Miracle-dz/UniFAR-FTUs huggingface dataset:
Transgene-mediated RNA silencing of TYLCV genes affecting the accumulation of viral DNA in plants

Post-transcriptional gene silencing (PTGS) is a nucleotide sequence specific RNA turnover mechanism produced by plant cell as a natural mechanism against virus infection. Double strands of short (21-25 nt) interference RNA (siRNA) mediate this natural defense mechanism. The PTGS mechanism is becoming powerful tools for reducing expression of a certain viral gene and controlling infection. In the purpose of controlling the tomato yellow leaf curl virus (TYLCV), three regions from the viral genome located in the overlap regions between C1/C2, C2/C3 and V1/V2 were used for studying their efficiency in working as siRNA to target viral DNA accumulation in plant cells. Constructs were prepared by cloning each of the three regions both in the sense or sense/antisense directions in the binary vector pFGC5941 and introduced into tomato and tobacco plant tissues via Agro-infiltration technique. Additional construct containing the three regions together in the sense/antisense directions was also used as a control to prove that either one of the selected regions may activate the siRNA mechanism. All plants were challenged with virus using the TYLCV-Eg infectious clone 10 days post infiltration. The obtained results revealed that only sense/antisense constructs inhibit or reduce accumulation of viral genome due to the induction of siRNA mechanism. However, infiltered plants with the construct containing the as C1/C2 region proved to be the best region for initiating PTGS as it inhibited the accumulation of the viral genome completely as well as it prevented the appearance of viral symptoms in all tested plants. This may be due to its role in silencing the expression of two very important viral genes which express the replication associated protein (Rep) and transactivator protein for the viral sense promoter. However, the other two regions showed a high, but not a complete, level of interference for genome accumulation and viral infection symptoms. The obtained results may also be explained based on the length of the cloned fragments, as it was only 1١٦ bp for C1/C2 region compared to the other regions (280 bp for C2/C3 and 260 bp for V1/V2) and / or the type of the genes they interfere. It can be concluded that this mechanism can result in higher viral resistance in tomato against TYLCV
Geochemistry and catagenetic transformation of kerogen from the bazhenov horizon

A representative suite of 276 samples was used to study the isotopic and element geochemistry of kerogens from the Bazhenov horizon (Bazhenov Formation and its time equivalents) of the West Siberian sedimentary basin and to construct maps reflecting changes in the elemental composition of kerogen. The elemental composition of kerogen was used to determine the types of organic matter (H and C contents), the initial components of the living matter, the sources of kerogen (H and N contents), diagenetic history of organic matter (S content), the level of catagenetic transformation (C and O contents). Kerogen from the central, western and southern regions of the West Siberian basin toward the boundary of the Bazhenov horizon pinch-out shows strong enrichment in hydrogen (up to 8–9%) and 12С (δ13С‰ from -35 to -29), suggesting its derivation from the polymer lipids of aquatic origin. Kerogen from the Bazhenov horizon (catagenetic grade MC1) in the northeast of the basin contains much lower hydrogen concentrations (2–4%). A map of organic matter types in the Bazhenov horizon was constructed.
Two forms of DNA‐dependent RNA polymerase α subunit in streptomycetes

We demonstrated two different DNA-dependent RNA polymerase (RNAP) α subunits in spores of Streptomyces granaticolor with apparent molecular masses of 40 and 43 kDa. The 43-kDa subunit was also found in vegetative cells. These two proteins are highly similar to each other as well as to other bacterial RNAP α subunits. The 40-kDa subunit is shortened from its C-terminus, in the portion of the protein, required for binding of DNA and transcription regulators. The gene for RNAP α from S. granaticolor was cloned and sequenced and the corresponding protein was overproduced in Escherichia coli. In vitro experiments using purified RNAP α showed that the cell free extract from spores of S. granaticolor exhibits proteolytic activity responsible for the α subunit shortening, whereas that from vegetative cells does not. This modification of α subunit might point to a novel mechanism of transcriptional control in streptomycetes.
Negative effects of UVB-irradiated phytoplankton on life history traits and fitness of Daphnia magna

1. We tested the effect of ultraviolet-B (UVB)-irradiated phytoplankton on life history characteristics of Daphnia magna . Two phytoplankton species were used, Chlamydomonas reinhardtii and Cryptomonas pyrenoidifera . The phytoplankton species were cultured under photosynthetically active radiation (PAR) conditions, and under PAR supplemented with ultraviolet-A and ultraviolet-B radiation, and fed to Daphnia . 2. Life history traits of Daphnia were negatively affected when fed on UVB-irradiated Cryptomonas . Size at maturity was depressed and fewer juveniles with lower fitness were produced in the UVB treatments. In the Chlamydomonas experiment, no significant effects were found. 3. The cause of the observed UVB effects is likely to be constraints in food quality. Ultraviolet-B radiation thus has the potential of inhibiting energy transfer from the first to the second trophic level.
The influence of family-correlated survival on Nb/N for progeny from integrated multi- and single-generation hatchery stocks of coho salmon (Oncorhynchus kisutch)

There exist surprisingly few data on the final variance and mean of family sizes for hatchery-born fish at the adult stage. Thus, it is difficult to predict, for a conservation hatchery operation that minimizes the variance in progeny number, how much lower the true effective population size (Ne) of a cohort of hatchery-born adults will be than Ne predicted simply by the number of parents that produced them. We used parentage analysis to estimate the survival and Ne for two integrated stocks of hatchery coho salmon (Oncorhynchus kisutch). One hatchery is a multigeneration stock obtained by spawning 70% hatchery with 30% naturally reproducing fish, whereas the second is a single-generation stock derived from naturally reproducing coho. There was no significant difference in average overall survival between stocks, but observed Ne was significantly less than expected for each stock. Family-correlated survival contributed to roughly a 20% reduction in Ne over the freshwater and marine life stages. This reduction is similar to previous esti- mates and suggests a value that can be used when estimating the effective number of hatchery parents in applications of the Ryman-Laikre formula (at least for programs such as ours that attempt to equalize sex ratios and family sizes). Resume : Il existe etonnamment peu de donnees sur la variance et la moyenne finales des tailles des familles au stade adulte chez les poissons nes en pisciculture. Il est ainsi difficile, dans une pisciculture de conservation qui minimise la va- riance des nombres dans la progeniture, de predire de combien inferieure sera la veritable taille effective de la population (Ne) d'une cohorte d'adultes nes en pisciculture par rapport au Ne predit simplement par le nombre des parents qui les ont produits. Nous utilisons une analyse de parente pour estimer la survie et le Ne chez deux stocks integres de saumons coho (Oncorhynchus kisutch) de pisciculture. Une des piscicultures utilise un stock de plusieurs generations obtenu en croisant 70 % de poissons de pisciculture avec 30 % de poissons a reproduction naturelle, alors que l'autre est forme d'un seul stock de saumons coho a reproduction naturelle. Il n'y a pas de difference de survie globale entre les stocks, mais le Ne observe est significativement inferieur a la valeur attendue pour chacun des stocks. La survie en fonction de la famille contribue grosso modo 20 % de la reduction de Ne au cours des stades du cycle en eau douce et en mer. Cette reduction est semblable a celle des estimations anterieures, ce qui fournit une valeur qui peut etre utilisee pour calculer le nombre effectif de parents de pisciculture lors de l'application de la formule de Ryman-Laikre (au moins dans les programmes comme le notre qui cherchent a egaliser les rapports mâles-femelles et les tailles des familles). (Traduit par la Redaction) Moyer et al. 1265
A new method to measure plant water uptake and transpiration simultaneously

A new weighing lysimeter system is described measuring transpiration and water uptake simultaneously on one plant, growing in water culture. The measurements may be made for short time intervals (min) making it possible to monitor quick responses to changing environmental conditions. Fresh weight change, a combination of growth and water status alterations in the plant, may be calculated from transpiration and water uptake. The system consists of two communicating vessels filled with nutrient solution; each placed on an electronic balance. One of these vessels carries the plant and is connected to the other by a flexible tube. Water uptake will cause an equal decrease of the solution level in each vessel
Effect of Surfactants on Activity and Stability of Native and Chemically Modified Lipases A and B from Candida Rugosa

The effect of sodium dodecyl sulfate (SDS) and Triton X-100 on the hydrolytic activity of lipases A and B from Candida rugosa has been studied. Lipase B is significantly more affected than lipase A by the presence of both surfactants; Triton X-100 produces a more deleterious effect than SDS with both isoenzymes. In addition, the stability of lipases A and B in the presence of different concentrations of SDS was investigated; lipase A was more stable than isoform B. Both isoenzymes were chemically modified by reaction of their amino groups with octanoyl chloride or activated polyethylene glycol (PEG, mol. wt. 5000). In all cases the modification produced a protective effect against denaturation by SDS. In particular, PEG5000-liPases A and B were significantly more stable (stabilization factor: 3-4) than the native enzymes at the surfactant concentrations tested.
Spatial Heterogeneity and Characteristic Scales of Species–Habitat Relationships

Abstract Determining the characteristic spatial scales at which species respond most strongly to the amount of available habitat is crucial for developing cross-species scaling rules and for predicting species' responses to landscape modification. A Biologist's Toolbox article by Holland and colleagues (“Determining the Spatial Scale of Species' Response to Habitat,” BioScience 54: 227–233) presents a multiscale approach and computer program (Focus) for detecting characteristic scales using a resampling procedure, species–habitat regression models, and nonoverlapping sampling sites. Holland and colleagues refer to these nonoverlapping areas as “spatially independent sites,” when in fact spatial independence includes additional concerns not addressed by the Focus approach. Here I discuss issues of spatial heterogeneity—spatial autocorrelation and spatial dependence—as they relate to measuring the spatial scaling of organism–environment relationships with regression models. I present an empirical example with cactus bugs (Chelinidea vittiger), demonstrating how spatial heterogeneity complicates the task of determining characteristic scales of species–habitat relationships. Finally, I provide some cautions and suggestions for researchers who are considering using Focus to examine scaling patterns with existing data sets.
COVID-19 preventive behaviors among people with anxiety and depression: Findings from Japan

Little is known about COVID-19 preventive behaviors among individuals with mental health problems. This study used cross-sectional online survey data from 2000 Japanese adults collected in April and May, 2020, to examine the association between anxiety and depression and COVID-19 preventive behaviors. Results from logistic regression analyses showed that both anxiety and depression were associated with lower odds for engaging in preventive behaviors such as wearing a face mask and hand washing. Our results highlight the importance of facilitating the performance of preventive behaviors in individuals with mental health problems to prevent the spread of COVID-19 in this population.
Association of Assisted Reproductive Technologies with offspring cord blood DNA methylation across cohorts.

Study question: Is DNA methylation at birth associated with having been conceived by assisted reproductive technologies (ART)? Summary answer: This study shows does not provide strong evidence of an association of conception by ART with variation in infant blood cell DNA methylation. What is known already: Assisted reproductive technologies (ART) are procedures used to help infertile/subfertile couples conceive. Due to its importance in gene regulation during early development programming, DNA methylation and its perturbations associated with ART could reveal new insights into the biological effects of ART and potential adverse offspring outcomes. Study design: We investigated the association of DNA methylation and ART using a case-control study design (N=205 ART cases and N=2439 non-ART controls in discovery cohorts; N=149 ART cases and N=58 non-ART controls in replication cohort). Participants/materials, settings, method: We assessed the association between ART and DNA methylation at birth in cord blood (205 ART conceptions and 2439 naturally conceived controls) at >450000 CpG sites across the genome in two sub-samples of the UK Avon Longitudinal Study of Parents and Children (ALSPAC) and two sub-samples of the Norwegian Mother, Father and Child Cohort Study (MoBa) by meta-analysis. We explored replication of findings in the Australian Clinical review of the Health of adults conceived following Assisted Reproductive Technologies (CHART) study (N=149 ART conceptions and N=58 controls). Main results and the role of chance: The ALSPAC and MoBa meta-analysis revealed evidence of association between conception by ART and DNA methylation (false-discovery-rate-corrected p-value < 0.05) at 5 CpG sites which are annotated to 2 genes. Methylation at 3 of these sites has been previously linked to cancer, aging, HIV infection and neurological diseases. None of these associations replicated in the CHART cohort. There was evidence of a functional role of ART-induced hypermethylation at CpG sites located within regulatory regions as shown by putative transcription factor binding and chromatin remodelling. Limitations, reasons for cautions: While insufficient power is likely, heterogeneity in types of ART and between populations may also contribute. Larger studies might identify replicable variation in DNA methylation at birth due to ART. Wider implications of the findings: ART-conceived newborns present with divergent DNA methylation in cord blood white cells. If these associations are true and causal, they might have long-term consequences for offspring health.
Clinical practice guidelines and recommendations in the context of the COVID-19 pandemic: systematic review and critical appraisal

Background: The number of published clinical practice guidelines and recommendations related to SARS-CoV-2 infections causing COVID-19 has rapidly increased. However, insufficient consideration of appropriate methodologies in the guideline development could lead to misleading information, uncertainty among professionals, and potentially harmful actions for patients. Purpose: Rapid systematic review of clinical practice guidelines and recommendations in the context of COVID-19 to explore if basic methodological standards of guideline development have been met. Data sources: MEDLINE [PubMed], CINAHL [Ebsco], Trip and manual search; from Feb 1st 2020 until April 27th 2020. Study selection: All types of healthcare workers providing any kind of healthcare to any patient population in any setting. Data extraction: At least two reviewers independently extracted guideline characteristics, conducted critical appraisal according to The Appraisal of Guidelines for Research and Evaluation Instrument (AGREE II) and classified the guidelines using the Association of the Scientific Medical Societies (AWMF) Guidance Manual and Rules for Guideline Development. We plan six-month updates (living review). Data synthesis: There were 1342 titles screened and 188 guidelines included. The highest average AGREE II domain score was 89% for scope and purpose, the lowest for rigor of development (25%). Only eight guidelines (4%) were based on a systematic literature search and a structured consensus process by representative experts (classified as the highest methodological quality, S3 according to AWMF). Patients were only included in the development of one guideline. A process for regular updates was described in 27 guidelines (14%). Limitations: Methodological focus only. Conclusions: Despite clear scope, most publications fell short of basic methodological standards of guideline development. Future research should monitor the evolving methodological quality of the guidelines and their updates over time. Registration/Publication: The protocol was published at www.researchgate. net, DOI: 10.13140/RG.2. 2.21293. 51689. Preliminary results are publicly available on medRxiv. Funding Source: This study was partly funded by the COVID-19 Rapid Response Funding Scheme of the Wiener Wissenschafts-, Forschungs- und Technologiefonds (WWTF)/Vienna Science and Technology Fund (project number COV20-028). The funding institution had no influence on the results of this work.
Motherhood and Female Self- Employment: Theory and Evidence

Having young children can push women into self-employment to reconcile the demands of motherhood with their professional ambitions. However, if self-employment offers very few opportunities for decent pay and access to wage employment depends on education, then, motherhood may no longer matter to women’s self-employment. In this paper, we formalize this idea theoretically and test it empirically using data from Nigeria. We use an identification strategy that corrects selection bias and the endogeneity of fertility jointly. We find no evidence of a causal effect of motherhood on women’s self-employment. This result is robust to several alternative specifications. However, we also find that motherhood increases the probability of self-employment for single women but not for married women. These findings suggest that the social setting governs the importance of motherhood for women’s self-employment. JEL Classification: H52, I26, J21, J24, J46.
Gz Can Mediate the Acute Actions of μ- and κ-Opioids but Is Not Involved in Opioid-Induced Adenylyl Cyclase Supersensitization

The three subtypes of opioid receptors (δ, μ, and κ) are known to regulate multiple effectors through either pertussis toxin-sensitive or -insensitive G proteins. In opioid-induced inhibition of adenylyl cyclase, both G i and G z proteins can serve as the signal transducer. Our previous study showed that opioid-induced adenylyl cyclase supersensitization in human embryonic kidney (HEK) 293 cells expressing the δ-opioid receptor requires G i but not G z proteins. Herein, we studied the ability of μ- and κ-opioid receptors to regulate the activities of adenylyl cyclase through G z . In HEK 293 cells coexpressing G z with the μ- or κ-opioid receptors, opioid agonists induced inhibition of adenylyl cyclase in a pertussis toxin-insensitive manner. However, adenylyl cyclase supersensitization induced by chronic opioid treatments remained sensitive to pertussis toxin. We also showed that the responsiveness of cAMP-dependent response element-binding proteins to forskolin was not altered after prolonged opioid treatment but was higher in cells coexpressing G z . Although the μ- and κ-opioid receptors mediated acute activation of extracellular signal-regulated protein kinase 1/2 via both G i and G z , these responses were abolished by chronic opioid treatment. These studies showed that G z could mediate acute actions of μ- and κ-opioids but G z alone was insufficient to mediate adenylyl cyclase supersensitization induced by the chronic activation of opioid receptors.
Long term diet differences between morphs in trophically polymorphic Percichthys trucha (Pisces : Percichthyidae) populations from the southern Andes

Divergent natural selection is often believed to be the driving force behind phenotypic differentiation in characters related to resource acquisition, leading to trophic polymorphism in fishes. Here we use variation in the fatty acid composition of adipose and muscle tissues to look at differences in resource use by two recently described sympatric morphs of Percichthys trucha, a common freshwater fish of the Andean and Patagonian regions of South America. Because dietary fatty acids are often stored in carnivorous animals with litde modification after consumption, they can be used to infer information about dietary habits of individuals. We found that the two morphs differed in the overall composition of fatty acids in both adipose and muscle tissue, but that there were some differences in how die morphs differed in lakes from the northern vs southern part of the range. Furthermore, we found that certain fatty acids were correlated with diet as determined by gut content analysis. Consumption of anisopteran larvae was highly correlated widi 14:0 in adipose and muscle tissue; and higher levels of longer chain unsaturated fatty acids (i.e. 20 and 22 carbons) were correlated with die presence offish and also amphipods in die diets. Taken togetiier, die results suggest that diere are marked differences in die foraging ecology of die two morphs of P. trucha inhabiting southern Andean lakes.
Questionnaire based Prediction of Hypertension using Machine Learning

Machine Learning has proven its ability in healthcare as an assisting technology for health care providers either by saving precious time or timely alerts or vitals monitoring. However, their application in real world is limited by availability of data. In this paper, we show that simple machine learning algorithms especially neural networks, if designed carefully, are extremely effective even with limited amount of data. Specifically with exhaustive experiments on standard Modified National Institute of Standards and Technology database (MNIST) dataset we analyse the impact of various parameters for effective performance. Further, on a custom dataset collected at a tertiary care hospital for hypertension analysis, we apply these design considerations to achieve better performance as compared to competitive baselines. On a real world dataset of only a few hundred patients, we show the effectiveness of these design choices and report an accuracy of 75% in determining whether a patient suffers from hypertension.
Investigating Human Evolution Using Digital Imaging & Craniometry

area of biology (Alles & Stevenson, 2003). The significance of evolution as a component of biology curricula, at all levels, can not be overstated; the need to make the most of opportunities to effectively educate students in evolution as a central and unifying realm of biology is paramount. Developing engaging laboratory or classroom activities that investigate human evolution (e.g., DeSilva, 2004) can therefore be of significant value to students and educators.