bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling Slag Behavior When Using Micro‐Bubble Swarms for the Deep Cleaning of Liquid Steel in Tundishes
Authors: Chang Sheng , Ge Sa , Zou Zongshu , Isac Mihaiela M. , Guthrie Roderick I. L.
Published: November 2016

Gas bubbling through a ladle shroud can be an effective approach for the removal of inclusions. However, an exposed eye of steel often appears in the slag cover surrounding the ladle shroud, owing to re‐surfacing bubbles leading to the formation of an exposed eye of steel, termed a “slag eye,” resulting in heat losses and re‐oxidation of the liquid steel. In order to control the formation of such a “slag eye” during gas injection into the shroud, a novel ladle shroud is employed to produce micro‐bubbles, as small as 0.54 mm in diameter. The water model results revealed that reducing the sizes of bubbles that are created in the ladle shroud could effectively limit the formation of a “slag eye,” provided the bubbles are sufficiently small and dispersed. This allows them to pass through the top layer of slag without breaking it up. For a given inflow velocity and shroud configuration, the critical condition for forming a “slag eye” depends on a balance between the gas flow rate and the individual sizes of bubbles penetrating the upper slag layer. Slag layer behavior is also simulated numerically, using a three‐dimensional CFD model. Numerical predictions are in good agreement with corresponding experimental results.
Causal inference based fault localization for numerical software with NUMFL
Authors: Bai Zhuofu , Shu Gang , Podgurski Andy
Published: November 2016

This paper presents NUMFL, a value‐based causal inference technique for localizing faults in numerical software. NUMFL combines causal and statistical analyses to characterize the causal effects of individual numerical expressions on output errors. Given value‐profiles for an expression's variables, NUMFL uses generalized propensity scores or covariate balancing propensity scores to reduce confounding bias caused by evaluation of other, faulty expressions. It estimates the average failure‐causing effect of an expression using statistical regression models fit within generalized propensity score or covariate balancing propensity score subclasses (strata). This paper also reports on an empirical evaluation of NUMFL involving components from four Java numerical libraries, in which it was compared with five alternative statistical fault localization metrics. The results indicate that NUMFL is more effective than competitive statistical fault localization techniques. The results also indicate NUMFL that works surprisingly well with data from failing runs alone. Copyright © 2016 John Wiley & Sons, Ltd.
Breaking bad news
Authors: Kirby Roger
Published: November 2016

Looking back over my career, I think one of the very hardest things that I have ever had to do was tell the parents of a teenage motorcyclist, brought in seriously injured to Accident and Emergency, that we were unable to save him from the catastrophic bleeding resulting from his shattered liver and spleen. Breaking bad news goes with the territory of being a doctor, yet we seldom stop and think how best it can and should be done.
The ‘burnout complex’ in surgical practice
Authors: O'Kelly Fardod
Published: November 2016

Burnout among healthcare professionals is a growing problem. Surgeons appear particularly vulnerable and the consequences can be significant for both the sufferer and those around them. In this article the author describes burnout, its manifestations, and how institutions and individuals can avoid it.
Screening for hypogonadism: real‐world considerations
Authors: Heald Adrian , Jones Richard , Khan Adnan , Donnahey Gemma , Downie Paul , Duff Christopher , Livingston Mark
Published: November 2016

Testosterone levels are increasingly being checked in primary care as awareness of the risks of male hypogonadism grows. The authors looked at what tests are performed in general practice in Cheshire to screen for hypogonadism and to rule out secondary hypogonadism.
Characteristics of day‐ahead wind power forecast errors in Nordic countries and benefits of aggregation
Authors: Miettinen Jari Johannes , Holttinen Hannele
Published: November 2016

The growing proportion of wind power in the Nordic power system increases day‐ahead forecasting errors, which have a link to the rising need for balancing power. However, having a large interconnected synchronous power system has its benefits, because it enables to aggregate imbalances from large geographical areas. In this paper, day‐ahead forecast errors from four Nordic countries and the impacts of wind power plant dispersion on forecast errors in areas of different sizes are studied. The forecast accuracy in different regions depends on the amount of the total wind power capacity in the region, how dispersed the capacity is and the forecast model applied. Further, there is a saturation effect involved, after which the reduction in the relative forecast error is not very large anymore. The correlations of day‐ahead forecast errors between areas decline rapidly when the distance increases. All error statistics show a strong decreasing trend up to the area sizes of 50,000 km2. The average mean absolute error (MAE) in different regions is 5.7% of installed capacity. However, MAE of a smaller area can be over 8% of the capacity, but when all the Nordic regions are aggregated together, the capacity‐normalized MAE decreases to 2.5%. The average of the largest errors for different regions is 39.8% and when looking at the largest forecast errors for smaller areas, the largest errors can exceed 80% of the installed capacity, whereas at the Nordic level, the maximum forecast error is only 13.5% of the installed capacity. Copyright © 2016 John Wiley & Sons, Ltd.
Comparison of survey techniques on detection of northern flying squirrels
Authors: Diggins Corinne A. , Gilley L. Michelle , Kelly Christine A. , Ford W. Mark
Published: November 2016

The ability to detect a species is central to the success of monitoring for conservation and management purposes, especially if the species is rare or endangered. Traditional methods, such as live capture, can be labor‐intensive, invasive, and produce low detection rates. Technological advances and new approaches provide opportunities to more effectively survey for species both in terms of accuracy and efficiency than previous methods. We conducted a pilot comparison study of a traditional technique (live‐trapping) and 2 novel noninvasive techniques (camera‐trapping and ultrasonic acoustic surveys) on detection rates of the federally endangered Carolina northern flying squirrel (Glaucomys sabrinus coloratus) in occupied habitat within the Roan Mountain Highlands of North Carolina, USA. In 2015, we established 3 5 × 5 live‐trapping grids (6.5 ha) with 4 camera traps and 4 acoustic detectors systematically embedded in each grid. All 3 techniques were used simultaneously during 2 4‐day survey periods. We compared techniques by assessing probability of detection (POD), latency to detection (LTD; i.e., no. of survey nights until initial detection), and survey effort. Acoustics had the greatest POD (0.37 ± 0.06 SE), followed by camera traps (0.30 ± 0.06) and live traps (0.01 ± 0.005). Acoustics had a lower LTD than camera traps (P = 0.017), where average LTD was 1.5 nights for acoustics and 3.25 nights for camera traps. Total field effort was greatest with live traps (111.9 hr) followed by acoustics (8.4 hr) and camera traps (9.6 hr), although processing and examination for data of noninvasive techniques made overall effort similar among the 3 methods. This pilot study demonstrated that both noninvasive methods were better rapid‐assessment detection techniques for flying squirrels than live traps. However, determining seasonal effects between survey techniques and further development of protocols for both noninvasive techniques is necessary prior to widespread application in the region. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
Question mark ear deformity-revisited
Authors: Al-Qattan Mohammad M. , Al-Qattan Noha M.
Published: November 2016

We report on two unusual cases of Cosman (question mark) ear; both required modifications of the standard techniques for surgical correction. The first patient presented with a unilateral question mark ear and concurrent ear prominence and bulging of the cartilage of the anti-helix. Simultaneous correction was done using a combination of cartilage suturing/scoring (for the prominence and the cartilage bulge) as well as Al-Qattan’s “v-y skin flap-cartilage graft-z-plasty” technique (for the correction of the ear cleft deformity). The second patient had aurico-condylar syndrome with bilateral ear deformity and complete separation of ear lobes from the external ear. Staged transposition followed by Al-Qattan’s technique resulted in a satisfactory outcome.

Level of evidence: Level V, therapeutic study.
Is Routine Prophylactic Cholecystectomy Necessary During Gastrectomy for Gastric Cancer?
Authors: Kimura Jun , Kunisaki Chikara , Takagawa Ryo , Makino Hirochika , Ueda Michio , Ota Mitsuyoshi , Oba Mari , Kosaka Takashi , Akiyama Hirotoshi , Endo Itaru
Published: November 2016

Background

Performing routine prophylactic cholecystectomy during gastrectomy in gastric cancer patients has been controversial. The frequency of cholelithiasis, cholecystitis, and cholangitis after gastrectomy has not been reported for large patient populations, so we carried out this retrospective study to aid the assessment of the necessity for prophylactic cholecystectomy.

Methods

This retrospective study reviewed 969 patients with gastric cancer who underwent distal gastrectomies with Billroth I reconstructions (DG) or total gastrectomies with Roux‐en‐Y reconstructions (TG), preserving the gallbladder, between January 2000 and May 2012. Risk factors for cholelithiasis, cholecystitis, and cholangitis after gastrectomy were evaluated using logistic regression analysis.

Results

The median follow‐up period after gastrectomy was 48 months (range 12–159 months). After gastrectomy, cholelithiasis occurred in 6.1% (59/969) patients and cholecystitis and/or cholangitis occurred in 1.2% (12/969) patients. The method used for gastrectomy was an independent risk factor for both cholelithiasis (TG/DG: OR (95%CI): 1.900 (1.114–3.240), p = 0.018) and cholecystitis and/or cholangitis (TG/DG: OR (95%CI): 8.325 (1.814–38.197), p = 0.006). In patients who developed cholelithiasis, the incidence of cholecystitis and/or cholangitis was 31.3% (10/32) after TG, but only 7.4% after DG.

Conclusions

Prophylactic cholecystectomy may be unnecessary in distal gastrectomy with Billroth I reconstruction.
The Effects of Intravenous Lidocaine Infusions on the Quality of Recovery and Chronic Pain After Robotic Thyroidectomy: A Randomized, Double‐Blinded, Controlled Study
Authors: Choi Kwan Woong , Nam Kee‐Hyun , Lee Jeong‐Rim , Chung Woong Youn , Kang Sang‐Wook , Joe Young Eun , Lee Jae Hoon
Published: November 2016

Background

The effect of the systemic lidocaine on postoperative recovery has not been definitively investigated despite its analgesic efficacy after surgery. The aim of this randomized, double‐blinded, controlled study was to evaluate the effect of intravenously administered lidocaine on the quality of recovery and on acute and chronic postoperative pain after robot‐assisted thyroidectomy.

Methods

Ninety patients who were undergoing robotic thyroidectomy were randomly assigned to the lidocaine or the control groups. The patients received 2 mg/kg of lidocaine followed by continuous infusions of 3 mg/kg/h of lidocaine (Group L) or the same volume of 0.9% normal saline (Group C) intravenously during anesthesia. The acute pain profiles and the quality of recovery, which was assessed using the quality of recovery‐40 questionnaire (QoR‐40), were evaluated for 2 days postoperatively. Chronic postsurgical pain (CPSP) and sensory disturbances at the surgical sites were evaluated 3 months after surgery.

Results

The QoR‐40 and pain scores that were assessed during the 2 days that followed surgery were largely comparable between the groups. However, CPSP was more prevalent in the Group C than in the Group L (16/43 vs. 6/41; p = 0.025). The tactile sensory score 3 months after the operation was significantly greater in the Group L than in the Group C (7 vs. 5; p = 0.001).

Conclusion

Systemic lidocaine administration was associated with reductions in CPSP and sensory impairment after robot‐assisted thyroidectomy although it was not able to reduce acute postsurgical pain or improve the quality of recovery.

Trial registry number NCT01907997 (http://clinicaltrials.gov).
Acetaldehyde kinetics of enological yeast during alcoholic fermentation in grape must
Authors: Li Erhu , Mira de Orduña Ramón
Published: November 2016

Acetaldehyde strongly binds to the wine preservative SO2 and, on average, causes 50–70 mg l−1 of bound SO2 in red and white wines, respectively. Therefore, a reduction of bound and total SO2 concentrations necessitates knowledge of the factors that affect final acetaldehyde concentrations in wines. This study provides a comprehensive analysis of the acetaldehyde production and degradation kinetics of 26 yeast strains of oenological relevance during alcoholic fermentation in must under controlled anaerobic conditions. Saccharomyces cerevisiae and non-Saccharomyces strains displayed similar metabolic kinetics where acetaldehyde reached an initial peak value at the beginning of fermentations followed by partial reutilization. Quantitatively, the range of values obtained for non-Saccharomyces strains greatly exceeded the variability among the S. cerevisiae strains tested. Non-Saccharomyces strains of the species C. vini, H. anomala, H. uvarum, and M. pulcherrima led to low acetaldehyde residues (<10 mg l−1), while C. stellata, Z. bailii, and, especially, a S. pombe strain led to large residues (24–48 mg l−1). Acetaldehyde residues in S. cerevisiae cultures were intermediate and less dispersed (14–34 mg l−1). Addition of SO2 to Chardonnay must triggered significant increases in acetaldehyde formation and residual acetaldehyde. On average, 0.33 mg of residual acetaldehyde remained per mg of SO2 added to must, corresponding to an increase of 0.47 mg of bound SO2 per mg of SO2 added. This research demonstrates that certain non-Saccharomyces strains display acetaldehyde kinetics that would be suitable to reduce residual acetaldehyde, and hence, bound-SO2 levels in grape wines. The acetaldehyde formation potential may be included as strain selection argument in view of reducing preservative SO2 concentrations.
Teaching policy analysis in China and the United States: Implications for curriculum design of public policy programs
Authors: He Alex Jingwei , Lai Allen , Wu Xun
Published: November 2016

Rapid worldwide growth in public policy education now offers excellent opportunities to assess the development of the field from a comparative perspective. Our analysis, which examines recent trends in public policy education by comparing public policy analysis courses taught in professional degree programs in China and in the United States, reveals considerable disparities in these curricula as taught in the two countries. Surprisingly, these differences have emerged primarily through disciplinary foci, expertise in policy analysis, and practical experience among instructors, rather than through the distinctive social, political, institutional, and historical characteristics of the two countries. Our findings also suggest that a positivist approach to policy analysis continues to dominate classroom discussions in US programs, despite intense debates in the literature regarding the utility of that approach in guiding actual practice.
Plant MITEs: Useful Tools for Plant Genetics and Genomics
Authors: Feng Ying
Published: November 2016

MITEs (Miniature inverted-repeat transposable elements) are reminiscence of non-autonomous DNA (class II) elements, which are distinguished from other transposable elements by their small size, short terminal inverted repeats (TIRs), high copy numbers, genic preference, and DNA sequence identity among family members. Although MITEs were first discovered in plants and still actively reshaping genomes, they have been isolated from a wide range of eukaryotic organisms. MITEs can be divided into Tourist-like, Stowaway-like, and pogo-like groups, according to similarities of their TIRs and TSDs (target site duplications). In despite of several models to explain the origin and amplification of MITEs, their mechanisms of transposition and accumulation in eukaryotic genomes remain poorly understood owing to insufficient experimental data. The unique properties of MITEs have been exploited as useful genetic tools for plant genome analysis. Utilization of MITEs as effective and informative genomic markers and potential application of MITEs in plants systematic, phylogenetic, and genetic studies are discussed.
The E Protein is a Multifunctional Membrane Protein of SARS-CoV
Authors: Wu Qingfa , Zhang Yilin , Lü Hong , Wang Jing , He Ximiao , Liu Yong , Ye Chen , Lin Wei , Hu Jianfei , Ji Jia , Xu Jing , Ye Jia , Hu Yongwu , Chen Wenjun , Li Songgang , Wang Jun , Wang Jian , Bi Shengli , Yang Huanming
Published: November 2016

The E (envelope) protein is the smallest structural protein in all coronaviruses and is the only viral structural protein in which no variation has been detected. We conducted genome sequencing and phylogenetic analyses of SARS-CoV. Based on genome sequencing, we predicted the E protein is a transmembrane (TM) protein characterized by a TM region with strong hydrophobicity and α-helix conformation. We identified a segment (NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH) in the carboxyl-terminal region of the E protein that appears to form three disulfide bonds with another segment of corresponding cysteines in the carboxyl-terminus of the S (spike) protein. These bonds point to a possible structural association between the E and S proteins. Our phylogenetic analyses of the E protein sequences in all published coronaviruses place SARS-CoV in an independent group in Coronaviridae and suggest a non-human animal origin.
Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese
Authors: Li Shuangding , Yan Chunxia , Deng Yajun , Wang Ruilin , Wang Jian , Yang Huanming , Li Shengbin
Published: November 2016

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amelogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05×10−10 within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelogenin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.
Integration of G-Protein Coupled Receptor Signaling Pathways for Activation of a Transcription Factor (EGR-3)
Authors: Tan Xuehai , Sanders Pam , Bolado Jack , Whitney Mike
Published: November 2016

We recently reported the use of a gene-trapping approach to isolate cell clones in which a reporter gene had integrated into genes modulated by T-cell activation. We have now tested a panel of clones from that report and identified the one that responds to a variety of G-protein coupled receptors (GPCR). The β-lactamase tagged EGR-3 Jurkat cell was used to dissect specific GPCR signaling in vivo. Three GPCRs were studied, including the chemokine receptor CXCR4 (Gi-coupled) that was endogenously expressed, the platelet activation factor (PAF) receptor (Gq-coupled), and β2 adrenergic receptor (Gs-coupled) that was both stably transfected. Agonists for each receptor activated transcription of the β-lactamase tagged EGR-3 gene. Induction of EGR-3 through CXCR4 was blocked by pertussis toxin and PD58059, a specific inhibitor of MEK (MAPK/ERK kinase). Neither of these inhibitors blocked isoproterenol or PAF-mediated activation of EGR-3. Conversely, β2- and PAF-mediated EGR-3 activation was blocked by the p38, specific inhibitor SB580. In addition, both β2- and PAF-mediated EGR-3 activation could be synergistically activated by CXCR4 activation. This combined result indicates that EGR-3 can be activated through distinct signal transduction pathways by different GPCRs and that signals can be integrated and amplified to efficiently tune the level of activation.
The Epitope Study on the SARS-CoV Nucleocapsid Protein
Authors: Li Shuting , Lin Liang , Wang Hao , Yin Jianning , Ren Yan , Zhao Zhe , Wen Jie , Zhou Cuiqi , Zhang Xumin , Li Xiaolei , Wang Jingqiang , Zhou Zhengfeng , Liu Jinxiu , Shao Jianmin , Lei Tingting , Fang Jianqiu , Xu Ningzhi , Liu Siqi
Published: November 2016

The nucleocapsid protein (N protein) has been found to be an antigenic protein in a number of coronaviruses. Whether the N protein in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is antigenic remains to be elucidated. Using Western blot and Enzyme-linked Immunosorbent Assay (ELISA), the recombinant N proteins and the synthesized peptides derived from the N protein were screened in sera from SARS patients. All patient sera in this study displayed strong positive immunoreactivities against the recombinant N proteins, whereas normal sera gave negative immunoresponses to these proteins, indicating that the N protein of SARS-CoV is an antigenic protein. Furthermore, the epitope sites in the N protein were determined by competition experiments, in which the recombinant proteins or the synthesized peptides competed against the SARS-CoV proteins to bind to the antibodies raised in SARS sera. One epitope site located at the C-terminus was confirmed as the most antigenic region in this protein. A detailed screening of peptide with ELISA demonstrated that the amino sequence from Codons 371 to 407 was the epitope site at the C-terminus of the N protein. Understanding of the epitope sites could be very significant for developing an effective diagnostic approach to SARS.
Genome Organization of the SARS-CoV
Authors: Xu Jing , Hu Jianfei , Wang Jing , Han Yujun , Hu Yongwu , Wen Jie , Li Yan , Ji Jia , Ye Jia , Zhang Zizhang , Wei Wei , Li Songgang , Wang Jun , Wang Jian , Yu Jun , Yang Huanming
Published: November 2016

Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves. Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions. The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs.
Molecular Advances in Severe Acute Respiratory Syndrome-Associated Coronavirus (SARS-CoV)
Authors: Chow Ken Yan Ching , Hon Chung Chau , Hui Raymond Kin Hi , Wong Raymond Tsz Yeung , Yip Chi Wai , Zeng Fanya , Leung Frederick Chi Ching
Published: November 2016

The sudden outbreak of severe acute respiratory syndrome (SARS) in 2002 prompted the establishment of a global scientific network subsuming most of the traditional rivalries in the competitive field of virology. Within months of the SARS outbreak, collaborative work revealed the identity of the disastrous pathogen as SARS-associated coronavirus (SARS-CoV). However, although the rapid identification of the agent represented an important breakthrough, our understanding of the deadly virus remains limited. Detailed biological knowledge is crucial for the development of effective countermeasures, diagnostic tests, vaccines and antiviral drugs against the SARS-CoV. This article reviews the present state of molecular knowledge about SARS-CoV, from the aspects of comparative genomics, molecular biology of viral genes, evolution, and epidemiology, and describes the diagnostic tests and the anti-viral drugs derived so far based on the available molecular information.
Bioinformatics Data Distribution and Integration via Web Services and XML
Authors: Li Xiao , Zhang Yizheng
Published: November 2016

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biological data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.
HLA-A Gene Polymorphism Defined by High-Resolution Sequence-Based Typing in 161 Northern Chinese Han People
Authors: Yan Chunxia , Wang Ruilin , Li Jingxiang , Deng Yajun , Wu Dongying , Zhang Hongbo , Zhang Hongxing , Wang Lidong , Zhang Chunrong , Sun Haiyan , Zhang Xiuqing , Wang Jian , Yang Huanming , Li Shengbin
Published: November 2016

Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods—sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.
Molecular Phylogenetics and Functional Evolution of Major RNA Recognition Domains of Recently Cloned and Characterized Autoimmune RNA-Binding Particle
Authors: Süleymanoğlu Erhan
Published: November 2016

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are spliceosomal macromolecular assemblages and thus actively participate in pre-mRNA metabolism. They are composed of evolutionarily conserved and tandemly repeated motifs, where both RNA-binding and protein-protein recognition occur to achieve cellular activities. By yet unknown mechanisms, these ribonucleoprotein (RNP) particles are targeted by autoantibodies and hence play significant role in a variety of human systemic autoimmune diseases. This feature makes them important prognostic markers in terms of molecular epidemiology and pathogenesis of autoimmunity. Since RNP domain is one of the most conserved and widespread scaffolds, evolutionary analyses of these RNA-binding domains can provide further clues on disease-specific epitope formation. The study presented herein represents a sequence comparison of RNA-recognition regions of recently cloned and characterized human hnRNP A3 with those of other relevant hnRNP A/B-type proteins. Their implications in human autoimmunity are particularly emphasized.
Structure Prediction of Membrane Proteins
Authors: Zhou Chunlong , Zheng Yao , Zhou Yan
Published: November 2016

There is a large gap between the number of membrane protein (MP) sequences and that of their decoded 3D structures, especially high-resolution structures, due to difficulties in crystal preparation of MPs. However, detailed knowledge of the 3D structure is required for the fundamental understanding of the function of an MP and the interactions between the protein and its inhibitors or activators. In this paper, some computational approaches that have been used to predict MP structures are discussed and compared.
Isolation and Characterization of 2′-Amino-Modified RNA Aptamers for Human TNFα
Authors: Yan Xinrui , Gao Xuwen , Zhang Zhiqing
Published: November 2016

Human tumor necrosis factor α (hTNFα), a pleiotropic cytokine with activities ranging from host defense mechanisms in infection and injury to severe toxicity in septic shock or other related diseases, is a promising target for drug screening. Using the SELEX (systematic evolution of ligands by exponential enrichment) process, we isolated oligonucleotide ligands (aptamers) with high affinities for hTNFα. Aptamers were selected from a starting pool of 40 randomized sequences composed of about 1015 RNA molecules. Representative aptamers were truncated to the minimal length with high affinity for hTNFα and were further modified by replacement of 2′-OH with 2′-F and 2′-NH2 at all ribopurine positions. These modified RNA aptamers were resistant to nuclease. The specificity of these aptamers for hTNFα was confirmed, and their activity to inhibit the cytotoxicity of hTNFα on mouse L929 cells was determined. Results demonstrated that four 2′-NH2-modified aptamers bound to hTNFα with high affinity and blocked the binding of hTNFα to its receptor, thus protecting the L929 cells from the cytotoxicity of hTNFα. Oligonucleotide aptamers described here are potential therapeutics and diagnostics for hTNFα-related diseases.
Identification and Expression Analysis of EST-Based Genes in the Bud of Lycoris Longituba
Authors: Cui Yonglan , Zhang Xinye , Zhou Yan , Yu Hong , Tao Lin , Zhang Lu , Zhou Jian , Zhuge Qiang , Cai Youming , Huang Minren
Published: November 2016

To obtain a primary overview of gene diversity and expression pattern in Lycoris longituba, 4,992 ESTs (Expressed Sequence Tags) from L. longituba bud were sequenced and 4,687 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 967 contigs and 1,343 singlets were obtained. Blast search showed that 179 contigs and 227 singlets (totally 1,066 ESTs) had homologues in GenBank and 3,621 ESTs were novel.
Identification and Characterization of 177 Unreported Genes Associated with Liver Regeneration
Authors: Xu Cunshuan , Chang Cuifang , Yuan Jinyun , Han Hongpeng , Yang Kejin , Zhao Lifeng , Li Wenqiang , Li Yuchang , Zhang Huiyong , Rahman Salman , Zhang Jingbo
Published: November 2016

The mammalian liver has a very strong regeneration capacity after partial hepatectomy (PH). To further learn the genes participating in the liver regeneration (LR), 551 cDNAs selected from subtracted cDNA libraries of the regenerating rat liver were screened by microarray, and their expression profiles were studied by cluster and generalization analyses. Among them, 177 genes were identified unreported and up- or down-regulated more than twofold at one or more time points after PH, of which 62 genes were down-regulated to less than 0.5; 99 genes were up-regulated to 2–10 folds, and 16 genes were either up- or down-regulated at different time points during LR. By using BLAST and GENSCAN, these genes were located on responsible chromosomes with 131 genes on the long arms of the chromosomes. The cluster and generalization analyses showed that the gene expression profiles are similar in 2 and 4, 12 and 16, 96 and 144 h respectively after PH, suggesting that the actions of the genes expressed in the same profiles are similar, and those expressed in different profiles have less similarity. However, the types, characteristics and functions of the 177 genes remain to be further studied.
Construction of A Non-Redundant Human SH2 Domain Database
Authors: Huang Haiming , Jiao Yuchen , Xu Rui , Gao Youhe
Published: November 2016

Domain database is essential for domain property research. Eliminating redundant information in database query is very important for database quality. Here we report the manual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in 110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree was generated. In this tree, proteins with similar known function were classified into the same group. Some proteins in the same group have been reported to have similar binding motifs experimentally. The tree might provide clues about possible functions of hypothetical proteins for further experimental verification.
Proteomics Reveals that Proteins Expressed During the Early Stage of Bacillus Anthracis Infection are Potential Targets for the Development of Vaccines and Drugs
Authors: Huang Chun-Ming , Elmets Craig A. , Tang De-chu C. , Li Fuming , Yusuf Nabiha
Published: November 2016

In this review, we advance a new concept in developing vaccines and/or drugs to target specific proteins expressed during the early stage of Bacillus anthracis (anthrax) infection and address existing challenges to this concept. Three proteins (immune inhibitor A, GPR-like spore protease, and alanine racemase) initially identified by proteomics in our laboratory were found to have differential expressions during anthrax spore germination and early outgrowth. Other studies of different bacillus strains indicate that these three proteins are involved in either germination or cytotoxicity of spores, suggesting that they may serve as potential targets for the design of anti-anthrax vaccines and drugs.
A Novel Algorithm for Finding Interspersed Repeat Regions
Authors: Li Dongdong , Wang Zhengzhi , Ni Qingshan
Published: November 2016

The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together. The complexity of our projection-assemble algorithm is nearly linear to the length of the genome sequence, and its memory usage is limited by the hardware. We tested our algorithm with both simulated data and real biology data, and the results show that our projection-assemble algorithm is efficient. By means of this algorithm, we found an un-labeled repeat region that occurs five times in Escherichia coli genome, with its length more than 5,000 bp, and a mismatch probability less than 4%.
Fast Tree Search for A Triangular Lattice Model of Protein Folding
Authors: Li Xiaomei , Wang Nengchao
Published: November 2016

Using a triangular lattice model to study the designability of protein folding, we overcame the parity problem of previous cubic lattice model and enumerated all the sequences and compact structures on a simple two-dimensional triangular lattice model of size 4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, and achieved 223+212 different sequences excluding the reverse symmetry sequences. The total string number of distinct compact structures was 219,093, excluding reflection symmetry in the self-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fast search algorithm by constructing a cluster tree. The algorithm decreased the computation by computing the objective energy of non-leaf nodes. The parallel experiments proved that the fast tree search algorithm yielded an exponential speed-up in the model of size 4+5+6+5+4. Designability analysis was performed to understand the search result.
SARS-CoV Genome Polymorphism: A Bioinformatics Study
Authors: Pavlović-Lažetić Gordana M. , Mitić Nenad S. , Tomović Andrija M. , Pavlović Mirjana D. , Beljanski Miloš V.
Published: November 2016

A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a “profile”, were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
DCCP and DICP: Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins
Authors: Wu Hao , Yang Yan , Jiang Sheng-Juan , Chen Ling-Ling , Gao Hai-Xia , Fu Qing-Shan , Li Feng , Ma Bin-Guang , Zhang Hong-Yu
Published: November 2016

Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases (DCCP and DICP) containing the known copper- and iron-chelating proteins, which are freely available from the website http://sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.
A Hybrid SOM-SVM Approach for the Zebrafish Gene Expression Analysis
Authors: Wu Wei , Liu Xin , Xu Min , Peng Jin-Rong , Setiono Rudy
Published: November 2016

Microarray technology can be employed to quantitatively measure the expression of thousands of genes in a single experiment. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large amount of expression data generated by this technology makes the study of certain complex biological problems possible, and machine learning methods are expected to play a crucial role in the analysis process. In this paper, we present our results from integrating the self-organizing map (SOM) and the support vector machine (SVM) for the analysis of the various functions of zebrafish genes based on their expression. The most distinctive characteristic of our zebrafish gene expression is that the number of samples of different classes is imbalanced. We discuss how SOM can be used as a data-filtering tool to improve the classification performance of the SVM on this data set.
FAMCS: Finding All Maximal Common Substructures in Proteins
Authors: Yao Zhen , Xiao Juan , Tung Anthony K.H. , Sung Wing Kin
Published: November 2016

Finding the common substructures shared by two proteins is considered as one of the central issues in computational biology because of its usefulness in understanding the structure-function relationship and application in drug and vaccine design. In this paper, we propose a novel algorithm called FAMCS (Finding All Maximal Common Substructures) for the common substructure identification problem. Our method works initially at the protein secondary structural element (SSE) level and starts with the identification of all structurally similar SSE pairs. These SSE pairs are then merged into sets using a modified Apriori algorithm, which will test the similarity of various sets of SSE pairs incrementally until all the maximal sets of SSE pairs that deemed to be similar are found. The maximal common substructures of the two proteins will be formed from these maximal sets. A refinement algorithm is also proposed to fine tune the alignment from the SSE level to the residue level. Comparison of FAMCS with other methods on various proteins shows that FAMCS can address all four requirements and infer interesting biological discoveries.
Non-Destructive Analysis of the Nuclei of Transgenic Living Cells Using Laser Tweezers and Near-Infrared Raman Spectroscopic Technique
Authors: Tang Wei , Newton Ronald J. , Xie Chang-An , Li Yong-Qing , Whitley Nicki
Published: November 2016

Transgenic cell lines of loblolly pine (Pinus taeda L.) were analyzed by a compact laser-tweezers-Raman-spectroscopy (LTRS) system in this investigation. A low power diode laser at 785 nm was used for both laser optical trapping of single transgenic cells and excitation for near-infrared Raman spectroscopy of the nuclei of synchronized cells, which were treated as single organic particles, at the S-phase of the cell cycle. Transgenic living cells with gfp and uidA genes were used as biological samples to test this LTRS technique. As expected, different Raman spectra were observed from the tested biological samples. This technique provides a high sensitivity and enables real-time spectroscopic measurements of transgenic cell lines. It could be a valuable tool for the study of the fundamental cell and molecular biological process by trapping single nucleus and by providing a wealth of molecular information about the nuclei of cells.
An Improved Biclustering Algorithm and Its Application to Gene Expression Spectrum Analysis
Authors: Qu Hua , Wang Liu-Pu , Liang Yan-Chun , Wu Chun-Guo
Published: November 2016

Cheng and Church algorithm is an important approach in biclustering algorithms. In this paper, the process of the extended space in the second stage of Cheng and Church algorithm is improved and the selections of two important parameters are discussed. The results of the improved algorithm used in the gene expression spectrum analysis show that, compared with Cheng and Church algorithm, the quality of clustering results is enhanced obviously, the mining expression models are better, and the data possess a strong consistency with fluctuation on the condition while the computational time does not increase significantly.
LZ Complexity Distance of DNA Sequences and Its Application in Phylogenetic Tree Reconstruction
Authors: Li Bin , Li Yi-Bing , He Hong-Bo
Published: November 2016

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet (A, C, T, G). As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals (Eutheria) with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.
Economic Growth
Authors: de La Grandville Olivier
Published: November 2016

In the second edition of this user-friendly book, Olivier de La Grandville provides a clear and original introduction to the theory of economic growth, its mechanisms and its challenges. The book has been fully updated to incorporate several important new results and proofs since the first edition. In addition to a progressive treatment of dynamic optimization, readers will find intuitive derivations of all central equations of the calculus of variations and of optimal control theory. It offers a new solution to the fundamental question: How much should a nation save and invest? La Grandville shows that the optimal savings rule he suggests not only corresponds to the maximization of future welfare flows for society, but also maximizes the value of society's activity, as well as the total remuneration of labour. The rule offers a fresh alternative to dire current predictions about an ever-increasing capital–output ratio and a decrease of the labour share in national income.
Super-premium Fruit and Vegetable Beverages: A Retail Sales Analysis and Demand Estimation
Authors: Bardzik Alec , Ishdorj Ariun , Jang Ju Won
Published: November 2016

Super-premium fruit and vegetable juices and drinks are a rapidly emerging product subcategory. We use retail-level scanner data to analyze trends in sales of and demand for super-premium and other fruit and vegetable beverages. We find that super-premium beverages represent a small share—about 6 percent in terms of dollar sales in 2012—of the overall fruit and vegetable juice and drink market and are priced considerably higher. Total sales more than doubled between 2007 and 2012 with 16 percent annual growth, and the beverages were more responsive to changes in price than other fruit and vegetable juices and drinks.