Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative and Qualitative Antibody Response to Pneumococcal Conjugate Vaccine Among African Human Immunodeficiency Virus-Infected and Uninfected Children

Objective: To determine the quantitative and qualitative antibody responses to a pneumococcal conjugate vaccine (PnCV) in human immunodeficiency virus (HIV)-exposed infected and uninfected children. Methods: Children were randomized to receive either a PnCV or placebo at 6, 10 and 14 weeks of age. PnCV serotype-specific antibody concentrations were measured by a standard enzyme immunoassay (EIA) and a 22F modified EIA (22F EIA) on single serum samples drawn at 21–42 days post-dose 3. Functional activities of the serotype-specific antibody to serotypes 6B, 19F and 23F were measured with an opsonophagocytic assay (OPA). Results: The geometric mean antibody concentrations (GMC) were similar in HIV-infected and HIV-uninfected PnCV recipients for 7 of the 9 vaccine serotypes. In placebo recipients, the GMCs were significantly higher in HIV-infected than in uninfected children for 7 of the serotypes. In HIV-infected PnCV recipients, the GMCs were lower for 5 of the serotypes in children with severe acquired immunodeficiency syndrome than in children who were asymptomatic or mildly symptomatic with acquired immunodeficiency syndrome. HIV-infected PnCV recipients were less likely to have measurable functional antibody (OPA titer ≥1/8) to all 3 studied serotypes (6B, 19F and 23F) than in HIV-uninfected children. HIV-infected children required a higher concentration of anticapsular antibody to achieve 50% of the maximum uptake of labeled Streptococcus pneumoniae in the OPA assay than HIV-uninfected children for 2 of the 3 serotypes, although this was significant only for serotype 6B (P = 0.0005). Conclusion: HIV-infected children have similar quantitative antibody responses but poorer qualitative antibody responses to the PnCV.
Testing a spatially distributed tracer‐aided runoff model in a snow‐influenced catchment: Effects of multicriteria calibration on streamwater ages

Integrating stable isotope tracers into rainfall‐runoff models allows investigation of water partitioning and direct estimation of travel times and water ages. Tracer data have valuable information content that can be used to constrain models and, in integration with hydrometric observations, test the conceptualization of catchment processes in model structure and parameterization. There is great potential in using tracer‐aided modelling in snow‐influenced catchments to improve understanding of these catchments' dynamics and sensitivity to environmental change. We used the spatially distributed tracer‐aided rainfall‐runoff (STARR) model to simulate the interactions between water storage, flux, and isotope dynamics in a snow‐influenced, long‐term monitored catchment in Ontario, Canada. Multiple realizations of the model were achieved using a combination of single and multiple objectives as calibration targets. Although good simulations of hydrometric targets such as discharge and snow water equivalent could be achieved by local calibration alone, adequate capture of the stream isotope dynamics was predicated on the inclusion of isotope data in the calibration. Parameter sensitivity was highest, and most local, for single calibration targets. With multiple calibration targets, key sensitive parameters were still identifiable in snow and runoff generation routines. Water ages derived from flux tracking subroutines in the model indicated a catchment where runoff is dominated by younger waters, particularly during spring snowmelt. However, resulting water ages were most sensitive to the partitioning of runoff sources from soil and groundwater sources, which was most realistically achieved when isotopes were included in the calibration. Given the paucity of studies where hydrological models explicitly incorporate tracers in snow‐influenced regions, this study using STARR is an important contribution to satisfactorily simulating snowpack dynamics and runoff generation processes, while simultaneously capturing stable isotope variability in snow‐influenced catchments.
Osteonecrosis of the Knee and Related Conditions

Abstract Osteonecrosis (ON) of the knee is a progressive disease that often leads to subchondral collapse and disabling arthritis. Recent studies have identified three distinct pathologic entities, all of which were previously described as knee ON: secondary ON, spontaneous ON of the knee, and postarthroscopic ON. Radiographic and clinical assessment is useful for differentiating these conditions, predicting disease progression, and distinguishing these conditions from other knee pathologies. The etiology, pathology, and pathogenesis of secondary ON of the knee are similar to those found at other sites (eg, hip, shoulder). Spontaneous ON is a disorder of unknown etiology. Postarthroscopic ON has been described as an infrequent but potentially destructive complication. Various treatment modalities (eg, core decompression, bone grafting, high tibial osteotomy, arthroplasty), have been used with varying degrees of success for each type of ON. Secondary ON frequently progresses to endstage disease, and early surgical intervention is recommended. Initial management of spontaneous ON of the knee and postarthroscopic ON is typically nonsurgical, with observation for clinical or radiographic progression.
Durability of the effects of cognitive–behavioural therapy in the treatment of chronic schizophrenia: 12-month follow-up

Background Persistent drug-resistant psychotic symptoms are a pervasive problem in the treatment of schizophrenia. Aims To evaluate the durability of the treatment effects of cognitive–behavioural therapy for chronic schizophrenia one year after treatment termination. Method A comparison of clinical outcomes was made at one-year follow-up from a randomised trial of cognitive–behavioural therapy, supportive counselling and routine care alone in the treatment of chronic schizophrenia. Results Seventy out of the 72 patients (97%) who completed treatment were assessed at follow-up. There were significant differences between the three groups when positive and negative symptoms were analysed by means of ANCOVAs. Between-group comparisons indicated significant differences between cognitive–behavioural therapy and routine care at follow-up for positive symptoms. There was a trend towards significance for both cognitive–behavioural therapy and supportive counselling to be superior to routine care alone on negative symptoms. Conclusions At 12-month follow-up the significant advantage of cognitive– behavioural therapy compared to routine care alone remained.
The impact of HIV on maternal quality of life in Uganda

Abstract To study the effect of HIV infection on quality of life (QOL) during pregnancy and puerperium, QOL was measured in a cohort study at St. Francis Hospital Nsambya, Kampala, Uganda. Dartmouth COOP charts were administered to 132 HIV-positive and 399 HIV-negative women at 36 weeks of pregnancy and six weeks post-partum. Responses were coded from 0 = best health-status to 4 = worst health-status and scores of 3–4 defined as poor. Odds ratios (OR) (95% confidence intervals(CI)) for poor scores were calculated and independent predictors of poor QOL examined using logistic regression. In pregnancy, HIV-positive women were more likely to have poor scores in feelings: OR = 3.2(1.9–5.3), daily activities: OR = 2.8(1.4–5.5), pain: OR = 2.1(1.3–3.5), overall health: OR = 1.7(1.1–2.7) and QOL: OR = 7.2(3.6–14.7), all p= ≤ 0.01. Differences in physical fitness, change in health, social activities and social support were not statistically significant (all p>0.2). HIV infection was independently associated with poor QOL: OR = 8.5(3.8–19). Findings in puerperium were similar to those in pregnancy except more HIV-positive women had poor scores in social activities: OR = 2.5(1.4–4.7) and change in health: OR = 5.4(2–14.5) and infant death also predicted poor QOL: OR = 6.7(2.4–18.5). The findings reflect HIV's adverse impact on maternal QOL and the need for interventions to alleviate this infection's social and emotional effects.
Impact of biomass burning on cloud properties in the Amazon Basin

[1] We used a one-dimensional (1-D) cloud parcel model to assess the impact of biomass-burning aerosol on cloud properties in the Amazon Basin and to identify the physical and chemical properties of the aerosol that influence droplet growth. Cloud condensation nuclei (CCN) measurements were performed between 0.15% and 1.5% supersaturation at ground-based sites in the states of Amazonas and Rondonia, Brazil during several field campaigns in 1998 and 1999 as part of the Large-Scale Biosphere–Atmosphere (LBA) Experiment in Amazonia. CCN concentrations measured during the wet season were low and resembled concentrations more typical of marine conditions than most continental sites. During the dry season, smoke aerosol from biomass burning dramatically increased CCN concentrations. The modification of cloud properties, such as cloud droplet effective radius and maximum supersaturation, is most sensitive at low CCN concentrations. Hence, we could expect larger interannual variation of cloud properties during the wet season that the dry season. We found that differences between CCN spectra from forested and deforested regions during the wet season are modest and result in modifications of cloud properties that are small compared to those between wet and dry seasons. Our study suggests that the differences in surface albedo, rather than cloud albedo, between forested and deforested regions may dominate the impact of deforestation on the hydrological cycle and convective activity during the wet season. During the dry season, on the other hand, cloud droplet concentrations may increase by up to 7 times, which leads to a model-predicted decrease in cloud effective radius by a factor of 2. This could imply a maximum indirect radiative forcing due to aerosol as high as ca. −27 W m−2 for a nonabsorbing cloud. Light-absorbing substances in smoke darken the Amazonian clouds and reduce the net radiative forcing, and a comparison of the Advanced Very High Resolution Radiometer (AVHRR) analysis and our modeling studies suggests that absorption of sunlight due to smoke aerosol may compensate for about half of the maximum aerosol effect. Sensitivity tests show that complete characterization of the aerosol is necessary when kinetic growth limitations become important. Subtle differences in the chemical and physical makeup are shown to be particularly influential in the activation and growth behavior of the aerosol. Knowledge of the CCN spectrum alone is not sufficient to fully capture the climatic influence of biomass burning.
What’s in a Name? Some Early and Current Issues in Dendritic Cell Nomenclature

The name dendritic cell (DC) was given by Steinman to describe the unusual cell type he saw in spleen cell suspensions. This morphological description is not sufficient to specify the cell of so much interest to immunologists; many cells can adopt a similar form. A useful functional definition evolved as Steinman and colleagues explored the immunological properties of this novel cell type (1). DCs were considered as antigen collecting and processing cells able to present antigen on MHC molecules and efficiently activate even primary T-cells. Nowadays, immunologists would likely add to this definition, a capacity to sense the context in which the antigen was collected, via receptors for pathogen or damaged cell-derived material. Why might we need to go beyond the name “dendritic cell” for cells with these well-understood functions? Some limitations of this single name arose early in DC research. This article surveys some problems of definition encountered in past work from our own laboratory. The problems we encountered arose from two sources, the first the discovery of different DC subsets and the need to determine whether these represented different maturation states or separate sub-lineages. The second was the difficulty in distinguishing these DC subsets from macrophages.
Scaling of Architecture Level Soft Error Rate for Superscalar Processors ∗

Soft errors are a growing concern for processor reliability. Recent studies have motivated architecture level studies of soft errors. It has been shown that the architecture level has a large derating effect on the raw processor error rate. In this paper, we quantify the impact of technology scaling on the processor soft error rate, taking the architecture level derating effects and workload characteristics into consideration. For our evaluation, we use SoftArch to quantify the derating factor and soft error rate (SER) for different structures in a modern superscalar processor running SPEC2000 benchmarks. We compare the SERs across four different technologies ranging from 180nm to 65nm with the same microarchitecture. We find that with scaling, the derating factors for logic structures often decrease, the derating factors for storage elements remain roughly unchanged, and the FIT rate for the full processor roughly follows the trend for the raw SER of storage structures (i.e., the FIT rate.increases from 180nm to 90nm and decreases from 90nm to 65nm.)
Formulation development of a stable influenza recombinant neuraminidase vaccine candidate

ABSTRACT Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a “closed” to an “open” conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.
Leptin and the risk of Barrett’s oesophagus

Background: Obesity is associated with increased risks of Barrett’s oesophagus and oesophageal adenocarcinoma. Alterations in serum leptin and adiponectin, obesity-related cytokines, have been linked with several cancers and have been postulated as potential mediators of obesity-related carcinogenesis; however, the relationship with Barrett’s oesophagus remains unexplored. Methods: Serum leptin and adiponectin concentrations were measured on two subsets of participants within a case–control study conducted in Brisbane, Australia. Cases were people aged 18–79 years with histologically confirmed Barrett’s oesophagus newly diagnosed between 2003 and 2006. Population controls, frequency matched by age and sex to cases, were randomly selected from the electoral roll. Phenotype and medical history data were collected through structured, self-completed questionnaires. Odds ratios (OR) and 95% CI were calculated using multivariable logistic regression analysis. Results: In the pilot analysis (51 cases, 67 controls) risks of Barrett’s oesophagus were highest among those in the highest quartile of serum leptin (OR 4.6, 95% CI 0.6 to 33.4). No association was seen with adiponectin. In the leptin validation study (306 cases, 309 controls), there was a significant threefold increased risk of Barrett’s oesophagus among men in the highest quartile of serum leptin (OR 3.3, 95% CI 1.7 to 6.6) and this persisted after further adjustment for symptoms of gastro-oesophageal reflux (OR 2.4, 95% CI 1.1 to 5.2). In contrast, the risk of Barrett’s oesophagus among women decreased with increasing serum leptin concentrations. Conclusions: High serum leptin is associated with an increased risk of Barrett’s oesophagus among men but not women. This association is not explained simply by higher body mass or gastro-oesophageal reflux among cases. The mechanism remains to be determined.
N-Terminus-Mediated Degradation of ACS7 Is Negatively Regulated by Senescence Signaling to Allow Optimal Ethylene Production during Leaf Development in Arabidopsis

Senescence is the final phase of leaf development, characterized by key processes by which resources trapped in deteriorating leaves are degraded and recycled to sustain the growth of newly formed organs. As the gaseous hormone ethylene exerts a profound effect on the progression of leaf senescence, both the optimal timing and amount of its biosynthesis are essential for controlled leaf development. The rate-limiting enzyme that controls ethylene synthesis in higher plants is ACC synthase (ACS). In this study, we evaluated the production of ethylene and revealed an up-regulation of ACS7 during leaf senescence in Arabidopsis. We further showed that the promoter activity of ACS7 was maintained at a relatively high level throughout the whole rosette development process. However, the accumulation level of ACS7 protein was extremely low in the light-grown young seedlings, and it was gradually restored as plants aging. We previously demonstrated that degradation of ACS7 is regulated by its first 14 N-terminal residues, here we compared the phenotypes of transgenic Arabidopsis overexpressing a truncated ACS7 lacking the 14 residues with transgenic plants overexpressing the full-length protein. Results showed that seedlings overexpressing the truncated ACS7 exhibited a senescence phenotype much earlier than their counterparts overexpressing the full-length gene. Fusion of the 14 residues to SSPP, a PP2C-type senescence-suppressed protein phosphatase, effectively rescued the SSPP-induced suppression of rosette growth and development but had no effect on the delayed senescence. This observation further supported that N-terminus-mediated degradation of ACS7 is negatively regulated by leaf senescence signaling. All results of this study therefore suggest that ACS7 is one of the major contributors to the synthesis of ‘senescence ethylene’. And more importantly, the N-terminal 14 residue-mediated degradation of this protein is highly regulated by senescence signaling to enable plants to produce the appropriate levels of ethylene required.
Socio-Economic Status Determines Risk of Receptive Syringe Sharing Behaviors among Iranian Drug Injectors; A National Study

Background: Although needle and syringe sharing is one of the main routs of transmission of HIV in several countries in the middle east, very little is known about how socio-economic status of injecting drug users (IDUs) is linked to the receptive syringe sharing behaviors in these countries. Aim: To study socio-economic correlates of receptive needle and syringe sharing among IDUs in Iran. Methods: The study used data from the Unhide Risk Study, a national survey of IDUs. This study sampled 636 IDUs (91% male) via snowball sampling from eight provinces in Iran in 2009. Socio-demographic and drug use characteristics were collected. We used a logistic regression to determine factors associated with receptive needle and syringe sharing during the past 6 months. Results: From 636 IDUs enrolled in this study, 68% (n = 434) reported receptive needle and syringe sharing behaviors in the past 6 months. Odds of receptive needle and syringe sharing in the past 6 months was lower among IDUs who were male [odds ratios (OR) = 0.29, 95% confidence interval (CI) = 0.12–0.70], had higher education (OR = 0.74, 95% CI = 0.64–0.86) but higher among those who were unemployed (OR = 4.05, 95% CI = 1.50–10.94), and were single (OR = 1.47, 95% CI = 1.02–2.11). Conclusion: This study presented factors associated with risk of receptive needle and syringe sharing among Iranian IDUs. This information may be used for HIV prevention and harm reduction purposes. Socio-economic status of Iranian IDUs may be closely linked to high-risk injecting behaviors among them.
Exaggerated Effect of Urbanization in the Diurnal Temperature Range Via “Observation minus Reanalysis” and the Physical Causes

The observation minus reanalysis (OMR) method is widely used to investigate the impact of urbanization and land use changes on regional climate. Based on homogenized temperature observations and the National Centers for Environmental Prediction/Department of Energy Atmospheric Model Intercomparison Project II reanalysis surface temperatures, we estimate the trend in diurnal temperature range (DTR) using the OMR method to be −0.324 ± 0.063 °C per decade for the period of 1980–2009 in eastern China. However, we find that reanalysis data produce a positive trend in downward surface solar radiation, while the observations do not, because the reanalysis data significantly overestimate the negative trend in total cloud coverage in the region. Moreover, the reanalysis considerably overestimates the negative trend in the local precipitation. These systematic biases cause an overestimation of the warming rate in daily maximum temperature in the reanalysis and therefore lead to the exaggerated effect of urbanization on the DTR via the OMR analysis. After adjusting the systematic bias in the trend of daily maximum temperature in the reanalysis data, the regional mean OMR trend in the DTR is estimated to be −0.065 °C per decade, which becomes much smaller than previous OMR calculations, and is more consistent with the previous estimates based on the comparison of urban and rural stations. These results not only indicate the methodological problem of the OMR method in many studies of urbanization effects but also hint at important aspects for improving the current reanalysis system.
Fast Retrieval of Isolated Visual Shapes

Similarity-based retrieval from databases of isolated visual shapes has become an important information retrieval problem. The goal of the current work is to achieve high retrieval speed with reasonable retrieval effectiveness, and support for partial and occluded shape queries. In the proposed method, histograms of local shape parts are coded as index vectors. To increase retrieval accuracy, a rich set of parts at all scales of the shape is used; specifically, the parts are defined as connected sequences of regions in curvature scale space. To increase efficiency, structural indexing is used to compare the index vectors of the query and database shapes. In experimental evaluations, the method retrieved at least one similar shape in the top three retrieved items 99-100% of the time, depending on the database. Average retrieval times ranged from 0.7 ms on a 131-shape database to 7 ms on a 1310-shape database. The method is thus suitable for fast, approximate shape retrieval in comparison with more accurate but more costly structural matching.