Miracle-dz/UniFAR-FTUs huggingface dataset:
Sulfate reduction in surface sediments of the southeast Atlantic continental margin between 15°38'S and 27°57'S (Angola and Namibia)

Sulfate reduction rates in the surface sediments from 17 stations from an along‐slope transect (1,300 m) and from a cross‐slope transect (855–4,766 m) were determined in the continental margin sediments of the Benguela Upwelling system. Profiles at all sites in the upwelling area showed increasing sulfate reduction rates from near zero at the surface to a peak at 2–5 cm (up to 29 nmol cm−3 d−1) and then decreasing exponentially with depth to near background rates at 10–20 cm depth (<2 nmol cm−3 d−1). Depth‐integrated sulfate reduction rates were greatest at 1,300 m and decreased exponentially with water depth. Along the transect following the 1,300‐m isobath, depth‐integrated sulfate reduction rates were highest in the north Cape Basin (1.16 +/− 0.23 mmol m−2 d−1), decreased over the Walvis Ridge (0.67 +/− 0.02 mmol m−2 d−1), and were lowest in the south Angola Basin (0.31 +/− 0.23 mmol m−2 d−1). Depth‐integrated sulfate reduction rates were consistent with the known pattern of coastal upwelling intensities and were also strongly correlated with surface organic carbon concentrations. Sulfate reduction rates, both as a function of depth and in comparison with sediment trap data, indicated that lateral downslope transport of organic carbon occurs. Sulfate reduction was estimated to account for 20–90% of the published rates of total oxygen consumption for the sediments at 1,300 m depth and 3–16% of sediments from 2,000 to 3,000 m depth. Comparison of the sulfate reduction rate profiles with the published diffusive oxygen uptake rates showed that the kinetics of oxygen utilization in the surface sediments are much faster than those for anaerobic organic carbon remineralization, although the underlying cause of the difference was not clear.
Short-term effects of air pollution and temperature on daily morbidity in Chiang Mai Thailand

Air pollution is associated with mortality and morbidity worldwide. Hot and cold temperature is also related to increased deaths and possibly hospital visits and admissions in many settings. Climate change is anticipated to pose increasing risks of deaths and illnesses associated with air pollution and temperature variations, particularly in developing world. To date, research studies about health effects of air pollution and temperature have been conducted in developed countries with cool climate more than in developing countries with subtropical or tropical climate. Furthermore, studies to identify susceptible populations are still limited. This study aims to investigate heath effects of air pollution and temperature and to identify people who are more susceptible to air pollution and temperature in a developing, tropical country, Thailand. A regression analysis of retrospective time series data was employed to assess the shortterm effects of air pollution and temperature on daily out-patient visits and hospital admissions in Chiang Mai, Thailand, from October 2002 to September 2006. Generalised negative binomial regression was used to model the relationships between the exposure and health outcomes, controlling for seasonal patterns and other possible potential confounders. Lag effects up to 4 days for air pollution, and up to 13 days for temperature were considered. Effect modification by age, sex, occupation, season, and previous out-patient visits before admissions were also examined. There were positive, but not significant, effects of air pollution for some pollutants (particularly for S02), with notably larger effect sizes compared to previous studies in Western countries. There was evidence of hot temperature effects (though wide confidence intervals), with an increase in diabetic visits of 26.3% (95% Cl, 7.1% to 49.0%), and in circulatory visits of 19.2% (95% Cl, 7.0% to 32.8%) for each 1°C increase in temperature above 29°C. There was a rise of both the visits (3.7% increase, 95% Cl, 1.5% to 5.9%) and admissions (5.8% increase, 95% Cl, 2.3% to 9.3%) due to intestinal infectious disease for each 1°C increase across the whole temperature range. Despite no statistically significant differences between subgroups, air pollution effects were stronger in the elderly, females and manual workers, whereas temperature effects were stronger in the elderly, male and unemployed people. This study suggests that while there was little evidence of air pollution effects, there was significant evidence of high temperature effects on daily morbidity in Chiang Mai. The elderly seemed to be more vulnerable to the daily changes of both air pollution and temperature.
One Hundred-one Canoes on the Shore – 3–5,000 year old Canoes from Newnans Lake, Florida

Abstract Newnans Lake is located east of the city of Gainesville in Alachua County, Florida. As the lake level dropped during extreme drought conditions in April 2000, hikers and bird watchers noticed wooden objects, including dugout canoes, appearing on the newly exposed shoreline. In the summer of 2000, with emergency funds furnished by the Florida Department of State, Division of Historical Resources many of the canoes were partially excavated, measured, photographed, drawn to scale, mapped using GPS, and sampled for radiocarbon analyses and wood identification. In subsequent months, additional canoes were exposed and recorded bringing the total to one hundred-one. In this paper we describe what is currently known about what is likely the world's largest cache of prehistoric dugout canoes – ages, sizes, styles, tree species and their significance.
The Effect of Different Types of Musculoskeletal Injuries on Blood Concentration of Serum Amyloid A in Thoroughbred Racehorses

Background Training-induced muscle, skeletal and joint trauma may result in acute phase response reflected by the changes in the blood concentration of serum amyloid A (SAA) in racehorses. It remains yet unclear if such systemic reaction could be triggered by sport injuries and what is the impact of different types of musculoskeletal trauma on SAA concentrations in racehorses. This study aimed to determine changes in the SAA blood concentration in racehorses with different types of injuries of musculoskeletal system. Materials and Methods The study involved 28 racehorses diagnosed after the race with bone fractures (n = 7), dorsal metacarpal disease (n = 11), joint trauma (n = 4) or tendon and muscle trauma (n = 6) and 28 healthy control racehorses. Serum samples were collected twice, between 1 and 4 days of the injury or succesful completion of the race. SAA concentration was measured using the commercial ELISA kit. Differences between mean SAA concentration in respective groups were analyzed using ANOVA and Tukey post-hoc test. Results Mean SAA concentration within the first 4 days of the injury of muscle and tendon was significantly higher than in bone fractures, dorsal metacarpal disease, joint trauma or in the healthy horses (p<0,001). There were no significant differences between the other groups. Conclusions Strain injuries of muscle and tendons can cause a moderate increase in SAA blood concentration in racehorses, reflecting the occurrence of the acute phase response. Similar reaction is not observed in the stress-related bone injuries.
Comparison of three Models of Avalanche Dynamics

Results and characteristics of three models for estimating avalanche flow speeds, flow heights, and run-out distances are compared: (1) Voellmy–Salm equation used with the traditional release, track, and run-out segmentation method; (2) Voellmy–Salm differential equation solved numerically along longitudinal profiles of avalanche paths, combined with modified assumptions for the flow in the run-out zone; (3) a granular-flow model introduced by Salm and Gubler. Within the limits of the accuracy of the field observations, all models are able to predict run-out distances correctly, at least for large avalanches, but the Voellmy–Salm type models significantly underestimate flow speeds. Modelling different flow regimes (sliding and partial fluidization) increases the range of avalanche sizes for which correct run-out modelling is possible without recalibration of model parameters.
Bcl-XL Inhibits Membrane Permeabilization by Competing with Bax

Although Bcl-XL and Bax are structurally similar, activated Bax forms large oligomers that permeabilize the outer mitochondrial membrane, thereby committing cells to apoptosis, whereas Bcl-XL inhibits this process. Two different models of Bcl-XL function have been proposed. In one, Bcl-XL binds to an activator, thereby preventing Bax activation. In the other, Bcl-XL binds directly to activated Bax. It has been difficult to sort out which interaction is important in cells, as all three proteins are present simultaneously. We examined the mechanism of Bax activation by tBid and its inhibition by Bcl-XL using full-length recombinant proteins and measuring permeabilization of liposomes and mitochondria in vitro. Our results demonstrate that Bcl-XL and Bax are functionally similar. Neither protein bound to membranes alone. However, the addition of tBid recruited molar excesses of either protein to membranes, indicating that tBid activates both pro- and antiapoptotic members of the Bcl-2 family. Bcl-XL competes with Bax for the activation of soluble, monomeric Bax through interaction with membranes, tBid, or t-Bid-activated Bax, thereby inhibiting Bax binding to membranes, oligomerization, and membrane permeabilization. Experiments in which individual interactions were abolished by mutagenesis indicate that both Bcl-XL–tBid and Bcl-XL–Bax binding contribute to the antiapoptotic function of Bcl-XL. By out-competing Bax for the interactions leading to membrane permeabilization, Bcl-XL ties up both tBid and Bax in nonproductive interactions and inhibits Bax binding to membranes. We propose that because Bcl-XL does not oligomerize it functions like a dominant-negative Bax in the membrane permeabilization process.
Perceptions of emergency medicine residents and fellows regarding competence, adverse events and reporting to supervisors: a national survey.

OBJECTIVE We sought to characterize the perceptions of emergency medicine (EM) residents and fellows of their clinical and procedural competence, as well as their attitudes, practices and perceived barriers to reporting these perceptions to their supervisors. METHODS A Web-based survey was distributed to residents and fellows, via their residency directors, in all Canadian EM residency programs outside of Quebec. RESULTS Of 220 residents and fellows contacted in 9 of 10 EM programs of the Royal College of Physicians and Surgeons of Canada and 12 of 13 EM programs of The College of Family Physicians of Canada, 82 (37.3%) completed all or part of the survey. Response rates varied slightly by question; 25 of 82 re-spondents (30.5% [95% confidence interval (CI) 19.9%-41.1%]) agreed with the statement, "I sometimes feel unsafe or un-qualified with undertaking unsupervised responsibilities or procedures, but I do not report this to my senior physician" and 32 of 81 (39.5% [95% CI 28.2%-50.8%]) had felt this within the past 6 months. Moreover, 34 of 82 (41.5% [95% CI 30.2%-52.7%]) reported their lack of competence to a supervisor half the time or less. Trainees reported worry about loss of trust, autonomy or respect (38/80, 47.5% [95% CI 35.9%-59.1%]) or reputation (32/80, 40.0% [95% CI 28.6%-51.4%]). Nights on-call (30/79, 38% [95% CI 26.6%-49.3%]), admission decisions (13/79, 16.5% [7.6%-25.3%]) and central line insertion (13/79, 16.5% [95% CI 7.6%-25.3%]) were reported to be frequently undertaken despite not feeling competent. Suggestions to improve reporting included encouragement to report without penalty (41/82, 50.0% [95% CI 38.6%-61.4%]) and a less judgmental environment (32/82, 39.0% [95% CI 27.9%-50.2%]). CONCLUSION Emergency medicine trainees report that they frequently do not feel competent when undertaking responsibilities without supervision. Barriers to reporting these feelings or reporting adverse events appear to relate to social pressures and authority gradients. Modifications to the training culture are encouraged to improve patient safety.
Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata

The movements of larvae between marine populations are difficult to follow directly and have been the subject of much controversy, especially in the Caribbean. The debate centres on the degree to which populations are demographically open, such that depleted populations can be replenished by recruitment from distant healthy populations, or demographically closed and thus in need of local management. Given the depressed state of many tropical reef populations, the understanding of these movements now bears critically on the number, placement, and size of marine reserves. Most genetic analyses assume that dispersal patterns have been stable for thousands of generations, thus they commonly reflect past colonization histories more than ongoing dispersal. Recently developed multilocus genotyping approaches, however, have the demonstrated ability to detect both migration and population isolation over far shorter timescales. Previously, we developed five microsatellite markers and demonstrated them to be both Mendelian and coral‐specific. Using these markers and Bayesian analyses, we show here that populations of the imperiled reef‐building coral, Acropora palmata, have experienced little or no recent genetic exchange between the western and the eastern Caribbean. Puerto Rico is identified as an area of mixing between the two subregions. As a consequence of this regional isolation, populations in the western and eastern Caribbean should have the potential to adapt to local conditions and will require population‐specific management strategies.
Notch Signaling Mediates the Age-Associated Decrease in Adhesion of Germline Stem Cells to the Niche

Stem cells have an innate ability to occupy their stem cell niche, which in turn, is optimized to house stem cells. Organ aging is associated with reduced stem cell occupancy in the niche, but the mechanisms involved are poorly understood. Here, we report that Notch signaling is increased with age in Drosophila female germline stem cells (GSCs), and this results in their removal from the niche. Clonal analysis revealed that GSCs with low levels of Notch signaling exhibit increased adhesiveness to the niche, thereby out-competing their neighbors with higher levels of Notch; adhesiveness is altered through regulation of E-cadherin expression. Experimental enhancement of Notch signaling in GSCs hastens their age-dependent loss from the niche, and such loss is at least partially mediated by Sex lethal. However, disruption of Notch signaling in GSCs does not delay GSC loss during aging, and nor does it affect BMP signaling, which promotes self-renewal of GSCs. Finally, we show that in contrast to GSCs, Notch activation in the niche (which maintains niche integrity, and thus mediates GSC retention) is reduced with age, indicating that Notch signaling regulates GSC niche occupancy both intrinsically and extrinsically. Our findings expose a novel role of Notch signaling in controlling GSC-niche adhesion in response to aging, and are also of relevance to metastatic cancer cells, in which Notch signaling suppresses cell adhesion.
B cells from hyper-IgM patients carrying UNG mutations lack ability to remove uracil from ssDNA and have elevated genomic uracil

The generation of high-affinity antibodies requires somatic hypermutation (SHM) and class switch recombination (CSR) at the immunoglobulin (Ig) locus. Both processes are triggered by activation-induced cytidine deaminase (AID) and require UNG-encoded uracil-DNA glycosylase. AID has been suggested to function as an mRNA editing deaminase or as a single-strand DNA deaminase. In the latter model, SHM may result from replicative incorporation of dAMP opposite U or from error-prone repair of U, whereas CSR may be triggered by strand breaks at abasic sites. Here, we demonstrate that extracts of UNG-proficient human B cell lines efficiently remove U from single-stranded DNA. In B cell lines from hyper-IgM patients carrying UNG mutations, the single-strand–specific uracil-DNA glycosylase, SMUG1, cannot complement this function. Moreover, the UNG mutations lead to increased accumulation of genomic uracil. One mutation results in an F251S substitution in the UNG catalytic domain. Although this UNG form was fully active and stable when expressed in Escherichia coli, it was mistargeted to mitochondria and degraded in mammalian cells. Our results may explain why SMUG1 cannot compensate the UNG2 deficiency in human B cells, and are fully consistent with the DNA deamination model that requires active nuclear UNG2. Based on our findings and recent information in the literature, we present an integrated model for the initiating steps in CSR.
Financial Repression in Transition: Evidence from Ukraine

This paper provides a rationale for the relatively poor macroeconomic performance in the post-Soviet transition economies based upon the concept of financial repression. Policies undertaken to assist in financing government expenditures caused financial repression and financial fragmentation, to use the terms introduced by McKinnon (1973). After an introductory section, I introduce a theoretical model of real and financial sectors in transition. The dynamic path to equilibrium from transition is derived. It is shown to have a tendency toward output contraction and hyperinflation when government policies promote financial repression. In the third section this hypothesis is examined with macroeconomic data from Ukraine for the period 1992 - 2001. These data are consistent with the hypothesis, although other factors (e.g., recession in trading partners) are also shown to be important.
HIV gp120 Binds to Mannose Receptor on Vaginal Epithelial Cells and Induces Production of Matrix Metalloproteinases

Background During sexual transmission of HIV in women, the virus breaches the multi-layered CD4 negative stratified squamous epithelial barrier of the vagina, to infect the sub-epithelial CD4 positive immune cells. However the mechanisms by which HIV gains entry into the sub-epithelial zone is hitherto unknown. We have previously reported human mannose receptor (hMR) as a CD4 independent receptor playing a role in HIV transmission on human spermatozoa. The current study was undertaken to investigate the expression of hMR in vaginal epithelial cells, its HIV gp120 binding potential, affinity constants and the induction of matrix metalloproteinases (MMPs) downstream of HIV gp120 binding to hMR. Principal Findings Human vaginal epithelial cells and the immortalized vaginal epithelial cell line Vk2/E6E7 were used in this study. hMR mRNA and protein were expressed in vaginal epithelial cells and cell line, with a molecular weight of 155 kDa. HIV gp120 bound to vaginal proteins with high affinity, (Kd = 1.2±0.2 nM for vaginal cells, 1.4±0.2 nM for cell line) and the hMR antagonist mannan dose dependently inhibited this binding. Both HIV gp120 binding and hMR exhibited identical patterns of localization in the epithelial cells by immunofluorescence. HIV gp120 bound to immunopurified hMR and affinity constants were 2.9±0.4 nM and 3.2±0.6 nM for vaginal cells and Vk2/E6E7 cell line respectively. HIV gp120 induced an increase in MMP-9 mRNA expression and activity by zymography, which could be inhibited by an anti-hMR antibody. Conclusion hMR expressed by vaginal epithelial cells has high affinity for HIV gp120 and this binding induces production of MMPs. We propose that the induction of MMPs in response to HIV gp120 may lead to degradation of tight junction proteins and the extracellular matrix proteins in the vaginal epithelium and basement membrane, leading to weakening of the epithelial barrier; thereby facilitating transport of HIV across the vaginal epithelium.
Stability of Solitary Waves and Global Existence of a Generalized Two-Component Camassa–Holm System

We study here the existence of solitary wave solutions of a generalized two-component Camassa–Holm system. In addition to those smooth solitary-wave solutions, we show that there are solitary waves with singularities: peaked and cusped solitary waves. We also demonstrate that all smooth solitary waves are orbitally stable in the energy space. We finally give a sufficient condition for global strong solutions to the equation in some special case.
Evaluation of a Capacitance Probe Frequency Response Model Accounting for Bulk Electrical Conductivity: Comparison with TDR and Network Analyzer Measurements

Soils ranging in texture from sand to clay were used to compare permittivity measurements made using a Surface Capacitance Insertion Probe (SCIP) and time domain reflectometer (TDR). Measurements were made using the same electrodes embedded in each soil, making the measurements directly comparable. The objective of the work was to test a model describing the frequency response of the SCIP to both permittivity and electrode conductance, and to compare results with TDR and network analyzer measurements. The model was tested using liquids of known permittivity and in saline, dielectric solutions. Surface Capacitance Insertion Probe and TDR determined permittivity values are similar for sandy soils but diverge for loam and clay soils. Using Topp's values as a reference, the SCIP‐determined permittivities for loams and clays lay close to the curve at water contents <0.25 m3 m−3, then often rose above the curve with increasing water content. Surface Capacitance Insertion Probe permittivity correction, using electrical conductivity (EC) measured at 1 kHz, corrected the results in sands reasonably well but not enough in loams and clays for reliable calibration. We propose three possible reasons for the higher than expected permittivity values observed using the SCIP: (i) higher than expected real permittivity created by dielectric dispersion, (ii) a large contribution of the imaginary permittivity due to relaxation processes assumed to be negligible, and (iii) poor model prediction of permittivity due to excessive damping of the oscillator circuit with high EC and dielectric losses. Results from network analyzer measurements for one of the clay soils were used to aid data interpretation. The TDR measurements were much more consistent, producing apparent relative permittivity values below those of the Topp curve for the finer textured soils.
Tree growth in carbon dioxide enriched air and its implications for global carbon cycling and maximum levels of atmospheric CO2

In the longest carbon dioxide enrichment experiment ever conducted, well-watered and adequately fertilized sour orange tree seedlings were planted directly into the ground at Phoenix, Arizona, in July 1987 and continuously exposed, from mid-November of that year, to either ambient air or air enriched with an extra 300 ppmv of CO2 in clear-plastic-wall open-top enclosures. Only 18 months later, the CO2-enriched trees had grown 2.8 times larger than the ambient-treated trees; and they have maintained that productivity differential to the present day. This tremendous growth advantage is due to two major factors: a CO2-induced increase in daytime net photosynthesis and a CO2-induced reduction in nighttime dark respiration. Measurements of these physiological processes in another experiment have shown three Australlian tree species to respond similarly; while an independent study of the atmosphere's seasonal CO2 cycle suggests that all earth's trees, in the mean, probably share this same response. A brief review of the plant science literature outlines how such a large growth response to atmospheric CO2 enrichment might possibly be maintained in light of resource limitations existing in nature. Finally, it is noted that a CO2 “fertilization effect” of this magnitude should substantially slow the rate at which anthropogenic carbon dioxide would otherwise accumulate in the atmosphere, possibly putting an acceptable upper limit on the level to which the CO2 content of the air may ultimately rise.