Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of an Aggregative Adhesion Fimbria (AAF) Type III-Encoding Operon in Enteroaggregative Escherichia coli as a Sensitive Probe for Detecting the AAF-Encoding Operon Family

ABSTRACT Enteroaggregative Escherichia coli (EAEC) is recognized as an emerging cause of diarrhea in children and adults worldwide, and recent studies have implicated EAEC in persistent diarrhea in patients infected with human immunodeficiency virus (HIV). In this study, we identified aggregative adhesion fimbria type III (AAF-III) in isolate 55989, a typical EAEC strain. Analysis of the sequence of the plasmid-borne agg-3 gene cluster encoding AAF-III showed this cluster to be closely related to the agg and aaf operons and to the afa operons carried by diffusely adherent pathogenic E. coli. We investigated the adhesion properties of a collection of 25 EAEC strains isolated from HIV-infected patients presenting with persistent diarrhea. We found that a minority of strains (36%) carried sequences similar to those of the agg and aaf operons, which encode AAF-I and AAF-II, respectively. We developed PCR assays specific for the agg-3 operon. In our collection, the frequency of AAF-III strains was similar (12%) to that of AAF-I strains (16%) but higher than that of AAF-II isolates (0%). Differences between EAEC strains in terms of the virulence factors present render detection of these strains difficult with the available DNA probes. Based on comparison of the agg, aaf, and agg-3 operons, we defined an AAF probe internal to the adhesion gene clusters and demonstrated that it was efficient for the identification of EAEC strains. We investigated 32 EAEC isolates, of which only 34.4% were detected with the classical CVD432 probe (detecting pAA virulence plasmids) whereas 65.6% were detected with the AAF probe.
Speeding up tensor based recommenders with clustered tag space and improving quality of recommendations with Non-negative tensor factorization

Social tagging facilitates users to annotate and categorize items (Web links, pictures, movies, etc.). Assigned tags express the user preferences. Social tagging systems (STS) have become popular hence various tag based recommenders have been developed. The state-of-the-art STS model three types of entities (i.e. tag-user-item) and relationships between them are encoded into a 3-order tensor. Latent relationships and patterns can be discovered by applying tensor factorization techniques like Higher Order Singular Value Decomposition (HOSVD), Canonical Decomposition (CD), etc. STS accumulate large amount of data that significantly slows down the process of a tensor factorization. Firstly, we propose to reduce tag space by exploiting clustering techniques so that execution time is improved and memory requirements are decreased while preserving the quality of the recommendations. The clustering is motivated by the fact that many tags in a tag space are semantically similar thus the tags can be grouped. Secondly, we propose to incorporate the personal prior knowledge to increase the precision of tensor based recommenders. In addition, we take an advantage of Non-negative Tensor Factorization (NTF) to get rid of negative values from the factorized tensor that are difficult to interpret. Finally, we combine all the approaches to improve the quality and time of computations and present the promising experimental results.
Correlates of Sexual Abuse in Women with Anorexia Nervosa and Bulimia Nervosa*

Of 184 female outpatients meeting the DSM-III-R criteria, for anorexia nervosa, bulimia nervosa, or anorexia nervosa with bulimia, approximately 25% reported previous sexual abuse. Furthermore, previous sexual abuse was associated with greater psychological disturbance, measured by the Eating Disorder Inventory and Eating Attitudes Test. Sexual functioning did not differ among women who did or did not report sexual abuse. This finding suggests that sexual abuse or its correlates may affect severity rather than type of eating disorder.
Modeling the Impact of Convective Entrainment on the Tropical Tropopause

Abstract Simulations with the Weather Research and Forecasting (WRF) cloud-resolving model of deep moist convective events reveal net cooling near the tropopause (∼15–18 km above ground), caused by a combination of large-scale ascent and small-scale cooling by the irreversible mixing of turbulent eddies overshooting their level of neutral buoyancy. The turbulent cooling occurred at all CAPE values investigated (local peak values ranging from 1900 to 3500 J kg−1) and was robust to grid resolution, subgrid-scale turbulence parameterization, horizontal domain size, model dimension, and treatment of ice microphysics. The ratio of the maximum downward heat flux in the tropopause to the maximum tropospheric upward heat flux was close to 0.1. This value was independent of CAPE but was affected by changes in microphysics or subgrid-scale turbulence parameterization. The convective cooling peaked roughly 1 km above the cold point in the background input sounding and the mean cloud- and (turbulent kinetic energy) T.
Signaling domain of the aspartate receptor is a helical hairpin with a localized kinase docking surface: cysteine and disulfide scanning studies.

Cysteine and disulfide scanning has been employed to probe the signaling domain, a highly conserved motif found in the cytoplasmic region of the aspartate receptor of bacterial chemotaxis and related members of the taxis receptor family. Previous work has characterized the N-terminal section of the signaling domain [Bass, R. B. , and Falke, J. J. (1998) J. Biol. Chem. 273, 25006-25014], while the present study focuses on the C-terminal section and the interactions between these two regions. Engineered cysteine residues are incorporated at positions Gly388 through Ile419 in the signaling domain, thereby generating a library of receptors each containing a single cysteine per receptor subunit. The solvent exposure of each cysteine is ascertained by chemical reactivity measurements, revealing a periodic pattern of buried hydrophobic and exposed polar residues characteristic of an amphipathic alpha-helix, denoted helix alpha8. The helix begins between positions R392 and Val401, then continues through the last residue scanned, Ile419. Activity assays carried out both in vivo and in vitro indicate that both the buried and exposed faces of this amphipathic helix are critical for proper receptor function and the buried surface is especially important for kinase downregulation. Patterns of disulfide bond formation suggest that helix alpha8, together with the immediately N-terminal helix alpha7, forms a helical hairpin that associates with a symmetric hairpin from the other subunit of the homodimer, generating an antiparallel four helix bundle containing helices alpha7, alpha7', alpha8, and alpha8'. Finally, the protein-interactions-by-cysteine-modification (PICM) method suggests that the loop between helices alpha7 and alpha8 interacts with the kinase CheA and/or the coupling protein CheW, expanding the receptor surface implicated in kinase docking.
The extratropical transition of tropical cyclones. Part I: Cyclone evolution and direct impacts

AbstractExtratropical transition (ET) is the process by which a tropical cyclone, upon encountering a baroclinic environment and reduced sea surface temperature at higher latitudes, transforms into an extratropical cyclone. This process is influenced by, and influences, phenomena from the tropics to the midlatitudes and from the meso- to the planetary scales to extents that vary between individual events. Motivated in part by recent high-impact and/or extensively observed events such as North Atlantic Hurricane Sandy in 2012 and western North Pacific Typhoon Sinlaku in 2008, this review details advances in understanding and predicting ET since the publication of an earlier review in 2003. Methods for diagnosing ET in reanalysis, observational, and model-forecast datasets are discussed. New climatologies for the eastern North Pacific and southwest Indian Oceans are presented alongside updates to western North Pacific and North Atlantic Ocean climatologies. Advances in understanding and, in some cases, mode.
Assessment of a novel lung sealant for performing endoscopic volume reduction therapy in patients with advanced emphysema

AeriSeal® Emphysematous Lung Sealant is a novel endoscopic lung-volume reduction therapy designed to reduce hyperinflation and improve pulmonary function and quality of life in patients with advanced emphysema. The device is administered to the subsegmental bronchus via a catheter as a 20 ml volume of liquid–foam. It flows into the peripheral airways and alveoli where it polymerizes and functions as a tissue glue, forming a film of material on the lung surface that seals the target region to cause durable absorption atelectasis. The AeriSeal System received CE mark approval for the treatment of patients with advanced upper lobe predominant and homogeneous emphysema based upon favorable results from clinical studies, and is commercially available in Europe. Patient and treatment site selection algorithms have been developed to simplify product use and optimize outcomes. This manuscript summarizes how the device is used, its mechanism of action and clinical trial results supporting its safety and efficacy.
Molecular picture of community- and healthcare-associated methicillin-resistant Staphylococcus aureus circulating in a teaching hospital in Milan

Abstract The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) has dramatically changed over the past 10 y with the emergence of community-associated MRSA (CA-MRSA). Recent studies have reported a frequent association of these strains with hospital outbreaks, and an incidence varying over time and by region. In order to evaluate the MRSA lineages circulating in our area of Italy, we performed a molecular characterization of CA-MRSA isolates prospectively collected from April 2006 to July 2007 at the San Paolo Hospital of Milan. We investigated the protein A-encoding gene (spa-typing), the staphylococcal chromosomal cassette SCCmec, the presence of Panton–Valentine leukocidin (PVL), and 3 adhesin genes. Twenty-five CA-MRSA isolates cultured from 25 patients were collected; an equal number of healthcare-associated (HA)-MRSA strains, from 25 patients hospitalized in various wards, were collected for comparison purposes. SCCmec type IV emerged as the most frequent genotype in both CA- and HA-MRSA. Seventeen different spa types were identified: t515 was the most common (36%), followed by t008 (20%). We detected 3 PVL-positive strains, only among the CA-MRSA. On the whole, our local MRSA epidemiology appears to be heterogeneous, with a predominant t515 spa type, only recently considered to belong to clonal EMRSA-15.
Response.

We wish to make some comments in response to the letter by Hung and others regarding our results published in the American Journal of Tropical Medicine and Hygiene. Using death certificate data, we identified human immunodeficiency virus (HIV) infection as a coexisting condition in 14 (10.4%) of 134 amebiasis-associated deaths in the United States over the period, 1990–2007. HIV infection was more common among amebiasis-associated deaths than in the control, nonamebiasis group (matched odds ratio = 7.7, 95% confidence interval, 3.16, 18.77). Twelve (86%) of the 14 HIV and amebiasis co-infected cases were male. Interpretation of these results is challenging. Whether HIV is directly associated with amebiasis is unclear from our study because the observed association may be confounded by the greater likelihood of exposure and infection with Entamoeba histolytica among men who have sex with men (MSM), who are also at increased risk of HIV infection. Death certificates do not contain information regarding sexual orientation precluding further analysis. Small numbers of females co-infected with HIV and amebiasis prevents us from stratifying by gender to see if this association is even specific to males. Additional confounders may be present. The limitations of death certificate data should also be considered. We thank Hung and others for their interest in our results and agree that further research is necessary to define any relationship between HIV infection and E. histolytica infection, especially in MSM.
Multiscale Modeling of Dye Solar Cells and Comparison With Experimental Data

In this paper, we investigate the electrical properties of dye solar cells (DSCs) under illumination and in dark conditions when an external bias is applied. The measurements performed on the cells will be compared with theoretical calculations. The modeling is made using two approaches: a finite-element code based on Tiber computer-aided design (CAD) software to describe in detail the electrical properties of the cell and a circuital model implemented on PSpice. The latter has been developed in the perspective of simulating larger systems, such as modules and panels. It should be a phenomenological model to fit I-V characteristics of real cells. The CAD instead allows to calculate steady-state properties and I-V characteristics of the cell, solving a set of differential equations on meshes in one, two, and three dimensions. The two models are compared to experimental values, and the microscopic model is used to shine light over the fitting parameters of the circuital model.
In Vivo Detection of Age- and Disease-Related Increases in Neuroinflammation by 18F-GE180 TSPO MicroPET Imaging in Wild-Type and Alzheimer's Transgenic Mice

Alzheimer's disease (AD) is the most common cause of dementia. Neuroinflammation appears to play an important role in AD pathogenesis. Ligands of the 18 kDa translocator protein (TSPO), a marker for activated microglia, have been used as positron emission tomography (PET) tracers to reflect neuroinflammation in humans and mouse models. Here, we used the novel TSPO-targeted PET tracer 18F-GE180 (flutriciclamide) to investigate differences in neuroinflammation between young and old WT and APP/PS1dE9 transgenic (Tg) mice. In vivo PET scans revealed an overt age-dependent elevation in whole-brain uptake of 18F-GE180 in both WT and Tg mice, and a significant increase in whole-brain uptake of 18F-GE180 (peak-uptake and retention) in old Tg mice compared with young Tg mice and all WT mice. Similarly, the 18F-GE180 binding potential in hippocampus was highest to lowest in old Tg > old WT > young Tg > young WT mice using MRI coregistration. Ex vivo PET and autoradiography analysis further confirmed our in vivo PET results: enhanced uptake and specific binding (SUV75%) of 18F-GE180 in hippocampus and cortex was highest in old Tg mice followed by old WT, young Tg, and finally young WT mice. 18F-GE180 specificity was confirmed by an in vivo cold tracer competition study. We also examined 18F-GE180 metabolites in 4-month-old WT mice and found that, although total radioactivity declined over 2 h, of the remaining radioactivity, ∼90% was due to parent 18F-GE180. In conclusion, 18F-GE180 PET scans may be useful for longitudinal monitoring of neuroinflammation during AD progression and treatment. SIGNIFICANCE STATEMENT Microglial activation, a player in Alzheimer's disease (AD) pathogenesis, is thought to reflect neuroinflammation. Using in vivo microPET imaging with a novel TSPO radioligand, 18F-GE180, we detected significantly enhanced neuroinflammation during normal aging in WT mice and in response to AD-associated pathology in APP/PS1dE9 Tg mice, an AD mouse model. Increased uptake and specific binding of 18F-GE180 in whole brain and hippocampus were confirmed by ex vivo PET and autoradiography. The binding specificity and stability of 18F-GE180 was further confirmed by a cold tracer competition study and a metabolite study, respectively. Therefore, 18F-GE180 PET imaging may be useful for longitudinal monitoring of neuroinflammation during AD progression and treatment and may also be useful for other neurodegenerative diseases.
Human resources for health in Africa

Better training and firm national policies might manage the brain drain A frican countries have a very low density health workforce, compounded by poor skill mix and inadequate investment.1 Yet trained healthcare staff continue to migrate from Africa to more developed countries. The World Health Organization has estimated that, to meet the ambitious targets of the millennium development goals, African health services will need to train and retain an extra one million health workers by 2010.2 It is too simplistic and misleading to define or try to resolve the crisis in human resources for health in Africa by looking only at overall numbers and density of workers, not least because these vary from country to country.3 4 Furthermore, the poor performance of health services in African countries is often compounded by shortages of drugs and other essential supplies, broken equipment, and poor …
Molecular Epidemiology of Avian Infectious Bronchitis in Brazil from 2007 to 2008 in Breeders, Broilers, and Layers

Abstract Multiple lineages of Brazilian strains from 2007 to 2008 of avian infectious bronchitis virus (IBV) were detected in flocks of breeders, broilers, and layers. Organs samples from 20 IBV-positive flocks with variable clinical signs were submitted to the partial amplification of S gene (nucleotides 726-1071) of IBV. Fifteen of the 20 sequenced strains segregated in a unique Brazilian cluster subdivided in three subclusters (Brazil 01, 02, and 03). Whereas three strains could be classified as Massachusetts (Mass) genotype, the remaining two strains, originating from flocks with reproductive and respiratory disorders, grouped within the 4/91-793B genotype, a genotype that has not been detected before in Brazil. The potential relevance of the findings to the poultry industry is discussed because the low level of identity of the sequenced part of the S gene from 17 of 20 detected field strains and the vaccines of the Massachusetts serotype used suggest that the level of cross-protection by the Massachusetts vaccines might be low.
The regulation of autophagy – unanswered questions

Autophagy is an intracellular lysosomal (vacuolar) degradation process that is characterized by the formation of double-membrane vesicles, known as autophagosomes, which sequester cytoplasm. As autophagy is involved in cell growth, survival, development and death, the levels of autophagy must be properly regulated, as indicated by the fact that dysregulated autophagy has been linked to many human pathophysiologies, such as cancer, myopathies, neurodegeneration, heart and liver diseases, and gastrointestinal disorders. Substantial progress has recently been made in understanding the molecular mechanisms of the autophagy machinery, and in the regulation of autophagy. However, many unanswered questions remain, such as how the Atg1 complex is activated and the function of PtdIns3K is regulated, how the ubiquitin-like conjugation systems participate in autophagy and the mechanisms of phagophore expansion and autophagosome formation, how the network of TOR signaling pathways regulating autophagy are controlled, and what the underlying mechanisms are for the pro-cell survival and the pro-cell death effects of autophagy. As several recent reviews have comprehensively summarized the recent progress in the regulation of autophagy, we focus in this Commentary on the main unresolved questions in this field.
Macroprolactinaemia: validation and application of the polyethylene glycol precipitation test and clinical characterization of the condition

The clinical characteristics and natural history of macroprolactinaemia are yet to be fully established and there is currently no widely accepted simple in vitro test for routine identification of the condition. This study was designed to further validate the polyethylene glycol (PEG) precipitation test with assessment of percentage prolactin recovery (%R), for the detection of macroprolactinaemia and clinically characterize cases identified using the test.
A 120-kDa Alkaline Peptidase from Trypanosoma cruzi Is Involved in the Generation of a Novel Ca2+-signaling Factor for Mammalian Cells (*)

Trypomastigotes, the infective stages of the intracellular parasite Trypanosoma cruzi, induce rapid and repetitive cytosolic free Ca2+ transients in fibroblasts. Buffering or depletion of intracellular free Ca2+ inhibits cell entry by trypomastigotes, indicating a role for this signaling event in invasion. We show here that the majority of the Ca2+-signaling activity is associated with the soluble fraction of parasites disrupted by sonication. Distinct cell types from different species are responsive to this soluble factor, and intracellular free Ca2+ transients occur rapidly and reach concentrations comparable to responses induced by thrombin and bombesin. The Ca2+-signaling activity does not bind concanavalin A and is strongly inhibited by a specific subset of protease inhibitors. The only detectable protease in the fractions with Ca2+-signaling activity is an unusual alkaline peptidase of 120 kDa, to which no function had been previously assigned. The activity of the protease and cell invasion by trypomastigotes are blocked by the same specific inhibitors that impair Ca2+-signaling, suggesting that the enzyme is required for generating the response leading to infection. We demonstrate that the 120-kDa peptidase is not sufficient for triggering Ca2+-signaling, possibly being involved in the processing of precursors present only in infective trypomastigotes. These findings indicate a biological function for a previously identified unusual protozoan protease and provide the first example of a proteolytically generated parasite factor with characteristics of a mammalian hormone.
Human Replication Protein A

Although the mechanical aspects of the single-stranded DNA (ssDNA) binding activity of human replication protein A (RPA) have been extensively studied, only limited information is available about its interaction with other physiologically relevant DNA structures. RPA interacts with partial DNA duplexes that resemble DNA intermediates found in the processes of DNA replication and DNA repair. Limited proteolysis of RPA showed that RPA associated with ssDNA is less protected against proteases than RPA bound to a partial duplex DNA containing a 5′-protruding tail that had the same length as the ssDNA. Modification of both the 70- and 32-kDa subunits, RPA70 and RPA32, respectively, by photoaffinity labeling indicates that RPA can bind the primer-template junction of partial duplex DNAs by interacting with the 3′-end of the primer. The identification of the protein domains modified by the photoreactive 3′-end of the primer showed that domains located in the central part of the RPA32 subunit (amino acids 39–180) and the C-terminal part of the RPA70 subunit (amino acids 432–616) are involved in these interactions.