Miracle-dz/UniFAR-FTUs huggingface dataset:
Lansoprazole and secnidazole with clarithromycin, amoxycillin or pefloxacin in the eradication of Helicobacter pylori in a developing country

A number of triple drug regimens using proton pump inhibitors and two antibiotics have been evaluated in the West and reported to achieve Helicobacter pylori eradication rates of over 90%. In developing countries however, these combinations have neither been well evaluated, nor the optimum treatment for H. pylori infection well defined.
Symptom Prevalence of ADHD and ODD in a Pediatric Population in Argentina

Objective: To assess the prevalence of DSM III-R symptoms of attention deficit hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD) in an outpatient pediatric population; to compare oppositional behavior and grade retention rates; and to establish local means and standard deviations (SD) for the ADHD rating scale. Method: 300 children (149m, 151f; 6 to12 yrs) were evaluated for ADHD and ODD symptoms with the DuPaul and an author-designed rating scale, respectively. Scores 1.5 SD above the mean were considered positive for each disorder. Results: A total of 27 subjects (13m, 14f), 9%, had positive scores consistent with ADHD. These children had an oppositional behavior rate of 33.3% and a grade retention rate of 30.7%. Those who did not have positive scores for ADHD had a rate of 5.5% and 7.3%, respectively. The mean scores for the boys on the ADHD rating scale was 17.1 (SD = 8.6); the girls had a mean of 14.7 (SD = 7.3). Conclusion: The prevalence rates in our study are similar to those found in other countries (J. of Att. Dis. 2007; Vol 11(3) 363-367)
Association Between Total Hip Replacement Characteristics and 3-Year Prosthetic Survivorship: A Population-Based Study.

IMPORTANCE Total hip replacement (THR) is successful in treating hip arthritis. Prosthetic survivorship may depend on characteristics of the implant, notably THR fixation technique and bearing surface type. OBJECTIVE To compare THR short-term survivorship according to cement type and bearing surface. DESIGN, SETTING, AND PARTICIPANTS The cohort included all French patients aged 40 years or older covered by the general scheme of the French national health insurance system who had undergone THR from April 1, 2010, through December 31, 2011, for arthritis, according to French national health insurance databases. The cohort was followed up until December 31, 2013. The THR survivorship was assessed according to cement type and bearing surface in univariate and multivariate Cox proportional hazards regression models adjusted for patient and implanting center characteristics. EXPOSURES Antibiotic-free cemented THRs and antibiotic-impregnated cemented THRs were compared with uncemented THRs. Ceramic-on-ceramic (CoC), ceramic-on-polyethylene (CoP), and metal-on-metal (MoM) THRs were compared with metal-on-polyethylene (MoP) THRs. MAIN OUTCOMES AND MEASURES Revision, including any surgical reintervention in which the implant or any of its components was changed or removed. RESULTS The study cohort comprised 100 191 individuals: mean age at baseline, 69.5 years; women, 56.6%; uncemented THR, 74.8%; antibiotic-free cemented THR, 3.8%; antibiotic-impregnated cemented THR, 21.4%; CoC, 40.9%; MoP, 33.9%; CoP, 20.8%; and MoM, 4.4%. During the median 33-month follow-up period, 3142 individuals underwent prosthetic revision. Antibiotic-impregnated cemented THRs had a better prognosis than uncemented THRs: cumulative revision rates were 2.4% and 3.3%, respectively (P < .001), and the multivariate adjusted hazard ratio was 0.75 (95% CI, 0.67-0.84; P < .001). This association was particularly significant in women. The CoP and CoC THRs were no different from the MoP THR. The MoM THR had slightly shorter survivorship compared with the MoP THR (adjusted hazard ratio, 1.20; 95% CI, 1.01-1.43; P < .001). CONCLUSIONS AND RELEVANCE Characteristics of THR are related to early prosthetic revision: antibiotic-impregnated cemented THRs have a better prognosis and MoM THRs a worse one. These findings are useful in helping surgeons select a THR fixation technique and helpful for both patient and surgeon in the decision-making process.
New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina

ABSTRACT The symbiotic association between aphids (Homoptera) and Buchnera aphidicola (Gammaproteobacteria) started about 100 to 200 million years ago. As a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. The downsize genome process starts when the bacterium enters the host and will probably end with its extinction and replacement by another healthier bacterium or with the establishment of metabolic complementation between two or more bacteria. Nowadays, several complete genomes of Buchnera aphidicola from four different aphid species (Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistacea, and Cinara cedri) have been fully sequenced. C. cedri belongs to the subfamily Lachninae and harbors two coprimary bacteria that fulfill the metabolic needs of the whole consortium: B. aphidicola with the smallest genome reported so far and “Candidatus Serratia symbiotica. ” In addition, Cinara tujafilina, another member of the subfamily Lachninae, closely related to C. cedri, also harbors “Ca. Serratia symbiotica” but with a different phylogenetic status than the one from C. cedri. In this study, we present the complete genome sequence of B. aphidicola from C. tujafilina and the phylogenetic analysis and comparative genomics with the other Buchnera genomes. Furthermore, the gene repertoire of the last common ancestor has been inferred, and the evolutionary history of the metabolic losses that occurred in the different lineages has been analyzed. Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts.
Demystifying ResNet

The Residual Network (ResNet), proposed in He et al. (2015), utilized shortcut connections to significantly reduce the difficulty of training, which resulted in great performance boosts in terms of both training and generalization error. It was empirically observed in He et al. (2015) that stacking more layers of residual blocks with shortcut 2 results in smaller training error, while it is not true for shortcut of length 1 or 3. We provide a theoretical explanation for the uniqueness of shortcut 2. We show that with or without nonlinearities, by adding shortcuts that have depth two, the condition number of the Hessian of the loss function at the zero initial point is depth-invariant, which makes training very deep models no more difficult than shallow ones. Shortcuts of higher depth result in an extremely flat (high-order) stationary point initially, from which the optimization algorithm is hard to escape. The shortcut 1, however, is essentially equivalent to no shortcuts, which has a condition number exploding to infinity as the number of layers grows. We further argue that as the number of layers tends to infinity, it suffices to only look at the loss function at the zero initial point. Extensive experiments are provided accompanying our theoretical results. We show that initializing the network to small weights with shortcut 2 achieves significantly better results than random Gaussian (Xavier) initialization, orthogonal initialization, and shortcuts of deeper depth, from various perspectives ranging from final loss, learning dynamics and stability, to the behavior of the Hessian along the learning process.
Association between dietary fiber and incident cases of colon polyps: the adventist health study.

BACKGROUND Colorectal cancer (CRC) is a leading cause of cancer death in the United States. Most cases of CRC arise in adenomatous polyps. It has been estimated that 25%-35% of colon adenoma risk could be avoidable by modification of dietary and life-style habits. METHODS We estimated the association between total dietary fiber and fiber intake from fruits, vegetables, and grains, and the risk of physician-diagnosed colon polyps among 2818 men and women who had undergone colonoscopy. Data were drawn from 2 cohort studies-the Adventist Health Study-1 (AHS-1) of 1976 and the Adventist Health Study-2 (AHS-2) conducted from 2002 to 2005. Dietary information was obtained from the self-administered questionnaire from AHS-1, while outcome was assessed from AHS-2 data. Multivariate logistic regression analysis was used to estimate the period risk of incident cases of polyps. RESULTS A total of 441 incident cases of colon polyps were identified. After adjusting for age, sex, body mass index, physical activity, education, and alcohol and meat consumption, total fiber intake was inversely associated with the risk of colon polyps (odds ratio [OR] for highest vs lowest quartile = 0.71, 95% confidence interval [CI] 0.51-0.99). This association showed a dose-response effect (p = .04). Analyses of various sources of fiber showed the most clear effect of fiber from vegetables including legumes (OR for highest vs lowest quartile = 0.65; 95% CI 0.47-0.90; p = .02). CONCLUSIONS In this population comprising a high proportion of vegetarians, persons who consumed low amounts of fiber, especially fiber contained in vegetables, had a higher risk of developing colon polyps.
Intraocular pressure fluctuations: how much do they matter?

Purpose of review To review the current literature with regard to the importance of IOP fluctuation/variation as independent risk factors for glaucoma progression. Recent findings There are conflicting reports in the literature assessing the relative importance of ‘intraocular pressure (IOP) fluctuation’ and ‘mean IOP’ as risk factors for glaucoma progression. There has been a trend toward more studies concluding that IOP fluctuation is an important independent risk factor for such progression but there is considerable variability in the quality of such studies. In particular, assumptions regarding causality have created doubt regarding some conclusions. Recent studies have also suggested that we should not abandon mean IOP as the important predictor of glaucoma progression. It should be noted that several analyses pertaining to this subject have emerged from large prospective randomized clinical trials primarily designed to answer other questions. Summary A review of the literature reveals that there is no conclusive evidence that IOP fluctuation/variation are independent risk factors for glaucoma progression. One should not discount the importance of mean IOP as a predictor of such progression. A major factor limiting all analyses pertaining to this issue is the inability to continuously measure IOP and thus optimally assess mean and variability.
Surface ultrastructure of larval mouthpart sensilla of the muga silkmoth, Antheraea assamensis, an endemic species of North‐East India

Scanning electron microscopy of different larval stages of the muga silk moth Antheraea assamensis revealed the presence of sensilla chaetica, sensilla trichoidea, sensilla styloconica, gustatory sensilla, sensory pegs, placoid sensilla, etc., on their mouth parts. Some variations were observed in the number and sub‐types of sensilla in certain larval stages indicating some differences in sensitivity of the worms in different instars to the food plant and microhabitat. Microsc. Res. Tech., 2010. © 2010 Wiley‐Liss, Inc.
The ALS6 and ALS7 genes of Candida albicans

ALS genes of Candida albicans encode a family of cell‐surface glycoproteins that are composed of an N‐terminal domain, a central domain of a tandemly repeated motif, and a relatively variable C‐terminal domain. Although several ALS genes have been characterized, more ALS‐like sequences are present in the C. albicans genome. Two short DNA sequences with similarity to the 5′ domains of known ALS genes were detected among data from the C. albicans genome sequencing project. Probes developed from unique regions of these sequences were used to screen a genomic library from which two full‐length genes, designated ALS6 and ALS7, were cloned. ALS6 and ALS7 encode features similar to other genes in the ALS family and map to chromosome 3, a chromosome previously not known to encode ALS sequences. ALS6 and ALS7 are present in all C. albicans strains examined. Additional analysis suggested that some C. albicans strains have another ALS gene with a 5′ domain similar to that of ALS6. Characterization of ALS7 revealed a novel tandemly repeated sequence within the C‐terminal domain. Unlike other ALS family tandem repeats, the newly characterized ALS7 repeat does not appear to define additional genes in the ALS family. However, our data and information from the C. albicans genome sequencing project suggest that there are additional ALS genes remaining to be characterized. Gene sequences of ALS6 (Accession No. AF075293) and ALS7 (Accession Nos. AF075294 and AF201684) were deposited in the GenBank database. Copyright © 2000 John Wiley & Sons, Ltd.
Degeneration and Regeneration of GABAergic Interneurons in the Dentate Gyrus of Adult Mice in Experimental Models of Epilepsy

Mounting evidence showed that GABAergic interneurons play an important role in the generation of seizures by regulating excitatory/inhibitory balance in the hippocampus; however, there is a continuous debate regarding the alteration in the number of hippocampal GABAergic interneurons during epileptogenesis. Here, we investigated the degeneration and regeneration of GABAergic interneurons in the dentate gyrus during epileptogenesis using glutamic acid decarboxylase‐green fluorescence protein (GAD67‐GFP) knock‐in mice.
INTERNATIONAL SYMPOSIUM ON OLFACTION AND TASTE Age-related Changes in Associative Learning for Olfactory and Visual Stimuli in Rodents

Memory for olfactory stimuli may be particularly affected by age-related brain changes in humans and may be an early indicator of cognitive impairment and Alzheimer’s disease. Studies involving rats have offered insights into impaired cognition in aged animals, but few have examined odor memory. Therefore, it is unclear whether aged rats are a good model for possible age-related changes in odor memory in humans. Young (6-month-old) and old (24-month-old) rats were tested on associative learning tasks involving visual and olfactory stimuli. The first task examined age-related differences in discrimination and reversal learning for olfactory and visual stimuli; the second task utilized an associative contextual learning task involving olfactory and visual cues. Although old rats were able to perform the olfactory and visual discrimination tasks as well as young rats, old rats displayed significant age-related impairment on the reversal learning and contextual learning tasks. The results suggest that aging may have a similar deleterious effect on odor memory in rats and in humans. The findings may have important implications for the selection of memory paradigms for future research studies on aging. In addition, the use of an animal model to investigate the effects of aging on odor memory will allow researchers the ability to investigate how age-related neuroanatomical and neurochemical changes may result in impaired odor memory.
Temporal effect of tumor necrosis factor alpha on murine macrophages infected with Mycobacterium avium

Members of the Mycobacterium avium complex are a family of bacteria that persist within macrophages in the face of an immune response. Elimination of these organisms is likely due to cytokine-induced macrophage activation. Because macrophage activation by tumor necrosis factor alpha (TNF-alpha) appears critical for killing of intracellular M. avium, early downregulation of TNF-alpha levels in infected macrophages has been suggested as a survival mechanism for virulent strains of M. avium. We examined the relationship between TNF-alpha and growth of M. avium strains of differing virulence, as measured by their ability to grow in murine bone marrow-derived macrophages. When exogenous TNF-alpha was added immediately following macrophage infection, significant growth inhibition of virulent M. avium strains was observed. If TNF-alpha addition was delayed by 24 h or more, growth inhibition was abrogated. To determine if early downregulation of TNF-alpha levels could explain the differential growth of virulent and avirulent strains, levels of TNF-alpha and prostaglandin E2 (PGE2), which has been shown to suppress TNF-alpha production in uninfected macrophages, were quantified over time. Upregulation of both TNF-alpha and PGE2, as measured by enzyme-linked immunosorbent assay, was evident by 6 h postinfection, indicating that the ability of M. avium to replicate in macrophages was not directly correlated with early downregulation of TNF-alpha production. However, TNF-alpha bioactivity, as measured by cytotoxicity, was significantly decreased in virulent M. avium strains at all time periods examined. Treatment of infected macrophages with gamma interferon immediately after infection resulted in significantly increased levels of nitric oxide but did not affect the growth of virulent M. avium strains. These results suggest that while significant levels of TNF-alpha are present in supernatants from all M. avium strains, levels of biologically active TNF-alpha are significantly reduced in supernatants from virulent M. avium strains. Preliminary results suggest that upregulation of the soluble p75 TNF receptor may be one mechanism by which TNF-alpha bioactivity reduction occurs.
Uterine leiomyomas: MR imaging-based thermometry and thermal dosimetry during focused ultrasound thermal ablation.

PURPOSE To retrospectively evaluate magnetic resonance (MR) imaging-based thermometry and thermal dosimetry during focused ultrasound treatments of uterine leiomyomas (ie, fibroids). MATERIALS AND METHODS All patients gave written informed consent for the focused ultrasound treatments and the current HIPAA-compliant retrospective study, both of which were institutional review board approved. Thermometry performed during the treatments of 64 fibroids in 50 women (mean age, 46.6 years +/- 4.5 [standard deviation]) was used to create thermal dose maps. The areas that reached dose values of 240 and 18 equivalent minutes at 43 degrees C were compared with the nonperfused regions measured on contrast material-enhanced MR images by using the Bland-Altman method. Volume changes in treated fibroids after 6 months were compared with volume changes in nontreated fibroids and with MR-based thermal dose estimates. RESULTS While the thermal dose estimates were shown to have a clear relationship with resulting nonperfused regions, the nonperfused areas were, on average, larger than the dose estimates (means of 1.9 +/- 0.7 and 1.2 +/- 0.4 times as large for areas that reached 240- and 18-minute threshold dose values, respectively). Good correlation was observed for smaller treatment volumes at the lower dose threshold (mean ratio, 1.0 +/- 0.3), but for larger treatment volumes, the nonperfused region extended to locations within the fibroid that clearly were not heated. Variations in peak temperature increase were as large as a factor of two, both between patients and within individual treatments. On average, the fibroid volume reduction at 6 months increased as the ablated volume estimated by using the thermal dose increased. CONCLUSION Study results showed good correlation between thermal dose estimates and resulting nonperfused areas for smaller ablated volumes. For larger treatment volumes, nonperfused areas could extend within the fibroid to unheated areas.
3-D individual cell based computational modeling of tumor cell-macrophage paracrine signaling mediated by EGF and CSF-1 gradients.

High density of macrophages in mammary tumors has been associated with a higher risk of metastasis and thus increased mortality in women. The EGF/CSF-1 paracrine signaling increases the number of invasive tumor cells by both recruiting tumor cells further away and manipulating the macrophages' innate ability to open up a passage into blood vessels thus promoting intravasation and finally metastasis. A 3-D individual-cell-based model is introduced, to better understand the tumor cell-macrophage interactions, and to explore how changing parameters of the paracrine signaling system affects the number of invasive tumor cells. The simulation data and videos of the cell movements correlated well with findings from both in vitro and in vivo experimental results. The model demonstrated how paracrine signaling is necessary to achieve co-migration of tumor cells and macrophages towards a specific signaling source. We showed how the paracrine signaling enhances the number of both invasive tumor cells and macrophages. The simulations revealed that for the in vitro experiments the imposed no-flux boundary condition might be affecting the results, and that changing the setup might lead to different experimental findings. In our simulations, the 3 : 1 tumor cell/macrophage ratio, observed in vivo, was robust for many parameters but sensitive to EGF signal strength and fraction of macrophages in the tumor. The model can be used to identify new agents for targeted therapy and we suggest that a successful strategy to prevent or limit invasion of tumor cells would be to block the tumor cell-macrophage paracrine signaling. This can be achieved by either blocking the EGF or CSF-1 receptors or supressing the EGF or CSF-1 signal.
Uric acid in cachectic and noncachectic patients with chronic heart failure: relationship to leg vascular resistance.

BACKGROUND Chronic heart failure (CHF) is a hyperuricemic state, and capillary endothelium is the predominant site of xanthine oxidase in the vasculature. Upregulated xanthine oxidase activity (through production of toxic free radicals) may contribute to impaired regulation of vascular tone in CHF. We aimed to study the relationship between serum uric acid levels and leg vascular resistance in patients with CHF with and without cachexia and in healthy control subjects. METHODS In 23 cachectic and 44 noncachectic patients with CHF (age, 62 +/- 1 years, mean +/- SEM) and 10 healthy control subjects (age, 68 +/- 1 years), we assessed leg resting and postischemic peak vascular resistance (calculated from mean blood pressure and leg blood flow by venous occlusion plethysmography). RESULTS Cachectic patients, compared with noncachectic patients and control subjects, had the highest uric acid levels (612 +/- 36 vs 459 +/- 18 and 346 +/- 21 micromol/L, respectively, both P <.0001) and the lowest peak leg blood flow and vascular reactivity (reduction of leg vascular resistance from resting to postischemic conditions: 83% vs 88% and 90%, both P <.005). In all patients, postischemic vascular resistance correlated significantly and independently of age with uric acid (r = 0.61), creatinine (r = 0.47, both P <.0001), peak VO2 (r = 0.34), and New York Heart Association class (r = 0.33, both P <.01). This correlation was not present in healthy control subjects (r = -0.04, P =.9). In multivariate and stepwise regression analyses, serum uric acid emerged as the strongest predictor of peak leg vascular resistance (standardized coefficient = 0.61, P <.0001) independent of age, peak VO2, creatinine, New York Heart Association class, and diuretic dose. CONCLUSIONS Hyperuricemia and postischemic leg vascular resistance are highest in cachectic patients with CHF, and both are directly related independent of diuretic dose and kidney function. The xanthine oxidase metabolic pathway may contribute to impaired vasodilator capacity in CHF.