Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.
Adjuvant tamoxifen prescription in women 65 years and older with primary breast cancer.

PURPOSE We examined patterns of adjuvant tamoxifen discussion and prescription among breast cancer patients age 65 years and older. METHODS We selected from women diagnosed with primary breast cancer those with (1) stage I (tumor diameter > or = 1 cm), stage II, or stage IIIa disease; (2) age 65 years or older on the date of diagnosis; and (3) permission from the attending physician to contact. Data were collected from consenting patients' medical records, telephone interviews with patients, and mailed questionnaires completed by their physicians. RESULTS We obtained medical record and interview data for 698 patients. The oldest patients (odds ratio [OR], 0.45; 95% confidence interval [CI], 0.23 to 0.87 for those aged 80+ relative to those aged 65 to 69 years old), those with more comorbid conditions (each additional comorbid condition reduced the odds of discussion by 0.84; 95% CI, 0.73 to 0.96), and those who were estrogen receptor-negative (OR, 0.56; 95% CI, 0.32 to 0.99) were less likely to report discussion of tamoxifen therapy with a physician. Older patients (OR, 2.17; 95% CI, 1.18 to 4.01 for 70- to 79-year-olds relative to 65- to 69-year-olds; OR, 2.44; 95% CI, 1.11 to 5.34 for those aged 80+ relative to those aged 65 to 69 years old), those who reported a greater influence of information about tamoxifen on decision-making (an increase in 1 SD increased the odds by 7.43; 95% CI, 4.36 to 12.65), and those whose physicians believed that the benefits of tamoxifen outweighed its risks (an increase in 1 SD increased the odds by 1.87; 95% CI, 1.34 to 2.62) were more likely to be prescribed tamoxifen. CONCLUSION These findings highlight the key role of communication in the care of older women with breast cancer and its ultimate influence on the receipt of therapy.
Leukocyte protein calprotectin and outcome in rheumatoid arthritis

Objective: To determine if calprotectin is predictive for outcome in patients with rheumatoid arthritis (RA). Methods: Fifty six RA in-patients with variable disease duration were prospectively followed for five years. Clinical and laboratory data were collected to assess disease activity. Health Assessment Questionnaire (HAQ) and radiographic scores (of hands and wrists) as described by Larsen were used as outcome measures. Plasma calprotectin levels were determined with ELISA technique. Results: Significant correlations (r) were found cross-sectionally at follow-up between calprotectin concentration and other known parameters of disease activity and severity: CRP (r= 0.67), investigator's global assessment of disease activity (r= 0.57), Waaler titre (r= 0.50), HAQ score (r= 0.48) and number of swollen joints (r= 0.48). Calprotectin at baseline was not identified as an independent predictor for HAQ or radiographic progression in the multivariate analysis. Conclusion: The results confirm calprotectin as a good measure of disease activity and joint inflammation in RA. However, the level of calprotectin at baseline was not predictive for radiographic damage or functional impairment five years later.
The ubiquilin 1 gene and Alzheimer's disease.

2752 n engl j med 352;26 www.nejm. org june 30, 2005 the authors reply: Dr. Schwartz correctly notes that the majority of the participants in the Women’s Health Study were at low risk for coronary heart disease, as measured by the Framingham risk score. However, 1100 participants did have a risk of coronary heart disease that was 10 percent or greater. Among these high-risk participants, the findings were consistent with the overall findings of the trial, with no significant benefit with respect to the primary end point of major cardiovascular events for women taking aspirin as compared with those taking placebo (61 events in the aspirin group and 60 in the placebo group, P=0.74); there was a benefit for total stroke (17 events vs. 32, respectively; P=0.04) and a trend toward benefit for ischemic stroke (16 vs. 29, P=0.07), and there was no benefit for myocardial infarction (32 vs. 23, P=0.15). Thus, although overall the population had a low risk of cardiovascular events, it is important to note that there was no evidence of a modification of the effect of aspirin according to levels of the Framingham risk score in our study. Dr. Dalen is correct in pointing out that our trial demonstrated that the specific dose of 100 mg of aspirin every other day was not associated with a reduction in myocardial infarction overall, and he raises the important question of whether this very low dose was inadequate to produce a cardioprotective effect in women. Although we agree that it is certainly possible that the dose was inadequate, there was no direct evidence to support this in the Women’s Health Study. We showed that levels of thromboxane and prostacyclin were reduced with 100 mg of aspirin every other day; we observed the expected increased risk of gastrointestinal bleeding, hemorrhagic stroke, nongastrointestinal bleeding, and peptic ulcer, and 100 mg every other day was adequate both to lower the risk of stroke overall and to lower the risk of myocardial infarction as well as stroke in women 65 years of age or older. However, the issue of the lowest effective dose in both women and men requires further research.
Student Aid, Repayment Obligations and Enrolment in Higher Education in Germany - Evidence from a "Natural Experiment"

We evaluate the effect of the German Federal Educational Assistance Act (BAfoeG) on enrolment rates in higher education by exploiting the exogenous variation introduced through a discrete shift in the repayment regulations. While up to 1990, students receiving assistance had to repay their loans in full, since the BAfoeG reform, 50 percent thereof has been offered as a non-repayable grant. Our results from simple difference-in-difference estimates suggest that student aid is ineffective in raising enrolment rates. Our findings may have important implications for the current debate on the reform of financing higher education in Germany and elsewhere.
Adjunctive Minocycline in Clozapine-Treated Schizophrenia Patients With Persistent Symptoms

Objective Clozapine is the most effective antipsychotic for treatment refractory people with schizophrenia, yet many patients only partially respond. Accumulating preclinical and clinical data suggest benefits with minocycline. We tested adjunct minocycline to clozapine in a 10-week, double-blind, placebo-controlled trial. Primary outcomes tested were positive, and cognitive symptoms, while avolition, anxiety/depression, and negative symptoms were secondary outcomes. Methods Schizophrenia and schizoaffective participants (n = 52) with persistent positive symptoms were randomized to receive adjunct minocycline (100 mg oral capsule twice daily; n = 29) or placebo (n = 23). Results Brief Psychiatric Rating Scale (BPRS) psychosis factor (P = 0.098; effect size [ES], 0.39) and BPRS total score (P = 0.075; ES, 0.55) were not significant. A change in total BPRS symptoms of more than or equal to 30% was observed in 7 (25%) of 28 among minocycline and 1 (4%) of 23 among placebo participants, respectively (P = 0.044). Global cognitive function (MATRICS Consensus Cognitive Battery) did not differ, although there was a significant variation in size of treatment effects among cognitive domains (P = 0.03), with significant improvement in working memory favoring minocycline (P = 0.023; ES, 0.41). The Scale for the Assessment of Negative Symptoms total score did not differ, but significant improvement in avolition with minocycline was noted (P = 0.012; ES, 0.34). Significant improvement in the BPRS anxiety/depression factor was observed with minocycline (P = 0.028; ES, 0.49). Minocycline was well tolerated with significantly fewer headaches and constipation compared with placebo. Conclusions Minocycline's effect on the MATRICS Consensus Cognitive Battery composite score and positive symptoms were not statistically significant. Significant improvements with minocycline were seen in working memory, avolition, and anxiety/depressive symptoms in a chronic population with persistent symptoms. Larger studies are needed to validate these findings.
Pragmatic Transfer in Compliment Responses by Chinese Learners of English

This paper reports a study on the pragmatic transfer in compliment responses by Chinese Learners of English. It has three aims: (1) to discover similarities and differences in compliment responses between the American English speakers (AES) and Chinese Learners of English (CLE); (2) to provide empirical evidence for or against existing theories of pragmatic transfer in compliment responses and (3) to reveal differences of social values between the two groups. The results of this study are compared with those of R. Chen who made a similar study in 1993. The changes in the past ten years are discussed at the end.
TESTING INTRAVITREAL TOXICITY OF BEVACIZUMAB (AVASTIN)

Purpose: To evaluate the retinal toxicity of varying doses of bevacizumab when injected intravitreally in rabbits. Bevacizumab has been approved by the US Food and Drug Administration for the treatment of metastatic colorectal cancer. Materials and Methods: Twelve New Zealand albino rabbits were used for this study and divided into four groups. Four concentrations of bevacizumab were prepared: 500 &mgr;g/0.1 mL, 1.0 mg/0.1 mL, 2.5 mg/0.1 mL, and 5.0 mg/0.2 mL. Each concentration was injected intravitreally in one eye of each of three rabbits; 0.1 mL volume of sterile balanced saline solution was injected into the contralateral eyes. Slit-lamp and funduscopic examinations were performed and the animals were observed for 2 weeks for signs of infection, inflammation, or toxicity. A baseline electroretinogram (ERG) was performed before the drug treatment and at day 14 before the animals were killed. The enucleated eyes were prepared for histologic evaluation of retinal toxicity. Results: Histologic and ERG results in all groups showed no retinal toxicity. However, some inflammatory cells were found in the vitreous at the 5–mg dose. Conclusions: Intravitreal bevacizumab did not appear toxic to the retina in albino rabbits at a concentration of 2.5 mg. Intravitreally injected bevacizumab should be evaluated for efficacy in choroidal neovascularization and macular edema.
The reaction of stock market returns to anticipated unemployment

We empirically investigate the short-run impact of anticipated and unanticipated unemployment rates on stock prices. We particularly examine the nonlinearity in stock market's reaction to unemployment rate and study the effect at each individual point (quantile) of stock return distribution. Using nonparametric Granger causality and quantile regression based tests, we find that, contrary to the general findings in the literature, only anticipated unemployment rate has a strong impact on stock prices. Quantile regression analysis shows that the causal effects of anticipated unemployment rate on stock return are usually heterogeneous across quantiles. For quantile range (0.35, 0.80), an increase in the anticipated unemployment rate leads to an increase in the stock market price. For the other quantiles the impact is statistically insignificant. Thus, an increase in the anticipated unemployment rate is in general good news for stock prices. Finally, we offer a reasonable explanation of why unemployment rate should affect stock prices and how it affects them. Using Fisher and Phillips curve equations, we show that high unemployment rate is followed by monetary policy action of Federal Reserve (Fed). When unemployment rate is high, the Fed decreases the interest rate, which in turn increases the stock market prices.
Clinical Grade Manufacturing of Human Alloantigen‐Reactive Regulatory T Cells for Use in Transplantation

Regulatory T cell (Treg) therapy has the potential to induce transplantation tolerance so that immunosuppression and associated morbidity can be minimized. Alloantigen‐reactive Tregs (arTregs) are more effective at preventing graft rejection than polyclonally expanded Tregs (PolyTregs) in murine models. We have developed a manufacturing process to expand human arTregs in short‐term cultures using good manufacturing practice‐compliant reagents. This process uses CD40L‐activated allogeneic B cells to selectively expand arTregs followed by polyclonal restimulation to increase yield. Tregs expanded 100‐ to 1600‐fold were highly alloantigen reactive and expressed the phenotype of stable Tregs. The alloantigen‐expanded Tregs had a diverse TCR repertoire. They were more potent than PolyTregs in vitro and more effective at controlling allograft injuries in vivo in a humanized mouse model.
Calcium Currents and Calcium Signaling in Rod Bipolar Cells of Rat Retinal Slices

Combined electrophysiological and imaging techniques were used to study calcium currents (ICa) and their sites of origin at rod bipolar cells in rat retinal slices. We report here for the first time the successful whole-cell patch-clamp recording from presynaptic boutons that were compared with somatic recordings. TTX-resistant inward currents were elicited in response to depolarization. The kinetic and pharmacological properties ofICa were very similar for recordings obtained from the soma and the presynaptic terminals.ICa activated maximally between −30 and −20 mV was enhanced by Bay K 8644 and was blocked by isradipine and nifedipine. Peak amplitude and time to peak were −31.3 ± 1.2 pA and 3.2 ± 0.2 msec with somatic recordings (n= 54), whereas the corresponding values were −31.6 ± 6.1 pA and 3.2 ± 0.7 msec in recordings obtained directly from terminals (n = 6). ICa showed little inactivation during sustained depolarizations. No T-typeICa was observed with depolarizations from −90 mV. Concomitant with Ca2+ entry, depolarization induced the appearance of transient outward currents that resembled IPSCs and were blocked by GABA and glycine receptor antagonists, suggesting that they arise from activation of amacrine feedback synapses. Upon depolarization, intracellular Ca2+([Ca2+]i) rises were restricted to the presynaptic terminals with no somatic or axonal changes and were linearly dependent on pulse duration when using a low-affinity Ca2+ indicator. In cone bipolar cells,ICa inactivated markedly, and [Ca2+]i rises occurred in the axon, as well as in the presynaptic terminals.
Assessing New Perspectives on Country Risk

We examine in a unified framework three recent perspectives on country risk=debt intolerance, original sin, and currency mismatches. We find statistical evidence supporting aspects of all three, though the strength of that support varies considerably across hypotheses and a number of open questions remain. Our evidence is consistent with the view that good domestic macroeconomic and structural policies hold the key to addressing country risk.
Effect of Lactobacillus rhamnosus GG and vitamin D supplementation on the immunologic effectiveness of grass-specific sublingual immunotherapy in children with allergy.

BACKGROUND An important issue in sublingual immunotherapy (SLIT) is how to improve efficacy. OBJECTIVE To compare the clinical and immunologic efficacy of SLIT given alone and, to enhance clinical efficacy, given with probiotic or vitamin D supplementation. METHODS One hundred children, ages 5-12 years, sensitive to grass pollen, with allergic rhinitis participated in a 5-month prospective, randomized, double-blind, placebo-controlled trial. Children received 5-grass SLIT 300 IR tablets with either vitamin D 1000 IU daily supplementation, probiotic, or placebo. The control group included children with allergy who did not qualify for immunotherapy. Primary end points included a symptom-medication score, lung function, and exhaled nitric oxide concentration. The secondary end point was the immunologic efficacy measured by the following: CD4(+)CD25(+)Foxp3(+) (forkhead box P3) cells, Toll-like receptor (TLR) 4, interleukin (IL) 1, IL-6, tumor necrosis factor, IL-10, and transforming growth factor β-1 levels in cell culture supernatants. RESULTS Reduction in the symptom-medication score and improvement in lung function as well as a significant increase in the percentage of CD4(+)CD25(+)Foxp3(+) in children who received SLIT in all the groups were observed compared with control group. In the SLIT-probiotic group, between-group analysis showed significantly higher CD4(+)CD25(+)Foxp3(+) induction compared with the SLIT group and higher reduction in the percentage of TLR-positive cell group compared with the SLIT-vitamin D group (Fig. 1). An increase in CD4(+)CD25(+)Foxp3(+) induction, reduction in TLR-positive cells recruitment and an increase in transforming growth factor β-1 production were independently associated with a better clinical effect of SLIT in children. CONCLUSIONS We demonstrated the clinical and immunologic effect of probiotic and vitamin D supplementation on SLIT. Probiotic supplementation showed better clinical and immunologic response in children with allergic rhinitis.
West‐northwest directed obduction of the Batain Group on the eastern Oman continental margin at the Cretaceous‐Tertiary boundary

The Batain coast area in eastern Oman is dominated by allochthonous Permian to Late Maastrichtian sedimentary and volcanic rocks (Batain Group), unconformably overlain by neoautochthonous Tertiary sediments. The allochthonous rocks of the Batain coast were previously attributed to the Hawasina complex, the Permian to Coniacian/Santonian sedimentary infill of the neo‐Tethyan Hawasina basin off northern Oman. Previous structural interpretations suggested that the Batain Group, along with the Hawasina complex and the Semail ophiolite, was obducted in the Coniacian to Campanian from NE to SW onto the northern Oman continental margin. Results of our work in the Batain area differ from previous interpretations, with most significant differences concerning timing and direction of obduction. Our results show that WNW directed tectonic movements formed a fold‐and‐thrust belt and led to the obduction of allochthonous rocks onto the east Oman continental margin during latest Maastrichtian/earliest Paleocene times. This is coeval with emplacement of ophiolitic fragments along the eastern coast of Oman (eastern ophiolite belt) but is about 15–20 Myr later than emplacement of Hawasina complex and Semail ophiolite in northern Oman. Postemplacement structural evolution during the Tertiary involved intraplate extension, possibly reflecting the Red Sea/Gulf of Aden opening, and late Tertiary shortening related to convergence between Arabia and Eurasia. Late Tertiary contractional deformation resulted in refolding of the Batain nappes and in folding of the overlying Tertiary sediments. A palinspastic reconstruction of the Batain area indicates that the Permian to Upper Cretaceous sediments were formerly deposited in the Batain basin, a part of the proto‐Indian Ocean, along the present‐day eastern Oman margin. This leads us to propose that Permian breakup of Gondwanaland created both continental margins of Oman and led to the opening of two major basins: the neo‐Tethyan Hawasina basin in the north and the proto‐Indian Ocean Batain basin in the east, the latter separating Arabia from greater India.
Identification of Amino Acid Sequences with Good Folding Properties

Folding properties of a toy protein model containing only two amino-acid types, hydrophobic and hydrophilic respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences. irback@thep.lu. se carsten@thep.lu. se frank@thep.lu. se
Multi-Objective Reliability-Based Optimization with Stochastic Metamodels

This paper addresses continuous optimization problems with multiple objectives and parameter uncertainty defined by probability distributions. First, a reliability-based formulation is proposed, defining the nondeterministic Pareto set as the minimal solutions such that user-defined probabilities of nondominance and constraint satisfaction are guaranteed. The formulation can be incorporated with minor modifications in a multiobjective evolutionary algorithm (here: the nondominated sorting genetic algorithm-II). Then, in the perspective of applying the method to large-scale structural engineering problems—for which the computational effort devoted to the optimization algorithm itself is negligible in comparison with the simulation—the second part of the study is concerned with the need to reduce the number of function evaluations while avoiding modification of the simulation code. Therefore, nonintrusive stochastic metamodels are developed in two steps. First, for a given sampling of the deterministic variables, a preliminary decomposition of the random responses (objectives and constraints) is performed through polynomial chaos expansion (PCE), allowing a representation of the responses by a limited set of coefficients. Then, a metamodel is carried out by kriging interpolation of the PCE coefficients with respect to the deterministic variables. The method has been tested successfully on seven analytical test cases and on the 10-bar truss benchmark, demonstrating the potential of the proposed approach to provide reliability-based Pareto solutions at a reasonable computational cost.