Theoretical bound of the efficiency of learning with coarse-graining

A thermodynamic formalism describing the efficiency of information learning is proposed, which is applicable for stochastic thermodynamic systems with multiple internal degree of freedom. The learning rate, entropy production rate (EPR), and entropy flow from the system to the environment under coarse-grained dynamics are derived. The Cauchy-Schwarz inequality has been applied to demonstrate the lower bound on the EPR of an internal state. The inequality of EPR is tighter than the Clausius inequality, leading to the derivative of the upper bound on the efficiency of learning. The results are verified in cellular networks with information processes

NMR structure and Mg(2+) binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit

Helix 42 of Domain II of Escherichia coli 23S ribosomal RNA underlies the L7/L12 stalk in the ribosome and may be significant in positioning this feature relative to the rest of the 50S ribosomal subunit. Unlike the Haloarcula marismortui and Deinococcus radiodurans examples, the lower portion of helix 42 in E.coli contains two consecutive G•A oppositions with both adenines on the same side of the stem. Herein, the structure of an analog of positions 1037–1043 and 1112–1118 in the helix 42 region is reported. NMR spectra and structure calculations support a cis Watson–Crick/Watson–Crick (cis W.C.) G•A conformation for the tandem (G•A)(2) in the analog and a minimally perturbed helical duplex stem. Mg(2+) titration studies imply that the cis W.C. geometry of the tandem (G•A)(2) probably allows O6 of G20 and N1 of A4 to coordinate with a Mg(2+) ion as indicated by the largest chemical shift changes associated with the imino group of G20 and the H8 of G20 and A4. A cross-strand bridging Mg(2+) coordination has also been found in a different sequence context in the crystal structure of H.marismortui 23S rRNA, and therefore it may be a rare but general motif in Mg(2+) coordination

Spectroscopy 16 (2002) 1-13 1 IOS Press Protein dynamics measurements by 3D HNCO based NMR experiments

Abstract. Protein dynamics can be characterized by relaxation parameters obtained from traditional 2D HSQC based NMR experiments. This approach is hampered when applied to proteins with severe spectral overlap. In the present work, several novel 3D TROSY-HNCO and 3D HSQC-HNCO based NMR experiments were applied for measuring 15 N T1, T2 and 1 H-15 N NOE with improved spectral dispersion by introducing a third 13 C dimension. The number of phase cycling steps in these 3D pulse sequences was restricted to two in order to minimize the time required to perform the dynamics measurements. For a uniformly 100% 15 N, 100% 13 C, and 70% 2 H-labelled trichosanthin sample (∼27 kDa, 1.0 mM) at 30 • C, the sensitivity of 3D TROSY-HNCO based experiment was, on the average, enhanced by 72% compared to that of 3D HSQC-HNCO based experiments. However, the 3D HSQC-HNCO based experiments should be more effective for non-deuterated proteins with smaller molecular weights and seriously overlapped 2D HSQC spectra. Results from the 3D TROSY-HNCO and 3D HSQC-HNCO based experiments were in good agreement with those obtained from traditional 2D HSQC based experiments

Effect of Pomegranate Juice on Dextran Sulfate Sodium Salt-Induced Ulcerative Colitis in Mice

Ulcerative colitis is a chronic inflammatory bowel disease with unclear pathogenesis and is difficult to cure. The incidence rate is increasing year by year, and there is high drug dependence for the treatment of ulcerative colitis, which leads to obvious the treatment resistance to s side effects. Therefore, seeking natural health products for nutritional therapy has become an attention focus of attention. In this articlestudy, dextran sulfate sodium salt (DSS) was used to establish a mouse model of ulcerative colitis. The mice were intervened with 5-aminosalicylic acid (5-ASA) (130 mg/(kg mb∙d)) or pomegranate juice (30% and 100%, 10 mL/d). Body mass, disease activity index (DAI) and colon length were measured, liver and kidney function and oxidative stress were measured by biochemical kits, the levels of inflammatory factors were measured by enzyme-linked immunosorbent assay (ELISA), colon tissue sections were observed, and the contents of fecal short-chain fatty acids (SCFAs) were determined by gas chromatography-mass spectrometry (GC-MS). Finally, a comprehensive evaluation of the effect and mechanism of pomegranate juice against ulcerative colitis in mice was exploredperformed. Compared with the DSS group, body mass and colon length in the pomegranate juice intervention group was increased, DAI was decreased, liver and kidney functions were improved, and could the expression of proinflammatory factors was significantly decreased (P < 0.01). In addition, anti-inflammatory factor expression was significantly enhanced (P < 0.01), reduce the level of oxidative stress and the activity of inflammatory marker myeloperoxidase (MPO) were significantly reduced (P < 0.01), the level of up-regulate fecal SCFAs was up-regulated, andimprove the colonic epithelial structure was improved. Pomegranate juice can attenuate intestinal mucosal damage and liver and kidney dysfunction, and has a good therapeutic effect on DSS-induced ulcerative colitis in mice

Integrated Dual-Band Filtering/Duplexing Antennas

In this paper, the state-of-the-art integrated filtering antennas with dual-band operation are first reviewed. Then, two designs of dual-band microstrip filtering antennas with a low frequency-ratio are presented. The 1st design is a dual-band dual-polarization (DBDP) antenna with a frequency ratio of 1.2 on a single patch, by employing the coupled resonator technique. Two bands at each polarization are achieved by vertically coupling a hairpin resonator with a patch through a slot in the ground plane and then coupled to a dual-mode stub loaded resonator (SLR). Each band exhibits a 2nd-order filtering performance with improved bandwidth and out-of-band rejection. Such an integration technique could significantly reduce the dimension and complexity of traditional DBDP antennas/arrays. In the 2nd design, a novel dual-port dual-band antenna (with a frequency ratio of 1.38) with the integrated filtering and duplexing functions is proposed. The frequency duplexing function is implemented by coupling a single patch with two sets of resonator-based filtering channels via a U-slot resonator inserted in the ground. This device seamlessly integrates the functions of duplexers, filters and antennas in a very compact structure

Effectiveness and cost-effectiveness of eliminating cervical cancer through a tailored optimal pathway: a modeling study.

BACKGROUND: The World Health Assembly has adopted a global strategy to eliminate cervical cancer. However, neither the optimal pathway nor the corresponding economic and health benefits have been evaluated. We take China as an example to assess the optimal pathway towards elimination and the cost-effectiveness of tailored actions. METHODS: A validated hybrid model was used to assess the costs and benefits of alternative strategies combining human papillomavirus vaccination, cervical screening, and treatment of pre-invasive lesions and invasive cancer for females with different immunization history. All Chinese females living or projected to be born during 2015-2100, under projected trends in aging, urbanization, and sexual activity, were considered. Optimal strategies were determined by cost-effectiveness efficiency frontiers. Primary outcomes were cervical cancer cases and deaths averted and incremental cost-effectiveness ratios (ICERs). We employed a lifetime horizon from a societal perspective. One-way and probabilistic sensitivity analyses evaluate model uncertainty. RESULTS: The optimal pathway represents an integration of multiple tailored strategies from females with different immunization history. If China adopts the optimal pathway, the age-standardized incidence of cervical cancer is predicted to decrease to fewer than four new cases per 100,000 women (i.e., elimination) by 2047 (95% confidence interval 2043 to 2050). Compared to the status quo, the optimal pathway would avert a total of 7,509,192 (6,922,744 to 8,359,074) cervical cancer cases and 2,529,873 (2,366,826 to 2,802,604) cervical cancer deaths in 2021-2100, with the discounted ICER being $- 339 (- 687 to - 79) per quality-adjusted life-year. CONCLUSIONS: By adopting an optimal pathway from 2021 (namely, the year of the first Chinese Centennial Goals) onwards, cervical cancer could be eliminated by the late 2040s (namely, ahead of the second Chinese Centennial Goals) while saving net economic costs in China

Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean

Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in Soy- Base (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database

A Comprehensive Sequence and Disease Correlation Analyses for the C-Terminal Region of CagA Protein of Helicobacter pylori

Chronic Helicobacter pylori infection is known to be associated with the development of peptic ulcer, gastric cancer and gastric lymphoma. Currently, the bacterial factors of H. pylori are reported to be important in the development of gastroduodenal diseases. CagA protein, encoded by the cagA, is the best studied virulence factor of H. pylori. The pathogenic CagA protein contains a highly polymorphic Glu-Pro-Ile-Tyr-Ala (EPIYA) repeat region in the C-terminal. This repeat region is reported to be involved in the pathogenesis of gastroduodenal diseases. The segments containing EPIYA motifs have been designated as segments A, B, C, and D; however the classification and disease relation are still unclear. This study used 560 unique CagA sequences containing 1,796 EPIYA motifs collected from public resources, including 274 Western and 286 East Asian strains with clinical data obtained from 433 entries. Fifteen types of EPIYA or EPIYA-like sequences are defined. In addition to four previously reported major segment types, several minor segment types (e.g., segment B′, B′′) and more than 30 sequence types (e.g., ABC, ABD) were defined using our classification method. We confirm that the sequences from Western and East Asian strains contain segment C and D, respectively. We also confirm that strains with two EPIYA segment C have a greater chance of developing gastric cancer than those with one segment C. Our results shed light on the relationships between the types of CagAs, the country of origin of each sequence type, and the frequency of gastric disease

MicroRNAome of Porcine Pre- and Postnatal Development

The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies