Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of sexual transmission of HV: implications for control

The extent to which ART (anti-retroviral therapy) reduces HIV transmission has received attention in recent years. Using data on the relationship between transmission and viral load we show that transmission saturates at high viral loads. We fit a power-law model and an exponential converging to an asymptote. Using data on the viral load in HIV-positive people we show that ART is likely to reduce transmission by 91.6% (81.7%-96.2%) under the first and 99.5% (98.5%-99.8%) under the second model. The role of the acute phase in HIV transmission is still debated. High levels of transmission during the acute phase have been used to argue that failure to identify people in the acute phase of HIV may compromise the impact of treatment on preventing new infections and that having concurrent sexual partners during the acute phase is an important driver of the epidemic. We show that the acute phase probably accounts for less than 1% of overall transmission. We also show that even if a significant proportion of infections are transmitted during the acute phase, this will not compromise the impact of treatment on population levels of transmission given the constraint implied by the doubling time of the epidemic. This analysis leads to other relevant conclusions. First, it is likely that discordant-couple studies significantly underestimate the risk of infection. Second, attention should be paid to the variability in set point viral load which determines both the infectiousness of HIV-positive people and the variability in the susceptibility of HIV-negative people. Third, if ART drugs are in short supply those with the highest viral load should be given priority, others things including age, gender and opportunistic infections being equal, but to reduce transmission ART should be offered to all those with a viral load above about 10k/mm.3
Identifying infection reservoirs of digital dermatitis in dairy cattle

7 Acknowledgements . 9 List of knowledge exchange contributions relating to this thesis . 10 Abbreviations . 11 Chapter 1: Introduction . 14 1.1 Bovine digital dermatitis – overview . 14 1.2. 1 Anatomical location of DD lesions . 14 1.2. 2 Clinical appearance and histopathology of DD lesions . 15 1.2. 3 DD lesion classification. 17 1.3 Epidemiology of DD. 18 1.3. 1 Geographic spread of DD . 18 1.3. 2 Prevalence . 18 1.3. 3 Seasonality . 19 1.4 The implications of DD . 19 1.4. 1 Welfare of affected cattle . 19 1.4. 2 Economic impact . 20 1.5 The aetiology of DD . 21 1.5. 1 A polymicrobial disease . 21 1.5. 2 Treponemes associated with DD . 23 1.5. 3 Experimental models of DD . 24 1.6 The Treponema genus . 25 1.6. 1 Treponema biology . 25 1.6. 2 Pathogenic treponemes important in medical and veterinary health . 27 1.6. 3 Non-pathogenic commensal treponemes . 28 1.6. 4 Detection methods for treponemes . 28 1.7 The promiscuous nature of DD treponemes . 31 1.7. 1 Manifestations of DD in animals other than dairy cattle . 31 1.7. 2 Detection of DD treponemes in other types of dairy cattle infections. 31 1.8 Diagnosis, treatment and control of DD . 32
Engineered Retroviruses as Fluorescent Biological Reference Particles for Small Particle Flow Cytometry

There has been renewed interest in the use of flow cytometry for single particle phenotypic analysis of particles in the nanometer size-range such as viruses, organelles, bacteria and extracellular vesicles (EVs). However, many of these particles are smaller than 200 nm in diameter, which places them at the limit of detection for many commercial flow cytometers. The use of reference particles of diameter, fluorescence, and light-scattering properties akin to those of the small biological particles being studied is therefore imperative for accurate and reproducible data acquisition and reporting across different instruments and analytical technologies. We show here that an engineered murine leukemia virus (MLV) can act as a fluorescence reference particle for other small particles such as retroviruses and EVs. More specifically, we show that engineered MLV is a highly monodisperse enveloped particle that can act as a surrogate to demonstrate the various effects of antibody labeling on the physical properties of small biological particles in a similar diameter range.
The learning curve for laparoscopic cholecystectomy. The Southern Surgeons Club.

BACKGROUND The use of laparoscopic surgical procedures without previous training has grown rapidly. At the same time, there have been allegations of increased complications among less experienced surgeons. METHODS Using multivariate regression analyses, we evaluated the relationship between bile duct injury rate and experience with laparoscopic cholecystectomy for surgeons in the Southern Surgeons Club. RESULTS Fifty-five surgeons performed 8,839 procedures. Fifteen bile duct injuries (by 13 surgeons) resulted with 90% of the injuries occurring within the first 30 cases performed by an individual surgeon. Multivariate analyses indicated that the only significant factor associated with an adverse outcome was the surgeon's experience with the procedure. A regression model predicted that a surgeon had a 1.7% chance of a bile duct injury occurring in the first case and a 0.17% chance of a bile duct injury at the 50th case. CONCLUSIONS While surgeons appear to learn this procedure rapidly, institutions might consider requiring surgeons to move beyond the initial learning curve before awarding privileges.
Immunoadsorption Techniques and Its Current Role in the Intensive Care Unit

Immunoadsorption is an extracorporeal technique used for the removal of antibodies and molecules from the blood. A large number of different adsorbents are now avail able allowing for the non-selective removal of all subclasses of immunoglobulins such as IgG or more selective removal of disease specific molecules such as lipoprotein(a) and CRP. This selectivity, coupled with its highly efficient removal of the molecule, along with a favourable side-effect profile, has made immunoadsorption an attractive option in a range of autoimmune diseases. Here we discuss the mechanism and technique of immunoadsorption and review the current evidence and indications for its use, particu larly in relation to sepsis.
Scheduling of hard-aperiodic requests in dynamic priority systems

In this paper, we discuss the problem of jointly scheduling both hard deadline of periodic and aperiodic tasks in dynamic priority systems. The proposed scheduling scheme has extended the APS (Alternative Priority Scheduling) algorithm which is developed by the authors. The APS algorithm has a simple slack calculation method which in consequence makes it be practical. The paper develops an efficient acceptance test method for hard-aperiodic requests. The on-line acceptance test performs to determine whether the timing requirements of the arriving hard aperiodic tasks can be met while guaranteeing all the deadlines of periodic tasks and any already accepted but not yet completed aperiodic tasks.
Experimental evidence of nitrogen control on pCO2 in phosphorus-enriched humic and clear coastal lagoon waters

Natural and human-induced controls on carbon dioxide (CO2) in tropical waters may be very dynamic (over time and among or within ecosystems) considering the potential role of warmer temperatures intensifying metabolic responses and playing a direct role on the balance between photosynthesis and respiration. The high magnitude of biological processes at low latitudes following eutrophication by nitrogen (N) and phosphorus (P) inputs into coastal lagoons waters may be a relevant component of the carbon cycle, showing controls on partial pressure of CO2 (pCO2) that are still poorly understood. Here we assessed the strength of N control on pCO2 in P-enriched humic and clear coastal lagoons waters, using four experimental treatments in microcosms: control (no additional nutrients) and three levels of N additions coupled to P enrichments. In humic coastal lagoons waters, a persistent CO2 supersaturation was reported in controls and all nutrient-enriched treatments, ranging from 24- to 4-fold the atmospheric equilibrium value. However, both humic and clear coastal lagoons waters only showed significant decreases in pCO2 in relation to the controlled microcosms in the two treatments with higher N addition levels. Additionally, clear coastal lagoons water microcosms showed a shift from CO2 sources to CO2 sinks, in relation to the atmosphere. Only in the two more N-enriched treatments did pCO2 substantially decrease, from 650 µatm in controls and less N-enriched treatments to 10 µatm in more N-enriched microcosms. Humic substrates and N inputs can modulate pCO2 even in P-enriched coastal lagoons waters, thereby being important drivers on CO2 outgassing from inland waters.
Twelve months fixed duration WHO multidrug therapy for multibacillary leprosy: incidence of relapses in Agra field based cohort study

Background & objectives: The reported low relapse rates after 24 months multidrug therapy (MDT) for multibacillary leprosy (MB) led to the recommendation of reducing duration of therapy to 12 months. However, only a few reports exist on long term follow up data after 12 months fixed duration therapy (FDT). The present study was done to assess the incidence of relapse in MB leprosy patients after 12 months treatment. Methods: The leprosy patients detected in field surveys during 2001-2006 in Agra district, Uttar Pradesh, India, were put on WHO-MDT and followed up for treatment completion, relapse, reactions and development of disability. The assessment was done clinically by following up the patients until January 2011. Data collected were analyzed for risk and survival analysis. Results: The incidence of relapse was found to be 1.97/100 person years of follow up. The incidence of relapse by age (34 yr vs >34 yr), sex (male vs female), delay in detection (<36 months vs >36 months) and smear status (smear +ve vs -ve) was not found to be significantly different but patients with no nerve involvement were observed to have significantly higher relapses than those with three or more nerve involvement (P<0.05). Similarly, borderline-borderline and BB with reaction (BB/BBR) patients were observed to have significantly high relapses than among those with borderline tuberculoid or BT with reaction (BT/BTR) or borderline lipromatous/lepromatous/neuritic (BL/LL/N) type of leprosy (P<0.01). Interpretation & conclusion: From the observations in the study, it can be suggested that relapses occur in 12 months FDT and almost as much as reported in 24 months FDT for MB leprosy. Although, early relapses may be due to insufficient treatment, late relapses may be due to persistent dormant mycobacteria. However, a study relating to immunological response of treatment and change in immunological profile relating to the occurrence of relapses and its clinical correlates may suggest better information on causes of relapses.
Authentication of Ecological, Biochemical and Molecular Features for Some Lamiaceae Species from Saudi Arabia

THE FAMILY Lamiaceae (Labiatae) contains several genera, such as sage (Salvia), mint (Mentha) and basil (Ocimum) with a rich diversity of ethno botanical uses. It has an important role as a source of medicinal and aromatic of commercial importance. Medicinal plants represent an important health and economic component of biodiversity. It is essential to make the complete inventory of the medicinal component of the flora of any country for conservation and sustainable use. The conservation of the threatened and endangered medicinal species in the wild is indispensable. Therefore, protein, isozymes, RAPD and ISSR markers were employed for molecular characterization, variability evaluation and genetic relationships of some Lamiaceae species collected from various areas of Saudi Arabia. All biochemical and molecular markers revealed high polymorphism percentage among the studied genotypes. The UPGMA clusters result indicated that all genotypes could be distinguished by these markers. The polymorphism information obtained through biochemical and molecular analyses may also help for further studies for other Lamiaceae genotypes in Saudi Arabia.
MULTIPLE ANTIBIOTIC RESISTANCE IN STAPHYLOCOCCUS AUREUS AND STAPHYLOCOCCUS EPIDERMIDIS: PLASMIDS IN STRAINS ASSOCIATED WITH NOSOCOMIAL INFECTION

Summary The plasmid DNA profiles were compared to phenotypically‐similar, antibiotic‐resistant strains of Staphylococcus aureus and Staphylococcus epidermidis associated with nosocomial infections in a Melbourne hospital. Whereas resistance to gentamicin, tobramycin and kanamycin was encoded by one of 3 plasmids [pSK1,18 megadalton (Md); pSK4, 22 Md; pSK9,17 Md] in S. aureus no similar plasmids were detected in S. epidermidis. Mediated exclusively by the chromosome in S. aureus tetracycline resistance was encoded either by the chromosome or by a 2.8 Md plasmid in strains of S. epidermidis. The inability to detect common resistance plasmids in strains of S. aureus and S. epidermidis recovered from this outbreak is in contrast to recent observations with staphylococci from other geographic areas; nevertheless, on the basis of restriction endonuclease analyses of 3 Md chloramphenicol resistance plasmids, it is suggested that a common gene pool does exist within isolates of S. aureus and S. epidermidis from Melbourne hospitals.
Cytoskeletal changes in osteoclasts during the resorption cycle

Osteoclasts are large, multinucleated cells which change their shape and polarity according to their resorptive activity. At least in vitro, nonresorbing osteoclasts move on the bone surface and do not show clear evidence of apical‐basolateral polarity. When stimulated for resorption, osteoclasts undergo a rapid reorganization of the cytoskeleton and appear clearly polarized. The detailed nature of different membrane domains in polarized osteoclasts is still far from clear, but a remarkable feature is the formation of a tight sealing zone between the ruffled border and the rest of the cell membrane. Characteristic organization of F‐actin into a belt or ring‐like structure with a double circle of vinculin around it is needed for the formation of the sealing zone. This type of microfilament organization is typical only for resorbing osteoclasts and can thus be used as a marker for resorbing cells. These characteristic changes in the molecular organization of the cytoskeleton in osteoclasts during the resorption cycle offer several potential targets to inhibit bone resorption, perhaps cell‐specific. © 1996 Wiley‐Liss, Inc.
Selective Increase of Vβ2+ T Cells in the Small Intestinal Mucosa in Kawasaki Disease

The current study tested the hypothesis that the gastrointestinal tract could be one of the primary sites of entry for etiologic agents in Kawasaki disease (KD). In an attempt to elucidate the pathogenic role of certain superantigenic agents in KD, T cell receptor Vβ expression by T cells in the small intestinal mucosa of KD patients was investigated using MAb on frozen tissue sections. Twelve Japanese patients with KD and eight controls were enrolled in the study. The numbers of cells stained by an immunofluorescence from each study group were counted and analyzed statistically by the t test. The occurrence of Vβ2+ T cells was found to be selectively increased in the small intestinal mucosa of patients in the acute phase of KD compared with controls (p < 0.01). In our previous study, five kinds of streptococci and two kinds of staphylococci, not detected in control patients, were isolated from the lumen of the jejunum of KD patients. These data suggest that the increased occurrence of Vβ2+ T cells in the jejunal mucosa of KD patients may be caused by exotoxins acting as superantigens produced by bacteria colonizing the small intestinal mucosa of these patients.
Effect of Sinecatechins on HPV-Activated Cell Growth and Induction of Apoptosis.

BACKGROUND Green tea catechins possess a wide range of pharmacological properties, including antiviral, anti-infective, and immunostimulatory properties. They also have demonstrated inhibitory effects on a variety of enzymatic and metabolic pathways involved in cancer development. Catechins have been shown to have antiproliferative properties in various cell lines and may have direct virucidal effect. The United States Food and Drug Administration has approved a topical ointment formulation of sinecatechins, derived from green tea catechins and other tea components, for the treatment of external genital and perianal warts. The exact mechanism of action of sinecatechins in eradication of human papillomavirus-induced external genital and perianal warts is unknown, but may be due to one or more of the mechanisms mentioned. OBJECTIVE This study was conducted to investigate the growth inhibitory potential of the sinecatechins in human cervical carcinoma cell lines infected with human papillomavirus. METHODS The viability of tumor cell lines (CaSki and SiHa infected with human papillomavirus-16; HeLa and C4-I infected with human papillomavirus-18) was investigated as one parameter in a short-term viability assay (48 hours). This was followed by a long-term clonogenic assay (12-23 days) to determine the cytotoxic potential of sinecatechins as a parameter for cell viability and proliferation. This assay determined if the effect observed in the viability assay was due to retardation in cell proliferation or to a reduction of total cell number, leading to cell death. RESULTS Based on the data collected, sinecatechins inhibited cell growth in all four tumor cell lines by 50 percent (GI(50)) at concentrations ranging from 160 to 360µM. C4-I cells were the most sensitive to treatment with sinecatechins, with a lower GI(50) (~34µM). Total GI was achieved in a 48-hour assay at 625µM sinecatechins (40µM for C4-I), with growth inhibitory potential detectable after one hour. Clonogenic assays confirmed the cytotoxic potential of sinecatechins with a reduction in clone numbers in a concentration-dependent fashion. Sinecatechins substantially reduced the number of surviving HeLa cells at a concentration of 200µM, while surviving SiHa cells were almost totally eradicated with a concentration of 600µM. CONCLUSION Sinecatechins demonstrated growth inhibitory potential in all four human papillomavirus-infected tumor cell lines, which may be attributed to the induction of apoptosis, mediated by cell cycle deregulation. In addition, this antiproliferative effect may contribute to the overall cancer-preventative function and possible direct antiviral activity of sinecatechins that may contribute to external genital and perianal warts clearance.
Exploring the DNA-recognition potential of homeodomains

The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recognition potential of HDs, we utilized a bacterial selection system to isolate HD variants, from a randomized library, that are compatible with each of the 64 possible 3′ triplet sites (i.e., TAANNN). The majority of these selections yielded sets of HDs with overrepresented residues at specific recognition positions, implying the selection of specific binders. The DNA-binding specificity of 151 representative HD variants was subsequently characterized, identifying HDs that preferentially recognize 44 of these target sites. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. These novel determinants, when grafted into different HD backbones, produce a corresponding alteration in specificity. This information was used to create more explicit HD recognition models, which can inform the prediction of transcriptional regulatory networks for extant HDs or the engineering of HDs with novel DNA-recognition potential. The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems.
Regional analysis of crop and natural vegetation in West Africa based on NDVI metrics

In West Africa, rainfall variability dynamics are often considered as the major driver of vegetation production. Land use shifts have also to be taken into account when analyzing changes in vegetation production. To study how land use changes may impact vegetation response along a climatic gradient, we used three MODIS NDVI metrics time series (2000-2012) and a land cover map from MODIS Land Cover product. We performed a trend analysis and analyzed temporal profiles of the three metrics according to three climatic zones (Sahelian, Sudanian and Guinean zones). Our results indicate differences in NDVI values of Croplands and Natural Vegetation and that these differences are in connection with climatic zones. In the Sahelian zone Croplands tend to have higher values than Natural vegetation, whereas the opposite is observed for the Sudanian and Guinean zones. These results could help improve the interpretation of vegetation trends in a context of climate and land management shifts.
Evaluation of Storytelling in Information Visualization

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COX-2–Dependent Cardiac Failure in Gh/tTG Transgenic Mice

Abstract— Gh is a GTP binding protein that couples to the thromboxane receptor (TP), but also functions as tissue transglutaminase II (tTG). A transgenic mouse model was generated in which Gh was overexpressed (GhOE) in ventricular myocytes under the control of the &agr;-myosin heavy chain promoter. Heart rate was elevated and both blood pressure and left ventricular ejection fraction were depressed in GhOEs. Left ventricular mass was increased, consistent with genetic and ultrastructural evidence of hypertrophy. Fibrosis and apoptosis were also augmented. Survival declined disproportionately in older GhOEs. Cardiomyocyte expression of COX-2, thromboxane synthase (TxS), and the receptors for TxA2 (the TP), PGF2&agr; (the FP), and PGI2 (the IP) were upregulated and urinary 8,12-iso-iPF2&agr;-VI,2,3-dinor-6-keto-PGF1&agr; and 2,3-dinor-thromboxane B2 were increased in GhOEs, reflecting increased lipid peroxidation and cyclooxygenase (COX) activation. Selective COX-2 inhibition, TP antagonism, and suppression of lipid peroxidation each rescued the cardiac phenotype. Infusion of an FP agonist exacerbated the phenotype, whereas administration of an IP agonist improved cardiac function. Directed cardiac overexpression of Gh/tTG causes both TG activation and increased TP/Gh-dependent signaling. The COX-2–dependent increase in TxA2 generation augments cardiac hypertrophy, whereas formation of PGI2 by the same isozyme ameliorates the phenotype. Oxidant stress may contribute, via regulation of COX-2 expression and/or ligation of the TP and the FP by isoprostanes. Gh/tTG activation regulates expression of COX-2 and its products may differentially modulate cardiomyocyte commitment to cell death or survival.