Biotechnology Information Center Research Articles

A trans-generation conundrum with implications in rehabilitation programs – what factors influence non-specific back pain in children?

Back pain in children and adolescents is one of the most frequent reasons for seeing a medical specialist worldwide. Many factors have been incriminated when it comes to influencing the appearance of non-specific back pain in children as well as in adults. For the younger population, some of the culprits seem to be sitting for long periods, us-ing harmful postural patterns, a forward head posture determined by incorrect positioning during prolonged studying hours, and carrying a too-heavy backpack, but do they really influence non-specific back pain in children? These ques-tions are valid for all generations and countries. This paper aimed to review the published literature to determine whether the factors mentioned above, sitting in mismatched school furniture, carrying heavy backpacks, and forward head posture, influence the incidence of non-specific back pain in children and whether there are any data or differences between the general population and Roma-nian students. For this purpose, we conducted database research using the keywords “non-specific back pain in chil-dren, sitting, school furniture, forward head posture, backpack carrying” and various combinations of these terms, which returned 37 eligible articles for this paper in PubMed - Center for Biotechnology Information (NCBI) and Sci-enceDirect. There was no time limit on the researched articles, and they had to refer to the pediatric population, be open-access and in extenso articles, and be written in English, French, or Spanish. After analyzing the results from these articles, the conclusion is that there is no evident or spe-cific connection between non-specific back pain in pediatric populations and harmful posture patterns while sitting or carrying a backpack. Also, more multicentered research using fewer variables and more objective measurement instruments is needed. Keywords: non-specific back pain in children, sitting, bad posture, school furniture, forward head posture, back-pack carrying

The impact of ovarian stimulation on the human endometrial microenvironment.

How does ovarian stimulation (OS), which is used to mature multiple oocytes for ART procedures, impact the principal cellular compartments and transcriptome of the human endometrium in the periovulatory and mid-secretory phases? During the mid-secretory window of implantation, OS alters the abundance of endometrial immune cells, whereas during the periovulatory period, OS substantially changes the endometrial transcriptome and impacts both endometrial glandular and immune cells. Pregnancies conceived in an OS cycle are at risk of complications reflective of abnormal placentation and placental function. OS can alter endometrial gene expression and immune cell populations. How OS impacts the glandular, stromal, immune, and vascular compartments of the endometrium, in the periovulatory period as compared to the window of implantation, is unknown. This prospective cohort study carried out between 2020 and 2022 included 25 subjects undergoing OS and 25 subjects in natural menstrual cycles. Endometrial biopsies were performed in the proliferative, periovulatory, and mid-secretory phases. Blood samples were processed to determine serum estradiol and progesterone levels. Both the endometrial transcriptome and the principal cellular compartments of the endometrium, including glands, stroma, immune, and vasculature, were evaluated by examining endometrial dating, differential gene expression, protein expression, cell populations, and the three-dimensional structure in endometrial tissue. Mann-Whitney U tests, unpaired t-tests or one-way ANOVA and pairwise multiple comparison tests were used to statistically evaluate differences. In the periovulatory period, OS induced high levels of differential gene expression, glandular-stromal dyssynchrony, and an increase in both glandular epithelial volume and the frequency of endometrial monocytes/macrophages. In the window of implantation during the mid-secretory phase, OS induced changes in endometrial immune cells, with a greater frequency of B cells and a lower frequency of CD4 effector T cells. The data underlying this article have been uploaded to the Genome Expression Omnibus/National Center for Biotechnology Information with accession number GSE220044. A limited number of subjects were included in this study, although the subjects within each group, natural cycle or OS, were homogenous in their clinical characteristics. The number of subjects utilized was sufficient to identify significant differences; however, with a larger number of subjects and additional power, we may detect additional differences. Another limitation of the study is that proliferative phase biopsies were collected in natural cycles, but not in OS cycles. Given that the OS cycle subjects did not have known endometrial factor infertility, and the comparisons involved subjects who had a similar and robust response to stimulation, the findings are generalizable to women with a normal response to OS. OS substantially altered the periovulatory phase endometrium, with fewer transcriptomic and cell type-specific changes in the mid-secretory phase. Our findings show that after OS, the endometrial microenvironment in the window of implantation possesses many more similarities to that of a natural cycle than does the periovulatory endometrium. Further investigation of the immune compartment and the functional significance of this cellular compartment under OS conditions is warranted. Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases (R01AI148695 to A.M.B. and N.C.D.), Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD109152 to R.A.), and the March of Dimes (5-FY20-209 to R.A.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or March of Dimes. All authors declare no conflict of interest.

Diagnosis of two local mushroom species (Pleurotus spp.) and their production management

The present study confirmed the identity of two Iraqi mushrooms by using the internal transcribed spacer (ITS) sequence; the genomic DNA of two isolates was amplified using ITS1 and ITS4 primers, and the data analyzed through Basic Local Alignment Tool( BLAST) search was achieved using the National Center for Biotechnology Information (NCBI) database. The result shows that the nucleotide sequence of two mushrooms blasted against the sequence from the Gene Bank database that Pleurotus ostreatus and Pleurotus eryngii matched 99% and 100%, respectively. The second stage of the current study was the comparison of different agro-waste, including wheat straw(WS), corncob(CC) and sawdust(SD) supplemented with 25% wheat bran(W) and 2% calcium carbonate (CaCo3) on mycelium growth, yield and biological efficiency (BE) of local oyster mushroom which comparison with Chinese strain pleurotus ostreatus121 and pleurotus eryngii 080. The highest growth average of local P. ostretus on the SD substrate was 1.50 cm, and P.eryngii was recorded at 1.18 cm. The substrate CC was the most suitable for the yield of mushroom local P. ostreatus and P. ostreatus121(485.40 and 418.50 g/bag, respectively), while local P. eryngii recorded 470.40 in the same substrate. It was also found that the WS substrate recorded the highest BE for each local isolate and Chinese strain. Keywords: Iraqi strains, Pleurotus spp., agricultural wastes, wild agricultural mushrooms

Chemoprophylaxis and Management of Venous Thromboembolism in Microvascular Surgery.

This review aims to highlight the common pharmacological and nonpharmacological interventions utilized for thromboprophylaxis as well as flap salvage in microsurgery. A literature review was conducted in PubMed/National Center for Biotechnology Information, Scopus, Web of Science, and MEDLINE databases. Articles with a focus on thromboprophylaxis in microsurgical procedures spanning head and neck surgery, breast and extremity microvascular reconstruction, deep venous thrombosis/pulmonary embolus in microvascular surgery, and flap thrombosis and salvage were included in this review. The majority of available evidence supports mechanical venous thromboembolism (VTE) prophylaxis in all patients undergoing microsurgery given the presence of multiple risk factors for VTE within this particular patient population. Based on the literature review, addition of VTE chemoprophylactic agents is beneficial and an algorithmic approach to thromboprophylaxis in microsurgery patients and management of patients with thrombosis based on literature review and senior authors' experience is recommended and outlined.

"Plutchik": artificial intelligence chatbot for searching NCBI databases.

As genetic testing gains ground in medicine, the ability to search across the suite of biomedical and clinical care databases offered through the National Library of Medicine/National Center for Biotechnology Information (NCBI)—such as PubMed, GENE, Structure, the Genetic Testing Registry, and others—holds the potential to enhance quality of clinical care best practices. “Plutchik” is a voice-enabled, embodied artificial intelligence (AI) chatbot that can perform highly technical medical searches in and across the NCBI suite of databases.

How user intelligence is improving PubMed.

PubMed is a widely used search engine for biomedical literature. It is developed and maintained by the US National Library of Medicine/National Center for Biotechnology Information and is visited daily by millions of users around the world. For decades, PubMed has used advanced artificial intelligence technologies that extract patterns of collective user activity, such as machine learning and natural language processing, to inform the algorithmic changes that ultimately improve a user's search experience. Although these efforts have led to objective improvements in search quality, the technical underpinnings remain largely invisible and go largely unnoticed by most users. Here we describe how these 'under-the-hood' techniques work within PubMed and report how their effectiveness and usage is assessed in real-world scenarios. In doing so, we hope to increase the transparency of the PubMed system and enable users to make more effective use of the search engine. We also identify open challenges and new opportunities for computational researchers to explore the potential of future improvements.

Buprenorphine Formulations: Clinical Best Practice Strategies Recommendations for Perioperative Management of Patients Undergoing Surgical or Interventional Pain Procedures

Starting with approval for clinical use in the treatment of opioid dependence in October 2002 by the Food and Drug Administration (FDA), buprenorphine has become an integral treatment option and in recent years, in chronic pain management. Buprenorphine possesses a unique pharmacodynamic and pharmacokinetic profile that can potentially make perioperative analgesia challenging. To date no unified guidelines or recommendations are available for buprenorphine product management during the perioperative period. The present investigation aims to review the literature and provide recommendations when encountering a patient on buprenorphine therapy who is scheduled for a surgical or interventional pain procedure. Clinical studies and reviews were searched using the PubMed National Center for Biotechnology Information database using MeSH terms buprenorphine, buprenorphine and naloxone, suboxone, perioperative, and postoperative pain. PubMed National Center for Biotechnology Information database search resulted in one randomized control trial, one prospective case matched cohort, one retrospective cohort, 0 case series, 4 case reports, and 6 review articles. Key literature is reviewed and summarized. Only 12 articles were included, which permits only limited recommendations drawn from this review. The perioperative management of buprenorphine and buprenorphine/naloxone are dependent on several key factors. The nature of the surgery, namely the postoperative opioid requirement, elective versus emergency surgery, patient characteristics, formulation of buprenorphine, and indication for buprenorphine or buprenorphine/naloxone therapy must be considered when devising a plan. Several options exist when formulating a plan for the perioperative management, including continuing buprenorphine therapy or holding buprenorphine therapy for a defined period of time with or without bridging to alternative opioids. Additionally, social support people and patient motivation should be addressed and optimized, as well as nonopioid adjuvant therapy should be maximized as applicable to each patient undergoing a surgical or interventional pain procedure. Buprenorphine, naloxone, surgery, pain management, anesthesia, suboxone, opioid abuse.

Immunoinformatics Prediction of Peptide-Based Vaccine Against African Horse Sickness Virus

Background: African horse sickness (AHS) is a viral disease of equidae. It is transmitted by hematophagous Culicoides midges (Diptera, Ceratopogonidae) and causes severe disease in horse that can lead to death. African Horse Sickness Virus (AHSV) is a double-stranded RNA (dsRNA) virus with ten genome segments encoding seven structural proteins (VP1-VP7) and four non-structural proteins (NS1, NS2, NS3, NS3A). The aim of this study is to analyze (VP2) protein of the African Horse Sickness Virus (AHSV) strains reported in the National Center for Biotechnology Information database (NCBI) database to select all possible epitopes that can be used to design a peptide vaccine. Materials and methods: A total of 27 outer capsid protein (VP2) sequences of African Horse Sickness Virus (AHSV) were retrieved from the National Center for Biotechnology Information database (NCBI) (https://www.ncbi.nlm. nih.gov/protein/?term=VP2+African+horse+sickness+virus) in the 7th of September 2016. On them, several tests were conducted using Immune Epitope Analysis Database (IEDB) to detect the highly conserved immunogenic epitopes of B and T cells from which all possible epitopes that can be used as a therapeutic peptide vaccine to be selected. Results and Discussion: Regarding epitopes that would elicit an antibody immune response, “FSPEYY, DKVVEDPESY and YDTDQNVV “were proposed to stimulate B cell. While 5 epitopes for each MHC I and II were addressed as potentially promising epitopes as they bound the highest number of alleles, all these epitopes were found to have a high binding affinity and the lowest binding energy to equine MHC class I molecule (ELA-A3) haplotype in the structural level. The epitopes “YAYCLILAL and YTFGNKFLL” were represented because they were bound to the largest number of alleles. In spite of binding to 4 alleles the epitope WFFDYYATL was represented because it has the lowest global energy. To our knowledge there is no epitope based vaccine for the African Horse Sickness Virus (AHSV) using in silico approaches.

An in silico framework for integrating epidemiologic and genetic evidence with health care applications: ventilation-related pneumothorax as a case illustration.

To illustrate an in silico integration of epidemiologic and genetic evidence that is being developed at the Center for Devices and Radiological Health/US Food and Drug Administration as part of regulatory research on postmarket device performance. In addition to using conventional epidemiologic evidence from registries, this innovative approach explores the vast potential of open-access omics databases for identifying genetic evidence pertaining to devices. A retrospective analysis of Agency for Healthcare Research and Quality (AHRQ)/Healthcare Cost and Utilization Project (HCUPNet) data (2002-2011) was focused on the ventilation-related iatrogenic pneumothorax (Vent-IP) outcome in discharges with mechanical ventilation (MV) and continuous positive airway pressure (CPAP). The derived epidemiologic evidence was analyzed in conjunction with pre-existing genomic data from Gene Expression Omnibus/National Center for Biotechnology Information and other databases. AHRQ/HCUPNet epidemiologic evidence showed that annual occurrence of Vent-IP did not decrease over a decade. While the Vent-IP risk associated with noninvasive CPAP comprised about 0.5%, the Vent-IP risk due to longer-term MV reached 2%. Along with MV posing an independent risk for Vent-IP, female sex and white race were found to be effect modifiers, resulting in the highest Vent-IP risk among mechanically ventilated white females. The Vent-IP risk was also potentiated by comorbidities associated with spontaneous pneumothorax (SP) and fibrosis. Consistent with the epidemiologic evidence, expression profiling in a number of animal models showed that the expression of several collagens and other SP/fibrosis-related genes was modified by ventilation settings. Integration of complementary genetic evidence into epidemiologic analysis can lead to a cost- and time-efficient discovery of the risk predictors and markers and thus can facilitate more efficient marker-based evaluation of medical product performance.

Local anaesthesia using Articaine and Lidocaine in oral and dental surgery: A comparative meta-analysis

Background: Articaine is an amide local anaesthetic, which is gaining popularity for use in dental and oral surgical anaesthesia in the United Kingdom. Hitherto there has been insufficient evidence to recommend articaine above the more commonly used lidocaine for dental procedures. The aim of this study is to compare the efficacy of 4% articaine with 1:100,000 adrenaline (4AA) with that of 2% lidocaine with 1:100,000 adrenaline (2LA) administered as buccal infiltrations for anaesthesia in mandibular permanent first molar teeth. Any significant advantage noted may obviate the need for regional blockage of the inferior dental nerve in dental or minor oral surgical procedure under local anaesthesia. Objectives: To review the published literature comparing the efficacies of 4AA and 2LA for achieving pulpal anaesthesia in human mandibular permanent first molar teeth. Null Hypothesis: 4AA and 2LA are of equal efficacy when used to anaesthetize mandibular permanent first molar teeth by buccal infiltration. Method: An electronic search encompassing Ovid MEDLINE?, PubMed (National Center for Biotechnology Information, US National Library of Medicine), SCOPUS?, SCIRUS?, EMBASE? databases and the Cochrane Library was performed to identify trials relating to the efficacy of 4AA and 2LA local anaesthetic solutions on mandibular first molars in adult participants. Study characteristics and outcome data were extracted as a basis for meta-analysis. Results: Three randomised controlled trials were identified for this meta-analysis. The relative efficacy of 4AA over 2LA in anesthetizing permanent first mandibular molars was calculated at 1.57 (95% CI = 1.27 to 1.95). Conclusion: Despite the promising results shown in the meta-analysis it is difficult to say from the evidence presented that 4AA should be used clinically in preference over 2LA.

RTTN Mutations Link Primary Cilia Function to Organization of the Human Cerebral Cortex

Polymicrogyria is a malformation of the developing cerebral cortex caused by abnormal organization and characterized by many small gyri and fusion of the outer molecular layer. We have identified autosomal-recessive mutations in RTTN, encoding Rotatin, in individuals with bilateral diffuse polymicrogyria from two separate families. Rotatin determines early embryonic axial rotation, as well as anteroposterior and dorsoventral patterning in the mouse. Human Rotatin has recently been identified as a centrosome-associated protein. The Drosophila melanogaster homolog of Rotatin, Ana3, is needed for structural integrity of centrioles and basal bodies and maintenance of sensory neurons. We show that Rotatin colocalizes with the basal bodies at the primary cilium. Cultured fibroblasts from affected individuals have structural abnormalities of the cilia and exhibit downregulation of BMP4, WNT5A, and WNT2B, which are key regulators of cortical patterning and are expressed at the cortical hem, the cortex-organizing center that gives rise to Cajal-Retzius (CR) neurons. Interestingly, we have shown that in mouse embryos, Rotatin colocalizes with CR neurons at the subpial marginal zone. Knockdown experiments in human fibroblasts and neural stem cells confirm a role for RTTN in cilia structure and function. RTTN mutations therefore link aberrant ciliary function to abnormal development and organization of the cortex in human individuals.

Species Identification of Rock Oysters Collected from the Dhofar Region, Sultanate of Oman

Oysters are commonly found on rocky shores along the Dhofar coast of Oman, but the species composition has not yet been studied. In an attempt to determine the species of these oysters, samples from four sites (Mirbat, Sadah, Hadbin, and Hasik) were collected and analyzed using DNA sequences that were compared with the database of GenBank/National Center for Biotechnology Information (NCBI) and Barcoding of Life Data Systems (BOLD). BLAST results of DNA sequences showed that there were no existing sequences available on NCBI/GenBank and BOLD. The DNA barcode sequences generated in this study can be employed as standards for this species and may be of use in taxonomic studies. Phylogenetic analysis demonstrated that the oysters from Oman exhibit homology with Saccostrea species cucullata or mordax.

Ureteral Injury in Gynecologic Laparoscopy

Purpose: To review incidence, presentation, diagnosticmethods, management, significance and avoidance of ureteralinjuries in gynecologic laparoscopy.Materials and methods: PubMed, National Center forBiotechnology Information Database, Journal of the Society ofLaparoendoscopic Surgeons, obstetrics and gynecology journal,google images were reviewed to gather information regardingureteral injuries in gynecologic laparoscopy.Results: Ureteral injury is one of the serious complications oflaparoscopic surgery, in particular, gynecologic laparoscopy. Itis very important to be familiar with presentation, diagnosticmethods and management as well as prevention of ureteralinjury at the time of gynecologic laparoscopy.Conclusion: Every gynecologic surgeon has to be familiar withsigns and symptoms as well as management of ureteral injuryat the time of gynecologic laparoscopy.

Proteomics analysis onpathogenesis of human atherosclerosis obliterans in human femoral artery

：Objective We usedproteomic profiling in an attempt to differentiate and identify histological proteins thatwere associated with atherosclerosis obliterans (ASO) of human femoral artery.Methods Wecomparatively analyzed the proteome of 8 atherosclerotic and 5 normal femoral arteries.The differentially expressed proteins were visualized by two dimensional electrophoresis(2-DE) and sequenced by matrix assisted laser desorption/ionization mass spectrometry(MALDI-TOF-MS). The protein identification program was used to search the National Centerfor Biotechnology Information (NCBI) database and International Protein Index (IPI).Results A total of 53 distinct spots corresponding to 13 different proteins wereidentified by MALDI-TOF-MS using the NCBI and IPI databases. The function information ofthese 13 proteins mainly involved the pathogenetic mechanisms such as inflammation, innateimmunity, oxidative stress, lipid metabolism, amyloid degeneration and so on. ConclusionASO is associated with distinct patterns of protein expression in the femoral arteries,and differentially expressed 13 proteins may contribute to the pathogenesis. Thesefindings might provide needed biomarkers for ASO and new insight into its pathophysiology.

Combination of Linkage Mapping and Microarray-Expression Analysis Identifies NF-κB Signaling Defect as a Cause of Autosomal-Recessive Mental Retardation

Autosomal-recessive inheritance accounts for nearly 25% of nonsyndromic mental retardation (MR), but the extreme heterogeneity of such conditions markedly hampers gene identification. Combining autozygosity mapping and RNA expression profiling in a consanguineous Tunisian family of three MR children with mild microcephaly and white-matter abnormalities identified the TRAPPC9 gene, which encodes a NF-kappaB-inducing kinase (NIK) and IkappaB kinase complex beta (IKK-beta) binding protein, as a likely candidate. Sequencing analysis revealed a nonsense variant (c.1708C>T [p.R570X]) within exon 9 of this gene that is responsible for an undetectable level of TRAPPC9 protein in patient skin fibroblasts. Moreover, TNF-alpha stimulation assays showed a defect in IkBalpha degradation, suggesting impaired NF-kappaB signaling in patient cells. This study provides evidence of an NF-kappaB signaling defect in isolated MR.

Microarray Standards

Microarray Standards

Review of the fourth Johns Hopkins Protein Folding Meeting

Review of the fourth Johns Hopkins Protein Folding Meeting