Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of Variants Identified in Caucasian Genome-Wide Association Studies for Plasma High-Density Lipoprotein Cholesterol and Triglycerides Levels in Mexican Dyslipidemic Study Samples

Background—Although epidemiological studies have demonstrated an increased predisposition to low high-density lipoprotein cholesterol and high triglyceride levels in the Mexican population, Mexicans have not been included in any of the previously reported genome-wide association studies for lipids. Methods and Results—We investigated 6 single-nucleotide polymorphisms associated with triglycerides, 7 with high-density lipoprotein cholesterol, and 1 with both triglycerides and high-density lipoprotein cholesterol in recent Caucasian genome-wide association studies in Mexican familial combined hyperlipidemia families and hypertriglyceridemia case-control study samples. These variants were within or near the genes ABCA1, ANGPTL3, APOA5, APOB, CETP, GALNT2, GCKR, LCAT, LIPC, LPL (2), MMAB-MVK, TRIB1, and XKR6-AMAC1L2. We performed a combined analysis of the family-based and case-control studies (n=2298) using the Z method to combine statistics. Ten of the single-nucleotide polymorphisms were nominally significant and 5 were significant after Bonferroni correction (P=2.20×10−3 to 2.6×10−11) for the number of tests performed (APOA5, CETP, GCKR, and GALNT2). Interestingly, our strongest signal was obtained for triglycerides with the minor allele of rs964184 (P=2.6×10−11) in the APOA1/C3/A4/A5 gene cluster region that is significantly more common in Mexicans (27%) than in whites (12%). Conclusions—It is important to confirm whether known loci have a consistent effect across ethnic groups. We show replication of 5 Caucasian genome-wide association studies lipid associations in Mexicans. The remaining loci will require a comprehensive investigation to exclude or verify their significance in Mexicans. We also demonstrate that rs964184 has a large effect (odds ratio, 1.74) and is more frequent in the Mexican population, and thus it may contribute to the high predisposition to dyslipidemias in Mexicans.
Vascular Hospitalization Rates and Costs in Patients With Peripheral Artery Disease in the United States

Background—Peripheral artery disease (PAD) is common and imposes a high risk of major systemic and limb ischemic events. The REduction of Atherothrombosis for Continued Health (REACH) Registry is an international prospective registry of patients at risk of atherothrombosis caused by established arterial disease or the presence of ≥3 atherothrombotic risk factors. Methods and Results—We compared the 2-year rates of vascular-related hospitalizations and associated costs in US patients with established PAD across patient subgroups. Symptomatic PAD at enrollment was identified on the basis of current intermittent claudication with an ankle-brachial index (ABI) <0.90 or a history of lower-limb revascularization or amputation. Asymptomatic PAD was diagnosed on the basis of an enrollment ABI <0.90 in the absence of symptoms. Overall, 25 763 of the total 68 236–patient REACH cohort were enrolled from US sites; 2396 (9.3%) had symptomatic and 213 (0.8%) had asymptomatic PAD at baseline. One- and cumulative 2-year follow-up data were available for 2137 (82%) and 1677 (64%) of US REACH patients with either symptomatic or asymptomatic PAD, respectively. At 2 years, mean cumulative hospitalization costs, per patient, were $7445, $7000, $10 430, and $11 693 for patients with asymptomatic PAD, a history of claudication, lower-limb amputation, and revascularization, respectively (P=0.007). A history of peripheral intervention (lower-limb revascularization or amputation) was associated with higher rates of subsequent procedures at both 1 and 2 years. Conclusions—The economic burden of PAD is high. Recurring hospitalizations and repeat revascularization procedures suggest that neither patients, physicians, nor healthcare systems should assume that a first admission for a lower-extremity PAD procedure serves as a permanent resolution of this costly and debilitating condition.
Isolation and characterization of osmotolerant bacteria from thar desert of western Rajasthan (India).

The Thar Desert harsher environment harbors a limited diversity of life forms due to extreme conditions like low moisture of sandy soils and high soil temperature. In the present study, osmotolerant bacteria from the Thar soils were isolated and characterized. Bacteria were isolated from 20 soil samples (100 g), collected from sand dunes, suspended in water and absolute alcohol. A total of 11 biochemical and morphological tests were carried out for generic identification of bacteria. Osmotic tolerance capacity of isolates was examined on glycerol, NaCI and alcohol; and sequencing of 16S rRNA gene was also performed for bacterial identification. 16S to 23S rRNA internal transcribed spacer analysis (RISA) was done for phylogenetic analysis of isolates. The soil suspended in water contained 2.5 x 10(6) bacteria/g of soil while alcohol suspended soil had 4.4 x 10(4) bacteria/g. The 24 bacterial isolates were found tolerant to 26% glycerol, 14% NaCI and 10% of alcohol, and 22 out of 24 isolates were found Gram positive. The results showed that 45.83% and 41.67% bacteria belong to Bacillus spp. and Corynebacterium spp. , respectively, while Acinetobacter spp. , Aeromonas spp. and Staphylococcus spp. were in equal proportion (4.16% each). Six isolates were selected for 16S rRNA gene sequencing and five were found 95% similar with Bacillus licheniformis whereas one isolate was identified as B. subtilis. All the isolates showed good growth up to 50 degrees C with gradual reduction on subsequent increment of temperature. Out of 24 isolates, six could survive at 65 degrees C while one isolate could grow at 63 degrees C. Growth kinetic studies revealed that the reduction in generation time in solute(s) and temperature stress was more as compared to generation time in plain medium. This study suggests that virgin sand dunes may be a rich source of bacteria, tolerant to osmotrophic solutes, and can be examined for plant growth promotion activity in agriculture. Moreover, study might help to resolve the tactic adopted by microbes to defeat desiccation induced by various types of solutes.
Fate of Pup inside the Mycobacterium Proteasome Studied by in-Cell NMR

The Mycobacterium tuberculosis proteasome is required for maximum virulence and to resist killing by the host immune system. The prokaryotic ubiquitin-like protein, Pup-GGE, targets proteins for proteasome-mediated degradation. We demonstrate that Pup-GGQ, a precursor of Pup-GGE, is not a substrate for proteasomal degradation. Using STINT-NMR, an in-cell NMR technique, we studied the interactions between Pup-GGQ, mycobacterial proteasomal ATPase, Mpa, and Mtb proteasome core particle (CP) inside a living cell at amino acid residue resolution. We showed that under in-cell conditions, in the absence of the proteasome CP, Pup-GGQ interacts with Mpa only weakly, primarily through its C-terminal region. When Mpa and non-stoichiometric amounts of proteasome CP are present, both the N-terminal and C-terminal regions of Pup-GGQ bind strongly to Mpa. This suggests a mechanism by which transient binding of Mpa to the proteasome CP controls the fate of Pup.
Origin of the matter-antimatter asymmetry

Although the origin of matter-antimatter asymmetry remains unknown, continuing advances in theory and improved experimental limits have ruled out some scenarios for baryogenesis, for example, sphaleron baryogenesis at the electroweak phase transition in the Standard Model. At the same time, the success of cosmological inflation and the prospects for discovering supersymmetry at the Large Hadron Collider have put some other models in sharper focus. We review the current state of our understanding of baryogenesis with emphasis on those scenarios that we consider most plausible.
Spatial relationships of microtubule-organizing centers and the contact area of cytotoxic T lymphocytes and target cells

Specific binding (conjugation) of cytotoxic T lymphocytes (CTL) to target cells (TC) is the first step in a multistage process ultimately resulting in dissolution of the TC and recycling of the CTL. We examined the position of the microtubule organizing center (MTOC) of immune CTL bound to specific TC. Immunofluorescence labeling of freshly prepared CTL-TC conjugates with tubulin antibodies indicated that the MTOC in essentially all conjugated CTL but not in the conjugated TC were oriented towards the intercellular contact site. This finding was corroborated by electron microscopy examination of CTL-TC conjugates fixed either immediately after conjugation or during the lytic process. Antibody-induced caps of membrane antigens of CTL such as H-2 and Thy 1, did not show a similar relationship to the MTOC. Incubation of CTL- TC conjugates, 10-15 min at room temperature, resulted in an apparent deterioration of the microtubular system of conjugated CTL. It is proposed that the CTL plasma membrane proximal to the MTOC is particularly active in forming stable intercellular contacts, resulting in CTL-TC conjugation, and that subsequent modulation of the microtubular system of the CTL may be related to the cytolytic response and to detachment of the effector cell.
Analytical characterization of the conformational transitions of polynucleotides by means of different molecular spectroscopies and multivariate curve resolution.

A general procedure for the study of conformational transitions of polynucleotides is described. The equilibria between different conformations induced by salt, ethidium bromide, and temperature of poly(dG-dC). poly(dG-dC) and induced by salt and temperature of poly(A). poly(U) are investigated using molecular absorption, circular dichroism, and fluorescence spectroscopies. Spectral data obtained from experiments are analyzed by means of a factor analysis method, namely, multivariate curve resolution, which allows possible intermediate states to be detected and the pure spectra and the concentration profiles of all species present in the system to be estimated. This work shows the application of this procedure for the analysis of data matrices obtained in individual experiments but also for the analysis of several data matrices simultaneously.
PREPARED FOR THE U.S. DEPARTMENT OF ENERGY, UNDER CONTRACT DE-AC02-76CH03073 PRINCETON PLASMA PHYSICS LABORATORY PRINCETON UNIVERSITY, PRINCETON, NEW JERSEY

It has been suggested that resonant mode conversion of compressional MHD waves into kinetic Alfvén waves at the magnetopause can explain the abrupt transition in wave polarization from compressional to transverse commonly observed during magnetopause crossings [Johnson and Cheng, 1997b]. We analyze magnetic field data for magnetopause crossings as a function of magnetic shear angle (defined as the angle between the magnetic fields in the magnetosheath and magnetosphere) and compare with the theory of resonant mode conversion. The data suggest that amplification in the transverse magnetic field component at the magnetopause is not significant up to a threshold magnetic shear angle. Above the threshold angle significant amplification results, but with weak dependence on magnetic shear angle. Waves with higher frequency are less amplified and have a higher threshold angle. These observations are qualitatively consistent with theoretical results obtained from the kinetic-fluid wave equations.
Sex Differences in the Genetic Risk for Alcoholism

One of the characteristics influencing a person’s risk for alcoholism is his or her sex, and various factors may contribute to sex differences in risk. Adoption studies have provided some evidence of possible sex differences in the heritability of alcoholism, but overall the findings have been inconclusive. Twin studies have consistently supported the role of genetic risk factors in the heritability of alcoholism in men, and shared environmental factors also play a role in the familiality of alcoholism among women. In addition, sex differences exist in the patterns of transmission of alcoholism between family members. However, the genetic epidemiology research conducted to date on this issue has several limitations, some of which may be resolved by future molecular genetic studies.
Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study

In the absence of an experimentally solved structure, a homology model of a protein target can be used instead for virtual screening of drug candidates by docking and scoring. This approach poses a number of questions regarding the choice of the template to use in constructing the model, the accuracy of the screening results, and the importance of allowing for protein flexibility. The present study addresses such questions with compound screening calculations for multiple homology models of five drug targets. A central result is that docking to homology models frequently yields enrichments of known ligands as good as that obtained by docking to a crystal structure of the actual target protein. Interestingly, however, standard measures of the similarity of the template used to build the homology model to the targeted protein show little correlation with the effectiveness of the screening calculations, and docking to the template itself often is as successful as docking to the corresponding homology model. Treating key side chains as mobile produces a modest improvement in the results. The reasons for these sometimes unexpected results, and their implications for future methodologic development, are discussed.
Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.
Helicobacter pylori in the mouth - negative isolation from dental plaque and saliva

Objective To determine the colonization of Helicobacter pylori in dental plaque and saliva of individuals with H. pylori-associated gastritis. Patients and methods One hundred and twenty adult dyspeptic patients attending for outpatient endoscopy were randomly selected. Saliva, dental plaques and antral biopsies were collected and cultured in Dent's medium. Antral biopsies were also taken for histological confirmation of colonization. Results Eleven patients were withdrawn owing to poor tolerance of endoscopy. Fifty-two patients (47%) were found to be H. pylori positive on culture from antral biopsies and on antral histology. H. pylori was not isolated from, saliva and dental plaques in any of the patients irrespective of their infective status. The H. pylori seropositivity rate was higher in the Japanese (72%) than in the Dutch (33%). Conclusion We failed to isolate H. pylori from saliva and dental plaque in a group of dyspeptic patients with H. py/ori-associated gastritis. We believe that our finding strongly suggests that oral to oral route is not an important mode of transmission in the adult population.
The interaction between model resolution, observation resolution and observation density in data assimilation: A one‐dimensional study

In this paper, the optimal configurations of model resolution, observation resolution and observation density are investigated in a simple one‐dimensional framework. In this context, the representativeness error is formalized and estimated before being used in the analysis‐error formulation. Some optimal and suboptimal assimilation‐schemes, differing from different approximations of observation‐error covariance and observation operator, are compared. The optimal observation‐extent is determined as a function of model resolution. Increasing the observation density is usually beneficial, except for suboptimal schemes similar to the ones used in operational practice. The impact of thinning the observations with correlated error is also studied from a suboptimal viewpoint. Copyright © 2002 Royal Meteorological Society
THE INTERACTION OF MAMMALIAN CELLS WITH ANTIBODIES. I

The single cell plating technique has been applied to quantitation of the reproductive killing of mammalian cells by specific antibodies. This method confirms previous demonstrations by other workers of localization of all the killing activity in the γ-globulin fraction of specific cell antisera but not of normal sera; the need for complement for the killing action in low doses of antibody and the leakage of cell constituents attending cell killing under these conditions. In concentrations of 4 per cent or higher of heated antiserum cell killing occurs without added complement. The cell plating technique permits highly reproducible quantitation of antibody action and demonstrates antibody activity in sera diluted 1:3000. It permits demonstration of very high degrees of species specificity as shown by virtually complete absence of cross-reaction between antisera to Chinese hamster and S3 HeLa cells, respectively. Somatic cells which have been sensitized by absorption of specific antibody lose their sensitization when incubated at 37° unless complement is added within 1 hour.
CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis

Chitin is a major component of fungal cell walls and serves as a microbe-associated molecular pattern (MAMP) for the detection of various potential pathogens in innate immune systems of both plants and animals. We recently showed that chitin elicitor-binding protein (CEBiP), plasma membrane glycoprotein with LysM motifs, functions as a cell surface receptor for chitin elicitor in rice. The predicted structure of CEBiP does not contain any intracellular domains, suggesting that an additional component(s) is required for signaling through the plasma membrane into the cytoplasm. Here, we identified a receptor-like kinase, designated CERK1, which is essential for chitin elicitor signaling in Arabidopsis. The KO mutants for CERK1 completely lost the ability to respond to the chitin elicitor, including MAPK activation, reactive oxygen species generation, and gene expression. Disease resistance of the KO mutant against an incompatible fungus, Alternaria brassicicola, was partly impaired. Complementation with the WT CERK1 gene showed cerk1 mutations were responsible for the mutant phenotypes. CERK1 is a plasma membrane protein containing three LysM motifs in the extracellular domain and an intracellular Ser/Thr kinase domain with autophosphorylation/myelin basic protein kinase activity, suggesting that CERK1 plays a critical role in fungal MAMP perception in plants.
Ecological stoichiometry: An elementary approach using basic principles

Based on the observation that organism‐specific elemental content creates ecologically relevant mismatches such as between plant and animal tissue, it was postulated—and experimentally verified—that this would profoundly affect trophic efficiency and nutrient fluxes in ecosystems. From its beginnings as a Daphnia‐centered perspective, the field of ecological stoichiometry (ES) has widened to include many organism groups, and ecosystem types, and the questions it addresses have broadened. We address some of the development of ES in aquatic sciences especially over the past 10 yr, focusing on homeostasis and mass balance in the consumer, and its effect on trophic efficiency and nutrient recycling in aquatic communities. We also discuss how ES has provided novel insights into genomic, proteomic, and cellular responses at one end of the biological scale as well as into large‐scale effects related to biogeochemical couplings at the ecosystem level. The coupling of global C, N, and P cycles via their biotic interactions and their responses to climate change accentuate ES as an important toolkit for ecosystem analysis. We also point to some of the major topics and principles where ES has provided new insights. For each of these topics we also point to some novel directions where the ES concepts likely will be useful in understanding and predicting biological responses.
CCN activation and cloud processing in sectional aerosol models with low size resolution

We investigate the influence of low size resolution, typical to sectional aerosol models in large scale applications, on cloud droplet activation and cloud processing of aerosol particles. A simplified cloud model with five approaches to determine the fraction of activated particles is compared with a detailed reference model under different atmospheric conditions. In general, activation approaches which assume a distribution profile within the critical model size sections predict the cloud droplet concentration most accurately under clean and moderately polluted conditions. In such cases, the deviation from the reference simulations is below 15% except for very low updraft velocities. In highly polluted cases, the concentration of cloud droplets is significantly overestimated due to the inability of the simplified model to account for the kinetic limitations of the droplet growth. Of the profiles examined, taking into account the local shape of the particle size distribution is the most accurate although in most cases the shape of the profile has little relevance. While the low resolution cloud model cannot reproduce the details of the out-of-the-cloud aerosol size distribution, it captures well the amount of sulphate produced in aqueous-phase reactions as well as the distribution of the sulphate between the cloud droplets. Overall, the simplified cloud model with low size resolution performs well for clean and moderately polluted regions that cover most of the Earth's surface and is therefore suitable for large scale models. It can, however, show uncertainties in areas with strong pollution from anthropogenic sources.