Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Chlorpyrifos from Plastic Bags used in Commercial Banana Production

Chlorpyrifos is an organophosphate pesticide used in Costa Rica and other countries around the world for banana and plantain production. In Costa Rica, chlorpyrifos is impregnated into blue plastic bags that are placed around ripening fruit to prevent insect damage to fruit skin. Much is known about chlorpyrifos movement and degradation rates from soils and foliage, but no studies are known on the movement and dissipation of chlorpyrifos from plastic bags. Our objective was to determine the rate of chlorpyrifos loss from plastic bags used in banana production, and to estimate the potential amount chlorpyrifos lost through volatilization or degradation annually in banana production in Costa Rica. Although chlorpyrifos bags were found to be very heterogeneous in chlorpyrifos concentration, approximately 90% of the chlorpyrifos was lost within the first 10 days during 3 replicated experiments, under average daily temperatures regimes between 19°C and 30°C. As the vast majority of chlorpyrifos is lost from plastic bags under these conditions, it is estimated than 22.5 metric tonnes of chlorpyrifos and degradation products may lost to the environment, annually during banana and plantain production in Costa Rica.
A DCE-MRI Driven 3-D Reaction-Diffusion Model of Solid Tumor Growth

Predicting tumor growth and its response to therapy remains a major challenge in cancer research and strongly relies on tumor growth models. In this paper, we introduce, calibrate, and verify a novel image-driven reaction-diffusion model of avascular tumor growth. The model allows for proliferation, death and spread of tumor cells, and accounts for nutrient distribution and hypoxia. It is constrained by longitudinal time series of dynamic contrast-enhancement-MRI images. Tumor specific parameters are estimated from two early time points and used to predict the spatio-temporal evolution of the tumor volume and cell densities at later time points. We first test our parameter estimation approach on synthetic data from 15 generated tumors. Our in silico study resulted in small volume errors (<5%) and high Dice overlaps (>97%), showing that model parameters can be successfully recovered and used to accurately predict the tumor growth. Encouraged by these results, we apply our model to seven pre-clinical cases of breast carcinoma. We are able to show promising preliminary results, especially for the estimation for early time points. Processes like angiogenesis and apoptosis should be included to further improve predictions for later time points.
Frankly, We Do Give a Damn

There are two conflicting perspectives regarding the relationship between profanity and dishonesty. These two forms of norm-violating behavior share common causes and are often considered to be positively related. On the other hand, however, profanity is often used to express one’s genuine feelings and could therefore be negatively related to dishonesty. In three studies, we explored the relationship between profanity and honesty. We examined profanity and honesty first with profanity behavior and lying on a scale in the lab (Study 1; N = 276), then with a linguistic analysis of real-life social interactions on Facebook (Study 2; N = 73,789), and finally with profanity and integrity indexes for the aggregate level of U.S. states (Study 3; N = 50 states). We found a consistent positive relationship between profanity and honesty; profanity was associated with less lying and deception at the individual level and with higher integrity at the society level.
Clinical and Bacteriological Aspects of Pyoderma

Pyoderma is one of the commonest clinical conditions encountered in dermatological practice. [1] Primary pyodermas are impetigo, follicultis, furuncle, carbuncle, ecthyma, erthyrasma, and sycosis barbae. Secondary pyodermas constitute tropic ulcer, infected pemphigus, infected contact dermatitis, infected scabies, and various other dermatoses infected with organisms. Various factors like poverty, malnutrition, overcrowding, and poor hygiene have been stated to be responsible for its higher incidence in the lower socio-economic class. Climatic conditions also play a major role. [2] Changing trends are being noted in the etiological aspects of primary pyoderma, and the problem of emergence of drug resistance strains is an even increasing one. Most common organism usually isolated in pyoderma is Staphyloccus aureus, which may be either methicilllin-sensitive (MSSA) or methicilllin-resistant (MRSA). MRSA is an important health care associated pathogen. Many of these isolates are becoming multidrug resistant. All β-lactams including carbapenams and high-end cephalosporins, piperacillin, tazobactum etc. are ineffective against MRSA. Knowledge of prevalence of MRSA and their current anti-microbial profile becomes necessary in the selection of appropriate empirical treatment of these infections. [3] Here, we report the clinical and bacteriological aspects of the pyodermas to guide for the selection of appropriate antibiotics and to prevent the emergence of resistant organisms. We found that the incidence of impetigo was maximum among pyoderma. The primary pyoderma cases were maximum in the age group of < 10 years, and prevalence rate was higher in male patients. Among the various diseases, scabies was found to be the commonest to be associated with primary pyoderma. Most common isolated organism was Staphylococcus aureus. Pyodermas are a common cause of skin infection in children and are associated with many multidrug-resistant organisms such as MRSA. A correct anti-microbial policy based on the knowledge of resistance patterns of the commonly isolated organisms is mandatory to prevent unnecessary medication and further emergence of drug-resistant organisms.
Rheology of fiber-enriched steamed bread: Stress relaxation and texture profile analysis

Wheat bran is one of the major dietary fiber sources widely used in the food industry in order to produce fiber-enriched foods. The effects of wheat bra n substitution (0-30%). water absorption (46-62%) and electric power (4-12 kW) of steamer on stress relaxation and textural parameters of steamed breads were evaluated by the Texture Analyzer. The results showed that mechanical stress relaxation data of steamed breads were fitted well by both the Peleg-Normand and three-element Maxwell models. At 10-40% strains tested, common and bran-enriched steamed breads were more elastic measured at low strain. It was suitable to perform the stress relaxation test of steamed bread at 10-30% strains. Generally, increasing the substitution of flour by bran resulted in less elasticity and higher hardness of steamed bread. Results of sensory evaluation indicated no significant difference in textural and overall acceptability among various steamed breads with 0, 10 and 20% of wheat bran. Medium and high water absorptions (54-62%) produced fiber-enriched steamed bread with better elasticity and texture. The elasticity of the steamed bread was the lowest at 4 kW e1eetric power of steamer. Significant correlations were found between textural characteristics and stress relaxation parameters. This study suggests that 20% bran-enriched steamed bread, with better elasticity and sensory acceptability, can be produced at 54% of water absorption and 12 kW of electric power of the steamer.
Retrieval of Inherent Optical Properties for Turbid Inland Waters From Remote-Sensing Reflectance

Remote estimation of inherent optical properties (IOPs) for water bodies cannot only provide indicators of water quality, but also be used in the study on biological and biogeochemical processes of waters. The quasi-analytical algorithm (QAA) is a simple and effective method to retrieve IOPs from remote-sensing reflectance (Rrs). The QAA has been widely validated and applied in oceans, but its application in inland waters is far less extensive. In this paper, the QAA was enhanced to retrieve IOPs for turbid inland waters based on the bandwidths of Medium Resolution Imaging Spectrometer (MERIS). The enhancement was achieved by proposing a semi-analytical model to estimate the spectral slope of particle backscattering, as well as a novel estimation model for phytoplankton absorption coefficient at 443 nm. Two data sets (i.e., noise-free synthetic data and in-situ data) were collected to assess the performance of the enhanced algorithm. Results show that the algorithm yields almost error-free estimations for total absorption and backscattering coefficients and estimations for phytoplankton absorption at 443 nm with acceptable accuracy in the case of synthetic data set. For the in-situ data set, the algorithm retrieves the total absorption coefficients (ranging 0.337-8.331 m-1) with root-mean-square-error in log scale (RMSE) and bias in log scale lower than 0.130 and 0.094, respectively, and phytoplankton absorption at 443 nm (ranging 0.378-4.669 m-1) with RMSE and bias in log scale of 0.151 and 0.096, respectively. These results indicate the potential of the enhanced QAA to accurately retrieve the IOPs from MERIS satellite observations for inland waters.
Variants of DNA Repair Genes and the Risk of Biliary Tract Cancers and Stones: A Population-Based Study in China

Biliary tract cancers, which encompass tumors of the gallbladder, extrahepatic ducts, and ampulla of Vater, are relatively rare tumors with a high fatality rate. Other than a close link with gallstones, the etiology of biliary tract cancers is poorly understood. We conducted a population-based case-control study in Shanghai, China, to examine whether genetic variants in several DNA repair genes are associated with biliary tract cancers or biliary stones. Genomic DNA from 410 patients with biliary tract cancers (236 gallbladder, 127 bile duct, and 47 ampulla of Vater), 891 patients with biliary stones, and 786 healthy subjects randomly selected from the Shanghai population were genotyped for putative functional single nucleotide polymorphisms in four DNA repair genes (MGMT, RAD23B, CCNH, and XRCC3). Of the five single nucleotide polymorphisms examined, only one (MGMT EX5-25C>T, rs12917) was associated with biliary tract cancer. Independent of gallstones, subjects carrying the CT genotype of the MGMT EX5-25C>T marker had a significantly reduced risk of gallbladder cancer [odds ratio (OR), 0.63; 95% confidence interval (95% CI), 0.41-0.97; P = 0.02] and nonsignificant reduced risks of bile duct (OR, 0.61; 95% CI, 0.35-1.06) and ampulla of Vater (OR, 0.85; 95% CI, 0.39-1.87) cancers. However, this marker was not associated with biliary stones, and the other markers examined were not significantly associated with either biliary tract cancers or stones. Findings from this population-based study in Shanghai suggest that MGMT gene variants may alter susceptibility to biliary tract cancer, particularly gallbladder cancer. Confirmation in future studies, however, is required. (Cancer Epidemiol Biomarkers Prev 2008;17(8):2123–7)
The Witten-Sakai-Sugimoto model: A brief review and some recent results

A brief review of the Witten-Sakai-Sugimoto model is given, which is a top-down holographic model of low-energy QCD with chiral quarks derived from type-IIA superstring theory. The main predictions of the model, in particular concerning meson spectra, the gluon condensate, the QCD string tension, the mass of the $\eta'$ and of baryons are discussed and compared quantitatively with available experimental and/or lattice results. Then some recent results of potential interest to the physics program at the future FAIR facility are presented: The spectrum of glueballs and their decay rates into pions, and the phase diagram of QCD at finite temperature, density, and magnetic field strength.
Physical Activity Contributes to Several Sleep-Cardiometabolic Health Relationships.

PURPOSE To estimate the contribution of accelerometer-derived physical activity to the relationship between sleep and cardiometabolic health. METHODS Data from the 2005 to 2006 US National Health and Nutritional Examination Survey were used (N = 1226; 20 years+). Metabolic syndrome (MetS) was defined by the Joint Interim Statement, and sleep quality and quantity by the Sleep Disorders Questionnaire. Physical activity intensities were defined by activity thresholds (counts per minute) as sedentary activity (0-99), light intensity (100-759), lifestyle activity (760-2019), moderate intensity (2020-5996), and vigorous intensity (≥5999). Outcomes were MetS, number of MetS components, waist circumference (WC), systolic and diastolic blood pressure (BP), triglycerides, HDL-cholesterol, fasting plasma glucose, and fasting insulin concentration. The bootstrap method was used to estimate the amount of mediation or contribution of activity intensities (ab) to the sleep-cardiometabolic health relationships, which were quantified as large (≥0.25) or moderate (≥0.09). RESULTS Lifestyle activity level contributes to several sleep duration and cardiometabolic health relationships, most notably for WC (ab: 0.28), systolic BP (0.39), and fasting insulin concentration (0.85). While moderate intensity and lifestyle activity intensities were large contributors to the sleep quality-fasting insulin concentration relationship (0.47 and 0.48, respectively), light intensity activity only moderately contributed to the relationship between sleep duration and quality with abdominal obesity (0.15). CONCLUSION Lifestyle and moderate intensity physical activity have a large effect on the relationship between sleep and cardiometabolic health, including WC, BP, and fasting insulin concentration. Appropriate sleep hygiene, in combination with regular physical activity should be considered mutually beneficial targets for cardiometabolic health.
GAIT: Gene expression Analysis for Interval Time

Motivation Despite the potential usefulness, the association analysis of gene expression with interval times of two events has been hampered because the occurrence of events can be censored and the conventional survival analysis is not suitable to handle two censored events. However, the recent advances of multivariate survival analysis considering multiple censored events together provide an unprecedented chance for this problem. Based on such advances, we have developed a software tool, GAIT, for the association analysis of gene expression with interval time of two events. Results The performance of GAIT was demonstrated by simulation studies and the real data analysis. The result indicates the usefulness of GAIT in a wide range of biomedical applications. Availability and implementation http://cdal.korea. ac.kr/GAIT/index.html
Attitudes and behavior of peripheral arterial disease patients toward influencing their physician’s prescription of cholesterol-lowering medication

Among 355 peripheral arterial disease (PAD) patients with low density lipoprotein cholesterol (LDL-C) levels ≥ 70 mg/dl, we assessed knowledge regarding optimal LDL levels and the importance of LDL-C-lowering therapy. We also assessed PAD participants’ behaviors and attitudes regarding their engagement with their physician in treatment decisions for LDL-C lowering. The average baseline LDL-C level of participants was 103.4 mg/dl ± 30.7 mg/dl. Seventy-six percent of participants were taking at least one cholesterol-lowering medication. Sixty-six percent were unable to define their optimal LDL-C. Only 47% strongly agreed that their own actions and decisions could reduce their LDL-C. Just 29.8% were aware that patients who request specific medications from their physician were more likely to receive them, and 16% had asked their physician whether they should be taking more cholesterol-lowering medication. These findings suggest that further study is needed to identify effective interventions to educate PAD patients and their physicians about the importance of cholesterol-lowering therapy and to encourage PAD patients to participate with their physician in decisions regarding cholesterol-lowering treatment. Clinical Trial Registration - URL: http://www.clinicaltrials. gov. Unique identifier: NCT00217919
Common germline variation in mismatch repair genes and survival after a diagnosis of colorectal cancer

The mismatch repair (MMR) genes are involved in the maintenance of genomic integrity. Recently, we showed that common variants in these genes are unlikely to contribute significantly to colorectal cancer risk. The aim of this study was to investigate the role of common variants in the mismatch repair pathway as prognostic markers in colorectal cancer patients. We genotyped 2,060 patients for 68 SNPs in 7 mismatch repair genes (MLH1, MLH3, MSH2, MSH3, MSH6, PMS1 and PMS2), using a single nucleotide polymorphism (SNP) tagging approach. Genotypes at the tag SNPs and multi‐SNP haplotypes were tested for association with overall survival (OS) and disease specific survival (DSS) using a Cox regression model. Eight SNPs and 10 haplotypes were significant at a nominal p < 0.05 in the univariate analyses. Stepwise analysis showed that haplotype effects were mainly due to associated SNPs carried by these haplotypes. After adjustment for sex, age at diagnosis and stage when using overall survival and stage only when using disease specific survival, prognostic values were unattenuated. The most significant SNP associated with disease specific survival after adjustment was rs863221, located in MSH3 (HR: 0.59, 95% confidence interval (CI) 0.42–0.82, p‐value: 0.001). In conclusion, we find some evidence that common variants in mismatch repair genes may contribute to survival of patients with colorectal cancer. © 2008 Wiley‐Liss, Inc.
Spontaneous Remission of Transient Leukemia in Down Syndrome: Extrinsic or Intrinsic Mechanism?

Myeloid leukemias in childhood Down syndrome (DS) comprise a unique disease entity. Transient Leukemia (TL) in neonates with DS is a neoplastic disorder characterized by Acute Myeloid Leukemia (AML)-like hematological abnormalities, which spontaneously resolves in several weeks or months. On the other hand, AML in young children with DS (AML-DS), which occurs several years later, usually after spontaneous remission of TL, does not resolve spontaneously and is a lethal disorder unless treated. These two types of myeloid leukemia in DS are a spectrum of disorders with common GATA1 gene mutations and a background of trisomy 21, but arise in different organs at different developmental stages. TL is thought to arise in the fetal liver and is often accompanied by hepatic fibrosis in severe cases, whereas AML-DS arises in the postnatal BM and is often accompanied by myelofibrosis, with fibrosis of both organs being caused by a common mechanism through cytokines produced by leukemic blasts. The mechanism of the spontaneous remission of TL is unclear and two major hypotheses have been proposed: 1) a transition of major hematopoietic organs from the liver to the BM after birth might stop TL blast growth (extrinsic/ environmental theory); and 2) the genetic mechanism controlling the switch from fetal- to adult-type haematopoiesis might trigger the end of TL blast growth (intrinsic/genetic theory).
Dectin-1-Syk-CARD9 Signaling Pathway in TB Immunity

One of the first steps toward mounting an effective immune response to Mycobacterium tuberculosis (Mtb) is recognition of the pathogen through pattern-recognition receptors (PRRs) expressed by innate immune cells. Activation of the PRR Dectin-1 by an unknown mycobacterial ligand triggers an intracellular signaling cascade involving numerous proteins, including spleen tyrosine kinase, protein kinase C-delta, and caspase recruitment domain family member 9, some of which have been shown to influence host immune response to TB infection. Here, we review the role of Dectin-1 signaling pathway in anti-mycobacterial immunity and discuss its contribution in the control of Mtb infection, and potential applications in TB vaccine adjuvanticity.
A better block partition and ligation strategy for individual haplotyping

MOTIVATION Haplotype played an important role in the association studies of disease gene and drug responsivity over the past years, but the low throughput of expensive biological experiments largely limited its application. Alternatively, some efficient statistical methods were developed to deduce haplotypes from genotypes directly. Because these algorithms usually needed to estimate the frequencies of numerous possible haplotypes, the partition and ligation strategy was widely adopted to reduce the time complexity. The haplotypes were usually partitioned uniformly in the past, but recent studies showed that the haplotypes had their own block structure, which may be not uniform. More reasonable block partition and ligation strategy according to the haplotype structure may further improve the accuracy of individual haplotyping. RESULTS In this article, we presented a simple algorithm for block partition and ligation, which provided better accuracy for individual haplotyping. The block partition and ligation could be completed within O(m(2) logm+m(2n)) time complexity, where m represented the length of genotypes and n represented the number of individuals. We tested the performance of our algorithm on both real and simulated dataset. The result showed that our algorithm yielded better accuracy with short running time. AVAILABILITY The software is publicly available at http://mail.ustc. edu.cn/~zyzh.
Association analysis of the GRN  rs5848 and MAPT rs242557 polymorphisms in Parkinson's disease and multiple system atrophy: a large-scale population-based study and meta-analysis

Background: Previous studies have found an association between the granulin gene rs5848 and microtubule-associated protein tau gene (MAPT) rs242557 polymorphisms and susceptibility to Parkinson's disease (PD). However, the results of association studies between the two polymorphisms and PD have been inconsistent. Given the overlap in clinical and pathological characteristics of PD and multiple system atrophy (MSA), we examined the associations of these two polymorphisms with PD and MSA in a subset of the Chinese population. Methods: In total, 1270 PD patients, 360 MSA patients and 830 healthy controls (HCs) were included in the study. All subjects were genotyped for the two polymorphisms using Sequenom iPLEX Assay technology. After combining our results with the available published data, a meta-analysis was conducted to investigate the association between MAPT rs242557 and the risk of PD. Results: The minor allele “T” of GRN rs5848 decreased the risk for PD (p = 0.0309, odds radio [OR], 0.86; 95% CI, 0.76–0.99). No differences in the genotype distributions and minor allele frequency (MAF) of MAPT rs242557 were observed between the PD and the HCs in our Chinese population. Our meta-analysis revealed an association between MAPT rs242557 and PD in Caucasian and Asian population in a recessive model (p = 0.049 and p = 0.046, respectively). However, no significant differences in the genotype distributions and MAFs of the two polymorphisms were found between the MSA patients and HCs. Conclusion: Our results indicate that GRN rs5458 may decrease the risk of PD in Chinese individuals, and the MAPT rs242557 is marginally associated with PD.