A qualitative interview study to determine barriers and facilitators of implementing automated decision support tools for genomic data access.

Data access committees (DAC) gatekeep access to secured genomic and related health datasets yet are challenged to keep pace with the rising volume and complexity of data generation. Automated decision support (ADS) systems have been shown to support consistency, compliance, and coordination of data access review decisions. However, we lack understanding of how DAC members perceive the value add of ADS, if any, on the quality and effectiveness of their reviews. In this qualitative study, we report findings from 13 semi-structured interviews with DAC members from around the world to identify relevant barriers and facilitators to implementing ADS for genomic data access management. Participants generally supported pilot studies that test ADS performance, for example in cataloging data types, verifying user credentials and tagging datasets for use terms. Concerns related to over-automation, lack of human oversight, low prioritization, and misalignment with institutional missions tempered enthusiasm for ADS among the DAC members we engaged. Tensions for change in institutional settings within which DACs operated was a powerful motivator for why DAC members considered the implementation of ADS into their access workflows, as well as perceptions of the relative advantage of ADS over the status quo. Future research is needed to build the evidence base around the comparative effectiveness and decisional outcomes of institutions that do/not use ADS into their workflows.

Investigating the Roles and Responsibilities of Institutional Signing Officials After Data Sharing Policy Reform for Federally Funded Research in the United States: National Survey.

BACKGROUND: New federal policies along with rapid growth in data generation, storage, and analysis tools are together driving scientific data sharing in the United States. At the same, triangulating human research data from diverse sources can also create situations where data are used for future research in ways that individuals and communities may consider objectionable. Institutional gatekeepers, namely, signing officials (SOs), are therefore at the helm of compliant management and sharing of human data for research. Of those with data governance responsibilities, SOs most often serve as signatories for investigators who deposit, access, and share research data between institutions. Although SOs play important leadership roles in compliant data sharing, we know surprisingly little about their scope of work, roles, and oversight responsibilities. OBJECTIVE: The purpose of this study was to describe existing institutional policies and practices of US SOs who manage human genomic data access, as well as how these may change in the wake of new Data Management and Sharing requirements for National Institutes of Health-funded research in the United States. METHODS: We administered an anonymous survey to institutional SOs recruited from biomedical research institutions across the United States. Survey items probed where data generated from extramurally funded research are deposited, how researchers outside the institution access these data, and what happens to these data after extramural funding ends. RESULTS: In total, 56 institutional SOs participated in the survey. We found that SOs frequently approve duplicate data deposits and impose stricter access controls when data use limitations are unclear or unspecified. In addition, 21% (n=12) of SOs knew where data from federally funded projects are deposited after project funding sunsets. As a consequence, most investigators deposit their scientific data into "a National Institutes of Health-funded repository" to meet the Data Management and Sharing requirements but also within the "institution's own repository" or a third-party repository. CONCLUSIONS: Our findings inform 5 policy recommendations and best practices for US SOs to improve coordination and develop comprehensive and consistent data governance policies that balance the need for scientific progress with effective human data protections.

Achieving Procedural Parity in Managing Access to Genomic and Related Health Data: A Global Survey of Data Access Committee Members.

Data access committees (DACs) are critical players in the data sharing ecosystem. DACs review requests for access to data held in one or more repositories and where specific constraints determine how the data may be used and by whom. Our team surveyed DAC members affiliated with genomic data repositories worldwide to understand standard processes and procedures, operational metrics, bottlenecks, and efficiencies, as well as their perspectives on possible improvements to quality review. We found that DAC operations and systemic issues were common across repositories globally. In general, DAC members endeavored to achieve an appropriate balance of review efficiency, quality, and compliance. Our results suggest a similarly proportionate path forward that helps DACs pursue mutual improvements to efficiency and compliance without sacrificing review quality.

Aligning NIH's existing data use restrictions to the GA4GH DUO standard.

It is widely accepted that large-scale genomic data (e.g., whole-genome sequencing, whole-exome sequencing, and genome-wide association study data) be shared through a controlled-access mechanism. This protects the privacy of research participants and ensures downstream uses of data align with participants' informed consent regarding future sharing of their data. In 2019, GA4GH approved the Data Use Ontology (DUO) standard to define data use terms with machine-readable representations to represent how a dataset can be used. We endeavored to determine the parity of existing data use restrictions ("Data Use Limitations" [DULs]) for datasets registered in the National Institutes of Health database for Genotypes and Phenotypes (dbGaP) with the DUO standard. We found substantial (93%) parity between the dbGaP DULs (n = 3,575) and DUO. This study demonstrates the comprehensiveness of the DUO standard and encourages data stewards to standardize data use restrictions in machine-readable formats to facilitate data sharing.

Metagenomic Mining and Functional Characterization of a Novel KG51 Bifunctional Cellulase/Hemicellulase from Black Goat Rumen.

A novel KG51 gene was isolated from a metagenomic library of Korean black goat rumen and its recombinant protein was characterized as a bifunctional enzyme (cellulase/hemicellulase). In silico sequence and domain analyses revealed that the KG51 gene encodes a novel carbohydrate-active enzyme that possesses a salad-bowl-like shaped glycosyl hydrolase family 5 (GH5) catalytic domain but, at best, 41% sequence identity with other homologous GH5 proteins. Enzymatic profiles (optimum pH values and temperatures, as well as pH and thermal stabilities) of the recombinant KG51 bifunctional enzyme were also determined. On the basis of the substrate specificity data, the KG51 enzyme exhibited relatively strong cellulase (endo-ß-1,4-glucanase [EC 3.2.1.4]) and hemicellulase (mannan endo-ß-1,4-mannosidase [EC 3.2.1.78] and endo-ß-1,4-xylanase [EC 3.2.1.8]) activities, but no exo-ß-1,4-glucanase (EC 3.2.1.74), exo-ß-1,4-glucan cellobiohydrolase (EC 3.2.1.91), and exo-1,4-ß-xylosidase (EC 3.2.1.37) activities. Finally, the potential industrial applicability of the KG51 enzyme was tested in the preparation of prebiotic konjac glucomannan hydrolysates.

Multistage Microfluidic Platform for the Continuous Synthesis of III-V Core/Shell Quantum Dots.

We present a fully continuous chip microreactor-based multistage platform for the synthesis of quantum dots with heterostructures. The use of custom-designed chip reactors enables precise control of heating profiles and flow distribution across the microfluidic channels while conducting multistep reactions. The platform can be easily reconfigured by reconnecting the differently designed chip reactors allowing for screening of various reaction parameters during the synthesis of nanocrystals. III-V core/shell quantum dots are chosen as model reaction systems, including InP/ZnS, InP/ZnSe, InP/CdS and InAs/InP, which are prepared in flow using a maximum of six chip reactors in series.

Laser parameters for efficient biomedical stimulation: A study to increase cognitive response rate.

BACKGROUND: The laser is able to irradiate the exact amount of stimulation to an area by a non contact method, and has the advantage of being able to stimulate the local target area. OBJECTIVE: This study examined an efficient method of laser tactile stimulation using laser parameter combinations. METHODS: The laser parameters that could cause an increase in the cognitive response rate of human subjects were examined without increasing the amount of total laser energy. RESULTS: As a result, the appropriate matching parameters such as duty ratio, pulse frequency, and exposure time of laser pulses showed a dominant influence in effectively increasing the tactile response rate of subjects with limited amount of total laser energy. CONCLUSIONS: This study can be applied to neurophysiology, cognitive research, and clinical laser application.

Isolation and characterization of a novel endo-beta-1, 4-glucanase from a metagenomic library of the black-goat rumen

ABSTRACT The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1 kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30-50 °C at a pH of 6-7. The thermostability was retained and the pH was stable in the range of 30-50 °C at a pH of 5-7.

Isolation and characterization of a novel endo-ß-1,4-glucanase from a metagenomic library of the black-goat rumen.

The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-ß-1,4-glucanase. The recombinant KG35 endo-ß-1,4-glucanase showed optimal activity within the range of 30-50°C at a pH of 6-7. The thermostability was retained and the pH was stable in the range of 30-50°C at a pH of 5-7.

A study on detection of glucose concentration using changes in color coordinates.

Glucose concentration is closely related to the metabolic activity of cells and it is the most important substance as the energy source of a living body which plays an important role in the human body. This paper proposes an optical method that can measure the concentration of glucose. The change in glucose concentration was observed by using CIE diagram, and wavelength and purity values were detected. Also, even small changes in glucose concentration can be evaluated through mathematical modeling. This system is simple, economical, and capable of quantifying optical signals with numerical values for glucose sensing. This method can be applicable to the clinical field that examines diabetes mellitus or metabolic syndrome.

Isolation and characterization of a novel glycosyl hydrolase family 74 (GH74) cellulase from the black goat rumen metagenomic library.

This study aimed to isolate and characterize a novel cellulolytic enzyme from black goat rumen by using a culture-independent approach. A metagenomic fosmid library was constructed from black goat rumen contents and screened for a novel cellulase. The KG37 gene encoding a protein of 858 amino acid residues (92.7 kDa) was isolated. The deduced protein contained a glycosyl hydrolase family 74 (GH74) domain and showed 77% sequence identity to two endo-1,4-ß-glucanases from Fibrobacter succinogenes. The novel GH74 cellulase gene was overexpressed in Escherichia coli, and its protein product was functionally characterized. The recombinant GH74 cellulase showed a broad substrate spectrum. The enzyme exhibited its optimum activity at pH 5.0 and temperature range of 20-50 °C. The enzyme was thermally stable at pH 5.0 and at a temperature of 20-40 °C. The novel GH74 cellulase can be practically exploited to convert lignocellulosic biomass to value-added products in various industrial applications in future.

Meta-analysis of factors predicting resistance to intravenous immunoglobulin treatment in patients with Kawasaki disease.

PURPOSE: Studies have been conducted to identify predictive factors of resistance to intravenous immunoglobulin (IVIG) for Kawasaki disease (KD). However, the results are conflicting. This study aimed to identify laboratory factors predictive of resistance to high-dose IVIG for KD by performing meta-analysis of available studies using statistical techniques. METHODS: All relevant scientific publications from 2006 to 2014 were identified through PubMed searches. For studies in English on KD and IVIG resistance, predictive factors were included. A meta-analysis was performed that calculated the effect size of various laboratory parameters as predictive factors for IVIG-resistant KD. RESULTS: Twelve studies comprising 2,745 patients were included. Meta-analysis demonstrated significant effect sizes for several laboratory parameters: polymorphonuclear leukocytes (PMNs) 0.698 (95% confidence interval [CI], 0.469-0.926), C-reactive protein (CRP) 0.375 (95% CI, 0.086-0.663), pro-brain natriuretic peptide (pro-BNP) 0.561 (95% CI, 0.261-0.861), total bilirubin 0.859 (95% CI, 0.582-1.136), alanine aminotransferase (AST) 0.503 (95% CI, 0.313-0.693), aspartate aminotransferase (ALT) 0.436 (95% CI, 0.275-0.597), albumin 0.427 (95% CI, -0.657 to -0.198), and sodium 0.604 (95% CI, -0.839 to -0.370). Particularly, total bilirubin, PMN, sodium, pro-BNP, and AST, in descending numerical order, demonstrated more than a medium effect size. CONCLUSION: Based on the results of this study, laboratory predictive factors for IVIG-resistant KD included higher total bilirubin, PMN, pro-BNP, AST, ALT, and CRP, and lower sodium and albumin. The presence of several of these predictive factors should alert clinicians to the increased likelihood that the patient may not respond adequately to initial IVIG therapy.

Simple LED spectrophotometer for analysis of color information.

A spectrophotometer is the basic measuring equipment essential to most research activity fields requiring samples to be measured, such as physics, biotechnology and food engineering. This paper proposes a system that is able to detect sample concentration and color information by using LED and color sensor. Purity and wavelength information can be detected by CIE diagram, and the concentration can be estimated with purity information. This method is more economical and efficient than existing spectrophotometry, and can also be used by ordinary persons. This contribution is applicable to a number of fields because it can be used as a colorimeter to detect the wavelength and purity of samples.

High throughput synthesis of uniform biocompatible polymer beads with high quantum dot loading using microfluidic jet-mode breakup.

Uniform polymer microbeads with highly loaded quantum dots (QDs) are produced using high-throughput coherent jet breakup of a biocompatible poly(ethylene glycol) diacrylate (PEGDA) prepolymer resin, followed by in-line photopolymerization. A spiraling and gradually widening channel enables maximum absorption of radiated UV light for the in-line photopolymerization without coalescence and clogging issues. Although the dripping mode in general provides superior uniformity to the jet mode, our nozzle design with tapered geometry brings controlled jet breakup leading to 3% of uniform particle size distribution, comparable to dripping-mode performance. We achieve a maximum production rate of 2.32 kHz, 38 times faster than the dripping mode, at a same polymer flow rate. In addition, the jet-mode scheme provides better versatility with 3 times wider range of size control as well as the compatibility with viscous fluids that could cause pressure buildup in the microsystem. As a demonstration, a QD-doped prepolymer resin is introduced to create uniform biocompatible polymer beads with 10 wt % CdSe/ZnSe QD loading. In spite of this high loading, the resulting polymer beads exhibits narrow bandwidth of 28 nm to be used for the ultrasensitive bioimaging, optical coding, and sensing sufficiently with single bead.

In vitro assessment of antibacterial activity and cytocompatibility of silver-containing PHBV nanofibrous scaffolds for tissue engineering.

Infections with bacteria have become a serious problem in joint arthroplasty. This study reports about in vitro antibacterial activity and in vitro cell compatibility of poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) nanofibers loaded with metallic silver particles of a size of 5-13 nm. In vitro antibacterial activity against Staphylococcus aureus and Klebsiella pneumoniae was studied by microplate proliferation tests. The adhesion, viability, and proliferation properties of fibroblasts (NIH 3T3) and differentiation of osteoblasts (MC3T3-E1) were done to study in vitro cell compatibility of the scaffolds. As the results, only silver-containing PHBV nanofibrous scaffolds showed a high antibacterial activity and an inhibitory effect on the growth of both Staphylococcus aureus and Klebsiella pneumoniae bacteria. The nanofibrous scaffolds having silver nanoparticles <1.0% were free of in vitro cytotoxicity. To sum up, the PHBV nanofibrous scaffolds having nanoparticles <1.0 wt % showed not only good antibacterial activity but also good in vitro cell compatibility. It is considered that the PHBV nanofibrous scaffolds with silver nanoparticles <1.0 wt % have a potential to be used in joint arthroplasty.

Systemic mast cell disease without associated hematologic disorder: a combined retrospective and prospective study.

OBJECTIVE: To study clinicopathologic correlations and identify prognostically important variables in patients with systemic mast cell disease (SMCD) who have no associated hematologic disorders. PATIENTS AND METHODS: We identified 40 adult patients with SMCD without associated hematologic disorders. Clinical, laboratory, and bone marrow (BM) histologic findings at the time of referral were evaluated (November 1980-February 2001) for possible correlations with a history of aggressive systemic mastocytosis (retrospectively analyzed) as well as survival (prospectively analyzed). RESULTS: The median follow-up time from diagnosis was 108 months and from BM examination was 24 months. A history of aggressive systemic mastocytosis correlated significantly with increased BM mast cell (MC) content, unfavorable MC infiltration pattern, BM eosinophilia, and elevated serum alkaline phosphatase (SAP) level, but not with BM angiogenesis, reticulin fibrosis, or levels of MC mediators. Of these factors, increased BM MC content and elevated SAP level were also associated with shortened survival from time of referral. CONCLUSIONS: This study suggests that the BM MC burden, BM eosinophilia, and SAP level are prognostically important in SMCD without associated hematologic disorders. In contrast, BM angiogenesis, reticulin fibrosis, and levels of MC mediators showed no prognostic relevance.

Mastocytosis and fibrosis: role of cytokines.

Mastocytosis is a rare stem cell disorder characterized by abnormal growth and accumulation of mast cells in one or more organ systems. Clinical heterogeneity is a hallmark of mastocytosis. Recent observations of activating mutations in c-kit may help to understand the abnormal growth of mast cells in mastocytosis. However, this mutation alone does not explain the entire clinical heterogeneity of the disease. Reticulin fibrosis is also commonly associated with systemic mastocytosis. Mast cells are known to be the source of fibrogenic cytokines, including platelet-derived growth factor, transforming growth factor-beta (TGF beta) and basic fibroblast growth factor (bFGF). Immunohistochemical studies show a close correlation between the mast cell expression of bFGF and the reticulin fibrosis of mastocytosis lesions. The study of cytokine receptor expression also demonstrates that the TGF beta receptor I (RI)-negative cases of mastocytosis are prognostically less favorable than the TGF beta RI-positive cases. This finding may be related to the fact that the TGF beta R complex functions as a tumor suppressor gene in neoplastic cells.

Bone marrow angiogenesis in systemic mast cell disease.

Mast cells may participate in tumor angiogenesis through the release of angiogenic cytokines from their secretory granules. To gain additional insight into the role of mast cells in bone marrow angiogenesis, we performed a semiquantitative measurement of bone marrow microvessel density in 52 consecutive adult patients with systemic mast cell disease (SMCD). The results were examined for potential correlations with mast cell expression of angiogenic cytokines and with other histologic features of the bone marrow. Standard immunohistochemical methods were used to visualize bone marrow microvessels (CD34 staining) and mast cell expression of transforming growth factor-beta, basic fibroblast growth factor, and their respective receptors. An increase in microvessel density was demonstrated in 32 of the 52 patients (62%) with SMCD, and the degree of bone marrow angiogenesis did not correlate with either the mast cell expression pattern of the study cytokines or the presence (23 patients) or absence (29 patients) of an associated hematologic disorder. In the 29 patients without an associated hematologic disorder, microvessel density was correlated significantly with the presence of an abnormal pattern of hematopoiesis but not with the degree of bone marrow involvement by mast cells. Furthermore, areas occupied by mast cell lesions were often devoid of neovascularization. We conclude that bone marrow angiogenesis characterizes a percentage of patients with SMCD and that the pathogenesis may not necessarily be linked to the mast cells themselves.