Miracle-dz/UniFAR-FTUs huggingface dataset:
Preliminary evidence from a multicenter prospective observational study of the safety and efficacy of chloroquine for the treatment of COVID-19

Background Effective therapies are urgently needed for the SARS-CoV-2 pandemic. Chloroquine has been proved to have antiviral effect against coronavirus in vitro. In this study, we aimed to assess the efficacy and safety of chloroquine with different doses in COVID-19. Method In this multicenter prospective observational study, we enrolled patients older than 18 years old with confirmed SARS-CoV-2 infection excluding critical cases from 12 hospitals in Guangdong and Hubei Provinces. Eligible patients received chloroquine phosphate 500mg, orally, once (half dose) or twice (full dose) daily. Patients treated with non-chloroquine therapy were included as historical controls. The primary endpoint is the time to undetectable viral RNA. Secondary outcomes include the proportion of patients with undetectable viral RNA by day 10 and 14, hospitalization time, duration of fever, and adverse events. Results A total of 197 patients completed chloroquine treatment, and 176 patients were included as historical controls. The median time to achieve an undetectable viral RNA was shorter in chloroquine than in non-chloroquine (absolute difference in medians -6.0 days; 95% CI -6.0 to -4.0). The duration of fever is shorter in chloroquine (geometric mean ratio 0.6; 95% CI 0.5 to 0.8). No serious adverse events were observed in the chloroquine group. Patients treated with half dose experienced lower rate of adverse events than with full dose. Conclusions Although randomised trials are needed for further evaluation, this study provides evidence for safety and efficacy of chloroquine in COVID-19 and suggests that chloroquine can be a cost-effective therapy for combating the COVID-19 pandemic.
On the relation between temporal variability and persistence time in animal populations

Summary 1 The relationship between temporal variability, spectral redness and population persistence for a large number of long-term time series was investigated. Although both intuition and theory suggest that more variability in population abundance would mean greater probability of extinction, previous empirical support for this view has not been conclusive. Possible reasons are the shortage of long-term data and the difficulties of adequately characterizing temporal variability, two issues that are explicitly addressed in this paper. 2 We examined the relationship between population variability and quasi-extinction time (measured as the time required to observe a 90% decline of population abundance) for a large set of data comprising 554 populations for 123 species that were censused for more than 30 years. Two aspects of temporal variability were considered in relation with the quasi-extinction time: a baseline value (coefficient of variation over a fixed, 30-year, time scale), and a measure of the rate of increase of the population variability over time (spectral exponent). 3 The results show that the quasi-extinction time was shorter for populations having higher temporal variability and redder dynamics. The relation between persistence time and population variability was compared for different taxa, trophic levels, habitat type (aquatic and terrestrial) and body sizes and compared with theoretical expectations.
HISTOCHEMICAL STUDY ON GUANYLATE CYCLASE ACTIVITY IN THE RETINA OF DEVELOPING RAT

The histo- and cytochemical localization of guanylate cyclase activity was examined in the newborn rat retina during the first three postnatal weeks. The reaction was first observed on the 3rd postnatal day on the apical plasmalemma of the retinal pigment epithelium. The reaction was seen on the disk and plasmalemma of the premature short outer segments from the 10th day. From the 14th day, the enzyme localization seemed to be the same as shown in the adult rat. The reaction products were restricted to the apical plasmalemma of the retinal pigment epithelium and disk and plasmalemma of the tip of the outer segments.
The Embryology and Relationships of Crypteronia (Crypteroniaceae)

Crypteronia shares its key embryological features with other genera of Crypteroniaceae and the order Myrtales. In common with Axinandra, it has such distinctive features as an ephemeral endothecium and a nucellar tissue that soon disintegrates. Crypteronia differs from Axinandra, however, in seed morphology and in having neither an endothelium nor the associated secondary multiplication of the inner integument. Although embryological evidence supports a relatively close relationship between Crypteronia and Axinandra, it seems likely that these genera are more distantly related than is indicated by their vegetative features. Nevertheless, their continued placement within a single family is consistent with our new evidence.
Disclaimer, copyright and distribution

5. The World Health Organization does not warrant that the information contained on the CD-ROM is complete and correct, and shall not be liable for any damages incurred as a result of use of the data or programmes. The designations employed and the presentation of this material do not imply the expression of any opinion whatsoever on the part of the Secretariat of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries.
SILVAngs - rDNA-based microbial community analysis using next-generation sequencing (NGS) data - User Guide

SILVAngs rDNA-based microbial community analysis using next-generation sequencing (NGS) data User Guide Contact: ngs-contact@arb-silva.de Motivation SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from highthroughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA sequence databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of result files (tables, graphs and sequence files) for download. The idea is to make you independent from time consuming installation and operating procedures which is typical for local solutions. Workflow The basic workflow of the pipeline can be divided into the following steps, pretty much reflecting the common process of analysing rDNA amplicon reads from next generation sequencing approaches: Alignment Quality management De-replication (identification of identical sequences) Clustering at a user-defined threshold (OTU definition) Classification of the OTUs/reads However, there are some specific features of SILVAngs compared to similar software pipelines, reflecting our philosophy on how to adequately analyse (and interpret) these kind of data in terms of quality and efficiency. They are discussed in the following description of the SILVAngs workflow. 1. Input data/Import The pipeline accepts input data in Multi-Fasta format with each input file representing one sample. Samples that belong to one project (a transect, timeseries etc.) should be uploaded as a single SILVAngs project. The results of a project are organized according to these samples (e.g. tax breakdown and fingerprint data are listed per sample) with the name of a sample defined by the file name of the corresponding Multi-Fasta input file.
Quilting with the Mosaic approach: smooth and striated spaces in early childhood research

Empirical data is taken from the Living Spaces study (Clark, 2010) a three year longitudinal study based in the UK, that set out to involve young children under five years old in the design and review of early childhood environments. A series of visual and participatory methods were brought together in order to support children’s reflections on their current and possible future environments. The research artefacts created including audio transcripts of child-led tours and maps composed of children’s photographs, emphasized the importance of surfaces, textures, furnishings and fittings.
An Unusual Case of Actinomucor elegans: A Challenging Diagnosis

Patient: Male, 70-year-old Final Diagnosis: Actinomucor elegans Symptoms: Bleeding • dizziness • eschar Medication: — Clinical Procedure: Culture • MALDI • sequencing • tooth extraction Specialty: Infectious Diseases Objective: Rare disease Background: Actinomucor elegans is an unusual cause of mucormycosis and can be difficult to identify by conventional methods. Mucormycosis has a very high mortality rate, especially among immunocompromised individuals. Due to the morbid and progressive nature of opportunistic fungal infections, early diagnosis is paramount for effective disease management. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI) and Sanger sequencing are useful methods for rapid diagnosis of unusual fungal pathogens. Case Report: We report a fatal case of mucormycosis caused by A. elegans in an immunocompromised man. The pathogen was isolated from a large nasal septal black eschar that developed rapidly during tooth extraction in a patient with myelodysplastic syndrome and diabetes mellitus. After unsuccessful identification by conventional methods, A. elegans was identified using MALDI and Sanger sequencing. Conclusions: Diagnosing fungal organisms poses many difficulties, but amidst the technological evolution in pathogen identification, there are useful methods for rapid identification, including MALDI and sequencing. With these powerful tools, earlier diagnosis will give health professionals an advantage against potentially fatal fungal infections.
Phylogenetic and Biogeographic Diversification in Osmorhiza (Apiaceae)

Osmorhiza Raf. (Apiaceae) consists of 10 species disjunctly distributed in temperate Asia (1 sp.) and the Americas (9 spp.). Osmorhiza berteroi and 0. depauperata show an American antitropical disjunction. Within North America, these two species are also disjunctly distributed in eastern and western North America and the Great Lakes regions. A phylogenetic analysis was conducted to clarify inter- and intraspecific relationships based on sequences of the ITS and 5.85 regions of nrDNA. With Anthriscus, Geocaryum, and Myrrhis as outgroups, the monophyly of Osmorhiza is strongly supported. The ITS phylogeny suggests the basal position of the Asiatic 0. aristata and the monophyly of the nine New World species. The ITS sequence of Osmorhiza aristata is relatively divergent from those of all other species even though it is morphologically similar to the eastern North American 0. claytonii and 0. longistylis (which form a Glade), suggesting early divergence followed by morphological stasis. Osmorhiza berteroi, 0. brachypoda, 0. depauperata, O. mexicana, O. occidentalis, and 0. purpurea constitute a monophyletic group (= western North American clade). The morphologically distinct 0. glabrata from the central Andes forms a trichotomy with the eastern North American Glade (O. claytonii and 0. longistylis) and the western North American clade in parsimony and maximum likelihood analyses. The 11 populations studied of the widespread 0. berteroi form a clade, and showed little sequence divergence, suggesting recent establishment of the widely disjunct populations following long-distance dispersal. Disjunct populations of 0. depauperata from the Rocky Mountains and eastern North America have an identical ITS profile. Osmorhiza occidentalis, however, shows a high level of infraspecific sequence divergence. The ITS phylogeny and the low sequence divergence values suggest rapid diversification of Osmorhiza in western North America.
SREBP pathway genes as candidate markers in country ham production

Country hams are dry-cured products from the Southeastern region of the USA. This high value product requires quality fresh meat to avoid later processing problems. The marker SREBF1 is a transcription factor involved in the regulation of fatty acid synthesis and anti-oxidative enzyme transcription. The SREBF1 gene and its regulators, SCAP and MBTPS1, were investigated for associations with several meat quality traits in country hams. After single nucleotide polymorphism (SNP) identification, PCR-RFLP tests were designed for one polymorphism in each of the three investigated genes. Meat quality and physical traits were collected on 299 fresh hams. Significant associations were found with ham yield (MBTPS1, P<0.05 and SREBF1×MBTPS1, P<0.05) and ham circumference (MBTPS1, P<0.05 and SREBF1×MBTPS1, P<0.01), Hunter A colour score on fresh meat (SREBF1, P<0.05), Hunter B colour score on cured meat (MBTPS1, P<0.05 and SREBF1×MBTPS1, P<0.01), moisture (SCAP×MBTPS1, P<0.05) and salt percentage (SREBF1×SCAP, P<0.05). Our findings provide initial evidence that SNPs in SREBF1, SCAP and MBTPS1 are associated with some country ham quality traits. Breeders could use these gene tests to improve their animals, which would in turn improve country ham processing and other desired production goals.
Is the effect of the femoral offset negligible? Œ JBJS eLetters

I read with interest the article by Bayram et al. [1] in the Volume 102 of the journal on critical limit of lower extremity lengthening in total hip arthroplasty. Authors reported that the critical limit of nerve lengthening was directly correlated with anthropometric measurements and found that the critical limb lengthening was up to 5% of femoral length and 2.6% of anterior superior iliac spine and the medial malleolus distance. This thoughtful clinical study presents meaningful information applicable to total hip arthroplasty and I commend the authors for their efforts in this regard.
The immune response in rohu, Labeo rohita (Actinopterygii: Cyprinidae) to Argulus siamensis (Branchiura: Argulidae) infection: kinetics of immune gene expression and innate immune response

Argulus siamensis is a major pathogen in freshwater aquaculture. The immune responses of Indian major carp, Labeo rohita to experimental infection of A. siamensis was evaluated by quantitation of immune-relevant gene expression in head kidney and skin, and serum innate immune parameters through the course of infection. In skin of infected fish, antioxidant genes like natural killer cell enhancing factor (NKEF-B) and superoxide dismutase (MnSOD) were significantly up-regulated in addition to lysozyme G and β2 microglobulin (β2M). Both tumour necrosis factor α (TNFα) and toll-like receptor 22 (TLR22) genes were significantly down-regulated in skin during early phases of the infection. Most of the genes exhibited significant down-regulation in head kidney; immunoglobulin (IgM) and β2M genes being the exceptions which were significantly up-regulated at 12 h and 3 days post infection. Most of the innate immune parameters like serum complement activity and ceruloplasmin levels showed significant reduction in infected fish. The observed results are indicative of A. siamensis modulating the immune response of rohu by down-regulation of many immune factors which may explain the susceptibility of rohu to A. siamensis infection. The interaction of this parasite with the host need to be further explored to understand its pathogenesis.
An examination of zinc uptake patterns by cultivars of sorghum and maize: differences amongst hybrids and their parents

Abstract Zinc absorption and transport patterns were examined in sorghum and maize hybrids and their parent cultivars with a view to observe, if any, and relate the differences amongst them meaningfully to traits like hybrid vigor. Short term uptake by excised roots or intact seedlings, from different concentrations of ZnCl2 or ZnEDDHA and also, time course from 50 μM ZnCl2, were measured. The results showed significant differences in the Zn absorption patterns by excised roots of sorghum cultivars. The rate of Zn transport to shoot in CSH‐8 was found to be higher than in others. The amount of Zn transported from ZnEDDHA was also more than that from ZnCl2 in all sorghum cultivars. Furthermore, significant hybrid vigor was observed in Zn transport from ZnEDDHA for the two hybrids CSH‐7 and CSH‐8. The resemblance of absorption and transport patterns of Zn in CSH‐8 to those of 36‐A strongly suggests that the trait is inherited from the female parent. No heterosis was observed in the absorption and transport .
Is Agrotourism Popular on the Internet

There is growing literature on the importance of the Internet, such as the growing importance of the agri/agrotourism role in the tourism industry, but with little inspection of the relationship in the context of word of mouth. The assumption is that online word of mouth makes the understanding of agrotourism more popular, so the aim of this paper is to examine whether the “popularity” of agrotourism has grown on the Internet during past years during which the Internet has recorded exceptional growth. According to that, this paper examines the distributions of using similar keywords with the same meaning - agritourism and agrotourism - during last four years (from June 2007 to June 2011) by use of Google alert and the word agroturizam which is the translation of these words in the Croatian language. Google alert was used as a monitoring tool. The paper analyzes the appearances of these three keywords monthly and daily on Google and additionally analyzes their use on Facebook as the most popular social group nowadays.
Interaction of long telomeric DNAs with macrocyclic hexaoxazole as a G-quadruplex ligand

The interactions of long telomeric DNAs, which mimic telomeres in living cells, with a macrocyclic hexaoxazole ligand L2H2-6OTD (2) were investigated by means of electrophoresis mobility shift assay, circular dichroism (CD) titration analysis, and DNA melting measurements. Our results indicate that G4 structure in long telomeric DNAs was mainly induced to take anti-parallel topology upon interaction with L2H2-6OTD (2). The overall higher-order G4 organizational structure of the long telomeric DNAs was suggested to be of beads-on-a-string type.
Land cover change in eastern Kansas: litter dynamics of closed-canopy eastern redcedar forests in tallgrass prairie

In the Great Plains region, eastern redcedar (Juniperus virginiana L.) abundance has increased dramatically in areas historically occupied by tallgrass prairie. This shift in dominant vegetation is likely to be accompanied by changes in ecosystem structure and function, including quantity, quality, and location (above- vs. below-ground) of litter inputs and subsequent effects on decomposition dynamics. The purpose of this study was to quantify and compare patterns of litterfall and decomposition in mature redcedar forests and adjacent prairie. Annual redcedar litterfall was 500 g·m-2·year-1, a large increase in foliar litter inputs compared with annually burned grassland (52 g·m-2·year-1). Using a reciprocal transplant decomposition study with four substrates, redcedar leaves and roots, and big bluestem (Andropogon gerardii Vitman) foliage and roots, we found marginal habitat effects, but greater differences between species, presumably owing to litter quality (including both C:N and lignin content). Decay.
Long-term cropping system studies support intensive and responsive cropping systems in the low-rainfall Australian Mallee

Abstract. Continuous-cropping systems based on no-till and crop residue retention have been widely adopted across the low-rainfall cereal belt in southern Australia in the last decade to manage climate risk and wind erosion. This paper reports on two long-term field experiments that were established in the late 1990s on texturally different soil types at a time of uncertainty about the profitability of continuous-cropping rotations in low-rainfall environments. Continuous-cereal systems significantly outyielded the traditional pasture–wheat systems in five of the 11 seasons at Waikerie (light-textured soil), resulting in a cumulative gross margin of AU$1600 ha–1 after the initial eight seasons, almost double that of the other treatments. All rotation systems at Kerribee (loam-textured soil) performed poorly, with only the 2003 season producing yields close to 3 t ha–1 and no profit achieved in the years 2004–08. For low-rainfall environments, the success of a higher input cropping system largely depends on the ability to offset the losses in poor seasons by capturing greater benefits from good seasons; therefore, strategies to manage climatic risk are paramount. Fallow efficiency, or the efficiency with which rainfall was stored during the period between crops, averaged 17% at Kerribee and 30% at Waikerie, also indicating that soil texture strongly influences soil evaporation. A ‘responsive’ strategy of continuous cereal with the occasional, high-value ‘break crop’ when seasonal conditions are optimal is considered superior to fixed or pasture–fallow rotations for controlling grass, disease or nutritional issues.
2-ALKOXY-5 (4H) -OXAZOLONES AND THE ENANTIOMERIZATION OF N-ALKOXYCARBONYLAMINO ACIDS

N-Alkoxycarbonylamino acids are chirally stable under normal conditions of coupling. In the presence of tert.amine (tertiary amine), most activated N-alkoxycarbonylamino acids generate 2-alkoxy-5(4H)-oxazolone, which is not chirally stable in the presence of the base. Consequently, enantiomerization occurs in the presence of tert.amine if the activated residue is not immediately consumed by aminolysis. This paper reviews the situations in which 2-alkoxy-5(4H)-oxazolones are generated from N-alkoxycarbonylamino acids, the enantiomerization that occurs during and after the incorporation of N-alkoxycarbonylamino acids into peptides, the properties and methods of preparation of 2-alkoxy-5(4H)-oxazolones, and the practical use that has been made from our knowledge of the chemistry of 2-alkoxy-5(4H)-oxazolones. © 1996 John Wiley & Sons, Inc.
An Extensible, Scalable Spark Platform for Alignment-free Genomic Analysis - Version 2

Motivation: Alignment-free distance and similarity functions (AF functions, for short) are a computationally convenient alternative to two and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Yet, their use is still to the proof of principle stage: only recently a benchmarking study has coherently evaluated a handful of the functions proposed over the years, identifying a pool of well performing ones. However, more is needed to make this pool usable on a day-to-day basis. In particular, a statistical significance quantification associated to the output of a given function would greatly help when no reference point is available. For most functions, such an analysis is bound to be based on Monte Carlo Hypothesis Test simulations, yielding a dramatic increase in computational time that transforms this into a Big Data problem. Surprisingly, it has been hardly considered, despite the increasing popularity of Big Data Technologies in Computational Biology. Results: We fill this important gap by providing the first user-friendly, extensible, efficient Spark platform for Alignment-free genomic analysis. Thanks to its scalability, Monte Carlo Hypothesis Test simulations on the output of AF functions can seamlessly be afforded for either small or huge collections of sequences. Thus, we are able to comparatively study for the first time AF functions in relation to the statistical significance of their output. Such novel analysis allows us to reduce the pool of well performing functions coming from the benchmarking study to a handful of them.