Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis of Recruitment of DNA Polymerase ζ by Interaction between REV1 and REV7 Proteins*

Background: REV1 and DNA polymerase ζ (Polζ), a complex of catalytic REV3 and non-catalytic REV7 subunits, are involved in translesion DNA synthesis (TLS). Results: The mechanism of REV1-Polζ interaction is revealed by the crystal structure of the REV1-Polζ complex. Conclusion: Polζ is recruited by REV1-REV7 interaction. Significance: Revealing the mechanism of REV1-Polζ interaction provides a new strategy to modulate TLS for cancer therapy. REV1, REV3, and REV7 are pivotal proteins in translesion DNA synthesis, which allows DNA synthesis even in the presence of DNA damage. REV1 and REV3 are error-prone DNA polymerases and function as inserter and extender polymerases in this process, respectively. REV7 interacts with both REV1 and REV3, acting as an adaptor that functionally links the two, although the structural basis of this collaboration remains unclear. Here, we show the crystal structure of the ternary complex, composed of the C-terminal domain of human REV1, REV7, and a REV3 fragment. The REV1 C-terminal domain adopts a four-helix bundle that interacts with REV7. A linker region between helices 2 and 3, which is conserved among mammals, interacts with the β-sheet of REV7. Remarkably, the REV7-binding interface is distinct from the binding site of DNA polymerase η or κ. Thus, the REV1 C-terminal domain might facilitate polymerase switching by providing a scaffold for both inserter and extender polymerases to bind. Our structure reveals the basis of DNA polymerase ζ (a complex of REV3 and REV7) recruitment to the stalled replication fork and provides insight into the mechanism of polymerase switching.
Reproduction and Vegetative Regeneration in Blutaparon portulacoides (Amaranthaceae) on Backshores in Southern Brazil

tT? ^mZ12m^ CORDAZZO, C. V. and SEELIGER, U. , 2003. Reproduction and Vegetative Regeneration in Blutaparon uJi^JeJ» portulacoides (Amaranthaceae) on Backshores in Southern Brazil. Journal of Coastal Research, SI 3 5 "■^J^^T^j^^L* (Proceedings of the Brazilian Symposium on Sandy Beaches: Morphodynamics, Ecology, Uses, ^^5SS522r Hazards and Management), 48 1 -485. Itajai, SC Brazil, ISSN 0749-0208.
Matrix analysis to model the invasion of alligatorweed (Alternanthera philoxeroides) on Kentucky lakes

Aims Alligatorweed (Alternanthera philoxeroides (Mart.) Griseb. ) is an invasive species indigenous to South America. With its rapid invasion of southeastern US waterways, understanding the invasiveness of this plant species is critical for providing possible mechanisms of prevention for resource managers. The aim of this project is to use a matrix model to study the invasion dynamics of alligatorweed under both terrestrial and aquatic environments. The use of this model allows for a deeper understanding of the invasiveness and life history–stage structure of alligatorweed. In particular, matrix analysis can further test the hypothesis that certain life stages of alligatorweed might be more sensitive to control and management. Methods A greenhouse experiment was conducted to study the spread of alligatorweed under both aquatic and terrestrial environments. Utilizing the growth data obtained during the summer of 2010, matrix analysis was used to model the growth of alligatorweed for six different treatments. Transition matrices were generated based on plant measurements taken at different life stages defined by the number of leaves or nodes. These matrices are population projection models whose eigenvalues represent the growth rate of alligatorweed. A high growth rate is a key feature of successful invaders. Residuals were calculated and sensitivity analysis was performed to test the accuracy of the model and importance of each life stage over the entire life cycle of alligatorweed. Important findings The results of this study indicate that in the aquatic habitat, plants at their early life cycle stage are most sensitive to potential control measures. Conversely, in the terrestrial habitat, the most sensitive stage of alligatorweed is at its late life cycle stage, characterized with large-sized plants, thus suggesting the best timing for management and eradication of this invasive species.
A statistical procedure for unsupervised classification of nutrient limitation bioassay experiments with natural phytoplankton communities

We describe a novel method for statistical analysis of bioassay experiments with natural plankton communities. The procedure allows unsupervised classification of the type of nutrient limitation in factorial experiments with two limiting nutrients, based on objective selection between several generic limitation patterns with direct biological interpretation, using the Akaike Information Criterion (AIC), which balances the concerns of model fit and model robustness. As such, it avoids the interpretation of nuisance parameters related to time effects in classical factorial design analysis of experiments with repeated measurements over time. The proposed limitation patterns discriminate between exclusive and primary limitation, depending on whether the initially nonlimiting nutrient has an effect or not. They also discriminate between two types of colimitation, depending on whether both nutrients only have an effect in combination, or also separately. The latter response is interpreted as the result of different phytoplankton community components being simultaneously limited by different nutrients. The capabilities of the classification procedure is demonstrated on a comprehensive set of 163 bioassay experiments with N and P additions to natural phytoplankton communities from the coast of Finland (NE Baltic Sea).
Using Manipulative Models to Develop Tree-Thinking

It is well known that students often struggle with tree-thinking, a core aspect of evolutionary education. Scientists consider phylogenetic trees multidimensional hypotheses of evolutionary relationships. However, student view textbook diagrams as static, two-dimensional images. Physical manipulatives have been used to facilitate learning science content in areas such as genetics, but these instructional tools have not yet been tested in tree-thinking. In order to circumvent students’ tree-thinking struggles, I investigated the use of manipulative, three-dimensional tree models in an introductory biology course designed for non-science majors (n=163). Specifically my research questions included: What are the differences in tree-thinking learning gains when exposed to one of three instructional treatment groups? ; How do students interact with manipulative tree models? I compared three treatment groups across three semesters: 1) control; 2) multichromatic model; and 3) monochromatic model. I used a mixed methods approach gathering data from pre/post assessments, course observations, and student reflections to measure student tree-thinking learning gains and interactions. I found that students had the highest tree-thinking learning gains when given explicit instruction tied with a multichromatic model (F(2,160)=15.608, p < 0.001). Students reported most challenges in the Control Treatment and the Monochromatic Treatment groups because they had difficulties distinguishing which branch represented which taxa when manipulating branches. The use of multiple colors aided students understanding of the major components of trees and facilitated easy distinction among the taxa represented. This investigation supports the use of manipulative models as interdisciplinary tools that provide a tangible, effective alternative for teaching abstract concepts.
Cities

tuna, and shrimp. Raising these species is an exercise in “reducing” fish to produce fish — turning smaller fish such as anchovy, herring, capelin, and whiting into feed for larger species. “Increasingly, we are fishing down the ocean chain so we can move up the fish-farming chain. Despite improvements in feed ingredients and technologies, rapid fish-farm growth in recent decades has effectively outweighed any gains in feeding efficiency. According to most estimates, modern fish farming is now a net drain on the world’s seafood supply. ” To avert the looming feed crisis and take pressure off edible wild fish, farmers could wean themselves off fish-based feed and pursue “integrated fish farming,” which can also improve water quality (shellfish eat algae, and can filter and cut excess nutrients that run into water). Governments can help by penalizing fish farms that pollute and rewarding farms that clean up.
Pandora's Box Contained Bait : The Global Problem of Introduced Earthworms

Introduced exotic earthworms now occur in every biogeographic region in all but the driest or coldest habitat types on Earth. The global distribution of a few species (e.g., Pontoscolex corethrurus) was noted by early natural- ists, but now approximately 120 such peregrine species are recognized to be widespread from regional to global scales, mainly via human activities. Species adapted to human transport and to colonization of disturbed habi- tats are most widespread and are the principal invasive species. We identify a number of endogenous and exogenous factors that may contribute to the successful establishment and spread of peregrine species. Quantification of these factors may help to determine why certain species become invasive while others do not. Recent advances in theory and modeling of biological invasions and in molecular techniques should prove fruitful in improving our understanding of invasive earthworms, as well as in predicting their impacts on ecosystems.
Utility of digitising point of care HIV test results to accurately measure, and improve performance towards, the UNAIDS 90-90-90 targets

Introduction High rates of pre-treatment loss to care among persons diagnosed with HIV persist. Linkage to care can be improved through active digitally-based surveillance. Currently, record-keeping for HIV diagnoses in South Africa is paper-based. Aggregated testing data are reported routinely, and only discordant findings result in a specimen being tested at a laboratory and digitised. The Western Cape Province in South Africa has a Provincial Health Data Centre (PHDC) where person-level routine electronic data are consolidated in a single database, leveraging the existence of a unique patient identifier. To facilitate improved HIV surveillance, a pre-carbonated point-of-care test (PoCT) form was piloted, where one copy was routed to a central point and digitised for PHDC inclusion. Methods We evaluated the utility of the intervention using cross-sectional and retrospective cohort analyses, as well as comparisons with aggregate data. Data were linked to the Patient Master Index of the PHDC using unique identifiers. Prior evidences of HIV within the PHDC were used to differentiate newly diagnosed patients and those retesting, as well as linkage to care and treatment. Results From May 2017 to June 2018, 11337 digitised point-of-care HIV testing records were linked to the PHDC. Overall, 96% of records in the aggregate dataset were digitised, with 97% linked to the PHDC. Of those tested, 79% were female (median age 27 years). Linkage demonstrated that 51.3% (95% CI 48.4–54.1%) of patients testing HIV-positive were retesting. Of those newly diagnosed, 81% (95% CI 77.9–84.3%) were linked to HIV care and 25% (95% CI 21.6–28.7%) were initiated on antiretroviral therapy immediately. Conclusion Digitisation of PoCT results provides individuated HIV testing data to assist in linkage to care and in differentiating newly diagnosed patients from positive patients retesting. Actionable and accurate data can improve the measurement of performance towards the UNAIDS 90-90-90 targets.
Contribution of various leaf morpho-physiological parameters towards grain yield in maize.

Knowledge of interrelationship between grain yield and its contributing components improves the efficiency of breeding programs through the use of appropriate selection indices. Significant differences were found among ten maize genotypes for grain yield and some leaf morpho-physiological parameters (excise leaf water content, stomata size, stomatal frequency, leaf venation, cell membrane thermostability & leaf area). Most leaf parameters, such as excise leaf water content, stomata size, leaf venation, cell membrane thermostability and leaf area had negative direct effect on grain yield. However, positive correlation due to indirect effects for stomata size, leaf venation and leaf area indicated that indirect selection for these parameters may be possible for grain yield improvement in maize. Stomatal frequency had positive direct effect on grain yield but negative correlation with it, which suggested that direct selection of this parameter might be effective to reduce the undesirable indirect effects on grain yield. Investigations of yield differences between maize genotypes using phenotypic and genotypic correlation showed that leaf area had significant and positive genotypic and phenotypic correlation with yield. Both genotypic and phenotypic correlations also confirmed leaf area as an indirect indicator for yield improvement in maize.
Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals

Summary Background Duration of persistence of SARS-CoV-2 in the upper respiratory tract of infected individuals has important clinical and epidemiological implications. Aim We aimed to establish the duration and risk factors for persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals. Methods Data of repeat rRT-PCR (real-time reverse transcription-polymerase chain reaction) test done for SARS-CoV-2 infected individuals at our institute at Jodhpur, India were analysed from 19 March to 21 May 2020. Duration of virus persistence was estimated with parametric regression models based on weibull, log-normal, log-logistic, gamma and generalized gamma distributions. Factors associated with prolonged viral persistence were analysed with the best-fitting model. Results Fifty-one SARS-CoV-2 infected individuals with repeat rRT-PCR test were identified with 44 asymptomatics. The asymptomatic individuals had median virus persistence duration of 8.87 days (95% CI: 7.65–10.27) and 95 percentile duration of 20.70 days (95% CI: 16.08–28.20). The overall median virus persistence including both symptomatic and asymptomatic individuals was found to be 9.18 days (95% CI: 8.04–10.48). Around one-fourth asymptomatics (10/44) demonstrated SARS-CoV-2 persistence beyond 2 weeks. Age <60 years and local transmission were found to be significantly associated with longer virus persistence among asymptomatic individuals on univariate regression but not in multivariate analysis. Conclusion Recommended home isolation duration for SARS-CoV-2 infected individuals in India should be extended from 17 days to at least 3 weeks. Prolonged persistence of SARS-CoV-2 in a considerable proportion of asymptomatic individuals merits attention with regard to ensuring universal infection prevention precautions irrespective of symptomatic status.
Innovative therapies for malignant brain tumors: the road to a tailored cure

Background: Immune tolerance, immune escape, neoangiogenesis, phenotypic changes, and glioma stem cells are all responsible for the resistance of malignant brain tumors to current therapies and persistent recurrence. The present study provides a panoramic view of innovative therapies for malignant brain tumors, especially glioblastoma, aimed at achieving a tailored approach. Methods: PubMed/Medline and ClinicalTrials.gov were the main sources of an extensive literature review in which “Regenerative Medicine,” “Cell-Based Therapy,” “Chemotherapy,” “Vaccine,” “Cell Engineering,” “Immunotherapy, Active,” “Immunotherapy, Adoptive,” “Stem Cells,” “Gene Therapy,” “Target Therapy,” “Brain Cancer,” “Glioblastoma,” and “Malignant Brain Tumor” were the search terms. Only articles in English published in the last 5 years were included. A further selection was made according to the quality of the studies and level of evidence. Results: Cell-based and targeted therapies represent the newest frontiers of brain cancer treatment. Active and adoptive immunotherapies, stem cell therapies, and gene therapies represent a tremendous evolution in recent years due to many preclinical and clinical studies. Clinical trials have validated the effectiveness of antibody-based immunotherapies, including an in-depth study of bevacizumab, in combination with standard of care. Preclinical data highlights the role of vaccines, stem cells, and gene therapies to prevent recurrence. Conclusion: Monoclonal antibodies strengthen the first-line therapy for high grade gliomas. Vaccines, engineered cells, stem cells, and gene and targeted therapies are good candidates for second-line treatment of both newly diagnosed and recurrent gliomas. Further data are necessary to validate this tailored approach at the bedside. (www.actabiomedica.it)
Identification of genes influencing wood fibre properties in Eucalyptus nitens

Eucalypts are a major forest resource globally and the area of eucalypt plantations for pulp and paper production is expanding rapidly in Australia. Consequently, there is an increasing need to breed eucalypts with improved wood properties. Since many high value wood traits are under strong genetic control, identification of DNA markers linked to these traits will have application in breeding programs. In recent years there has been a shift in marker strategy away from QTL mapping in pedigrees to association studies in unrelated populations. In the latter approach, single nucleotide polymorphisms (SNPs) in candidate genes are screened to identify SNPs that significantly associate with wood traits. Significant SNPs could be used for marker-assisted selection (MAS) in breeding programs. The objectives of this study were to identify candidate genes that may influence pulp yield in eucalypts and to identify SNP variants in those genes that associate with superior wood and pulp traits. Approximately 300 trees from a full-sib Eucalyptus nitens progeny derived from a wide intra specific cross were used for gene discovery. DNA microarrays containing ~5800 young xylem of cDNAs Eucalyptus grandis were screened with probes synthesised from RNA isolated from trees with either high or low pulp yield. Forty-six transcripts were differentially regulated, of which 27 were more abundant in high pulp trees and 19 were more abundant in low pulp trees. All differentially expressed cDNAs were partially sequenced and searched against existing gene databases. Six genes were selected as putative pulp yield candidate genes based on their significant similarity to genes with known function and were named EgrCesA3 (cellulose synthase), EgrNAM1 (NAM
Sarcopenia and myosteatosis in patients undergoing curative radiotherapy for head and neck cancer: Impact on survival, treatment completion, hospital admission and cost.

BACKGROUND Computed tomography (CT) is the gold standard of body composition analysis at the tissue-organ level. The present study aimed to determine the impact of CT-defined sarcopenia and myosteatosis on outcomes, including overall survival, unplanned hospital admissions and related costs, in patients who had completed treatment of curative intent for head and neck cancer (HNC). METHODS Retrospective observational study of patients undergoing radiotherapy of curative intent ± other treatment modalities for HNC. Tissue density data derived at the third lumbar vertebra (L3) were evaluated with sarcopenia defined per sex-specific published threshold values for skeletal muscle index, stratified by body mass index and mean skeletal muscle attenuation in HU (Hounsfield units). RESULTS Pre- or post-treatment images were available for 79/98 patients (80.6%) and 61/98 patients (62.2%), respectively. Sarcopenia was present in 42/79 patients pre-treatment and 36/61 patients post-treatment, whereas myosteatosis was present in 63/79 patients pre-treatment and 48/61 patients post-treatment. In patients with pre- and post-treatment images (n = 60), the median (range) percentage weight change was -8.5% (-29.9 to +11.7). On multivariable analysis, a post-treatment sarcopenia hazard ratio of 3.87 (95% confidence interval = 1.22-12.24, P = 0.021) and a pre-treatment myosteatosis hazard ratio of 8.86 (95% confidence interval = 1.12-69.88, P = 0.038) were independent predictors of reduced overall survival. There was no difference in radiotherapy or chemotherapy treatment completion based on pre-treatment sarcopenia status. The mean (SD) difference unplanned hospital admission cost was $15 846 ($17 707) for patients without sarcopenia versus $47 945 ($82 688) for patients with sarcopenia at any time point (P = 0.077). CONCLUSIONS As CT-defined sarcopenia and myosteatosis hold clinically meaningful prognostic value, muscle status evaluation is recommended in routine clinical practice.
Nest visits and capture events affect breeding success of Yellow-billed and Pacific loons

ABSTRACT Accurate estimates of breeding success are essential for understanding population dynamics and for managing populations. Unfortunately, research activities to collect these data can negatively impact the breeding success of the study species and bias estimates of breeding success. Despite the potential for negative impacts, few studies have documented the effect of capturing incubating adults on nest survival or compared nest survival following different capture methods. In this study we evaluate the impacts of investigator disturbance associated with captures and nest visits on nest survival of Yellow-billed Loons (Gavia adamsii) and Pacific Loons (Gavia pacifica) in the National Petroleum Reserve-Alaska (NPR-A), an area of conservation concern, in 2011–2013. In an effort to reduce capture-related nest failures, we developed a new suspended dive net technique to catch territorial aquatic birds while off their nests. We then compared nest survival following suspended dive net captures to bow-net trap captures of breeding adult loons. Daily nest survival following bow-net trap or suspended dive net capture was about 30% lower than when adults were not captured. The effect of captures on nest survival was similar between bow-net trap and suspended dive net capture methods. Nest visits without captures also negatively impacted nest survival, although less than captures. If not accounted for, nest visitation biased daily survival rates of nests downward 6%. Effects of investigator disturbance did not differ by species or between years. Our results suggest that any source of disturbance that displaces incubating adult loons could potentially reduce nest survival. To maximize breeding success, human disturbance factors should be limited near loon nests.
Resource Communication. Identification of single nucleotide polymorphisms (SNPs) at candidate genes involved in abiotic stress in two Prosopis species and hybrids

Aim of the study: Identify and compare SNPs on candidate genes related to abiotic stress in Prosopis chilensis, Prosopis flexuosa and interspecific hybrids Area of the study: Chaco arido, Argentina. Material and Methods: Fragments from 6 candidate genes were sequenced in 60 genotypes. DNA polymorphisms were analyzed. Main Results: The analysis revealed that the hybrids had the highest rate of polymorphism, followed by P. flexuosa and P. chilensis, the values found are comparable to other forest tree species. Research highlights: This approach will help to study genetic diversity variation on natural populations for assessing the effects of environmental changes.