Nucleic acid structure and sequence probing using fluorescent base analogue tC^o

The fluorescent cytosine analog tC(o) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(o), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tCo is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(o) represents a new method of characterization. Furthermore, we find that tCo may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched

Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment

Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase–DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA–protein interaction than do tethered fluorophores. Here we report the incorporation of the 5′-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tCO), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication

Technical Language Supervision for Intelligent Fault Diagnosis in Process Industry

In the process industry, condition monitoring systems with automated fault diagnosis methods assist human experts and thereby improve maintenance efficiency, process sustainability, and workplace safety. Improving the automated fault diagnosis methods using data and machine learning-based models is a central aspect of intelligent fault diagnosis (IFD). A major challenge in IFD is to develop realistic datasets with accurate labels needed to train and validate models, and to transfer models trained with labeled lab data to heterogeneous process industry environments. However, fault descriptions and work-orders written by domain experts are increasingly digitised in modern condition monitoring systems, for example in the context of rotating equipment monitoring. Thus, domain-specific knowledge about fault characteristics and severities exists as technical language annotations in industrial datasets. Furthermore, recent advances in natural language processing enable weakly supervised model optimisation using natural language annotations, most notably in the form of natural language supervision (NLS). This creates a timely opportunity to develop technical language supervision (TLS) solutions for IFD systems grounded in industrial data, for example as a complement to pre-training with lab data to address problems like overfitting and inaccurate out-of-sample generalisation. We surveyed the literature and identify a considerable improvement in the maturity of NLS over the last two years, facilitating applications beyond natural language; a rapid development of weak supervision methods; and transfer learning as a current trend in IFD which can benefit from these developments. Finally we describe a general framework for TLS and implement a TLS case study based on Sentence-BERT and contrastive learning based zero-shot inference on annotated industry data

Mediation by Thyroid Hormone in the Relationships Between Gestational Exposure to Methylmercury and Birth Size

Our previous studies have linked gestational methylmercury exposure, originating from seafood, to changes in maternal thyroid hormones and infant birth size in a Swedish birth cohort. Herein we aimed to determine associations between maternal thyroid hormones and infant birth size and elucidate if maternal hormones could mediate the relationship between methylmercury and lower birth size. In 515 women, without known thyroid disease, we assessed metal exposure by erythrocyte mercury concentrations (mainly methylmercury, reflecting exposure over the past months) in early third trimester measured with inductively coupled plasma-mass spectrometry. Plasma concentrations of total and free thyroxine (tT4 and fT4) and triiodothyronine (tT3 and fT3), and thyroid-stimulating hormone (TSH) were measured at an accredited clinical laboratory. In multivariable-adjusted linear regression models, maternal tT3 (per 1\ua0nmol/L increase) was positively associated with birth weight (B: 125\ua0g; 95% CI 36, 214) and length (B: 0.59\ua0cm; 95% CI 0.21, 0.97). Maternal fT4 was inversely associated with birth weight (B: −\ua033\ua0g; 95% CI −\ua057, −\ua09.5), driven by obese women (n = 76). Causal mediation analyses suggested that a doubling of erythrocyte mercury (> 1\ua0\ub5g/kg; n = 374) was associated with a mean tT3-mediated decrease in birth weight of 11\ua0g (95% CI −\ua025, −\ua01.6) and in birth length of 0.1\ua0cm (95% CI −\ua00.12, −\ua00.01), both equivalent to about 12% of the total effect. To conclude, tT3 was positively associated with infant birth size. Reduced tT3 levels appeared to mediate a minor part of the inverse association between methylmercury exposure and birth size

The ERA2 facility: towards application of a fiber-based astronomical spectrograph for imaging spectroscopy in life sciences

Astronomical instrumentation is most of the time faced with challenging requirements in terms of sensitivity, stability, complexity, etc., and therefore leads to high performance developments that at first sight appear to be suitable only for the specific design application at the telescope. However, their usefulness in other disciplines and for other applications is not excluded. The ERA2 facility is a lab demonstrator, based on a high-performance astronomical spectrograph, which is intended to explore the innovation potential of fiber-coupled multi-channel spectroscopy for spatially resolved spectroscopy in life science, material sciences, and other areas of research.Comment: 10 pages, 9 figures, SPIE Conference "Astronomical Telescopes and Instrumentation" 2012, Amsterda

A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels.

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low

Scale dependency in the hydromorphological control of a stream ecosystem functioning

Physical habitat degradation is prevalent in river ecosystems. Although still little is known about the ecological consequences of altered hydromorphology, understanding the factors at play can contribute to sustainable environmental management. In this study we aimed to identify the hydromorphological features controlling a key ecosystem function and the spatial scales where such linkages operate. As hydromorphological and chemical pressures often occur in parallel, we examined the relative importance of hydromorphological and chemical factors as determinants of leaf breakdown. Leaf breakdown assays were investigated at 82 sites of rivers throughout the French territory. Leaf breakdown data were then crossed with data on water quality and with a multi-scale hydro- morphological assessment (i.e. upstream catchment, river segment, reach and habitat) when quantitative data were available. Microbial and total leaf breakdown rates exhibited differential responses to both hydromorphological and chemical alterations. Relationships between the chemical quality of the water and leaf breakdown were weak, while hydromorphological integrity explained independently up to 84.2% of leaf breakdown. Hydrological and morphological parameters were the main predictors of microbial leaf breakdown, whereas hydrological parameters had a major effect on total leaf breakdown, particularly at large scales, while morphological parameters were important at smaller scales. Microbial leaf breakdown were best predicted by hydromorphological features defined at the upstream catchment level whereas total leaf breakdown were best predicted by reach and habitat level geomorphic variables. This study demonstrates the use of leaf breakdown in a biomonitoring context and the importance of hydromorphological integrity for the functioning of running water. It provides new insights for envi- ronmental decision-makers to identify the management and restoration actions that have to be un- dertaken including the hydromorphogical features that should be kept in minimal maintenance to support leaf breakdown

Quality Measures for the Diagnosis and Non-Operative Management of Carpal Tunnel Syndrome in Occupational Settings

Introduction: Providing higher quality medical care to workers with occupationally associated carpal tunnel syndrome (CTS) may reduce disability, facilitate return to work, and lower the associated costs. Although many workers’ compensation systems have adopted treatment guidelines to reduce the overuse of unnecessary care, limited attention has been paid to ensuring that the care workers do receive is high quality. Further, guidelines are not designed to enable objective assessments of quality of care. This study sought to develop quality measures for the diagnostic evaluation and non-operative management of CTS, including managing occupational activities and functional limitations. Methods: Using a variation of the well-established RAND/UCLA Appropriateness Method, we developed draft quality measures using guidelines and literature reviews. Next, in a two-round modified-Delphi process, a multidisciplinary panel of 11 U.S. experts in CTS rated the measures on validity and feasibility. Results: Of 40 draft measures, experts rated 31 (78%) valid and feasible. Nine measures pertained to diagnostic evaluation, such as assessing symptoms, signs, and risk factors. Eleven pertain to non-operative treatments, such as the use of splints, steroid injections, and medications. Eleven others address assessing the association between symptoms and work, managing occupational activities, and accommodating functional limitations. Conclusions: These measures will complement existing treatment guidelines by enabling providers, payers, policymakers, and researchers to assess quality of care for CTS in an objective, structured manner. Given the characteristics of previous measures developed with these methods, greater adherence to these measures will probably lead to improved patient outcomes at a population level

Genetic Structure Among 50 Species of the Northeastern Pacific Rocky Intertidal Community

Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI) mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1–0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine dispersal break the coast into separate demographic zones that may require their own management plans