A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users

Allometric models for liana aboveground biomass in old-growth and secondary tropical forests of Tanzania

\ua9 2024 The AuthorsLianas are common in tropical forests, where they influence forest dynamics, thus impacting the global carbon sink, with implications for climate change mitigation. Despite their increasing competitiveness with trees at the global scale, robust measurements of liana aboveground biomass (AGB) have been limited. Here we use data from destructive sampling to develop two separate allometric equations for estimating liana AGB from stem diameter in old-growth (n = 15 lianas) and secondary forests (n = 22 lianas). We compared estimates of AGB using our equations for 3141 lianas (≥ 1 cm diameter) in Tanzania\u27s Kilombero Valley against estimates from previously published equations in other tropical regions. Our equations demonstrated stronger correlations between diameter and destructively measured AGB, than those from previously published equations (R2 = 0.86–0.89, versus R2 = 0.82–0.88). Across all stems, the average stem-level liana AGB estimated using the equation for old-growth forests was 52 % higher than that estimated by the equation for secondary forests, showing that lianas have lower biomass per unit diameter in forests impacted by disturbance. In such forests, liana stems are damaged, deformed, or cannot reach maximum height due to reduced structural support. At the scale of the forest stand, our equations estimated a mean liana AGB of 3.25 Mg ha−1 (95 % Confidence Interval: 1.52–6.96) in old-growth forests and 10.19 Mg ha−1 (5.91–17.64) in secondary forests. These estimates roughly aligned with estimates from other equations, although there was considerable variation. Depending on the equation used, mean stand-level estimates of liana AGB ranged from 2.49–9.76 Mg ha−1 in old-growth forests and 10.19–20.74 Mg ha−1 in secondary forests. Our findings show the variability in liana allometry and AGB with disturbance and successional stage, further underscoring a need for caution when comparing estimates of liana biomass across studies and regions

Proteína C-reativa não é um marcador útil de infecção em unidade de terapia intensiva cirúrgica

CONTEXT AND OBJECTIVE: C-reactive protein (CRP) is commonly used as a marker for inflammatory states and for early identification of infection. This study aimed to investigate CRP as a marker for infection in patients with postoperative septic shock. DESIGN AND SETTING: Prospective, single-center study, developed in a surgical intensive care unit at Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo. METHODS: This study evaluated 54 patients in the postoperative period, of whom 29 had septic shock (SS group) and 25 had systemic inflammatory response syndrome (SIRS group). All of the patients were monitored over a seven-day period using the Sequential Organ Failure Assessment (SOFA) score and daily CRP and lactate measurements. RESULTS: The daily CRP measurements did not differ between the groups. There was no correlation between CRP and lactate levels and the SOFA score in the groups. We observed that the plasma CRP concentrations were high in almost all of the patients. The patients presented an inflammatory state postoperatively in response to surgical aggression. This could explain the elevated CRP measurements, regardless of whether the patient was infected or not. CONCLUSIONS: This study did not show any correlation between CRP and infection among patients with SIRS and septic shock during the early postoperative period.CONTEXTO E OBJETIVO: A proteína C reativa (PCR) é muito usada como marcador de estados inflamatórios e na identificação precoce de infecção. Este estudo teve como proposta investigar a PCR como marcadora de infecção em pacientes em choque séptico no período pós-operatório. TIPO DE ESTUDO E LOCAL: Estudo prospectivo, monocêntrico, desenvolvido numa unidade de terapia intensiva pós-operatória do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. MÉTODOS: Foram avaliados 54 pacientes no pós-operatório, sendo 29 deles com choque séptico (grupo SS) e 25 com síndrome da resposta inflamatória sistêmica (grupo SI). Todos os pacientes foram acompanhados durante sete dias pelo escore SOFA (Sequential Organ Failure Assessment) e com dosagens diárias de PCR e lactato. RESULTADOS: As dosagens de PCR não diferiram entre os grupos. Não foi observada correlação entre dosagem de PCR e lactato ou escore SOFA nos grupos estudados. Observamos que as concentrações plasmáticas de PCR estavam elevadas em quase todos os pacientes avaliados. Os pacientes no pós-operatório apresentam estado inflamatório em resposta à agressão cirúrgica, sendo este fato capaz de explicar as dosagens de PCR elevadas, independentemente de o paciente estar ou não infectado. CONCLUSÕES: Este estudo não evidenciou correlação entre PCR e infecção nos pacientes com síndrome da resposta inflamatória sistêmica e choque séptico no período pós-operatório precoce

Leadership and decision-making practices in public versus private universities in Pakistan

The goal of this study is to examine differences in leadership and decision-making practices in public and private universities in Pakistan, with a focus on transformational leadership (TL) and participative decision-making (PDM). We conducted semi-structured interviews with 46 deans and heads of department from two public and two private universities in Pakistan. Our findings indicate that leadership and decision-making practices are different in public and private universities. While differences were observed in all six types of TL-behaviour, the following three approaches emerged to be crucial in both public and private universities: (1) articulating a vision, (2) fostering the acceptance of group goals, and (3) high-performance expectations. In terms of PDM, deans and heads of department in public and private universities adopt a collaborative approach. However, on a practical level this approach is limited to teacher- and student-related matters. Overall, our findings suggest that the leadership and decision-making practices in Pakistani public and private universities are transformational and participative in nature

Observation of contemporaneous optical radiation from a gamma-ray burst

The origin of gamma-ray bursts (GRBs) has been enigmatic since their discovery. The situation improved dramatically in 1997, when the rapid availability of precise coordinates for the bursts allowed the detection of faint optical and radio afterglows - optical spectra thus obtained have demonstrated conclusively that the bursts occur at cosmological distances. But, despite efforts by several groups, optical detection has not hitherto been achieved during the brief duration of a burst. Here we report the detection of bright optical emission from GRB990123 while the burst was still in progress. Our observations begin 22 seconds after the onset of the burst and show an increase in brightness by a factor of 14 during the first 25 seconds; the brightness then declines by a factor of 100, at which point (700 seconds after the burst onset) it falls below our detection threshold. The redshift of this burst, approximately 1.6, implies a peak optical luminosity of 5 times 10^{49} erg per second. Optical emission from gamma-ray bursts has been generally thought to take place at the shock fronts generated by interaction of the primary energy source with the surrounding medium, where the gamma-rays might also be produced. The lack of a significant change in the gamma-ray light curve when the optical emission develops suggests that the gamma-rays are not produced at the shock front, but closer to the site of the original explosion.Comment: 10 pages, 2 figures. Accepted for publication in Nature. For additional information see http://www.umich.edu/~rotse

Haptoglobin Phenotype, Preeclampsia Risk and the Efficacy of Vitamin C and E Supplementation to Prevent Preeclampsia in a Racially Diverse Population

Haptoglobin's (Hp) antioxidant and pro-angiogenic properties differ between the 1-1, 2-1, and 2-2 phenotypes. Hp phenotype affects cardiovascular disease risk and treatment response to antioxidant vitamins in some non-pregnant populations. We previously demonstrated that preeclampsia risk was doubled in white Hp 2-1 women, compared to Hp 1-1 women. Our objectives were to determine whether we could reproduce this finding in a larger cohort, and to determine whether Hp phenotype influences lack of efficacy of antioxidant vitamins in preventing preeclampsia and serious complications of pregnancy-associated hypertension (PAH). This is a secondary analysis of a randomized controlled trial in which 10,154 low-risk women received daily vitamin C and E, or placebo, from 9-16 weeks gestation until delivery. Hp phenotype was determined in the study prediction cohort (n = 2,393) and a case-control cohort (703 cases, 1,406 controls). The primary outcome was severe PAH, or mild or severe PAH with elevated liver enzymes, elevated serum creatinine, thrombocytopenia, eclampsia, fetal growth restriction, medically indicated preterm birth or perinatal death. Preeclampsia was a secondary outcome. Odds ratios were estimated by logistic regression. Sampling weights were used to reduce bias from an overrepresentation of women with preeclampsia or the primary outcome. There was no relationship between Hp phenotype and the primary outcome or preeclampsia in Hispanic, white/other or black women. Vitamin supplementation did not reduce the risk of the primary outcome or preeclampsia in women of any phenotype. Supplementation increased preeclampsia risk (odds ratio 3.30; 95% confidence interval 1.61-6.82, p<0.01) in Hispanic Hp 2-2 women. Hp phenotype does not influence preeclampsia risk, or identify a subset of women who may benefit from vitamin C and E supplementation to prevent preeclampsia

FAK acts as a suppressor of RTK-MAP kinase signalling in Drosophila melanogaster epithelia and human cancer cells

Receptor Tyrosine Kinases (RTKs) and Focal Adhesion Kinase (FAK) regulate multiple signalling pathways, including mitogen-activated protein (MAP) kinase pathway. FAK interacts with several RTKs but little is known about how FAK regulates their downstream signalling. Here we investigated how FAK regulates signalling resulting from the overexpression of the RTKs RET and EGFR. FAK suppressed RTKs signalling in Drosophila melanogaster epithelia by impairing MAPK pathway. This regulation was also observed in MDA-MB-231 human breast cancer cells, suggesting it is a conserved phenomenon in humans. Mechanistically, FAK reduced receptor recycling into the plasma membrane, which resulted in lower MAPK activation. Conversely, increasing the membrane pool of the receptor increased MAPK pathway signalling. FAK is widely considered as a therapeutic target in cancer biology; however, it also has tumour suppressor properties in some contexts. Therefore, the FAK-mediated negative regulation of RTK/MAPK signalling described here may have potential implications in the designing of therapy strategies for RTK-driven tumours