Miracle-dz/UniFAR-FTUs huggingface dataset:
Prokaryotic Communities in Pit Mud from Different-Aged Cellars Used for the Production of Chinese Strong-Flavored Liquor

ABSTRACT Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4 +, lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.
Evaluation of the Impact of the Cancer Therapy Everolimus on the Central Nervous System in Mice

Cancer and treatments may induce cognitive impairments in cancer patients, and the causal link between chemotherapy and cognitive dysfunctions was recently validated in animal models. New cancer targeted therapies have become widely used, and their impact on brain functions and quality of life needs to be explored. We evaluated the impact of everolimus, an anticancer agent targeting the mTOR pathway, on cognitive functions, cerebral metabolism, and hippocampal cell proliferation/vascular density in mice. Adult mice received everolimus daily for 2 weeks, and behavioral tests were performed from 1 week after the last treatment. Everolimus-treated mice displayed a marked reduction in weight gain from the last day of the treatment period. Ex vivo analysis showed altered cytochrome oxidase activity in selective cerebral regions involved in energy balance, food intake, reward, learning and memory modulation, sleep/wake cycle regulation, and arousal. Like chemotherapy, everolimus did not alter emotional reactivity, learning and memory performances, but in contrast to chemotherapy, did not affect behavioral flexibility or reactivity to novelty. In vivo hippocampal neural cell proliferation and vascular density were also unchanged after everolimus treatments. In conclusion, two weeks daily everolimus treatment at the clinical dose did not evoke alteration of cognitive performances evaluated in hippocampal- and prefrontal cortex-dependent tasks that would persist at one to four weeks after the end of the treatment completion. However, acute everolimus treatment caused selective CO modifications without altering the mTOR effector P70S6 kinase in cerebral regions involved in feeding behavior and/or the sleep/wake cycle, at least in part under control of the solitary nucleus and the parasubthalamic region of the hypothalamus. Thus, this area may represent a key target for everolimus-mediating peripheral modifications, which has been previously associated with symptoms such as weight loss and fatigue.
Location tracking of fast-paced mobile entity using CDS for VANETs

Location tracking of mobile entity becomes a research challenge for applications in vehicular networks, mobile sensor networks and mobile adhoc networks. The GPS based tracking in vehicular networks has limitations in certain scenarios such as inside tunnels, tall buildings, dense forests, etc. Tracking of fast-paced mobile entity (say mobile node) finds applications in vehicular networks such as chasing, hit-and-run accidents, etc. Connected dominating set(CDS) provides a virtual backbone in adhoc network. This paper uses connected dominating set(CDS) based virtual backbone in vehicular adhoc networks for tracking of fast-paced mobile node's location. We show that using a simple heuristics that the location updates for mobile node can be reduced to the tune of 40%.
Fast Compressed Sensing SAR Imaging Based on Approximated Observation

In recent years, compressed sensing (CS) has been applied in the field of synthetic aperture radar (SAR) imaging and shows great potential. The existing models are, however, based on application of the sensing matrix acquired by the exact observation functions. As a result, the corresponding reconstruction algorithms are much more time consuming than traditional matched filter (MF)-based focusing methods, especially in high resolution and wide swath systems. In this paper, we formulate a new CS-SAR imaging model based on the use of the approximated SAR observation deducted from the inverse of focusing procedures. We incorporate CS and MF within an sparse regularization framework that is then solved by a fast iterative thresholding algorithm. The proposed model forms a new CS-SAR imaging method that can be applied to high-quality and high-resolution imaging under sub-Nyquist rate sampling, while saving the computational cost substantially both in time and memory. Simulations and real SAR data applications support that the proposed method can perform SAR imaging effectively and efficiently under Nyquist rate, especially for large scale applications.
Characterization of Cell Populations Isolated from Aortas of Rhesus Monkeys with Experimental Atherosclerosis

We used enzyme digestion to isolate cells from aortas of Rhesus monkeys (Macaca mulatto) fed on control or atherogenic diets for 19-21 months and subjected them to Metrizamide density gradient centrifugation. A majority of the cells from both control and experimental animals equilibrated in the density range of 1.08-1.12, but an additional population of cells (about 10% of the total) equilibrating at lower densities (p = 1.04-1.07) was present in preparations from diseased vessels. Except for a 10-fold increase in esterified cholesterol in cells from diseased aortas, the high density cells of both groups exhibited similar levels of marker enzymes of organelles [iV-acetyl-/? -glucosaminidase and /? -galactosidase (lysosomes), neutral a-glucosidase (endoplasmic reticulum), 5′-nucleotidase (plasma membrane), and catalase (catalase-bearing particles)] and contained similar amounts of unesterified cholesterol. Electron microscopy revealed the high density cells as smooth muscle cells, with many of those from diseased vessels containing cytoplasmic lipid droplets and lipid-containing lysosomes. The latter were identified by acid phosphatase cytochemistry. The low density cells were enriched in both free and esterified cholesterol, acid hydrolases, and catalase. They appeared morphologically as foam cells heavily laden with lipid, which was present as cytoplasmic lipid droplets and as lipid-containing lysosomes. The cytoplasmic lipid droplets occupied 34-38% and the lipid-filled lysosomes another 18-23% of the cytoplasmic volume of the foam cells. The proportion of total aortic cholesterol associated with cells was found to be 22.1 ± 7% (n = 3) in the control aortas and 17.0 ± 4% (n = 4) in the diseased aortas. Circ Res 46: 520-530, 1980
What affect the contribution of it to firm performance? an exploratory study in China

This paper integrates the strategic management perspectives of “resource-based” and “positioning” to simultaneously examine the mediating effect of knowledge management (KM) and the moderating effect of industry setting on the performance impact of information technology (IT). Data collected from 236 firms operating in China replicated and extended research findings of previous studies, based on structural model equations. Consistent with previous studies, KM capability was found to be a partial mediator of the IT-performance relationship. Extending previous studies, industry setting was found to be a moderator of the IT-performance and IT-KM capability relationships. Theoretical contributions and managerial implications are discussed accordingly.
Variational PET/CT Tumor Co-Segmentation Integrated With PET Restoration

Positron emission tomography (PET) and computed tomography (CT) are widely used imaging modalities in radiation oncology. PET imaging has a high contrast but often leads to blurry tumor edges due to its limited spatial resolution, while CT imaging has a high resolution but a low contrast between a tumor and its surrounding normal soft tissues. Tumor segmentation from either a single PET or CT image is difficult. It is known that co-segmentation methods utilizing the complementary information between PET and CT can improve the segmentation accuracy. This complementary information can be either consistent or inconsistent in the image level. How to correctly localize tumor edges with the inconsistent information is one major challenge for co-segmentation. This paper proposes a novel variational method for tumor co-segmentation in PET/CT, with a fusion strategy specifically designed to handle the information inconsistency between PET and CT in an adaptive way—the method can automatically decide which modality should be more trustful when PET and CT disagree to each other for localizing the tumor boundary. A PET restoration process is further integrated into the co-segmentation process, which further eliminates the uncertainty for tumor segmentation introduced by tumor edge blur in PET. The performance of the proposed method is validated on 50 nonsmall cell lung cancer patients. It achieves an average dice similarity indexes (DSIs) of 0.85 ± 0.06, volume error (VE) of 0.09 ± 0.08, and classification error (CE) of 0.31 ± 0.13. The proposed method has a high accuracy for PET/CT tumor co-segmentation and PET restoration.
Detecting the small island effect and nestedness of herpetofauna of the West Indies

Abstract To detect the small island effect (SIE) and nestedness patterns of herpetofauna of the West Indies, we derived and updated data on the presence/absence of herpetofauna in this region from recently published reviews. We applied regression‐based analyses, including linear regression and piecewise regressions with two and three segments, to detect the SIE and then used the Akaike's information criterion (AIC) as a criterion to select the best model. We used the NODF (a nestedness metric based on overlap and decreasing fill) to quantify nestedness and employed two null models to determine significance. Moreover, a random sampling effort was made to infer about the degree of nestedness at portions of the entire community. We found piecewise regression with three segments performed best, suggesting the species–area relationships possess three different patterns that resulted from two area thresholds: a first one, delimiting the SIE, and a second one, delimiting evolutionary processes. We also found that taxa with lower resource requirement, higher dispersal ability, and stronger adaptation to the environment generally displayed lower corresponding threshold values, indicating superior taxonomic groups could earlier end the SIE period and start in situ speciation as the increase of island size. Moreover, the traditional two‐segment piecewise regression method may cause poor estimations for both slope and threshold value of the SIE. Therefore, we suggest previous SIE detection works that conducted by two‐segment piecewise regression method, ignoring the possibility of three segments, need to be reanalyzed. Antinestedness occurred in the entire system, whereas high degree of nestedness could still occur in portions within the region. Nestedness may still be applicable to conservation planning at portions even if it is antinested at the regional scale. However, nestedness may not be applicable to conservation planning at the regional scale even if nestedness does exist among sampling islands from a portion.
Characterization of Major Histocompatibility Complex (MHC) DRB Exon 2 and DRA Exon 3 Fragments in a Primary Terrestrial Rabies Vector (Procyon lotor)

The major histocompatibility complex (MHC) presents a unique system to explore links between genetic diversity and pathogens, as diversity within MHC is maintained in part by pathogen driven selection. While the majority of wildlife MHC studies have investigated species that are of conservation concern, here we characterize MHC variation in a common and broadly distributed species, the North American raccoon (Procyon lotor). Raccoons host an array of broadly distributed wildlife diseases (e.g., canine distemper, parvovirus and raccoon rabies virus) and present important human health risks as they persist in high densities and in close proximity to humans and livestock. To further explore how genetic variation influences the spread and maintenance of disease in raccoons we characterized a fragment of MHC class II DRA exon 3 (250bp) and DRB exon 2 (228 bp). MHC DRA was found to be functionally monomorphic in the 32 individuals screened; whereas DRB exon 2 revealed 66 unique alleles among the 246 individuals screened. Between two and four alleles were observed in each individual suggesting we were amplifying a duplicated DRB locus. Nucleotide differences between DRB alleles ranged from 1 to 36 bp (0.4–15.8% divergence) and translated into 1 to 21 (1.3–27.6% divergence) amino acid differences. We detected a significant excess of nonsynonymous substitutions at the peptide binding region (P = 0.005), indicating that DRB exon 2 in raccoons has been influenced by positive selection. These data will form the basis of continued analyses into the spatial and temporal relationship of the raccoon rabies virus and the immunogenetic response in its primary host.
A Dynamic Approach for Modelling and Simulation of Motor Unit Discharge Behaviour Using Recurrent Fuzzy-techniques

A dynamic approach for modelling and simulation of motor unit discharge behaviour using recurrent fuzzy-techniques is presented. The model is able to generate a nominal force-time curve by means of the discharge behaviour of a single motor unit pool using the knowledge of various seemingly isolated findings that have been reported. In several simulations, it has been shown that recurrent fuzzy systems are able to approximate dynamic behaviour in terms of nominal/actual force value regulation. First results suggest that there might be optimal motor unit co-ordination patterns relating to a given task: in first MVC-simulations variation of about 10% has been shown. In spite of the difficulties to verify the model experimental examination is necessary to confirm the results. This kind of research is fundamental to understand mechanisms that yield to increased muscle performances in sports.
Correction: A Robust Model-free Approach for Rare Variants Association Studies Incorporating Gene-Gene and Gene-Environmental Interactions

Recently more and more evidence suggest that rare variants with much lower minor allele frequencies play significant roles in disease etiology. Advances in next-generation sequencing technologies will lead to many more rare variants association studies. Several statistical methods have been proposed to assess the effect of rare variants by aggregating information from multiple loci across a genetic region and testing the association between the phenotype and aggregated genotype. One limitation of existing methods is that they only look into the marginal effects of rare variants but do not systematically take into account effects due to interactions among rare variants and between rare variants and environmental factors. In this article, we propose the summation of partition approach (SPA), a robust model-free method that is designed specifically for detecting both marginal effects and effects due to gene-gene (G6G) and gene-environmental (G6E) interactions for rare variants association studies. SPA has three advantages. First, it accounts for the interaction information and gains considerable power in the presence of unknown and complicated G6G or G6E interactions. Secondly, it does not sacrifice the marginal detection power; in the situation when rare variants only have marginal effects it is comparable with the most competitive method in current literature. Thirdly, it is easy to extend and can incorporate more complex interactions; other practitioners and scientists can tailor the procedure to fit their own study friendly. Our simulation studies show that SPA is considerably more powerful than many existing methods in the presence of G6G and G6E interactions. Citation: Fan R, Lo S-H (2013) A Robust Model-free Approach for Rare Variants Association Studies Incorporating Gene-Gene and Gene-Environmental Interactions. PLoS ONE 8(12): e83057. doi:10.1371/journal.pone. 0083057 Editor: Zhi Wei, New Jersey Institute of Technology, United States of America Received May 24, 2013; Accepted October 30, 2013; Published December 17, 2013 Copyright: 2013 Lo, Fan. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. * E-mail: slo@stat.columbia. edu(SHL)
A PDZ-containing Scaffold Related to the Dystrophin Complex at the Basolateral Membrane of Epithelial Cells

Membrane scaffolding complexes are key features of many cell types, serving as specialized links between the extracellular matrix and the actin cytoskeleton. An important scaffold in skeletal muscle is the dystrophin-associated protein complex. One of the proteins bound directly to dystrophin is syntrophin, a modular protein comprised entirely of interaction motifs, including PDZ (protein domain named for PSD-95, discs large, ZO-1) and pleckstrin homology (PH) domains. In skeletal muscle, the syntrophin PDZ domain recruits sodium channels and signaling molecules, such as neuronal nitric oxide synthase, to the dystrophin complex. In epithelia, we identified a variation of the dystrophin complex, in which syntrophin, and the dystrophin homologues, utrophin and dystrobrevin, are restricted to the basolateral membrane. We used exogenously expressed green fluorescent protein (GFP)-tagged fusion proteins to determine which domains of syntrophin are responsible for its polarized localization. GFP-tagged full-length syntrophin targeted to the basolateral membrane, but individual domains remained in the cytoplasm. In contrast, the second PH domain tandemly linked to a highly conserved, COOH-terminal region was sufficient for basolateral membrane targeting and association with utrophin. The results suggest an interaction between syntrophin and utrophin that leaves the PDZ domain of syntrophin available to recruit additional proteins to the epithelial basolateral membrane. The assembly of multiprotein signaling complexes at sites of membrane specialization may be a widespread function of dystrophin-related protein complexes.
Association between polymorphisms in the metallophosphoesterase (MPPE1) gene and bipolar disorder

Genetic linkage studies in bipolar disorder (BPD) suggest that a susceptibility locus exists on chromosome 18p11. The metallophosphoesterase (MPPE1) gene maps to this region. Dysregulation of protein phosphorylation and subsequent abnormal cellular signaling has been postulated to be involved in neuropsychiatric disorders thus making MPPE1 a plausible biological candidate gene for BPD. In this study, we hypothesized that genetic variation in the MPPE1 gene contributes to BPD. We tested this hypothesis by genotyping four SNPs (rs871044; rs3974590; rs593713; rs602201) in BPD patients (n = 570) and healthy controls (n = 725). Genotypes and allele frequencies were compared between groups using Chi square contingency analysis. Linkage disequilibrium (LD) between markers was calculated and estimated haplotype frequencies were compared between groups. Single marker analysis revealed an association of rs3974590 with BPD (P = 0.009; permutation corrected P = 0.046). Haplotype analysis did not show any significant association with disease after permutation correction. Our results provide evidence of an association between a polymorphism in the MPPE1 gene and BPD. Additional studies are necessary to confirm and elucidate the role of MPPE1 as a susceptibility gene for BPD on chromosome 18p. © 2009 Wiley‐Liss, Inc.
Differential Gene Expression in Auristatin PHE-Treated Cryptococcus neoformans

ABSTRACT The antifungal pentapeptide auristatin PHE was recently shown to interfere with microtubule dynamics and nuclear and cellular division in the opportunistic pathogen Cryptococcus neoformans. To gain a broader understanding of the cellular response of C. neoformans to auristatin PHE, mRNA differential display (DD) and reverse transcriptase PCR (RT-PCR) were applied. Examination of approximately 60% of the cell transcriptome from cells treated with 1.5 times the MIC (7.89 μM) of auristatin PHE for 90 min revealed 29 transcript expression differences between control and drug-treated populations. Differential expression of seven of the transcripts was confirmed by RT-PCR, as was drug-dependent modulation of an additional seven transcripts by RT-PCR only. Among genes found to be differentially expressed were those encoding proteins involved in transport, cell cycle regulation, signal transduction, cell stress, DNA repair, nucleotide metabolism, and capsule production. For example, RHO1 and an open reading frame (ORF) encoding a protein with 91% similarity to the Schizophyllum commune 14-3-3 protein, both involved in cell cycle regulation, were down-regulated, as was the gene encoding the multidrug efflux pump Afr1p. An ORF encoding a protein with 57% identity to the heat shock protein HSP104 in Pleurotus sajor-caju was up-regulated. Also, three transcripts of unknown function were responsive to auristatin PHE, which may eventually contribute to the elucidation of the function of their gene products. Further study of these differentially expressed genes and expression of their corresponding proteins are warranted to evaluate how they may be involved in the mechanism of action of auristatin PHE. This information may also contribute to an explanation of the selectivity of auristatin PHE for C. neoformans. This is the first report of drug action using DD in C. neoformans.