Bridging the Pressure Gap in CO Oxidation.
Ontology highlight
ABSTRACT:
SUBMITTER: Blomberg S
PROVIDER: S-EPMC8397290 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Glycomics@ExPASy (https://www.expasy.org/glycomics) is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralize web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. The scarcity of data bridging these two disciplines led us to design tools as interactive as possible based on database connectivity to facilitate data exploration and support hypothesis building. Glycomics@ExPASy was designed, and is developed, with a long-term vision in close collaboration with glycoscientists to meet as closely as possible the growing needs of the community for glycoinformatics.
| S-EPMC6210229 | biostudies-literature
Project description:Purpose of reviewThe purpose of this paper is to identify strategies for a successful transition to sports in patients following rehabilitation for ACL reconstruction surgery (ACLR).Recent findingsRecent research continues to demonstrate a relatively low rate of return to previous level of play among athletes following ACLR combined with a significant risk of injury to either the ipsi or the contralateral ACL. Recent research also demonstrates a growing use of a varied battery of assessments to determine readiness to return to sport as well as a lack of consensus on the ideal rehabilitation program, the criteria for clearance for return to play (both in time from surgery and functional milestones), and the nature of a conditioning program designed specifically for transitioning the cleared athlete back to competition. Due to the lack of consensus and consistency regarding rehabilitation protocols and criteria for clearance to play after ACLR, deficits in strength, neuromuscular control, and psychological readiness may exist in "cleared" athletes. These deficits may not only negatively impact sports performance but also raise the risk of re-injury. Programs designed to successfully return an athlete to previous level of play should include not only strength and conditioning aimed at restoring fitness that was compromised as a result of the injury but also include attention to psychological readiness and address deficits in neuromuscular control. Problems that exist following ACLR cannot be solved by one professional; successful rehabilitation and return to play require a coordinated effort among the surgeon, physical therapist, athletic trainer, and fitness professional. Future research is needed to determine the optimal strategy to restore the neuromuscular control, functional strength, and psychological readiness necessary for a successful return to competition following ACLR.
| S-EPMC5577420 | biostudies-literature
Project description:PurposeTo establish the feasibility of embedding a flexible, exercise-based rehabilitation program into a cancer treatment unit to allow cancer survivors early exercise support.MethodA pre-post study was conducted using Bowen's Framework to describe key domains of feasibility: demand (referrals), acceptability (uptake, attendance, satisfaction), implementation (resources), practicality (adverse events, costs) and limited-efficacy (function, quality of life, self-efficacy). Participants were medically stable, adult cancer survivors receiving curative or palliative treatment for cancer at the health service. Participants completed an 8-week home or hospital-based exercise program. Data were analysed descriptively. Standardised mean differences (Hedge's g) and mean differences were calculated to determine effect size and clinical significance.ResultsThe exercise-based rehabilitation service received 155 referrals over 6 months. Of those eligible, 73/119 (61%) commenced. Participants opting for twice-weekly, hospital-based exercise attended 9/16 (56%) sessions. Participants reported high satisfaction and there were no major adverse events. The program utilised existing resources, with the predominant cost being staff. The average health service cost per participant was AUD $1,104. Participants made clinically significant gains in function (6-min walk distance; + 73 m, 95% confidence interval 49 to 96) and quality of life (EORTC QLQ-C30 Global quality of life; + 8 units, 95% confidence interval 3 to 13).ConclusionImplementation of exercise-based rehabilitation in a co-located cancer unit was safe and feasible. Access, patient and staff education and establishing funding streams are important implementation considerations. Implications for cancer survivors Access to exercise in a cancer unit provides opportunity for early intervention to optimise function during treatment.
| S-EPMC8105143 | biostudies-literature
Project description:Natural language processing (NLP) techniques are increasingly being used in biology to automate the capture of new biological discoveries in text, which are being reported at a rapid rate. Yet, information represented in NLP data structures is classically very different from information organized with ontologies as found in model organisms or genetic databases. To facilitate the computational reuse and integration of information buried in unstructured text with that of genetic databases, we propose and evaluate a translational schema that represents a comprehensive set of phenotypic and genetic entities, as well as their closely related biomedical entities and relations as expressed in natural language. In addition, the schema connects different scales of biological information, and provides mappings from the textual information to existing ontologies, which are essential in biology for integration, organization, dissemination and knowledge management of heterogeneous phenotypic information. A common comprehensive representation for otherwise heterogeneous phenotypic and genetic datasets, such as the one proposed, is critical for advancing systems biology because it enables acquisition and reuse of unprecedented volumes of diverse types of knowledge and information from text.A novel representational schema, PGschema, was developed that enables translation of phenotypic, genetic and their closely related information found in textual narratives to a well-defined data structure comprising phenotypic and genetic concepts from established ontologies along with modifiers and relationships. Evaluation for coverage of a selected set of entities showed that 90% of the information could be represented (95% confidence interval: 86-93%; n = 268). Moreover, PGschema can be expressed automatically in an XML format using natural language techniques to process the text. To our knowledge, we are providing the first evaluation of a translational schema for NLP that contains declarative knowledge about genes and their associated biomedical data (e.g. phenotypes).http://zellig.cpmc.columbia.edu/PGschema
| S-EPMC2879055 | biostudies-literature
Project description:PURPOSE OF REVIEW:Leber hereditary optic neuropathy (LHON) is the most common primary mitochondrial DNA (mtDNA) genetic disorder in the population. We address the clinical evolution of the disease, the secondary etiological factors that could contribute to visual loss, and the challenging task of developing effective treatments. RECENT FINDINGS:LHON is characterized by a preclinical phase that reflects retinal ganglion cell (RGC) dysfunction before rapid visual deterioration ensues. Children can present atypically with slowly progressive visual loss or an insidious/subclinical onset that frequently results in considerable diagnostic delays. The LHON mtDNA mutation is not sufficient on its own to precipitate RGC loss and the current body of evidence supports a role for smoking and estrogen levels influencing disease conversion. Clinical trials are currently investigating the efficacy of adeno-associated viral vectors-based gene therapy approaches for patients carrying the m.11778G>A mutation. Mitochondrial replacement therapy is being developed as a reproductive option to prevent the maternal transmission of pathogenic mtDNA mutations. SUMMARY:LHON is phenotypically more heterogeneous than previously considered and a complex interplay of genetic, environmental and hormonal factors modulates the risk of a LHON carrier losing vision. Advances in disease modelling, drug screening and genetic engineering offer promising avenues for therapeutic breakthroughs in LHON.
| S-EPMC5562441 | biostudies-literature
Project description:The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
| S-EPMC6723020 | biostudies-literature
Project description:Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important phenotypic effects. Although reference transcriptomes are inestimable for gene expression analysis, they may turn limiting in important medical applications. We discuss computational strategies for retrieving hidden transcript diversity.
| S-EPMC6545731 | biostudies-literature
Project description:Oxygen distribution is a major determinant of treatment success in radiotherapy, with well-oxygenated tumour regions responding by up to a factor of three relative to anoxic volumes. Conversely, tumour hypoxia is associated with treatment resistance and negative prognosis. Tumour oxygenation is highly heterogeneous and difficult to measure directly. The recent advent of functional hypoxia imaging modalities such as fluorine-18 fluoromisonidazole positron emission tomography have shown promise in non-invasively determining regions of low oxygen tension. This raises the prospect of selectively increasing dose to hypoxic subvolumes, a concept known as dose painting. Yet while this is a promising approach, oxygen-mediated radioresistance is inherently a multiscale problem, and there are still a number of substantial challenges that must be overcome if hypoxia dose painting is to be successfully implemented. Current imaging modalities are limited by the physics of such systems to have resolutions in the millimetre regime, whereas oxygen distribution varies over a micron scale, and treatment delivery is typically modulated on a centimetre scale. In this review, we examine the mechanistic basis and implications of the radiobiological oxygen effect, the factors influencing microscopic heterogeneity in tumour oxygenation and the consequent challenges in the interpretation of clinical hypoxia imaging (in particular fluorine-18 fluoromisonidazole positron emission tomography). We also discuss dose-painting approaches and outline challenges that must be addressed to improve this treatment paradigm.
| S-EPMC5603947 | biostudies-literature
Project description:Early diagnosis of pregnancy- and lactation-associated osteoporosis (PLO) is mandatory for a good outcome. Standard care is not a matter of conventional guidelines, rather it requires an individualized strategy while true overall incidence and pathogeny remain open issues. This is a narrative review based on full-length English articles, published between January 2021 and March 2023 and accessed via PubMed (no traumatic fractures or secondary osteoporosis are included). Our case-sample-based analysis included 836 females with PLO (the largest cohort based on published cases so far) through 12 studies and 24 single case reports. Except for one survey, these involved retrospective cohorts of small size (6-10 females/study) to medium size (23-47 women/study), and large cohorts with >50 subjects per study (a maximum of 379). Age of diagnosis: from 24 to 40 years for case reports (most subjects being over 30 and primigravida), while original studies indicated an average age between 31 and 34.18 years. Type of fractures underlined a most frequent vertebral phenotype (a mean of 2 to 5.8 vertebral fractures per patient) versus a most severe non-vertebral phenotype (hip and femoral neck fractures mostly requiring surgery). Potential contributors varied: smoking (1/3-1/2 of subjects), family history of osteoporosis (1/3), heparin and glucocorticoid use in pregnancy, low body mass index (majority of cases), hypovitaminosis D; and (with a low level of statistical significance) anti-psychotic medication, gestational diabetes, lupus, thrombophilia, anemia, in vitro fertilization (1/3 in one study), twin pregnancy, tocolysis with MgSO4, and postpartum thyroiditis. Most remarkably, up to 50% of PLO patients harbor mutations of LRP5, WNT1, and COL1A1/A2 (more damaged form with potential benefits from osteoanabolic drugs); gene testing might become the new norm in PLO. The low index of clinical suspicion should be supported by performing magnetic resonance imaging (gold standard in pregnancy) with DXA (in lactation). Low bone mineral density is expected (Z-score varying from -2.2 SD to -4 SD, unless normal which does not exclude PLO). Bone turnover markers might be useful in individuals with normal DXA, in pregnancy when DXA cannot be performed, and in following the response to anti-osteoporosis drugs. Alternatively, microarchitecture damage might be reflected by DXA-trabecular bone score and high-resolution peripheral quantitative computed tomography. Specific medical interventions are currently focused on teriparatide (TPT) use (3 studies; n = 99 females treated with TPT and an additional subgroup of 18 patients from the gene-analysis-based study, thus a total of 117 females) which seems to be the therapy of choice as reflected by these new data: 6-24 months, 20 µg/day, no sequential therapy needed; case selection based on high fracture risk is necessary). The first case using romosozumab was reported in 2022. PAO/LAO remains a challenging condition which is a battle for the wellbeing of two individuals, on one hand, considering maternal-fetal outcomes and taking care of the offspring, but it is a battle for a multidisciplinary team, on the other hand, since a standardized approach is lacking.
| S-EPMC10177839 | biostudies-literature
Project description:We evaluate a bridging intervention for a group of young people aged 18-29, with no formal educational qualifications, who are not in employment, education or training. The bridging intervention consisted of classroom training, educational internships and mentoring. Based on Danish register data with a large number of control variables, a propensity score matching estimator was applied to assess the effectiveness of the bridging intervention. The results show that the bridging intervention was effective in increasing educational enrollment and completion for all participants. The effects of the intervention were particularly large for participants assessed to be 'not ready for education' and those diagnosed with psychiatric disorders suggesting that the bridging intervention may be especially beneficial for these subgroups.
| S-EPMC6494054 | biostudies-literature