On de novo Bridging Paired-end RNA-seq Data

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced two ends in the absence of the reference genome - a problem here we refer to as de novo bridging. Solving this problem provides longer, more informative RNA-seq reads, and benefits downstream RNA-seq analysis such as transcript assembly, expression quantification, and splicing differential analysis. However, de novo bridging is a challenging and complicated task owing to alternative splicing, transcript noises, and sequencing errors. It remains unclear if the data provides sufficient information for accurate bridging, let alone efficient algorithms that determine the true bridges. Methods have been proposed to bridge paired-end reads in the presence of reference genome (called reference-based bridging), but the algorithms are far away from scaling for de novo bridging as the underlying compacted de Bruijn graph(cdBG) used in the latter task often contains millions of vertices and edges. We designed a new truncated Dijkstra's algorithm for this problem, and proposed a novel algorithm that reuses the shortest path tree to avoid running the truncated Dijkstra's algorithm from scratch for all vertices for further speeding up. These innovative techniques result in scalable algorithms that can bridge all paired-end reads in a cdBG with millions of vertices. Our experiments showed that paired-end RNA-seq reads can be accurately bridged to a large extent. The resulting tool is freely available at https://github.com/Shao-Group/rnabridge-denovo.Comment: 10 pages, 4 figure

Helina subpyriforma sp. n., a newmuscid fly (Diptera: Muscidae) from Yunnan, China

Helina subpyriforma Wang sp. n., a species from Yunnan, China, is described and illustrated as new to science. The new species can be assigned to the Helina quadrum-group, based on male morphological and genitalic structures. The species is also incorporated into the existing key of H. quadrum-group (males) from China

The correlation of osteoporosis to clinical features: a study of 4382 Female Cases of a Hospital Cohort with musculoskeletal symptoms in Southwest China

<p>Abstract</p> <p>Background</p> <p>By analyzing the clinical features and risk factors in female patients with musculoskeletal symptoms of Southwest China, this report presents the initial analysis of characteristics in this region and compared with international evaluative criteria.</p> <p>Methods</p> <p>Diagnosis of osteoporosis (OP) was made in female hospital patients age ≥ 18 years admitted from January 1998 to December 2008 according to WHO definition. Case data were analyzed by symptoms, age, disease course and risk factors to reveal correlation with diagnosis of OP. Logistic regression was used to identify the risks of osteoporosis.</p> <p>Results</p> <p>A total of 4382 patients were included in the analysis of the baseline characteristics, among which 1455 in the OP group and 2927 in the non-OP group. The morbidity of OP <b/>is significantly increased in females' ≥ 50 years. Both groups had symptoms related to pain and numbness; no significant difference was found in reported upper and lower back pain, or leg pain between two groups (<it>p </it>> 0.05). Neck, shoulder and arm pain, leg and arm numbness were more common in the non-osteoporosis group (p < 0.05, OR < 1, and upper limit of 95% CI of OR < 1). Hypertension, diabetes, hyperostosis were major risk factors for the patients with OP. The most common lifestyle-related risk factors for osteoporosis were smoking, body mass index, lack of physical activity and menopause.</p> <p>Conclusions</p> <p>The present study offers the first reference data of the relationship between epidemiologic distribution of osteoporosis and associated factors in adults Chinese women. These findings provide a theoretical basis for its prevention and treatment in developing country.</p

Central Asia in the Conditions of Conjugation of the Economic Belt of the Silk Way and the Eurasian Economic Union

The article analyzes soft power in the policices of China and Russia in Central Asia from the perspective of successful realization of interaction of the Economic Belt of the Silk Way and the Eurasian Economic Union. It especially emphasizes that in combination with the Eurasian Economic Union, the Economic Belt of the Silk Way presents new characters in configurations of international economic and political relations

Central Asia in the Conditions of Conjugation of the Economic Belt of the Silk Way and the Eurasian Economic Union

The article analyzes the main trends of development of Central Asia in the conditions of conjugation of the Economic Belt of the Silk Road and the Eurasian Economic Union, and the nature of interaction between the participants of this process, especially Russia, China and Kazakhstan. It occupies an important place in the study of China’s guildlines of foreign policy and geo-economy in relations with Central Asia. This is not overlooked and Central Asian countries themselves became active actors in these processes. It is especially emphasized that in order to improve its image in Central Asia, therefore, China and Russia widely use soft power to get the successful implementation of economic and humanitarian plans

Dexmedetomidine inhibits inflammation in microglia cells under stimulation of LPS and ATP by c-Fos/NLRP3/caspase-1 cascades

NOD-like receptor 3 (NLRP3) plays critical roles in the initiation of inflammasome-mediated inflammation in microglia, thus becomes an important therapeutic target of Alzheimer’s disease (AD). Dexmedetomidine (Dex), a new type of clinical anesthetic agent, shows anti-inflammatory properties and inhibits postoperative cognitive dysfunction in AD patients. The present study was aimed to investigate effect of Dex on NLRP3 activity in activated microglia and reveal the underlying mechanisms. The human microglia clone 3 (HMC3) cells were exposed to 100 ng/ml LPS and 5 mM ATP, in the presence and absence of doses of Dex. Data from ELISA and Western blot assays showed that Dex abrogated the promoting effects of LPS/ATP on the release of pro-inflammatory cytokines including IL-1ß and IL-18 in the cell medium and the expression of NLRP3 and its downstream target caspase-1 in HMC3 cells. Furthermore, the present study found that exposure of HMC3 cells to LPS/ATP increased nuclear protein levels of transcription factor c-Fos, but treatment with Dex reversed the increase in c-Fos, as indicated by Western blot and immunofluorescence measures. Luciferase reported assay revealed that c-Fos can bind to the promoter region of NLRP3 gene and positively regulate the expression. These results suggest that Dex inhibiting c-Fos nuclear protein levels promoted by LPS/ATP blocks the up-regulation of NLRP3. This suggestion is supported by co-immunoprecipitation and PCR studies, in which Dex decreased the amount of c-Fos that binds to NLRP3 under the stimulation of LPS/ATP. The present study revealed that Dex inhibits inflammation in microglia cells under stimulation of LPS and ATP by c-Fos/NLRP3/caspase-1 cascades, which adds new understanding of the anti-inflammatory mechanism of Dex

4-(2-Chloro­ethoxy)phthalonitrile

In the title compound, C10H7ClN2O, the O and both C atoms of the chloroethoxy group are disordered over two positions, the occupancy factor of the major disorder component refining to 0.54 (2)

Incorporating Ab Initio energy into threading approaches for protein structure prediction

<p>Abstract</p> <p>Background</p> <p>Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in <it>Ab Initio</it> methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the <it>Ab Initio</it> energy function can be used to improve threading, especially for the weakly/distant homologous templates.</p> <p>Results</p> <p>In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an <it>Ab Initio</it> energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function.</p> <p>Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison.</p> <p>Conclusions</p> <p>Incorporating <it>Ab Initio</it> energy functions into threading can greatly improve alignment accuracy.</p