Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence Characterisation of Salmonella enterica Isolates of Differing Antimicrobial Resistance Recovered from UK Livestock and Imported Meat Samples

Salmonella enterica is a foodborne zoonotic pathogen of significant public health concern. We have characterized the virulence and antimicrobial resistance gene content of 95 Salmonella isolates from 11 serovars by DNA microarray recovered from UK livestock or imported meat. Genes encoding resistance to sulphonamides (sul1, sul2), tetracycline [tet(A), tet(B)], streptomycin (strA, strB), aminoglycoside (aadA1, aadA2), beta-lactam (blaTEM), and trimethoprim (dfrA17) were common. Virulence gene content differed between serovars; S. Typhimurium formed two subclades based on virulence plasmid presence. Thirteen isolates were selected by their virulence profile for pathotyping using the Galleria mellonella pathogenesis model. Infection with a chicken invasive S. Enteritidis or S. Gallinarum isolate, a multidrug resistant S. Kentucky, or a S. Typhimurium DT104 isolate resulted in high mortality of the larvae; notably presence of the virulence plasmid in S. Typhimurium was not associated with increased larvae mortality. Histopathological examination showed that infection caused severe damage to the Galleria gut structure. Enumeration of intracellular bacteria in the larvae 24 h post-infection showed increases of up to 7 log above the initial inoculum and transmission electron microscopy (TEM) showed bacterial replication in the haemolymph. TEM also revealed the presence of vacuoles containing bacteria in the haemocytes, similar to Salmonella containing vacuoles observed in mammalian macrophages; although there was no evidence from our work of bacterial replication within vacuoles. This work shows that microarrays can be used for rapid virulence genotyping of S. enterica and that the Galleria animal model replicates some aspects of Salmonella infection in mammals. These procedures can be used to help inform on the pathogenicity of isolates that may be antibiotic resistant and have scope to aid the assessment of their potential public and animal health risk.
Studies on Autoimmunity For Initiation of β-Cell Destruction: V. Decrease of Macrophage-Dependent T Lymphocytes and Natural Killer Cytotoxicity in Silica-Treated BB Rats

Administration of silica, which is selectively toxic to macrophages, to young BB rats resulted in the prevention of insulitis and diabetes. However, the mechanism leading to the prevention of an autoimmune process in silica-treated BB rats is not known. This study was undertaken to investigate the mechanism involved in prevention of insulitis and diabetes. Neonates of diabetes-prone BB (DPBB) rats injected with concanavalin A (ConA)-activated spleen cells from silica-treated DPBB (STDPBB) rats did not develop insulitis or diabetes, whereas DPBB neonates injected with ConA-activated spleen cells from the untreated DPBB rats developed both insulitis and diabetes. Not only was there a decrease of natural killer (NK) cell activity in splenocytes from STDPBB rats, but there was also a significant reduction in the number of immunocytes such as T lymphocytes (helper/inducer and cytotoxic/suppressor) and NK cells. The number of macrophages in both spleen and peripheral blood was significantly decreased in STDP rats compared with untreated DP rats. In contrast to the changes in T lymphocytes and NK cell activity, there was no change in target β-cells in STDPBB rats with regard to the susceptibility to adoptive transfer of insulitis. It is concluded that the prevention of insulitis and diabetes in STDPBB rats is due to a decrease in macrophage-dependent T lymphocytes and NK cell cytotoxicity.
Searching Imagined Environments

Subjects read narratives describing directions of objects around a standing or reclimng observer, who was periodically reoriented. RTs were measured to identify which object was currently located beyond the observer's head, feet, front, back, fight, and left. When the observer was standing, head/feet RTs were fastest, followed by front/back and then right/left. For the reclining observer, front/back RTs were fastest, followed by head/feet and then right/left. The data support the spatial framework model, according to which space is conceptualized in terms of three axes whose accessibility depends on body asymmetries and the relation of the body to the world. The data allow rejection of the equiavailability model, according to which RTs to all directions are equal, and the mental transformation model, according to which RTs increase with angular disparity from front.
Biological Principles and Physiology of Bone Regeneration under the Schneiderian Membrane after Sinus Lift Surgery: A Radiological Study in 14 Patients Treated with the Transcrestal Hydrodynamic Ultrasonic Cavitational Sinus Lift (Intralift)

Introduction. Sinus lift procedures are a commonly accepted method of bone augmentation in the lateral maxilla with clinically good results. Nevertheless the role of the Schneiderian membrane in the bone-reformation process is discussed controversially. Aim of this study was to prove the key role of the sinus membrane in bone reformation in vivo. Material and Methods. 14 patients were treated with the minimal invasive tHUCSL-Intralift, and 2 ccm collagenous sponges were inserted subantrally and the calcification process followed up with CBCT scans 4 and 7 months after surgery. Results. An even and circular centripetal calcification under the sinus membrane and the antral floor was detected 4 months after surgery covering 30% of the entire augmentation width/height/depth at each wall. The calcification process was completed in the entire augmentation volume after 7 months. A loss of approximately 13% of absolute augmentation height was detected between the 4th and 7th month. Discussion. The results of this paper prove the key role of the sinus membrane as the main carrier of bone reformation after sinus lift procedures as multiple experimental studies suggested. Thus the importance of minimal invasive and rupture free sinuslift procedures is underlined and does not depend on the type of grafting material used.
HIV Envelope Binding by Macrophage-Expressed gp340 Promotes HIV-1 Infection1

The scavenger receptor cysteine-rich protein gp340 functions as part of the host innate immune defense system at mucosal surfaces. In the genital tract, its expression by cervical and vaginal epithelial cells promotes HIV trans-infection and may play a role in sexual transmission. Gp340 is an alternatively spliced product of the deleted in malignant brain tumors 1 (DMBT1) gene. In addition to its innate immune system activity, DMBT1 demonstrates instability in multiple types of cancer and plays a role in epithelial cell differentiation. We demonstrate that monocyte-derived macrophages express gp340 and that HIV-1 infection is decreased when envelope cannot bind it. Inhibition of infection occurred at the level of fusion of M-, T-, and dual-tropic envelopes. Additional HIV-1 envelope binding molecules, such as dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN), mannose-binding lectin, and heparan sulfate, enhance the efficiency of infection of the cells that express them by increasing the local concentration of infectious virus. Our data suggest that gp340, which is expressed by macrophages in vivo, may function to enhance infection in much the same manner. Its expression on tissue macrophages and epithelial cells suggests important new opportunities for HIV-1 pathogenesis investigation and therapy.
Finite element methods for a singularly perturbed transmission problem

Abstract We consider a one-dimensional singularly perturbed transmission problem with two different diffusion coefficients. The solution will contain boundary layers only in the part of the domain where the diffusion coefficient is high. We derive and analyze various finite element approaches for the approximation of the solution and conduct numerical computations that show the robustness (or lack thereof) of each approach.
Solution of the H+3 model on a disc

We determine all the correlators of the H+3 model on a disc with AdS2-brane boundary conditions in terms of correlators of Liouville theory on a disc with FZZT-brane boundary conditions. We argue that the Cardy-Lewellen constraints are weaker in the H+3 model than in rational conformal field theories due to extra singularities of the correlators, but strong enough to uniquely determine the bulk two-point function on a disc. We confirm our results by detailed analyses of the bulk-boundary two-point function and of the boundary two-point function. In particular we find that, although the target space symmetry preserved by AdS2-branes is the group SL(2,), the open string states between two distinct parallel AdS2-branes belong to representations of the universal covering group.
Patient selection, cancer control, and complications after salvage local therapy for postradiation prostate‐specific antigen failure

Among men who experience prostate‐specific antigen (PSA) failure after external beam radiation or brachytherapy (RT), many will harbor occult micrometastases; however, a significant minority will have a true local‐only failure and, thus, potentially may benefit from a salvage local therapy. Those most likely to have a local‐only failure initially have low‐risk disease (PSA < 10 ng/mL, Gleason score ≤6, clinical T1c or T2a tumor status), pretreatment PSA velocity < 2.0 ng/mL per year at the time of initial presentation, interval to PSA failure > 3 years, PSA doubling time > 12 months, negative bone scan and pelvic imaging, and positive rebiopsy. In addition, men with presalvage PSA levels > 10 ng/mL, presalvage T3/T4 disease, or presalvage Gleason scores ≥7 on a rebiopsy sample without significant RT effects are unlikely to be cured by salvage local therapy. Based on a review of all series of post‐RT salvage prostatectomy, cryosurgery, and brachytherapy published in English since 1990, morbidity can be substantial. Although urinary incontinence appeared to be greater after salvage prostatectomy (41%) or cryosurgery (36%) than after brachytherapy (6%), patients who received salvage brachytherapy faced a 17% risk of grade 3 or 4 genitourinary complications and a fistula risk that averaged 3.4% across all series. From this review, the authors concluded that prospective randomized studies are needed to determine the relative efficacy of the 3 major local salvage modalities and that additional research is needed to identify factors associated with an increased risk of significant complications to improve patient selection and to augment the benefit/risk ratio associated with attempts to cure local‐only recurrences after radiation therapy. Cancer 2007. © 2007 American Cancer Society.
Deep sequencing of 10,000 human genomes

Significance Large-scale initiatives toward personalized medicine are driving a massive expansion in the number of human genomes being sequenced. Therefore, there is an urgent need to define quality standards for clinical use. This includes deep coverage and sequencing accuracy of an individual’s genome. Our work represents the largest effort to date in sequencing human genomes at deep coverage with these new standards. This study identifies over 150 million human variants, a majority of them rare and unknown. Moreover, these data identify sites in the genome that are highly intolerant to variation—possibly essential for life or health. We conclude that high-coverage genome sequencing provides accurate detail on human variation for discovery and clinical applications. We report on the sequencing of 10,545 human genomes at 30×–40× coverage with an emphasis on quality metrics and novel variant and sequence discovery. We find that 84% of an individual human genome can be sequenced confidently. This high-confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. We present the distribution of over 150 million single-nucleotide variants in the coding and noncoding genome. Each newly sequenced genome contributes an average of 8,579 novel variants. In addition, each genome carries on average 0.7 Mb of sequence that is not found in the main build of the hg38 reference genome. The density of this catalog of variation allowed us to construct high-resolution profiles that define genomic sites that are highly intolerant of genetic variation. These results indicate that the data generated by deep genome sequencing is of the quality necessary for clinical use.
Changing nursery practice gets inner-city infants in the supine position for sleep.

OBJECTIVE To determine whether an educational intervention to change nursery practice would result in more inner-city parents placing their infants in the supine position for sleep. DESIGN We conducted semistructured interviews at the 2-week health supervision visit with 1 convenience sample of parents before and a different convenience sample of parents after an educational intervention was conducted to change nursery practice in positioning infants for sleep. SETTING University hospital clinic located in an urban setting. PARTICIPANTS Parents of 2-week-old infants at their first health supervision visit in an urban, university-affiliated clinic. All parents who were approached agreed to participate. INTERVENTION Nurses were instructed to place infants exclusively in the supine position in the nursery and to instruct parents to exclusively place infants in the supine sleeping position at home. MAIN OUTCOME MEASURE The usual sleeping position in which parents reported placing their 2-week old infants. RESULTS Before the intervention, 41% of parents reported that a clinician had told them to place their infants to sleep in the supine position compared with 81% after the intervention (odds ratio [OR], 6.1; 95% confidence interval [CI], 3.1-12.3). Before the intervention, 37% of parents reported that the nursery staff placed their infants to sleep in the supine position, compared with 88% after the intervention (OR, 12.5; 95% CI, 5.7-27.7). Before the intervention, 42% of parents reported that they usually placed their infants to sleep in the supine position at home compared with 75% after the intervention (OR, 4.2; 95% CI, 2.1-7.9). CONCLUSION After an educational intervention to change practice in a well-newborn nursery, many more parents reported placing their infants in the supine position for sleep, which suggests that such an intervention may have an impact on the position in which parents place their children to sleep.
Proteomics study of rice embryogenesis: Discovery of the embryogenesis‐dependent globulins

The plant embryo is the germination center of the seed. How an embryo forms during seed maturation remains unclear, especially in the case of monocotyledonous plants. Generally, the complex processes of embryogenesis result from the action of a coordinated network of genes. Thus, a large‐scale survey of changes in protein abundance during embryogenesis is an effective approach to study the molecular events of embryogenesis. In this study, two‐dimensional gel electrophoresis (2DE) was applied to separate rice embryo proteins collected during the three phases of embryogenesis: 6 days after pollination (DAP), 12 DAP, and 18 DAP. We then employed matrix‐assisted laser desorption‐ionization time of flight/time of flight mass spectrometry(MALDI TOF/TOF MS) to identify the phase‐dependent differential 2DE spots. A total of 66 spots were discovered to be regulated during embryogenesis, and of these spots, 53 spots were identified. These proteins were further categorized into several functional classes, including storage, embryo development, stress response, glycolysis, and protein metabolism. Intriguingly, the major differential spots originated from three globulins. We further examined the possible mechanism underlying the globulins’ multiple forms using Western blotting, proteolysis, and blue native gel electrophoresis techniques and found that the multiple forms of globulins were produced as a result of enhanced proteolysis during embryogenesis, indicating that these globulin forms may serve as chaperone proteins participating in the formation of multiple protein complexes during embryogenesis.
Fast Computation of the Roots of Polynomials Over the Ring of Power Series

We give an algorithm for computing all roots of polynomials over a univariate power series ring over an exact field K. More precisely, given a precision d, and a polynomial Q whose coefficients are power series in x, the algorithm computes a representation of all power series f(x) such that Q(f(x)) = 0 mod xd. The algorithm works unconditionally, in particular also with multiple roots, where Newton iteration fails. Our main motivation comes from coding theory where instances of this problem arise and multiple roots must be handled. The cost bound for our algorithm matches the worst-case input and output size d deg(Q), up to logarithmic factors. This improves upon previous algorithms which were quadratic in at least one of d and deg(Q). Our algorithm is a refinement of a divide & conquer algorithm by Alekhnovich (2005), where the cost of recursive steps is better controlled via the computation of a factor of $Q$ which has a smaller degree while preserving the roots.
Laboratory Investigation of Compacted No-Fines Concrete for Paving Materials

In this study the physical and engineering characteristics of various no-fines concrete mixtures are investigated. No-fines concrete mixtures subjected to impact compaction are studied under unconfined compression, indirect tension, and static modulus of elasticity; and the results are interpreted as functions of mixture proportions. The effect of impact-compaction energies, consolidation techniques, mixture proportions, curing types, and testing conditions on physical and engineering properties are presented. The abrasion characteristics and resistance to freezing and thawing of no-fines concrete are also discussed. It was found that the strength of no-fines concrete is strongly related to its mixture proportion and compaction energy. A sealed compressive strength of 20.7 MPa (3,000 psi) can readily be achieved with an aggregate cement ratio of 4.5:1 or less and a minimum compaction energy of 165 J/m 3 (4,303 ft-lb/cu ft). The splitting tensile-compressive relationship followed a pattern similar to that .
The Effects of a Custom-Made Lead Collar on Dose Rates of Patients Treated with 131I

We studied the effects of a custom-made lead collar on dose rates and hospitalization days of patients treated with high doses (>400 MBq) of radioiodine (131I). Between October 2005 and March 2006, the dose rates of 28 consecutive patients were studied. Dose rates of patients with and without the collar (5.5 mm lead) were measured daily until the rate dropped below the discharge dose rate of 20 &mgr;Sv h−1 at 1 m. Age, sex, 131I dose, uptake, thyroid disorder, and days of isolated hospitalization were recorded. The difference in mean dose rate with or without the collar was analyzed by t test or Mann-Whitney test, as appropriate. Twenty-eight patients (7 male, 21 female; mean age, 57 y; range, 29–82 y) were analyzed. Nine patients suffered from Graves’ disease, 9 from toxic nodular goiter, and 10 from non-toxic nodular goiter. Patients were treated with a mean dose of 1,647 MBq 131I (range, 511–3,276 MBq). The mean anterior dose rates were 28 ± 12 &mgr;Sv h−1 at 1 m and 11 ± 6 &mgr;Sv h−1 at 1 m without and with the lead collar, respectively (p < 0.001). The mean reduction in dose rate for patients wearing the collar was 61 ± 13%. The mean hospital stay was 2.6 ± 1.3 days without the collar vs. 1.2 ± 0.6 days with the collar (p < 0.001). A custom-made lead collar significantly reduced dose rates and could reduce compulsory hospitalization, especially in toxic- and non-toxic nodular goiter.
Gamma Oscillation in Schizophrenia

Dysfunctional neural circuitry has been found to be involved in abnormalities of perception and cognition in patients with schizophrenia. Gamma oscillations are essential for integrating information within neural circuits and have therefore been associated with many perceptual and cognitive processes in healthy human subjects and animals. This review presents an overview of the neural basis of gamma oscillations and the abnormalities in the GABAergic interneuronal system thought to be responsible for gamma-range deficits in schizophrenia. We also review studies of gamma activity in sensory and cognitive processes, including auditory steady state response, attention, object representation, and working memory, in animals, healthy humans and patients with schizophrenia.
A Sero-epidemiological Study of Arboviral Fevers in Djibouti, Horn of Africa

Arboviral infections have repeatedly been reported in the republic of Djibouti, consistent with the fact that essential vectors for arboviral diseases are endemic in the region. However, there is a limited recent information regarding arbovirus circulation, and the associated risk predictors to human exposure are largely unknown. We performed, from November 2010 to February 2011 in the Djibouti city general population, a cross-sectional ELISA and sero-neutralisation-based sero-epidemiological analysis nested in a household cohort, which investigated the arboviral infection prevalence and risk factors, stratified by their vectors of transmission. Antibodies to dengue virus (21.8%) were the most frequent. Determinants of infection identified by multivariate analysis pointed to sociological and environmental exposure to the bite of Aedes mosquitoes. The population was broadly naïve against Chikungunya (2.6%) with risk factors mostly shared with dengue. The detection of limited virus circulation was followed by a significant Chikungunya outbreak a few months after our study. Antibodies to West Nile virus were infrequent (0.6%), but the distribution of cases faithfully followed previous mapping of infected Culex mosquitoes. The seroprevalence of Rift valley fever virus was 2.2%, and non-arboviral transmission was suggested. Finally, the study indicated the circulation of Toscana-related viruses (3.7%), and a limited number of cases suggested infection by tick-borne encephalitis or Alkhumra related viruses, which deserve further investigations to identify the viruses and vectors implicated. Overall, most of the arboviral cases' predictors were statistically best described by the individuals' housing space and neighborhood environmental characteristics, which correlated with the ecological actors of their respective transmission vectors' survival in the local niche. This study has demonstrated autochthonous arboviral circulations in the republic of Djibouti, and provides an epidemiological inventory, with useful findings for risk mapping and future prevention and control programs.
Safety checking of machine code

We show how to determine statically whether it is safe for untrusted machine code to be loaded into a trusted host system. Our safety-checking technique operates directly on the untrusted machine-code program, requiring only that the initial inputs to the untrusted program be annotated with typestate information and linear constraints. This approach opens up the possibility of being able to certify code produced by any compiler from any source language, which gives the code producers more freedom in choosing the language in which they write their programs. It eliminates the dependence of safety on the correctness of the compiler because the final product of the compiler is checked. It leads to the decoupling of the safety policy from the language in which the untrusted code is written, and consequently, makes it possible for safety checking to be performed with respect to an extensible set of safety properties that are specified on the host side. We have implemented a prototype safety checker for SPARC machine-language programs, and applied the safety checker to several examples. The safety checker was able to either prove that an example met the necessary safety conditions, or identify the places where the safety conditions were violated. The checking times ranged from less than a second to 14 seconds on an UltraSPARC machine.