lenhoso numa comunidade do cerrado

A biologia reprodutiva de especies arbustivo-arboreas foi avaliada em uma comunidade de cerrado (sensu stricto), em Mato Grosso, Brasil. O levantamento floristico revelou um total de 131 especies, distribuidas em 45 familias e 92 generos determinados, em uma area de 4,9 ha. Estudos sobre a estrutura da comunidade, usando metodos fitossociologicos, envolveram 69% (90/131) das especies lenhosas; os resultados apontaram densidade populacional mediana de 8 individuos/ha. A maioria das especies exibiu florescimento (83%, 109/131) e frutificacao (62%, 81/131), durante dois anos de acompanhamento fenologico. A producao de flores e frutos ocorreu com frequencia anual, episodica ou continua. Entre as especies com atividade reprodutiva foi observada interacao com animais, na polinizacao das flores (94,5%, 103/109) e na dispersao das sementes (53%, 43/81). A polinizacao por animais pode ser ordenada em seis sistemas basicos, definidos segundo a categoria de visitantes - abelhas, besouros, mariposas, animais diversos, morcegos e beijaflores. O vento tambem pode atuar como agente polinizador (5,5%, 6/109) e, principalmente, como dispersor (36%, 29/81). A dispersao de sementes ainda e desenvolvida atraves de mecanismos autocoricos (11 %, 9/81). Seis sistemas sexuais foram identificados no estrato estudado, com maior destaque para o hermafroditismo (77%,101/131) e a dioicia (15%, 20/131). Informacoes disponiveis para 60 especies, revelam que o sistema reprodutivo adotado, pela maioria, e a xenogamia (70%, 42/60), a xenogamia facultativa (25%, 15/60) e a autogamia (3,4%, 2/60). Apenas uma especie (1,6%, 1/60), deste total, apresenta indicios de agamospermia. Estudos envolvendo sistema subterrâneo, num grupo de 22 especies, descrevem a ocorrencia de propagacao vegetativa em sete (32%) e capacidade de regeneracao em 16 (73%). Entre as especies com propagacao vegetativa somente uma (Hexaclamys aft. edu/is) nao produziu sementes. A baixa densidade populacional registrada para muitas especies, dependencia por animais na polinizacao e dispersao e a existencia de varias especies com fecundacao cruzada obrigatoria (auto-incompativeis e dioicas) conferem fragilidade a comunidade. Para a conservacao da mesma, mantendo a integridade de seus processos ecologicos, e necessario que as pressoes (fragmentacao, isolamento, perturbacoes) sobre o cerrado estudado sejam minimizadas Abstract
The effects of ethanol on CA(2+) sensitivity in airway smooth muscle.

UNLABELLED Halothane and other volatile anesthetics relax air-way smooth muscle (ASM) in part by decreasing the amount of force produced for a given intracellular Ca(2+) concentration (the Ca(2+) sensitivity) during muscarinic receptor stimulation. To determine whether this is a unique property of the volatile anesthetics, we tested the hypothesis that ethanol, another compound with anesthetic properties, also inhibits calcium sensitization induced by muscarinic stimulation of ASM. A beta-escin permeabilized canine tracheal smooth muscle preparation was used. Ethanol was applied to permeabilized muscles stimulated with calcium in either the absence or presence of acetylcholine. In intact ASM, ethanol produced incomplete relaxation (approximately 40%) at concentrations up to 300 mM. Ethanol significantly increased Ca(2+) sensitivity both in the presence and the absence of muscarinic receptor stimulation. Although ethanol did not affect regulatory myosin light chain (rMLC) phosphorylation during stimulation with Ca(2+) alone, it decreased rMLC phosphorylation by Ca(2+) during muscarinic receptor stimulation. Ethanol, like volatile anesthetics, inhibits increases in rMLC phosphorylation produced by muscarinic receptor stimulation at constant [Ca(2+)](i). However, despite this inhibition, the net effect of ethanol is to increase Ca(2+) sensitivity (defined as the force maintained for a given [Ca(2+)](i)) by a mechanism that is independent of changes in rMLC phosphorylation. IMPLICATIONS In permeabilized airway smooth muscle, ethanol, like volatile anesthetics, inhibits increases in regulatory protein phosphorylation caused by stimulation of the muscle when intracellular calcium concentration is constant. However, unlike volatile anesthetics, ethanol causes a net increase in force through a process not dependent on protein phosphorylation, an action favoring bronchoconstriction.
Optimal Insurance Demand when Contract Nonperformance Risk is Perceived as Ambiguous

We study the optimal insurance demand of a riskand ambiguity-averse consumer if contract nonperformance risk is perceived as ambiguous. We find that the consumer’s optimal insurance demand is lower compared to a situation without ambiguity and that his degree of ambiguity aversion is negatively associated with the optimal level of coverage. We also determine sufficient conditions for biased beliefs or greater ambiguity to reduce the optimal demand for insurance and discuss wealth effects. Finally, we scrutinize several alternative model specifications to demonstrate the robustness of our main findings and discuss implications of our findings.
The reliability of cluster and switch scores for the Controlled Oral Word Association Test.

This study examined the interrater reliability and temporal stability of a scoring system developed by Troyer, Moscovich, and Winocur [Neuropsychologia 11 (1997) 138] to measure clustering and switching on verbal fluency (VF) tasks such as the Controlled Oral Word Association Test (COWAT) [Benton, A.L. , Hamsher, K. , & Sivan, A.B. (1983). Multilingual aphasia examination (3rd ed.). Iowa City, IA: AJA Associates]. Seven independent raters scored COWAT protocols of 125 healthy participants in accordance with the rules proposed by Troyer et al. Intraclass coefficients were near perfect, ranging from.96 for total number of clusters to.99 for total number of switches. Test-retest reliability coefficients (n=55) were poor to modest (r=.47 for clusters, r=.58 for switches, and r=.70 for total words). Significant improvement in performance was observed across most COWAT indices, suggesting a practice effect. Modifications to test administration are suggested to improve the stability of cluster and switch scores, as well as other variables for further study.
Robust Adaptive Position Mooring Control for Marine Vessels

In this paper, robust adaptive control with dynamic control allocation is proposed for the positioning of marine vessels equipped with a thruster assisted mooring system, in the presence of parametric uncertainties, unknown disturbances and input nonlinearities. Using neural network approximation and variable structure based techniques in combination with backstepping and Lyapunov synthesis, the positioning control is developed to handle the uncertainties, input saturation and dead-zone characteristics of the mooring lines and thrusters. Full state feedback with all states measurable and output feedback using high gain observer to estimate unmeasurable states are considered. Dynamic control allocation is presented for actuation of the position mooring system. Under the proposed robust adaptive control, semi-global uniform boundedness of the closed-loop signals are guaranteed. Numerical simulations are carried out to show the effectiveness of the proposed control.
Colorimetric Nucleic Acid Testing Assay for RNA Virus Detection Based on Circle-to-Circle Amplification of Padlock Probes

ABSTRACT We developed a molecular diagnostic method for detection of RNA virus based on padlock probes and colorimetric readout. The feasibility of our approach was demonstrated by using detection of Crimean-Congo hemorrhagic fever (CCHF) virus as a model. Compared with conventional PCR-based methods, our approach does not require advanced equipment, involves easier assay design, and has a sensitivity of 103 viral copies/ml. By using a cocktail of padlock probes, synthetic templates representing different viral strain variants could be detected. We analyzed 34 CCHF patient samples, and all patients were correctly diagnosed when the results were compared to those of the current real-time PCR method. This is the first time that highly specific padlock probes have been applied to detection of a highly variable target sequence typical of RNA viruses.
Long‐term antiepileptic drug therapy contributes to the acceleration of atherosclerosis

Purpose: Long‐term antiepileptic drug (AED) therapy has been associated with an increase in risk of atherosclerosis. At issue is whether this risk is related to the duration of AED therapy. We evaluated the hypothesis that the cumulative effect of long‐term exposure to AEDs plays a pivotal role in the pathogenesis of atherosclerosis in patients with epilepsy.
Spermine oxidase, a polyamine catabolic enzyme that links Helicobacter pylori CagA and gastric cancer risk

We have recently reported that Helicobacter pylori strains expressing the virulence factor cytotoxin-associated gene A (CagA) stimulate increased levels of spermine oxidase (SMO) in gastric epithelial cells, while cagA– strains did not. SMO catabolizes the polyamine spermine and produces H2O2 that results in both apoptosis and DNA damage. Exogenous overexpression of CagA confirmed these findings, and knockdown or inhibition of SMO blocked CagA-mediated apoptosis and DNA damage. The strong association of SMO, apoptosis, and DNA damage was also demonstrated in humans infected with cagA+, but not cagA– strains. In infected gerbils and mice, DNA damage was CagA-dependent and only present in epithelial cells that expressed SMO. We also discovered SMOhigh gastric epithelial cells from infected animals with dysplasia that are resistant to apoptosis despite high levels of DNA damage. Inhibition of polyamine synthesis or SMO could abrogate the development of this cell population that may represent precursors for neoplastic transformation.
Albumen foam stability and s-ovalbumin contents in eggs coated with whey protein concentrate

Food products such as breads, cakes, crackers, meringues, ice creams and several bakery items depend on air incorporation to maintain their texture and structure during or after processing. Proteins are utilized in the food industry since they improve texture attributes through their ability to encapsulate and retain air. The objectives of this work were to quantify s-ovalbumin contents in albumen and to determine alterations in egg white foam stability in fresh eggs, and in eggs coated and non-coated with a whey protein-based concentrate film (WPC), stored at 25°C for 28 days. The volume of drained liquid was higher in non-coated eggs than in coated eggs stored at 25°C at all storage periods. The difference on the third day of storage was in the order of 59% between coated and non-coated eggs, while on the twenty-eighth day it was 202%. During the storage period, an increase in pH and drainage volume was observed for non-coated eggs. After three days, the non-coated eggs showed a s-ovalbumin content 33% higher than coated eggs; this increase jumped to 205% at 28 days of storage. There was a positive correlation between s-ovalbumin content and the volume of drained liquid for coated and non-coated eggs; in other words, when the s-ovalbumin content increased, there was an increase in the volume of drained liquid and a decrease in foam stability. WPC coating maintain egg quality, since it is an effective barrier against the loss of CO2, avoiding changes in the pH of egg white.
More Than An Answer: Neural Pivot Network for Visual Qestion Answering

Most of existing works in visual question answering (VQA) are dedicated to improving the performance of answer predictions, while leaving the explanation of answering unexploited. We argue that, exploiting the explanations of question answering not only makes VQA explainable, but also quantitatively improves the prediction performance. In this paper, we propose a novel network architecture, termed Neural Pivot Network (NPN), towards simultaneous VQA and generating explanations in a multi-task learning architecture. NPN is trained by using both image-caption and image-question-answer pairs. In principle, CNN-based deep visual features are extracted and sent to both the VQA channel and the captioning module, the latter of which serves as a pivot to bridge the source image module to the target QA predictor. Such an innovative design enables us to introduce large-scale image-captioning training sets, e.g., MS-COCO Caption and Visual Genome Caption, together with cutting-edge image captioning models to benefit VQA learning. Quantitatively, the proposed NPN performs significantly better than alternatives and state-of-the-art schemes trained on VQA datasets only. Besides, by investigating the by-product of experiments, in-depth digests can be provided along with the answers.
Integration host factor is involved in transcriptional regulation of the Brucella abortus virB operon

Type IV secretion systems (T4SSs) are multicomponent machineries that play an essential role in pathogenicity of many facultative intracellular bacteria. The virB operon of Brucella abortus codes for a T4SS essential for virulence and intracellular multiplication. Here, virB expression analyses carried out using lacZ transcriptional fusions showed that virB promoter (PvirB) is temporally activated within J774 cells. Primer extension experiments revealed that virB transcription starts at 27 bp upstream of the first gene of the virB operon. Structural analyses showed that PvirB and regulatory sequences involved in intracellular regulation span 430 bp upstream of the transcription start site. A protein able to bind PvirB was isolated and identified. This protein, homologue to integration host factor (IHF), specifically interacts with PvirB and induces a DNA bending with an angle of 50.36°. DNAse I footprinting experiments showed that IHF protects a 51 bp region that contains two overlapped IHF binding consensus motifs. VirB expression experiments carried out with PvirB‐lacZ fusions showed that in B. abortus IHF participates in the regulation of PvirB activity during the intracellular and vegetative growth in different media. A mutant strain with a 20 bp IHF binding site replacement failed to turn on the virB operon during the initial stages of macrophage infection and displayed severe intracellular multiplication defects. These data indicate that IHF plays a key role during intracellular virB operon expression being required for the biogenesis of the endoplasmic reticulum‐derived replicative vacuole.
Weight gain profiles of new anti‐psychotics: public health consequences

Anti‐psychotic medications are an important therapeutic option for many individuals with schizophrenia. Recently, a growing interest has been observed on weight gain, which is now a well‐known adverse effect of many anti‐psychotics. As obesity is frequently a comorbid condition with schizophrenia, patients with schizophrenia are inherently at increased risk of developing obesity‐related conditions such as cardiovascular disease and type 2 diabetes. The consequences of excessive weight gain (obesity) associated with anti‐psychotic drugs are likely to include adverse effects on health, social burden and poor compliance or even discontinuation of therapy by the patients. In this article, we focus on different aspects of weight gain induced by anti‐psychotics. This review comprises the following sections: (i) the pharmacological basis of anti‐psychotic‐induced weight gain and metabolic effects with a review of all anti‐psychotics that can be used in patients with schizophrenia; (ii) the clinical impact of the body weight gain (morbidity, psychatric consequences, mortality); (iii) the management of obesity (identification of risk factors including pharmacogenetics, diet, behavioural therapies, pharmacological approach). An understanding of these aspects is important for those who prescribe anti‐psychotics in order to provide the patient the best therapeutic management.
Hospitalist involvement in internal medicine residencies.

CONTEXT The ways hospitalists interact with and contribute to internal medicine residencies in the United States have been described locally, but have not been documented on a national level. OBJECTIVES To describe the penetration of hospitalists into medicine residency faculty nationally, and document their contributions to teaching activities. DESIGN, SETTING, AND PARTICIPANTS Survey of all 386 internal medicine residency directors in the United States in 2005 (272 respondents) and 2007 (236 respondents). MEASUREMENTS Number of teaching hospitals utilizing hospitalists, number of programs utilizing hospitalists to teach, hospitalist teaching duties, and number with hospitalist tracks. RESULTS In 2005, program directors recalled 54% of teaching hospitals employed hospitalists before and 73% after implementation of work-hour limitations. Of those employing hospitalists, 92% of programs in the Northeast and West used them to teach. Two years later, the Midwest (78%) and South (76%) continued to lag behind in the proportion of teaching hospitalists. Specific teaching activities of hospitalists included: attending on teaching service (92%), conducting rounds (81%), observation of clinical skills (67%), lectures (68%), and morning report (52%). Seven percent of program directors reported other duties of hospitalists, including: supervising procedures, reviewing night float patients, serving as associate program directors, and writing curricula. Eleven percent of training programs had hospitalist tracks. CONCLUSIONS As hospitalists have become prevalent and have become efficient clinicians in community and university hospitals, the majority of internal medicine residencies have enlisted them to provide rounds, lectures, and bedside teaching. A small number of residencies are beginning to develop tracks to facilitate this new career option for graduates.
Overnight theophylline concentrations and effects on sleep and lung function in chronic obstructive pulmonary disease.

Circadian alterations in lung function occur in respiratory disorders, with the nadir during the sleep-related hours. Higher therapeutic serum theophylline concentrations (STC) during the night have been shown to improve lung function in reversible airway disease. To determine what effect higher nocturnal STC would have in patients with chronic obstructive pulmonary disease (COPD) on overnight lung function, oxygen saturation, and sleep quality, two different theophylline products were used to give higher or lower STC during the night. We found that with a higher STC (15.0 +/- 1.0 versus 11.0 +/- 1.0 micrograms/ml, p = 0.005) at 7:00 A.M., the overnight changes in FEV1 (+7.4 +/- 5.7% versus -18.9 +/- 7.9%, respectively) and FVC (+1.8 +/- 7.5% versus -17.2 +/- 3.9%, respectively) were significantly better. However, there was no apparent effect on oxygen saturation (mean sleep values for higher STC were 85.3 +/- 1.2%, and for lower STC they were 86.5 +/- 0.8%). The higher STC did not adversely affect sleep latency, sleep efficiency, or sleep staging. We conclude that a higher therapeutic STC during sleep will improve lung function without altering oxygen saturation in patients with COPD. In this group of patients, the higher STC did not interfere with sleep characteristics.