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As assessment of habitat pressure, oxygen fraction, and EVA suit design for space operations.

At high cabin pressure [e.g. 1013 hPa (14.7 psi) 21% O2] there are serious issues relative to specification of suit pressure and the need for prebreathing. A high pressure suit will be costly but use of the existing, flexible suit requires up to 6 h of prebreathing. Or one could use a cabin pressure of 700 hPa (10.2 psi) prior to extravehicular activity (EVA) in order to use the existing suit with only 1 h of prebreathing. If these normal cabin pressures and O2 levels are utilized, existing physiological and medical databases apply, providing a known basis for evaluating effects of long duration space missions. If a 345 hPa (5 psi), 70-100% O2 atmosphere is adopted the existing suit can be used with no prebreathing required. However, there is no reference database on physiological effects under the conditions of lower pressure and higher O2 concentration. This paper considers the major issues involved in defining habitat pressure, O2 fraction, and EVA suit design for operations in space. A preliminary model for evaluating habitat/suit pressure and O2% strategies is presented.

Aerospace Medicine↗

Metacarpal index and bone mineral density in healthy African-American women.

Bone mineral density (BMD) reference data of non-Caucasian women is scarce but greatly needed for African-American women. The objective of this study was to establish a metacarpal normative reference database for African-American women using digital X-ray radiogrammetry (DXR) and hand radiographs and compare these values to existing Caucasian data. Two hundred and fifty healthy African-American women between the ages of 20 and 79 years old, 14 of whom were excluded, were recruited to participate from four different clinical sites. The study population was recruited in approximately equal number into the following groups: 20-29, 30-39, 40-49, 50-59, 60-69 and 70-79 years of age. A radiograph was acquired of each subject's non-dominant hand. The radiographs were scanned and analyzed using radiogrammetric techniques, and the BMD, MCI (Metacarpal Index), bone width and cortical thickness were calculated. The regression curve that best fit the data was a second order polynomial. The BMD and MCI of young adult women (20-40 years of age) were used to calculate T-score parameters. The young reference BMD and MCI with their associated standard deviations were found to be 0.6045 g/cm2+/-0.0529 g/cm2 and 0.5096 and 0.0792, respectively. However, the MCI was found to be approximately 2.5% lower (-0.0118) compared to Caucasian women. The African-American metacarpal BMD was found to be 3.5% (0.0207 g/cm2) higher across all ages when compared to existing Caucasian reference data acquired in a similar way. The differences were found to be entirely due to larger bone size, cortical diameter and bone width in the African-American women.

Absorptiometry, Photon↗

Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.

SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health. AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

Metadata↗

[A definition of the nomenclature of allele variants and a description of allele polymorphism within a molecular-genetic individualization system based on the pentanucleotide tandem replication of HUMCD4].

While analyzing the available published data, we found significant differences in definition of alleles of the HUMCD4 polymorphic chromosome locus. It is an obstacle for comparing the expertise results obtained while using the locus as molecular individualization system in different laboratories and, as a consequence, it hinders the use of the said marker in building up a reference database. The structure of the HUMCD4 locus was analytically investigated and the distribution of the locus alleles was systemized in a sample of 407 persons (citizens of Russia who are not blood relatives) within the present case study for the purpose of a detailed definition of its allele's characteristics. We worked out recommendations related with the nomenclature standardization of alleles of the HIMCD4 locus and specified the main population features of the locus polymorphism on the bases of the studied sample of Russia's citizens. The results can be used as reference parameters in interpreting the findings of the molecular-genetic identification expertise and examinations and in building up databases.

Alleles↗

resLens: genomic language models to enhance antibiotic resistance gene detection.

The rise of antibiotic resistance necessitates advanced tools to detect and analyze antibiotic resistance genes (ARGs). We present resLens, a family of genomic language models that leverage latent genomic representations to enhance ARG detection and analysis. Unlike alignment-based methods constrained by reference databases, resLens fine-tunes a pre-trained DNA language model on curated ARG datasets, achieving competitive or superior performance in classifying resistance genes across multiple evaluation scenarios, including when ARGs exhibit sequences and mechanisms of resistance dissimilar to those in reference datasets.

Journal Article↗

Assessment of left ventricular perfusion, volumes, and motion in mice using pinhole gated SPECT.

UNLABELLED: Quantitative functional normal data should be a prerequisite before applying SPECT in murine models of cardiac disease. Therefore, we investigated the capability of in vivo pinhole gated SPECT for establishment of a reference database for left ventricular myocardial perfusion, volumes, and motion in normal mice. METHODS: A small-animal dedicated pinhole gamma-camera with a field of view of 17 cm and a focal distance of 12 cm was used with a 1.5-mm pinhole and a 2.5-cm radius of rotation. Phantoms were designed to test spatial resolution and microvolume measurements of accuracy. Eight adult normal mice (CD1) were studied using a heated mixture of air (0.3 L/min) and 1.5%-2.5% isoflurane for anesthesia. For myocardial perfusion, 350-450 MBq of (99m)Tc-tetrofosmin were used in 0.15-0.25 mL. Gated acquisitions (8 or 10 time bins per cardiac cycle) were obtained using a 180 degrees circular arc and 48 anterior projections of 300 R-R intervals. Image reconstruction was done using a specific Algebraic Reconstruction Technique (ART) cone-beam algorithm. For quantification, reconstructed images were processed using standard nuclear medicine software. RESULTS: Millimetric spatial resolution and volume calibration linear relationships (r(2) = 0.99) in the 10- to 100-muL range were obtained in phantoms and used to scale in vivo volume values. In mice, left ventricular perfusion was lower in the apex (65% +/- 6%) versus lateral (72% +/- 5%), inferior (74% +/- 5%), septum (75% +/- 4%), and anterior (74% +/- 2%) walls. The left ventricular ejection fraction was 60% +/- 9%, end-diastolic volume was 50 +/- 8 muL, end-systolic volume was 20 +/- 6 muL, stroke volume was 29.5 +/- 6 muL, and cardiac output was 9.6 +/- 1.6 mL/min. Wall thickening was higher in the apex (47% +/- 12%) versus lateral (30% +/- 9%), inferior (33% +/- 8%), septum (37% +/- 10%), and anterior (33% +/- 10%) walls. CONCLUSION: This work shows that in vivo pinhole gated SPECT can be used for assessment of left ventricular perfusion, volumes, and cardiac function in normal mice.

Animals↗

Identification of Mycobacterium species by multiple-fluorescence PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene.

Identification of mycobacteria to the species level by growth-based methodologies is a process that has been fraught with difficulties due to the long generation times of mycobacteria. There is an increasing incidence of unusual nontuberculous mycobacterial infections, especially in patients with concomitant immunocompromised states, which has led to the discovery of new mycobacterial species and the recognition of the pathogenicity of organisms that were once considered nonpathogens. Therefore, there is a need for rapid and sensitive techniques that can accurately identify all mycobacterial species. Multiple-fluorescence-based PCR and subsequent single-strand conformation polymorphism (SSCP) analysis (MF-PCR-SSCP) of four variable regions of the 16S rRNA gene were used to identify species-specific patterns for 30 of the most common mycobacterial human pathogens and environmental isolates. The species-specific SSCP patterns generated were then entered into a database by using BioNumerics, version 1.5, software with a pattern-recognition capability, among its multiple uses. Patient specimens previously identified by 16S rRNA gene sequencing were subsequently tested by this method and were identified by comparing their patterns with those in the reference database. Fourteen species whose SSCP patterns were included in the database were correctly identified. Five other test organisms were correctly identified as unique species or were identified by their closest relative, as they were not in the database. We propose that MF-PCR-SSCP offers a rapid, specific, and relatively inexpensive identification tool for the differentiation of mycobacterial species.

DNA Primers↗

Large scale database experiments to assess the significance of matching DNA profiles.

Over 5,700 three-probe VNTR DNA profiles collected by several United Kingdom (UK) laboratories have been compared to examine the probability of randomly matching 2 samples from different individuals. In over 16 million comparisons, using a matching rule corresponding to the matching guideline employed by the UK Forensic Science Service, no profiles were found to match at the 3 loci D1S7 (MS1), D7S21(MS31) and D12S11 (MS43a). The frequency of occurrence of a set of Caucasian profiles have been estimated with 6 reference databases. The results show that there were greater differences in the frequency estimates when using a database of Afro-Caribbean or Asian profiles, rather than a different Caucasian database. The results further demonstrate the power and robustness of the VNTR DNA profiling technique for forensic casework.

Bayes Theorem↗

Systematic analysis of stutter percentages and allele peak height and peak area ratios at heterozygous STR loci for forensic casework and database samples.

To assist the interpretation of STR DNA typing results from forensic casework samples containing mixtures, the range of heterozygous allele peak height and peak area ratios (HR) and stutter percentages (stutter %) for the loci comprised in the AmpFlSTR Profiler Plus (PP) kit were assessed on 468 database and 275 casework single source samples. Stutter % medians were similar for database and casework samples, ranging from 2% to 7%. The upper limit of the stutter value range was 16%, calculated as median +3 SD, although lower locus-specific values could be used. HR medians were 93 +/- 6.5% for database samples, 88 +/- 12% for casework samples. For casework samples, the maximum signal imbalance noted was 52%, calculated as median -3 SD. No significant difference was observed between peak height and peak area calculated values. This study shows the importance of selecting the proper reference database for the establishment of HR threshold values.

Alleles↗

A database for estimating normal spinal motion derived from noninvasive measurements.

STUDY DESIGN: A database for estimated normal spinal motion was derived using a noninvasive, high-resolution, computer-aided system, which tracks the motion of skin markers strategically placed on the spine. Forty normal subjects, selected from hundreds of possible subjects according to rigorous inclusion/exclusion criteria, were tested on the system. OBJECTIVES: Patterns of estimated spinal motion were analyzed as a function of load, age, and sex, confirming a correlation between the movement of spinal segments and the motion of skin markers. SUMMARY OF BACKGROUND DATA: The Workers Compensation Board of Quebec funded and supervised the experiments necessary to establish a normative reference database for a high-resolution motion analysis system that permits a noninvasive assessment of spinal function. A previous study examined the correlation between the movements of the skin markers and the underlying bony structures for trunk flexion. Skin movement cannot be random and contains information characterizing both the spine and its surrounding soft tissues. METHODS: A noninvasive dynamic imaging system was used to measure normal spinal function under free movement. A high-resolution three-dimensional camera system collected basic kinematic data from strategically placed skin markers over the lumbar spine while the activity of paraspinal muscles was being recorded with surface electromyography. The measurements were analyzed for consistent, specific patterns recognizable as normal lumbar spine skin motion and reflecting normal lumbar spine function. A comparison was made with previous radiographic studies to confirm the correlation between the motion of skin markers and lumbar spine function. RESULTS: Lumbar skin marker motion patterns in normal subjects were consistent and varied little with load; gender had no effect except in the initial phase of a movement. There was less mobility but similar coordination in older subjects. No inconsistencies with previous radiologic investigations were found for sagittal and lateral plane movement.

Adolescent↗

In vivo organ mass of Korean adults obtained from whole-body magnetic resonance data.

In vivo organ mass of the Korean adult, male and female were presented for the purpose of radiation protection. A total of 121 healthy volunteers (66 males and 55 females), whose body dimensions were close to that of average Korean adults, were recruited for this study. Whole-body magnetic resonance (MR) images were obtained, and contours of 15 organs (brain, eye, gall bladder, heart, kidney, liver, lung, pancreas, stomach, spleen, testes, thymus, thyroid, urinary bladder and uterus) and 9 bones (femur, tibia + fibula, humerus, radius + ulna, pelvis, cervical spine, thoracic and lumber spine, skull and clavicle) were segmented for organ volume rendering by anatomists using commercial software. Organ and bone masses were calculated by multiplying the Asian reference densities of the corresponding organs and bones by the measured volumes. The resulting organ and bone masses were compared with those of the International Commission of Radiological Protection (ICRP) and the Asian reference data. Significantly large standard deviation was shown in the moving organs of the respiratory and circulatory systems and in the alimentary and urogenital organs that are variable in volume in a single person. Gall bladder and pancreas showed unique Korean organ masses compared with those of ICRP and the Asian reference adults. Different from anatomical data based on autopsy, the in vivo volume and mass in this study can more exactly describe the organ volume of a living human subject for radiation protection. A larger sample size would be required for obtaining statistically more reliable results. It is also needed to establish the reference organ mass of younger age groups for which it is difficult to recruit volunteers and to immobilise the subjects for long-time MR scanning. At present, the data from this study will contribute to the establishment of a Korean reference database.

Adult↗

BioBuilder as a database development and functional annotation platform for proteins.

BACKGROUND: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. RESULTS: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. CONCLUSIONS: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.

Computational Biology↗

Automatic analysis of heart rate variation: I. Method and reference values in healthy controls.

Many patients referred to an electrophysiological laboratory may have autonomic dysfunction. Some parasympathetic tests are based on the assessment of heart rate variation induced by breathing, Valsalva maneuver, and standing. We have developed fast and practical computer-based methods to analyze heart rate variation using standard EMG equipment and a personal computer. For quantitative description we have evaluated different algorithms, both earlier described and new ones. Findings in patients with diabetes have been compared with those obtained from healthy subjects in order to determine the diagnostic utility of the various algorithms. The optimal algorithm has been chosen by this and other criteria, and a reference database from healthy subjects has been developed.

Adolescent↗

Suitability of the T-score for establishing bone mineral density categories.

The use of different reference ranges may give rise to different T-score values for the same bone mineral density (BMD) value. This study was designed to quantify the differences in the classification of a particular population on the basis of normal ranges obtained from other reference databases. The T-scores obtained in a sample of 148 women by applying the Spanish normal range were compared with the normal range obtained in NHANES III for femoral neck. Significant differences were found when T-scores were compared, but there were no differences in categorizations using the WHO criteria. The application of these reference ranges to a female population aged older than 45 years with known BMD showed significant differences in classification. In conclusion, the T-score can vary according to the normal range used as reference, but it has little influence on the categorization of individual patients. However, it may be important when applied to a general population.

Adult↗

RESOURCERER: a database for annotating and linking microarray resources within and across species.

Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding human disease states, one of the significant challenges is cross-referencing the data derived from different species, across diverse expression analysis platforms, in order to properly derive inferences regarding gene expression and disease state. To address this problem, we have developed RESOURCERER, a microarray-resource annotation and cross-reference database built using the analysis of expressed sequence tags (ESTs) and gene sequences provided by the TIGR Gene Index (TGI) and TIGR Orthologous Gene Alignment (TOGA) databases [now called Eukaryotic Gene Orthologs (EGO)].

Animals↗

A comparison study of the reference curves of bone mineral density at different skeletal sites in native Chinese, Japanese, and American Caucasian women.

To understand the differences among reference curves for bone mineral density (BMD) for Chinese, Japanese, and American Caucasian women, we measured the BMD at the anteroposterior (AP) lumbar spine (L1-L4), lateral lumbar spine (L2-L4), hip (including the femoral neck, trochanter, intertrochanter, Ward's triangle, and total hip), and ultradistal forearm by the dual-energy X-ray absorptiometry (DXA) in a total of 2728 healthy Chinese women, aged 5-96 years. Documented BMD data for Japanese women and device manufacturer's BMD new reference databases (including the NHANES III dataset) for American Caucasian women were also used in this study. The cubic regression model was found to fit best in analyzing the age-associated variations of BMD at various sites in Chinese women, i.e., the equations had the largest coefficient of determination (R2). At the AP/Lat spine, trochanter, intertrochanter, and Ward's triangle, BMD reference curves for Chinese women were lower than those for Japanese or Caucasian women, while at the femoral neck, total hip, and ultradistal forearm, the reference curves for Chinese women were higher than those for Japanese women, with overlaps and crossing of the curves for some age spans in comparing the Chinese and Caucasian women. There were significant differences in the peak BMD (PBMD) at various sites among the Chinese, Japanese, and Caucasian women (P = 0.000). The PBMDs for Chinese women at the lumbar spine and various sites of the hip were 5.7% +/- 2.1% (mean +/- SD, range, 2.7-7.9%) lower than those for Japanese women and 5.1% +/- 2.7% (range, 0.5-7.2%) lower than those for Caucasian women; however, the PBMDs for Chinese women were 26.2% higher than those for Japanese women and 10% higher than those for Caucasian women at the ultradistal forearm. After the PBMD, average T-scores of Chinese women for losses at the AP lumbar spine with increasing age were nearly identical to those for Japanese women, but both were greater than those for Caucasian women. The average T-scores for BMD loss at various sites in Chinese women were higher than those for both Japanese and Caucasian women except at the femoral neck, where the T-scores of Chinese women were exceeded by those of both Japanese and Caucasian women. Estimated from the T-score curve of BMD loss, the age of osteoporosis occurrence at the femoral neck in Chinese women was about 10 years later than that in Japanese or Caucasian women; at the AP spine, Chinese women were similar to Japanese women; at the other sites, the age for occurrence of osteoporosis in Chinese women was about 5-15 years earlier than that in either Japanese or Caucasian women. There are differences in prevalence or odds ratio (OR) of osteoporosis at the same skeletal region for Chinese, Japanese, and Caucasian women aged > or = 50 years or at different skeletal regions in women of the same race. The prevalences of osteoporosis at various regions of the hip in Chinese women are 10.1-19.8% and ORs are 22.0-32.3, of which prevalence at the femoral neck is the lowest (10.1%); the prevalences of osteoporosis in Japanese women are 11.6-16.8% and ORs are 21.1-26.3, of which prevalence at the femoral neck is the lowest (11.6%); and the prevalences of osteoporosis in Caucasian women are 13.0-20.0% and ORs are 19.4-48.9, of which prevalence at the femoral neck is the highest (20%). In conclusion, racial differences in BMD reference curves, prevalences, and risks of osteoporosis at various skeletal sites exist among native Chinese, Japanese, and American Caucasian women.

Absorptiometry, Photon↗

Comparative analysis of coiled-coil prediction methods.

In this study we compare commonly used coiled-coil prediction methods against a database derived from proteins of known structure. We find that the two older programs COILS and PairCoil/MultiCoil are significantly outperformed by two recent developments: Marcoil, a program built on hidden Markov models, and PCOILS, a new COILS version that uses profiles as inputs; and to a lesser extent by a PairCoil update, PairCoil2. Overall Marcoil provides a slightly better performance over the reference database than PCOILS and is considerably faster, but it is sensitive to highly charged false positives, whereas the weighting option of PCOILS allows the identification of such sequences.

Amino Acid Sequence↗

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗