Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Methods for the Discovery of Small Molecule Biological Probes

Advances in combinatorial chemistry have facilitated the production of large chemical libraries that can be used as tools to discover biological probes and therapeutics. High-throughput screening (HTS) strategies have emerged as the standard method to assess the biological activity of small molecules. These screens involve the individual analysis of each small molecule in multiwell plates, often requiring expensive automated methods and development of robust assays that may not translate to physiologically relevant contexts. In order to more efficiently analyze small molecules, a pooled approach would be useful. This dissertation describes the studies towards developing a pooled screening strategy for small molecules in cellular contexts. Through an initial screen, we set to phenotypically profile small molecule biological activity in a pooled fashion, while simultaneously gain insight about an individual, active molecule’s mechanism of action. I first describe the design of the pooled screen and define the goals necessary for successful application. Next, I outline the steps taken and challenges encountered during the invention of each component of the technology. Finally, I discuss a computational, target-based approach to design small molecules appropriate for future applications of the new screening technology. Thesis Defense in Chemistry Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, NY 10027, USA | 212-854-2202 | www.columbia. edu/cu/chemistry
Primary Care Providers' Attitudes Towards Recommending Cancer Screening to Patients With Intellectual Disability: A Cross-Sectional Survey

Individuals with intellectual disability (ID) obtain breast, cervical, and colorectal cancer screening at lower rates, relative to the general population. This cross-sectional survey study explored how primary care providers and trainees recommend cancer screening to patients with ID, using a standardized attitudes questionnaire and vignettes of fictional patients. In total, 106 primary care providers and trainees participated. Analyses revealed that participants' attitudes towards community inclusion predicted whether participants anticipated recommending breast and colorectal cancer screening to fictional patients. Further research is needed to explore these factors in decisions to recommend screening, and how these factors contribute to cancer screening disparities.
Design and analytical validation of a duplex PCR for Ehrlichia and Rickettsia detection in ticks

Background: Ehrlichia and Rickettsia are two major rickettsial genera transmitted by ticks that affect a number of wild and domestic animal species and human populations around the world. Objective: To design and validate a duplex PCR for Ehrlichia and Rickettsia in ticks. Methods:Assay validation included testing for sensitivity,specificity, reproducibility, and robustness of the PCR. The groELand 23sr RNAgenes were used for Ehrlichia and Rickettsia, respectively. Results: The limit of detection was one hundred gene copies per 50 μLof reaction for Ehrlichia spp, and one gene copy of Rickettsia per 50 μL of reaction. In general, the primers of the test only amplified in silico those bacterial agents for which they were originally designed, with the exception of the primers for Rickettsia that also amplified Methylocystis sp. The test was reproducible (intermediate precision) 96.7% of the times for both agents. The test was robust enough to tolerate concentration changes of all reagents with the exception of Taq DNA polymerase. Conclusions: The validation results indicated that this PCR is useful for detection in both bacterial genera and it is a good candidate for diagnostic validation.
Supplemental LED Increases Tomato Yield in Mediterranean Semi-Closed Greenhouse

Supplemental light (SL) is a technique used to increase horticulture yield, especially in northern countries, where the Daily Light Integral (DLI) is a limiting factor during fall and winter, and which could also be used to obtain higher tomato yield at the Mediterranean latitude. In this study, three tomato hybrid (F1) cultivars were grown for year-round production in a commercial semi-closed glasshouse in Southern Italy: two of the cherry fruit-type (‘Juanita’ and ‘Sorentyno’) and one mini plum fruit-type (‘Solarino’). From 120 to 243 days after transplant, light-emitting diode (LED) toplights were used as SL, with a photoperiod of 18 h. The main climatic parameters inside and outside the glasshouse were recorded, and tomato plants’ development and yield were examined. Plants grown with LEDs had longer stems as compared to control treatment (9.53 vs. 8.79 m), a higher stem thickness and yielded more trusses. On average, the yield was 21.7% higher with LEDs. ‘Sorentyno’ was the cultivar with the highest cumulated productivity when it was grown under SL. However, the cultivar with best light use efficiency under LEDs was ‘Solarino’. Therefore, supplemental LED from mid-December until March enhanced tomato growth and yield, opening a favorable scenario for large-scale application of this technology also in the Mediterranean area.
Renoprotective and anti-oxidant effects of coleus forskohlii against gentamicin induced nephrotoxicity in albino wistar rats

The aim of present study was to evaluate the protective effects of Coleus forskohlii against Gentamicin (GM)-induced nephrotoxicity in male albino wistar rats. Thirty rats were divided into five groups (n=6). Control rats received normal saline. Nephrotoxicity was induced in rats by gentamicin (80mg/Kg, IP) and treated with Silymarin (100mg/Kg, p.o,), aqueous and ethanolic extracts of (500mg/Kg, p.o) C. Forskohlii respectively for 15days. Markers of renal function (urea, uric acid and Creatinine), antioxidant markers were evaluated along with histopathological investigation in all experimental groups. GM-treated rats showed significant increase in serum levels of renal markers, TBARS and decrease in GSH, SOD, CAT. Histopathological examinations of GMtreated rats revealed degenerative changes in glomeruli and renal tubules. Administration of aqueous and ethanolic root extracts of Coleus forskohlii, protected the kidney tissues against toxic effects of gentamicin as evidenced by amelioration of histopathological changes and normalization of kidney biochemical parameters. The results of present study confirm the nephroprotective and anti-oxidant activity of C. forskohlii.
The influence of drought on flow‐ecology relationships in Ozark Highland streams

Funding information Arkansas Game and Fish Commission, Grant/Award Number: T-30-12; State Wildlife Grants Abstract 1. Drought and summer drying can have strong effects on abiotic and biotic components of stream ecosystems. Environmental flow-ecology relationships may be affected by drought and drying, adding further uncertainty to the already complex interaction of flow with other environmental variables, including geomorphology and water quality. 2. Environment–ecology relationships in stream communities in Ozark Highland streams, USA, were examined over two years with contrasting environmental conditions, a drought year (2012) and a flood year (2013). We analysed fish, crayfish and benthic macroinvertebrate assemblages using two different approaches: (1) a multiple regression analysis incorporating predictor variables related to habitat, water quality, geomorphology and hydrology and (2) a canonical ordination procedure using only hydrologic variables in which forward selection was used to select predictors that were most related to our response variables. 3. Reach-scale habitat quality and geomorphology were found to be the most important influences on community structure, but hydrology was also important, particularly during the flood year. We also found substantial between-year variation in environment–ecology relationships. Some ecological responses differed significantly between drought and flood years, while others remained consistent. We found that magnitude was the most important flow component overall, but that there was a shift in relative importance from low flow metrics during the drought year to average flow metrics during the flood year, and the specific metrics of importance varied markedly between assemblages and years. 4. Findings suggest that understanding temporal variation in flow-ecology relationships may be crucial for resource planning. While some relationships show temporal variation, others are consistent between years. Additionally, different kinds of hydrologic variables can differ greatly in terms of which assemblages they affect and how they affect them. Managers can address this complexity by focusing on relationships that are temporally stable and flow metrics that are consistently important across groups, such as flood frequency and flow variability.
Allele Mining for Crop Improvement

Identification and access to allelic variation that affects the plant phenotype is of the utmost importance for the efficient and purposeful utilization of genetic resources in plant variety development. Considering the huge numbers of accessions that are held collectively by gene-banks, genetic resource collections are deemed to harbour a wealth of undisclosed allelic variants. The challenge is how to unlock this variation. Allele mining is a research field aimed at identifying allelic variation of relevant traits within genetic resource collections. It can be defined as an approach that is used to dissect naturally occurring allelic variations or to suitable alleles of a candidate gene controlling key agronomic traits which have potential in crop improvement. It basically helps in tracing the evolution of alleles, identification of new haplotypes and development of allele-specific molecular markers for use in marker-assisted selection (MAS). True allele mining includes the analysis of non-coding and regulatory regions of the candidate gene(s), in addition to analyzing sequence variations in the coding regions of the agronomically important genes so as to cover most of the functional variations of relevance in the genes. Three major approaches such as Eco-tilling, sequencing and association mapping are available for the identification of sequence polymorphism for a given gene in the naturally occurring populations. Allele mining requires various sophisticated bio-informatic tools which are useful for sequence alignment in order to compare the new sequence to reference genome i.e, sequenced genome. Recently, the approaches and applications of allele mining along with the challenges associated have generated a lot of interest among scientists with emphasize on the need for more refined ‘mining’ strategies for accelerating the process of allele discovery and its utilization in molecular breeding.
Evaluating the Effects of Replacing Fish Meal with HP 300 on Nursery Pig Performance

A total of 350 barrows (Line 200 × 400 DNA, Columbus, NE; initially 13.6 lb) were used in a 21-d growth trial with 5 pigs per pen and 14 pens per treatment. Pigs were weaned at approximately 21-d of age, placed in nursery pens according to BW and fed a common pelleted starter diet for 3 d, at which time, pigs were weighed and then pens were blocked by BW to 1 of 5 dietary treatments in a randomized complete block design. A composite sample of fish meal and HP 300 was collected and analyzed for AA content and proximate analysis prior to formulation to determine nutrient loading values. Dietary treatments were corn-soybean-meal-based with 10% spray-dried whey and formulated to contain 1.35% standardized ileal digestible (SID) Lys and balanced on an NE basis. The 5 corn-soybean meal-based treatment diets were: 1) soybean meal control (no specialty protein products); 2) diet with 6% fish meal; 3) diet with 9.1% HP 300 replacing fish meal on a Lys basis; 4) diet with 6% HP 300 replacing fish meal on a lb/lb basis; and 5) diet with 15% HP 300 included at the expense of SBM and fish meal. All diets were fed in meal form. Overall (d 0 to 21), ADG and ADFI increased (P < 0.10 and P < 0.05, respectively) when pigs were fed the fish meal control diet compared to pigs fed HP 300 replacing fish meal on an SID Lys basis and 15% HP 300 diet, with pigs fed HP 300 replacing fish meal on lb/lb basis intermediate. In addition, ADG marginally decreased (P < 0.10) when pigs were fed the soybean meal control diet compared with pigs fed the fish meal diet. Furthermore, pigs fed the control diet had the poorest F/G among the dietary treatments. In addition, pigs fed the fish meal diet had improved (P < 0.05) final BW (d 21) compared to pigs fed the soybean meal control, HP 300 replacing fish meal on an SID Lys basis, and 15% HP 300 diet, with pigs fed diets with HP 300 replacing fish meal on a lb/lb basis intermediate. In conclusion, nursery pigs fed diets with fish meal had improved performance compared with the control diet, but 9% or greater HP 300 resulted in poorer feed intake and gain.
Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses

Post-transcriptional gene silencing in plants results from independent activities of diverse small RNA types. In anthers of grasses, hundreds of loci yield non-coding RNAs that are processed into 21- and 24-nt phased small interfering RNAs (phasiRNAs); these are triggered by miR2118 and miR2275. We characterized these “reproductive phasiRNAs” from rice panicles and anthers across seven developmental stages. Our computational analysis identified characteristics of the 21-nt reproductive phasiRNAs that impact their biogenesis, stability, and potential functions. We demonstrate that 21-nt reproductive phasiRNAs can function in cis to target their own precursors. We observed evidence of this cis regulatory activity in both rice (Oryza sativa) and maize (Zea mays). We validated this activity with evidence of cleavage and a resulting shift in the pattern of phasiRNA production. We characterize biases in phasiRNA biogenesis, demonstrating that the Pol II-derived “top” strand phasiRNAs are consistently higher abundance than the bottom strand. The first phasiRNA from each precursor overlaps the miR2118 target site, and this impacts phasiRNA accumulation or stability, evident in the weak accumulation of this phasiRNA position. Additional influences on this first phasiRNA duplex include the sequence composition and length, and we show that these factors impact Argonaute loading.
The Australian Labour Market and the Early Impact of COVID‐19: An Assessment

Abstract From March to June 2020 was the most dramatic four months in the history of the Australian labour market Never before has a such a substantial decrease in labour demand (and partial reversal) occurred so quickly In this article, we present an overview of the early impact of COVID-19: the main drivers it brought into play and the consequent labour market developments Aggregate effects and how impacts differed by type of job and worker are described We conclude with a brief review of the main government response to COVID-19, the JobKeeper program
Organic acids promote phosphorus release from Mollisols with different organic matter contents

Organic acids could improve the phosphorus (P) availability through enhancing the release of inorganic phosphorus (P<sub>i</sub>) in the soil. However, the effects of organic acids on the P<sub>i</sub> release are still poorly understood, especially from soils with different organic matter contents. Here, a biochemically produced humic acid and P fertiliser were added to the soil to modify the content of the soil organic matter (SOM) and soil P, respectively. And then the soil samples were incubated at 25 °C for 30 days. The release of P<sub>i</sub> fractions (such as H<sub>2</sub>O-P<sub>i</sub>, NaHCO<sub>3</sub>-P<sub>i</sub>, NaOH-P<sub>i</sub>, HCl-P<sub>i</sub>, and Residual-P) from the soils with different organic matter contents in the presence of citric, oxalic, and malic acids was evaluated using a sequential chemical fractionation method. The results showed that the release of the NaHCO<sub>3</sub>-P<sub>i</sub>, NaOH-P<sub>i</sub>, and HCl-P<sub>i</sub> fractions also showed a decreasing trend with an increasing content of soil organic matter, and more NaOH-P<sub>i</sub> than the other P<sub>i</sub> fractions was generally released in the presence of organic acids. Considering the types of organic acids, oxalic acid and malic acid most effectively and least effectively released P<sub>i</sub>, respectively. The path analysis indicated that the NaOH-P<sub>i</sub> release had the highest direct and indirect effects on the total inorganic P (TP<sub>i</sub>) release. NaOH-P<sub>i</sub> was, therefore, the most effective source of P<sub>i</sub> in the Mollisols.
Emerging Roles and New Paradigms in Signaling Mechanisms of Plant Cryptochromes

ABSTRACT Analogous to the opsin-based receptors in animals, plants contain a diverse and elaborate set of photoreceptors to perceive a much wider spectrum of light and adapt to varying light conditions. Cryptochromes (CRYs), the blue/UV-A light sensing receptors, represent one such class of photoreceptors found ubiquitously in plants. Although structurally similar to DNA photolyases which could repair UV-induced DNA damage, photoactivated CRYs, instead, initiate signal transduction pathways, which lead to gene expression changes and eventually more overt photomorphogenic responses. Apart from the well-established roles of CRYs in regulating seedling de-etiolation, flowering time, and circadian clock, recent reports have highlighted their roles in controlling other aspects of plant development as well. This review attempts to describe the novel/atypical roles of CRYs that have emerged in the past few years, and also present an account of the various signaling components involved in CRY signal transduction pathway.
Transient Heterologous Gene Expression Methods for Poison Ivy Leaf and Cotyledon Tissues

Poison ivy [ Toxicodendron radicans (L.) Kuntz] is a widely recognized native plant species because of its production of urushiol, which is responsible for delayed contact dermatitis symptoms in humans. Poison ivy is predicted to become both more prevalent and more noxious in response to projected patterns of climate change. Future studies on poison ivy chemical ecology will require reverse genetics to investigate urushiol metabolism. A prerequisite for reverse genetic procedures is the introduction and expression of recombinant DNA into poison ivy tissues. Poison ivy leaves and cotyledons were marginally susceptible to vacuum- and syringe-agroinﬁltration and expression of two ﬁreﬂy luciferase ( LUC )–based reporter genes. The efﬁcacy of agroinﬁltration and transient LUC expression was dependent on leaf age and plant growth environmental conditions, with young leaves grown in magenta boxes showing highest transient LUC expression levels. Agroinﬁltrated leaves showed an Agrobacterium-dependent accumulation of brown–colored pigments. Biolistic transformation of a LUC reporter gene did not show brown pigment accumulation and readily displayed transient LUC bioluminescence in both leaves and cotyledon tissues. These studies establish best practices for introducing and transiently expressing recombinant DNA into poison ivy leaf and cotyledon tissues, on which future reverse genetic procedures can be developed.
Contributions to some Corydiinae genera (Blattodea: Corydioidea: Corydiidae) from China

ABSTRACT New findings on Chinese Corydiinae are presented and new taxa are described and illustrated: Ctenoblatta impubis gen. and sp. nov., Minicorydia maoxiana gen. and sp. nov. and Ergaula nepalensis (Saussure) is newly recorded from China. The occurrence of two species of Polyphaga Brullé, P. plancyi Bolívar and P. obscura Chopard, in China are confirmed. A key to Chinese Corydiinae genera is provided as well as checklists for extant Polyphaga and Ergaula. http://zoobank.org/urn:lsid:zoobank.org:pub:F428E561-2A57-4DAD-8855-5879AB4599FB
WRF wind field assessment under multiple forcings using spatialized aircraft data

The performances of limited area weather models are affected by the choice of core solvers, domain resolutions, and initial and boundary conditions. To understand the extent of such differences on simulated wind fields, weather research and forecast (WRF) simulations initialized by different forcings were extensively compared with an aircraft‐derived high‐resolution data set. The two used forcings were the European Centre for Medium‐Range Weather Forecasts (ECMWF) ERA‐Interim reanalysis and the National Centers for Environmental Predictions (NCEP) Climate Forecast System Reanalysis (CFSR). The model domain covered a large portion of central western Italy (including part of the Tyrrhenian coast) encompassing the aircraft track and allowed the characterization of their performance across the simulation domain rather than a small set of point‐based observations. The WRF results show good agreement with the aircraft data across the whole flight track with both forcings (root mean square errors (RMSEs) < 2.3 m·s−1 and an average r2 = 0.7). Orography and coasts show an effect on simulated wind fields. The presence of a strong orography (which is smoothed by the model internal terrain elevation model) is associated with increased errors. Distance from the coast is also associated with a variation in RMSE (even if in a non‐straightforward manner) because of potential breeze effects. No forcing data set clearly outperforms the other, while the ECMWF has higher correlation co‐efficients when considering wind direction.
Genetic diversity within African tomato using next generation sequencing

Abstract Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. The findings of this study reveal significant morphological variation among African tomato contributed by plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.
Political turnover and corporate research and development: evidence from China

ABSTRACT This paper documents cycles in corporate research and development corresponding with the timing of political turnover. Utilising the data on local government officials and research and development activities at the firm level in China, firms’ intensity of research and development input is found to be negatively associated with a turnover in local political leaders. We investigate several potential explanations and find evidence supporting that political turnover reduces the incentives of firms to invest in research and development until the uncertainty is resolved.