String Programs Research Articles

In silico elucidation of protein-protein interaction network in fish pathogen Flavobacterium Columnare

Flavobacterium columnare is a virulent intracellular bacterial pathogen that causes an infection known as columnaris in many species of fish. Some economically important fish species are strongly affected by columnaris, leading to a high mortality rate and significant economic losses. Previous in silico studies have provided various biological insights into F. columnare, including its interaction with MHC class I alleles and the epitopic region within outer membrane proteins. However, the protein-protein interaction networks underlying the growth, defense, and pathogenesis of F. columnare remain largely unknown. This study was conducted to identify the protein-protein interaction (PPI) networks and hub proteins of F. columnare that can be used as drug or vaccine targets. A total of 500 protein sequences were retrieved from UniprotKB in FASTA format and analyzed using VaxiJen, PSORTb, STRING, Cytoscape, and BLASTp programs. The results demonstrated that 60% of F. columnare proteins were predicted as antigenic proteins, most of which were associated with catalytic activity and metabolic processes, identified as cytoplasmic proteins. Ten hub proteins with the highest number of functional interactions were identified, which were also antigenic and non-host homologous. In conclusion, F. columnare hub proteins represent potential therapeutic targets in drug and vaccine development against columnaris infection.

Fire on the Bayou: The Status of School Orchestra and String Programs in Louisiana

This study examined the status of school orchestra and string programs in Louisiana. A manual web search for string programs in parish school districts, student school affiliations from honor orchestra lists, Louisiana members of the American String Teachers Association (ASTA), and members of the Louisiana Music Educators Association was conducted to determine the approximate number of programs in the state. These data were cross-referenced with available data from the Louisiana Department of Education, which listed course offerings by school. A total of 44 teachers serving 97 schools were identified. Semi-structured interviews were then conducted with five-string teachers and two district arts coordinators from around the state to determine the strengths of current string programs and opportunities for growth. Findings from participant interviews revealed the legacy of school segregation, inadequate funding for public education, competition from non-public schools, and the challenges of maintaining program infrastructure due to limited funding and perennial natural disasters. The results of this study were compared with other statewide string program surveys to situate Louisiana string programs in a national context with implications for string teachers, music teacher education, and professional development offered.

In Silico Analysis of miRNA-Mediated Genes in the Regulation of Dog Testes Development from Immature to Adult Form.

High-throughput in-silico techniques help us understand the role of individual proteins, protein-protein interaction, and their biological functions by corroborating experimental data as epitomized biological networks. The objective of this investigation was to elucidate the association of miRNA-mediated genes in the regulation of dog testes development from immature to adult form by in-silico analysis. Differentially expressed (DE) canine testis miRNAs between healthy immature (2.2 ± 0.13 months; n = 4) and mature (11 ± 1.0 months; n = 4) dogs were utilized in this investigation. In silico analysis was performed using miRNet, STRING, and ClueGo programs. The determination of mRNA and protein expressions of predicted pivotal genes and their association with miRNA were studied. The results showed protein-protein interaction for the upregulated miRNAs, which revealed 978 enriched biological processes GO terms and 127 KEGG enrichment pathways, and for the down-regulated miRNAs revealed 405 significantly enriched biological processes GO terms and 72 significant KEGG enrichment pathways (False Recovery Rate, p < 0.05). The in-silico analysis of DE-miRNA's associated genes revealed their involvement in the governing of several key biological functions (cell cycle, cell proliferation, growth, maturation, survival, and apoptosis) in the testis as they evolve from immature to adult forms, mediated by several key signaling pathways (ErbB, p53, PI3K-Akt, VEGF and JAK-STAT), cytokines and hormones (estrogen, GnRH, relaxin, thyroid hormone, and prolactin). Elucidation of DE-miRNA predicted genes' specific roles, signal transduction pathways, and mechanisms, by mimics and inhibitors, which could perhaps offer diagnostic and therapeutic targets for infertility, cancer, and birth control.

Read/write factorizable programs

Abstract In the cons-free programming paradigm, we eschew constructors and program using only destructors. Cons-free programs in a simple first-order language with string data capture exactly P, the class of polynomial-time relations. By varying the underlying language and considering other data types, we can capture several other complexity classes. However, no cons-free programming language captures any functional complexity class for fundamental reasons. In this paper, we cleanly extend the cons-free paradigm to encompass functional complexity classes. Namely, we introduce programs with data that can either only be destructed or only be constructed, which we enforce by a type system on the program variables. We call the resulting programs read/write - (or RW -)factorizable, show that RW-factorizable string programs capture exactly the class FP of polynomial-time functions, and that tail-recursive RW-factorizable programs capture exactly the class FL of logarithmic-space functions. Finally, we state and solve the nontrivial problem of syntactic composition of two RW-factorizable programs.

Sex Differences in Diet-induced Obesity: Identification of Key Genes in Association With Phenotypes

ObjectivesObesity is associated with many metabolic disorders requiring personalized management. In this study, we examined sex-dependent metabolic changes in diet-induced fat accumulation and tissue-specific transcriptomics to identify responsible genes. Estrogen-dependency was also evaluated.MethodsMale, female and ovariectomized female C57BL/6J mice fed with high fat diet were maintained for 10wks. At sacrifice, body weight, tissue weight, fasting blood glucose and insulin, leptin and adiponectin were measured. Adipose tissue histology and the quantification of major proteins involved in fat synthesis and oxidation were carried out. Key genes in major tissues were identified based on microarray analyses followed by network analyses using protein-protein network and STRING programs.ResultsFemale animals showed significantly lower body weight, adipocyte size, and the macrophage infiltration in white adipose tissue, which are increased by ovariectomy. Not like leptin, adiponectin concentration is significantly higher in female animals, which is maintained even after the ovariectomy. The expressions of proteins related to the regulation of lipid metabolism in adipose tissue show sex differences with or without estrogen depletion. Microarray analyses reveal that ovariectomized female group-specific genes up-regulated in fat, liver and muscle tissue are 251,148, and 49 in numbers, respectively. The number of down-regulated genes are 329, 86, and 37, respectively. PPI network analysis identified Cxcr3, Il2ra, Il2rg, Lck, and Ccl5 as top five up-regulated genes showing highest interaction score, while Cyc1, Uqcrc1, Atp5d, Ndufa9, and Ndufs8 are down-regulated with highest scores. Similarly, the top 5 genes up-regulated in liver tissue are Emr1, Itgb2, Igsf6, Clec4a3, and Aif1, while Eed, Myh11, and Tjp2 are down-regulated with highest scores. Cd4, Slco2b1, Fbxw11, Tub, Wnt5b, U2af2, and Cd38 are up-regulated and the Egfr is down-regulated with highest score in muscle tissue.ConclusionsThis study suggests that biochemical alterations in abdominal obesity in females are different from males, and a part of mechanisms are estrogen-independent. Several key genes associated with these changes are suggested.Funding SourcesThis work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT).

Allogenic stem cell transplant-associated acute graft versus host disease: a computational drug discovery text mining approach using oral and gut microbiome signatures.

Acute graft versus host disease (aGVHD) is a major cause of non-relapse morbidity and mortality post-allogenic hematopoietic stem cell transplant (HSCT). Using conventional literature search and computational approaches, our objective was to identify oral and gut bacterial species associated with aGVHD, potentially affecting drug treatment via lipopolysaccharide (LPS) pathways. Medline, PubMed, PubMed Central, and Google Scholar were searched using MeSH terms. The top 100 hits per database were curated, and 25 research articles were selected to examine oral and gut microbiomes associated with health, HSCT, and aGVHD. Literature search validation, aGVHD drug targets, and microbial metabolic pathway identification were completed using BioReader, MACADAM, KEGG, and STRING programs. Our review determined that (1) oral genera Rothia, Solobacterium, and Veillonella were identified in HSCT patients' stool and associated with aGVHD; (2) shifts in gut enterococci profiles were determined in HSCT-associated aGVHD; (3) gut microbiome dysbiosis prior or during HSCT and lower Shannon diversity index at time of HSCT were also associated with increased risk of aGVHD and transplant related death; and (4) Coriobacteriaceae family was negatively correlated with gut aGVHD, whereas Eubacterium limosum was associated with decreased risk of chronic GVHD relapse. Additionally, we identified molecular pathways related to TLR4/ LPS, including candidate aGVHD drug targets, impacted by oral and gut bacterial taxa. Reduced microbial diversity reflects higher severity and mortality rate in HSCT patients with aGVHD. Multi-omics approaches to decipher oral and gut microbiome associations will be critical for developing aGVHD preventive therapies.

Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin

Curcumin is an important bioactive component of turmeric and also one of the important natural products, which has been investigated extensively. The precise mode of action of curcumin and its impact on system level protein networks are still not well studied. To identify the curcumin governed regulatory action on protein interaction network (PIN), an interectome was created based on 788 key proteins, extracted from PubMed literatures, and constructed by using STRING and Cytoscape programs. The PIN rewired by curcumin was a scale-free, extremely linked biological system. MCODE plug-in was used for sub-modulization analysis, wherein we identified 25 modules; ClueGo plug-in was used for the pathway’s enrichment analysis, wherein 37 enriched signalling pathways were obtained. Most of them were associated with human diseases groups, particularly carcinogenesis, inflammation, and infectious diseases. Finally, the analysis of topological characteristic like bottleneck, degree, GO term/pathways analysis, bio-kinetics simulation, molecular docking, and dynamics studies were performed for the selection of key regulatory proteins of curcumin-rewired PIN. The current findings deduce a precise molecular mechanism that curcumin might exert in the system. This comprehensive in-silico study will help to understand how curcumin induces its anti-cancerous, anti-inflammatory, and anti-microbial effects in the human body.

String Teacher Preparation Programs in the United States

The rise in demand for string teachers is a sign of support for string programs across the United States. Despite an increase in string teacher positions, there is growing concern regarding the lack of qualified string music education graduates to fill the vacancies, sometimes leading administrators to close programs. This study investigated the status of string teacher education programs in the United States. Participants for this study were degree-granting institutions ( N = 636) accredited by the National Association of Schools of Music (NASM). The NASM directory listings and institution websites were examined to determine what type of degrees were offered, and presence of a full-time string music education faculty member. Results indicated that while most NASM-accredited institutions offer some type of undergraduate degree in music education, very few institutions (16%) were shown to have a full-time string music education specialist. Results also indicated a significant relationship between the size of school and likelihood of having a full-time string music education specialist, χ2 (7, N = 526) = 80.03, p &lt; .001.

Identification of Potential Biomarkers and Survival Analysis for Head and Neck Squamous Cell Carcinoma Using Bioinformatics Strategy: A Study Based on TCGA and GEO Datasets.

The mechanism and gene markers of head and neck squamous cell carcinoma (HNSCC), a common malignant tumor, have not yet been identified. The aim of this study was to identify the key genes and pathways associated with HNSCC and to further analyze its molecular mechanism and prognostic significance. In this study, the expression profile chip data GSE6631 from Gene Expression Omnibus (GEO) included paired HNSCC tumor and normal samples from 22 patients; the RNAseq tertiary dataset of HNSCC and corresponding clinical information from The Cancer Genome Atlas (TCGA) included biological information of 12 normal head and neck tissues and 111 HNSCC sample tissues. Differentially expressed genes (DEGs) were screened by R software, and the pathway enrichment analysis of DEGs was performed by DAVID, String, and Sytoscape software programs. Combining the GEO and the TCGA databases, we used bioinformatics technology to screen out 50 DEGs in HNSCC and enrich the biological functions and key pathways of HNSCC. Then we performed Gene Ontology (GO) enrichment analysis, the Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, protein-protein interaction (PPI) analysis, and survival analysis on these DEGs. Using CMap, we identified candidate small molecules that might reverse HNSCC gene expression. Finally, four most important small molecules that could provide more reliable biomarkers for early diagnosis and individualized control of HNSCC were identified.

The Status of Strings and Orchestra Programs in U.S. Schools

The purpose of this study was to monitor the status of school string and orchestra programs in the United States and to gather descriptive information in the areas of program characteristics, curriculum, support, and student/teacher demographics. A second purpose was to document trends observed when compared with results of previous studies. Based on the review of literature, specific variables were identified as potential for trends: string student enrollment, symphonic orchestra offerings, enhancement offerings, private lesson enrollment, string teacher shortages, and student/teacher demographic information. All members of the American String Teachers Association indicating K-12 string teaching as part of their duties were contacted to complete a web-based survey ( N = 2,232). After follow-up contact, 369 respondents participated (16.5%). Although teachers indicated growth in both number and size of programs, increased utilization of approved curricula, and representative racial demographics among students, analysis revealed the following concerns: a decline in the offering of symphonic orchestra and other enhancements, a decline in student participation in private instruction, unrepresentative gender and racial demographics of string teachers, and factors that indicate a continuing string teacher shortage.

Quantitative Proteomic Analysis of the Metastasis-Inhibitory Mechanism of miR-193a-3p in Non-Small Cell Lung Cancer

Background: microRNAs can repress the expression of target genes by destabilizing their mRNAs or by inhibiting their translation. Our previous findings suggested that miR-193a-3p inhibited the progression of NSCLC both in vitro and in vivo. However, the biological processes and molecular pathways through which this miRNA exerts its positive effects are unknown. Methods: To explore the molecular mechanisms by which miR-193a-3p inhibited NSCLC metastasis, we investigated the changes in the protein profile of SPC-A-1sci (highly metastatic) cells in response to the up-regulation of miR-193a-3p expression using a proteomics approach (iTRAQ combined with NanoLC-MS/MS). Changes in the profiles of the expressed proteins were verified using western blotting and were analyzed using the DAVID and STRING programs. Results: In the two replicated experiments, 4962/4946 proteins were identified, and the levels of expression of 4923/4902 proteins were quantified. In total, 112 of these proteins were differentially expressed. Among them, the up-regulated levels of expression of two of the 62 proteins with up-regulated expression (PPP2R2A and GSN) and the down-regulated levels of expression four of the 50 proteins with down-regulated expression (LMNB2, UHRF1, G3BP1, and HNRNPU) were verified using western blotting. The bioinformatics analysis revealed the interactions and signaling networks of these differentially expressed proteins. Conclusion: miR-193a-3p inhibited the metastasis of lung cancer cells by deregulating the expression of tumor-related proteins. These findings may improve the understanding of the molecular mechanisms underlying the metastatic-inhibitory effect of miR-193a-3p on lung cancer cells.

The Status of Public School Orchestras in Kansas

The purpose of this study was to investigate string and orchestra programs in Kansas public schools. Website searches were conducted of all 285 Kansas public school districts for evidence of orchestra programs and names and contacts of teachers. A survey was administered to all known string and orchestra teachers in Kansas (N=150). A total of 67 participants fully completed the survey for a response rate of 45%. Data were collected on the prevalence of school districts with orchestra programs, the number of orchestra teachers employed in the state, demographic profiles of orchestra teachers, orchestra program information, and recent changes to programs. Approximately 13% of school districts in Kansas had string or orchestra programs during the 2012-2013 school year. As a whole, the data indicate that Kansas string and orchestra teachers and programs are very similar to those on a national level. This study provides an easily replicable methodological model and survey instrument that could be used by any state, with limited changes, to collect similar data.

String Music Educators’ Perceptions of the Impact of New String Programs on Student Outcomes, School Music Programs, and Communities

The purpose of this study was to examine the impact of newly initiated string programs on teachers, schools, districts, communities, and existing music program administration and students. Research questions pertained to (a) locations, student access, and instructional offerings; (b) educators; and (c) perceived impact on student outcomes. Data from 64 participants were analyzed. Results indicated that new string programs were largely developed at the middle and high school levels, located in suburban (59%), urban (23%), and rural (18%) areas, with instruction held during the regular school day. The majority (86%) of teachers were credentialed string specialists. While participants cited some frustrations, such as scheduling difficulties and lack of performance facilities, they identified several benefits from the new programs, including increased student participation in all music programs, more student collaborative opportunities, increased community and local music business support, and the more comprehensive nature of the music curriculum.

A History of the Michigan School Band and Orchestra Association: 1959-2009

The purpose of this study was to extend the documented history of the Michigan School Band and Orchestra Association (MSBOA) by providing a chronological account of the organization from 1959 to 2009 with historical context and insight into circumstances and individuals that influenced and shaped the organization during that period. Official records, Association publications, and first-hand accounts are compiled into a narrative of the organization. The study is a continuance of a previous historical examination of the formative years (1934-1959) of the MSBOA by James Burnham Hause. Formed in 1934, the MSBOA evolved from the need for leadership in school instrumental music and gave teachers the power to govern activities that affected their students through debate and the democratic process. The primary goal of the founders was to raise standards of musical performance through “competition-festivals.” The history of the MSBOA from 1959 to 2009 can be drawn into four periods. During the first period (1959 to 1973), the MSBOA abandoned its long-held practice of remaining autonomous to become a department of the Michigan Education Association; this decision was a post-Sputnik reaction to gain academic credibility and become “more than just a festival association” (a mantra used by MSBOA leaders of the period) by focusing on such matters as curriculum development and the creation of string programs. The organization began the second period (1973 to 1984) by separating from the Michigan Education Association and assuming an introspective posture, which led to a continual emphasis on revising its festival systems, especially the band and orchestra festival. After the celebration of its fiftieth anniversary in 1984, the MSBOA entered the third period (1984 to 1997), during which it largely addressed federal and state educational reform initiatives and computer technology development. During the final period (1997 to 2009), the Association focused on expanding its website to improve services to the membership, creating the state’s first all-state bands and orchestras, and helping establish a new conference for music educators. The author found that the MSBOA supported and served instrumental music education in Michigan in two important ways by 1) providing a strong system of festivals and other performance activities for students; and 2) offering multiple professional development opportunities for music teachers. The MSBOA cooperated at times with other arts and educational organizations in the state on various projects; however, because of the MSBOA’s determination to remain autonomous, its relationship with the Michigan Music Educators Association (the state chapter of the MENC) was contentious for decades. The lack of a strong partnership among the state’s four independent music education associations — the MSBOA, the Michigan School Vocal Association, the Michigan unit of the American String Teachers Association, and the Michigan Music Educators Association — weakened both their individual and collective attempts to address reforms affecting music education.

HnRNPL as a key factor in spermatogenesis: Lesson from functional proteomic studies of azoospermia patients with sertoli cell only syndrome

Sertoli cell only syndrome (SCOS) is one of the main causes leading to the abnormal spermatogenesis. However, the mechanisms for abnormal spermatogenesis in SCOS are still unclear. Here, we analyzed the clinical testis samples of SCOS patients by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF/TOF MS) to find the key factors contributing to SCOS. Thirteen differential proteins were identified in clinical testis samples between normal spermatogenesis group and SCOS group. Interestingly, in these differential proteins, Heterogeneous nuclear ribonucleoprotein L(HnRNPL) was suggested as a key regulator involved in apoptosis, death and growth of spermatogenic cells by String and Pubgene bioinformatic programs. Down-regulated HnRNPL in testis samples of SCOS patients was further confirmed by immunohistochemical staining and western blotting. Moreover, in vitro and in vivo experiments demonstrated that knockdown of HnRNPL led to inhibited proliferation, increased apoptosis of spermatogenic cell but decreased apoptosis of sertoli cells. Expression of carcinoembryonic antigen-related cell adhesion molecule 1 in GC-1 cells or expression of inducible nitric oxide synthases in TM4 sertoli cells, was found to be regulated by HnRNPL. Our study first shows HnRNPL as a key factor involved in the spermatogenesis by functional proteomic studies of azoospermia patients with sertoli cell only syndrome. This article is part of a Special Issue entitled: Proteomics: The clinical link.

The Perceived Impact of String Programs on K-12 Music Programs

We examined music teacher perceptions regarding the impact of string programs on overall music programs in K-12 schools. Research questions included: (1) What are the perceived positive and negative program and student outcomes? (2) What are the underlying issues of music teachers’ perceptions about the positive and negative impacts of string programs? (3) How do these underlying issues compare with one another (negative and positive)? and (4) What relationships, if any, exist between fixed factors and the perceptions of the impact of string programs? Questionnaires were sent to all MENC members in two Southwestern MENC states. Data from participants (n = 308) were analyzed using principal components analyses and correlation analyses. A majority of music teachers felt that string programs were beneficial and offered opportunities for student development as well as expanded opportunities within a music program. Concerns included program focus and support, logistical issues, budget concerns, and finding qualified instructors.

The Power of Unison: A Method for Including Fiddle Tunes in Classroom String Programs

The Power of Unison: A Method for Including Fiddle Tunes in Classroom String Programs

String Programs in Schools

String Programs in Schools

An Investigation of New String Programs Established in American Schools between 1999 and 2009

The purposes of this study were to identify string programs created between 1999 and 2009, compile a profile of those programs, and identify resources and strategies that were used to create them that may serve as a model for establishing future new programs. One hundred-fifty string programs were identified from 33 different states. A survey form to gather data about the programs was created and administered to 132 of the programs. Eighty-two completed the survey for a response rate of 62%. The survey asked questions about the history of the program, its current status, and projected future status. Data revealed that most programs began after one or less than one year of discussion, most often first suggested by local music teachers or superintendent. Those factors considered critical to successful establishment of the program included parent support, administrative support, competent string teaching, and funding. Respondents were willing to found additional programs. They suggested that a how-to manual and outside grant funding would help establish future new programs.

Reflecting on the Rationales for String Study in Schools

This essay will address the question of the value of string education by first examining arguments offered on behalf of string education in schools, and noting their somewhat mixed value. Then a set of arguments will be presented that may have greater promise. The focal point will be the establishment of excellence in string teaching and playing. When public school string programs are of the highest quality, they produce the kinds of musical outcomes that will draw strong support from students, communities, and administrators. While string programs should always have strong advocacy arguments at their disposal, these arguments should be balanced by a high level of musicianship and musicality in the public schools which will in turn draw fine teachers and students to string education.