Miracle-dz/UniFAR-FTUs huggingface dataset:
Neotropical Lycopodiaceae-An Overview

Approximately 185 species of Lycopodiaceae are known to occur in the Neotropics: ca. 150 belong in the genus Huperzia, ca. 8 in Lycopodium, and ca. 25 in Lycopodiella. The species are enumerated according to assumed relationship, with information of the most important synonyms, a summary of their distribution, comments on their morphology and variability, and reference to selected illustrations. Species delimitation is problematic throughout the family. This is due to the simple morphology and the plasticity of the characters. Morphogenesis seems unstable in many species and may be strongly affected by environmental factors (.)
SEXUAL REPRODUCTION, MATING SYSTEM, AND PROTOPLAST DYNAMICS OF SEMINAVIS (BACILLARIOPHYCEAE)1

Cell division, the mating system, and auxosporulation were studied in the marine epipelic diatom Seminavis cf. robusta Danielidis & D. G. Mann. The interphase protoplast contains two girdle‐appressed chloroplasts, each with an elongate bar‐like pyrenoid, and also a central nucleus, located in a bridge between two vacuoles. Before cell division, the chloroplasts divide transversely and translocate onto the valves. The nucleus relocates to the ventral side for mitosis. After cytokinesis and valve formation, the chloroplasts move back to the girdle, showing a constant clockwise movement relative to the epitheca of the daughter cell. Seminavis cf. robusta is dioecious, and sexual reproduction is possible once cells are less than 50 μm. In crosses of compatible clones, gametangia pair laterally, without the formation of a copulation envelope, and produce two gametes apiece. The intensity of sexualization increases as cells reduce further in size below the 50‐μm threshold. At plasmogamy, the gametangia dehisce fully and the gametes, which were morphologically and behaviorally isogamous, fuse in the space between the gametangial thecae. The auxospore forms a transverse and longitudinal perizonium. After expansion is complete, there is an unequal contraction of the protoplast within the perizonium, creating the asymmetrical shape of the vegetative cell. Apart from this last feature, almost all characteristics exhibited by the live cell and auxospores of Seminavis agree with what is found in Navicula sensu stricto, supporting the classification of both in the Naviculaceae. Haploid parthenogenesis and polyploid auxospores were found, lending support to the view that change in ploidy may be a significant mechanism in diatom evolution.
Inheritance of resistance in peanut to mixed infections of groundnut rosette virus (GRV) and groundnut rosette assistor virus and a single infection of GRV

Inheritance of resistance to the green form of groundnut rosette was studied in two ways—aphid inoculation in the field with a mixed culture of groundnut rosette virus (GRV) (plus its satellite RNA) and groundnut rosette assistor virus (GRAV) and mechanical inoculation in the greenhouse with GRV (plus its satellite RNA). Crosses were made with two resistant and six susceptible genotypes in a diallel test. In most crosses, the resistance was conditioned by two recessive genes. Furthermore, results were similar both with mixed infections and the single GRV infection, thus providing direct evidence that genetic control of resistance is to GRV and not to GRAV. In the RMP 12 × M1204.78I cross (and its reciprocal), F2 progeny segregated 1:3 susceptible/resistant. Mechanical inoculation with GRV provided an acceptable and rapid procedure to screen segregating populations for resistance to the virus
APL since 1978

The Evolution of APL, the HOPL I paper by Falkoff and Iverson on APL, recounted the fundamental design principles which shaped the implementation of the APL language in 1966, and the early uses and other influences which shaped its first decade of enhancements. In the 40 years that have elapsed since HOPL I, several dozen APL implementations have come and gone. In the first decade or two, interpreters were typically born and buried along with the hardware or operating system that they were created for. More recently, the use of C as an implementation language provided APL interpreters with greater longevity and portability. APL started its life on IBM mainframes which were time-shared by multiple users. As the demand for computing resources grew and costs dropped, APL first moved in-house to mainframes, then to mini- and micro-computers. Today, APL runs on PCs and tablets, Apples and Raspberry Pis, smartphones and watches. The operating systems, and the software application platforms that APL runs on, have evolved beyond recognition. Tools like database systems have taken over many of the tasks that were initially implemented in APL or provided by the APL system, and new capabilities like parallel hardware have also changed the focus of design and implementation efforts through the years. The first wave of significant language enhancements occurred shortly after HOPL I, resulting in so-called second-generation APL systems. The most important feature of the second generation is the addition of general arrays—in which any item of an array can be another array—and a number of new functions and operators aligned with, if not always motivated by, the new data structures. The majority of implementations followed IBM’s path with APL2 “floating” arrays; others aligned themselves with SHARP APL and “grounded” arrays. While the APL2 style of APL interpreters came to dominate the mainstream of the APL community, two new cousins of APL descended from the SHARP APL family tree: J (created by Iverson and Hui) and k (created by Arthur Whitney). We attempt to follow a reasonable number of threads through the last 40 years, to identify the most important factors that have shaped the evolution of APL. We will discuss the details of what we believe are the most significant language features that made it through the occasionally unnatural selection imposed by the loss of habitats that disappeared with hardware, software platforms, and business models. The history of APL now spans six decades. It is still the case, as Falkoff and Iverson remarked at the end of the HOPL I paper, that: Although this is not the place to discuss the future, it should be remarked that the evolution of APL is far from finished.
Lipi Gnani

A Kannada OCR, called Lipi Gnani, has been designed and developed from scratch, with the motivation of it being able to convert printed text or poetry in Kannada script, without any restriction on vocabulary. The training and test sets have been collected from more than 35 books published from 1970 to 2002, and this includes books written in Halegannada and pages containing Sanskrit slokas written in Kannada script. The coverage of the OCR is nearly complete in the sense that it recognizes all punctuation marks, special symbols, and Indo-Arabic and Kannada numerals. Several minor and major original contributions have been done in developing this OCR at different processing stages, such as binarization, character segmentation, recognition, and Unicode mapping. This has created a Kannada OCR that performs as good as, and in some cases better than, Google’s Tesseract OCR, as shown by the results. To the best of our knowledge, this is the maiden report of a complete Kannada OCR, handling all issues involved. Currently, there is no dictionary-based postprocessing, and the obtained results are due solely to the recognition process. Four benchmark test databases containing scanned pages from books in Kannada, Sanskrit, Konkani, and Tulu languages, but all of them printed in Kannada script, have been created. The word-level recognition accuracy of Lipi Gnani is 5.3% higher on the Kannada dataset than that of Google’s Tesseract OCR, 8.5% higher on the Sanskrit dataset, and 23.4% higher on the datasets of Konkani and Tulu.
OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.

Background Establishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary. Data sources Primary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform. Population 17,425,445 adults. Time period 1st Feb 2020 to 25th April 2020. Primary outcome Death in hospital among people with confirmed COVID-19. Methods Cohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings. Results There were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.43-1.82). Conclusions We have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients' records; we will update and extend these results regularly. Keywords COVID-19, risk factors, ethnicity, deprivation, death, informatics.
Using Administrative Data to Predict Suicide After Psychiatric Hospitalization in the Veterans Health Administration System

There is a very high suicide rate in the year after psychiatric hospital discharge. Intensive postdischarge case management programs can address this problem but are not cost-effective for all patients. This issue can be addressed by developing a risk model to predict which inpatients might need such a program. We developed such a model for the 391,018 short-term psychiatric hospital admissions of US veterans in Veterans Health Administration (VHA) hospitals 2010–2013. Records were linked with the National Death Index to determine suicide within 12 months of hospital discharge (n=771). The Super Learner ensemble machine learning method was used to predict these suicides for time horizon between 1 week and 12 months after discharge in a 70% training sample. Accuracy was validated in the remaining 30% holdout sample. Predictors included VHA administrative variables and small area geocode data linked to patient home addresses. The models had AUC=. 79–. 82 for time horizons between 1 week and 6 months and AUC=. 74 for 12 months. An analysis of operating characteristics showed that 22.4%–32.2% of patients who died by suicide would have been reached if intensive case management was provided to the 5% of patients with highest predicted suicide risk. Positive predictive value (PPV) at this higher threshold ranged from 1.2% over 12 months to 3.8% per case manager year over 1 week. Focusing on the low end of the risk spectrum, the 40% of patients classified as having lowest risk account for 0%–9.7% of suicides across time horizons. Variable importance analysis shows that 51.1% of model performance is due to psychopathological risk factors accounted, 26.2% to social determinants of health, 14.8% to prior history of suicidal behaviors, and 6.6% to physical disorders. The paper closes with a discussion of next steps in refining the model and prospects for developing a parallel precision treatment model.
Generation and Regeneration of Thymic Epithelial Cells

The thymus is unique in its ability to support the maturation of phenotypically and functionally distinct T cell sub-lineages. Through its combined production of MHC-restricted conventional CD4+ and CD8+, and Foxp3+ regulatory T cells, as well as non-conventional CD1d-restricted iNKT cells and invariant γδT cells, the thymus represents an important orchestrator of immune system development and control. It is now clear that thymus function is largely determined by the availability of stromal microenvironments. These specialized areas emerge during thymus organogenesis and are maintained throughout life. They are formed from both epithelial and mesenchymal components, and collectively they support a stepwise program of thymocyte development. Of these stromal cells, cortical, and medullary thymic epithelial cells represent functional components of thymic microenvironments in both the cortex and medulla. Importantly, a key feature of thymus function is that levels of T cell production are not constant throughout life. Here, multiple physiological factors including aging, stress and pregnancy can have either short- or long-term detrimental impact on rates of thymus function. Here, we summarize our current understanding of the development and function of thymic epithelial cells, and relate this to strategies to protect and/or restore thymic epithelial cell function for therapeutic benefit.
Targeted delivery of doxorubicin into cancer cells using a folic acid–dendrimer conjugate

We report here a general approach to using multifunctional poly(amidoamine) (PAMAM) dendrimer-based platform to encapsulate an anticancer drug doxorubicin (DOX) for targeted cancer therapy. In this approach, generation 5 (G5) PAMAM dendrimers modified with fluorescein isothiocyanate (FI) and folic acid (FA) via covalent conjugation, and with remaining terminal amines being acetylated (G5.NHAc-FI-FA) were used to complex DOX for targeted delivery of the drug to cancer cells overexpressing high-affinity folic acid receptors (FAR). We show that the formed G5.NHAc-FI-FA/DOX complexes with each dendrimer encapsulating approximately one DOX molecule are water soluble and stable. In vitro release studies show that DOX complexed with the multifunctional dendrimers can be released in a sustained manner. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell viability assay in conjunction with cell morphology observation demonstrates that the G5.NHAc-FI-FA/DOX complexes can specifically target and display specific therapeutic efficacy to cancer cells overexpressing high-affinity FAR. Findings from this study suggest that multifunctional dendrimers may be used as a general drug carrier to encapsulate various cancer drugs for targeting therapy of different types of cancer.
Growth and Essential Carotenoid Micronutrients in Lemna gibba as a Function of Growth Light Intensity

Duckweed is a promising food crop with multiple benefits for space applications. Fresh duckweed could deliver synergistically acting essential antioxidant nutrients to a crew – but only if growth conditions provide the plant with the right cues to trigger antioxidant formation. We grew Lemna gibba under continuous growth light ranging from low to very high intensities (photosynthetic photon flux densities = PPFDs) in order to investigate the effect on plant growth, photosynthesis, and level of carotenoid antioxidants that are essential human micronutrients. Lemna gibba achieved remarkably high growth rates under modest growth PPFD by virtue of superior light absorption resulting from minimal self-shading and high chlorophyll levels. Conversely, L. gibba’s growth rate remained high even under very high growth PPFDs. This notable ability of L. gibba to avoid inactivation of photosynthesis and diminished growth under very high growth PPFDs resulted from a combination of downregulation of chlorophyll synthesis and increased biochemical photoprotection that limited a build-up of excessive excitation energy. This biochemical photoprotection included accumulation of zeaxanthin (an essential human micronutrient) and high levels of zeaxanthin-catalyzed thermal energy dissipation of excess excitation. Compared to the light levels needed to saturate L. gibba photosynthesis and growth, higher light levels were thus required for strong induction of the essential antioxidant zeaxanthin. These results indicate a need for design of light protocols that achieve simultaneous optimization of plant yield, nutritional quality, and light-use efficiency to circumvent the fact that the light requirement to saturate plant growth is lower than that for production of high zeaxanthin levels. How this trade-off between light-use efficiency of growth and nutritional quality might be minimized or circumvented to co-optimize all desired features is discussed.
Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%–98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise FST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
Dealing with Uncertainty in pWCET Estimations

The problem of estimating a tight and safe Worst-Case Execution Time (WCET), needed for certification in safety-critical environment, is a challenging problem for modern embedded systems. A possible solution proposed in past years is to exploit statistical tools to obtain a probability distribution of the WCET. These probabilistic real-time analyses for WCET are, however, subject to errors, even when all the applicability hypotheses are satisfied and verified. This is caused by the uncertainties of the probabilistic-WCET distribution estimator. This article aims at improving the measurement-based probabilistic timing analysis approach providing some techniques to analyze and deal with such uncertainties. The so-called region of acceptance model based on state-of-the-art statistical test procedures is defined over the distribution space parameters. From this model, a set of strategies is derived and discussed to provide the methodology to deal with the trade-off safety/tightness of the WCET estimation. These techniques are then tested over real datasets, including industrial safety-critical applications, to show the increased value of using the proposed approach in probabilistic WCET analyses.
Effects of predator-induced spines on individual fitness in Daphnia pulex

We studied both the cues for spine induction and costs of spinc production in Daphnia pulex (Cladocera). A significant number of D. pulex cultured individually in water treated with Chaoborus crystallinus larvae that were fed carried spines to the end of the fourth instar. Water treated with Chaoborus that were starved induced only minor morphological changes in D. pulex. Treatments with crushed D. pulex did not affect neck spine induction. Spine production carries a cost evident in the timing Iof first reproduction of D. pulex. Over half (58%) of D. pulex grown in culture conditions with a high density of Chaoborus postponed first reproduction from the fifth to the sixth instar. A decrease in growth of the spined morphs was attributable to an increase in duration of instars. Fitness effects persisted through the third reproductive instar. The intrinsic rate of increase was lowest in D. p&x populations cultured in Chaoborus-treated water. Treatments with crushed D. pulex did not affect growth but did significantly increase clutch size of D. pulex.