Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Profiling, Pedigree Lineage Analysis and Monitoring in the Australian Breeding Program of Radiata Pine

Abstract Ten microsatellite loci were used to DNA profile 215 first and second generation breeding clones in the Australian radiata pine breeding program. The clones were essentially unique from one another and these DNA profiles were used to examine the sexual and asexual phases in the breeding program. Only 2.6% of ramets from 25 breeding clones were incorrect whereas 8.4% of progeny from 10 families were genetically incorrect. The lineages of second generation clones were checked for DNA profiles that were available for putative parents. Some parents appear to be incorrect on the basis of the DNA profiles and further sampling will be required to confirm these results across the breeding program. Microsatellite markers can now enable most questions to be resolved in breeding programs and also will allow novel breeding strategies to be used in the future.
Neural Reranking for Dependency Parsing: An Evaluation

Recent work has shown that neural rerankers can improve results for dependency parsing over the top k trees produced by a base parser. However, all neural rerankers so far have been evaluated on English and Chinese only, both languages with a configurational word order and poor morphology. In the paper, we re-assess the potential of successful neural reranking models from the literature on English and on two morphologically rich(er) languages, German and Czech. In addition, we introduce a new variation of a discriminative reranker based on graph convolutional networks (GCNs). We show that the GCN not only outperforms previous models on English but is the only model that is able to improve results over the baselines on German and Czech. We explain the differences in reranking performance based on an analysis of a) the gold tree ratio and b) the variety in the k-best lists.
Biochemistry and Molecular Biology of the Isoprenoid Biosynthetic Pathway in Plants

This review first summarizes the diverse nature of isoprenoids found in plants, emphasizing the wide range of physiological functions these compounds serve. The biosynthetic origins of isoprenoids have occupied chemists and biochemists for decades, and the second section of this review recaps some of the conceptual models used to rationalize key biosynthetic reactions in the isoprenoid pathway. The third section describes briefly some of the recently developed experimental systems that have helped researchers uncover much of the biochemistry and molecular biology of isoprenoids. The fourth section compares the deduced amino acid sequences of enzymes with similar catalytic functions and attempts to correlate these sequences with the known enzymology. The fifth and final section focuses on our limited understanding of how isoprenoid biosynthesis is regulated in plants.
Design of an Interactive Nostalgic Amusement Device with User-Friendly Tangible Interfaces for Improving the Health of Older Adults

To help older adults achieve active aging, an interactive device with tangible interfaces is proposed, which combines human–machine interaction techniques and older adults’ life experiences to provide three functions: nostalgia, leisure, and entertainment. Firstly, by a review of related theories and studies, principles for designing a desirable interactive device were established. Accordingly, a prototype device with an interactive game was constructed, which was then tested in a field experiment and improved according to the users’ opinions collected by interviews. Subsequently, in a second experiment the users’ and some experts’ feedback about the system’s usability and user interaction satisfaction was collected and analyzed, and found to be reliable and valid for further evaluations of the effectiveness of the proposed system, resulting in the following findings about the older adults who have played the game: the participants become more willing to use technological devices; involving them in the game creates positive aging effects; participants become more receptive to technology products; the participating older adults’ cognitive abilities are trained and their body exercises increased, creating sensory stimulation and health promotion effects; and considering users with cognitive impairments who have stress and difficulty operating the device, the system needs to be improved in the future.
Alterations in Herbage Yield, Antioxidant Activities, Phytochemical Contents, and Bioactive Compounds of Sabah Snake Grass (Clinacanthus Nutans L.) with Regards to Harvesting Age and Harvesting Frequency

Sabah snake grass or Clinacanthus nutans has drawn public interest having significant economic benefits attributable to the presence of phytochemicals and several interesting bioactive constituents that may differ according to harvesting age and harvesting frequency. The current study was aimed to evaluate the effect of harvesting age and harvesting frequency towards herbal yield, antioxidant activities, phytochemicals synthesis, and bioactive compounds of C. nutans. A factorial randomized completely block design with five replications was used to illustrate the relationship between herbal yield, DPPH (2, 2-diphenyl-1-picrylhydrazyl) and ferric reducing antioxidant power (FRAP) assays, total phenolic and flavonoid content affected by harvesting age (week 8, 12, and 16 after transplanting), and harvesting frequency (harvest 1, 2, and 3). The bioactive compounds by HPLC were also determined to describe the interaction effect between both harvesting age and harvesting frequency. The yield, antioxidant activities, and phytochemical contents were gradually increased as the plant grew, with the highest recorded during week 16. However, the synthesis and activities of phytochemicals were reduced in subsequent harvests despite the increment of the herbal yield. All bioactive compounds were found to be influenced insignificantly and significantly by harvesting age and harvesting frequency, respectively, specifically to shaftoside, iso-orientin, and orientin. Among all constituents, shaftoside was the main compound at various harvesting ages and harvesting frequencies. These results indicated that harvesting at week 16 with 1st harvest frequency might enhance the yield while sustaining the high synthesis of polyphenols and antioxidant activities of C. nutans.
Analysis of the Status of the Cutaneous Endogenous and Exogenous Antioxidative System of Smokers and the Short-Term Effect of Defined Smoking Thereon

The daily consumption of tobacco products leads to a boost in free radical production in tissues, promoting the risk for malignancies, metabolic alterations and chronic-inflammatory diseases. This study aimed to broaden the knowledge of the status of the antioxidative (AO) system in the skin, compared to the blood, of healthy appearing smokers. Both, the basic status compared to non-smokers and the short-term impact of controlled cigarette consumption in smokers were analyzed. Our study showed that the basic level of the AO system of smokers significantly differed from that of non-smokers. As determined by resonant Raman spectroscopy (RRS), the levels of exogenous AOs were decreased in both, the skin, in vivo (β-carotene and lycopene), and blood plasma (β-carotene only). In contrast, the levels of glutathione (GSH), the prototypical endogenous AO, which were analyzed by fluorimetric assays in cutaneous tape strips and blood plasma, were increased in the skin, although unchanged in the blood of smokers. Elevated cutaneous GSH levels were reflected by an elevated overall radical scavenging activity in the skin, as quantified by non-invasive electron paramagnetic resonance (EPR) spectroscopy. Analysis of the expression of selected stress-associated genes in blood immune cells by quantitative RT-PCR in subgroups of non-smokers and smokers additionally demonstrated the downregulation of AKR1C2 in smokers, and its negative correlation with blood plasma levels of the protective immune mediator interleukin-22, assessed by the ELISA technique. Controlled cigarette consumption did not alter exogenous or endogenous AOs in the skin of smokers, but decreased lycopene levels in blood plasma. Moreover, there was a decline in blood IL-22 levels, while no relevant response of blood cell gene expressions was found after the considered short time. Our data therefore demonstrate a strengthened endogenous AO status in the skin of smokers, which may indicate a long-term adaptation to chronic oxidative stress in this specific organ. While this effect was not clearly visible in the blood, this compartment seems to be useful as an immediate indicator of the body’s AO consumption. Moreover, decreased levels of AKR1C2, which we show for the first time to be expressed in immune cells, may be a candidate marker for long-term smoking. In addition, this study demonstrates that the rate constant of a spin probe decline determined by EPR spectroscopy mainly represents the endogenous AO status of a tissue.
CXCR3 chemokine receptor contributes to specific CD8+ T cell activation by pDC during infection with intracellular pathogens

Chemokine receptor type 3 (CXCR3) plays an important role in CD8+ T cells migration during intracellular infections, such as Trypanosoma cruzi. In addition to chemotaxis, CXCR3 receptor has been described as important to the interaction between antigen-presenting cells and effector cells. We hypothesized that CXCR3 is fundamental to T. cruzi-specific CD8+ T cell activation, migration and effector function. Anti-CXCR3 neutralizing antibody administration to acutely T. cruzi-infected mice decreased the number of specific CD8+ T cells in the spleen, and those cells had impaired in activation and cytokine production but unaltered proliferative response. In addition, anti-CXCR3-treated mice showed decreased frequency of CD8+ T cells in the heart and numbers of plasmacytoid dendritic cells in spleen and lymph node. As CD8+ T cells interacted with plasmacytoid dendritic cells during infection by T. cruzi, we suggest that anti-CXCR3 treatment lowers the quantity of plasmacytoid dendritic cells, which may contribute to impair the prime of CD8+ T cells. Understanding which molecules and mechanisms guide CD8+ T cell activation and migration might be a key to vaccine development against Chagas disease as those cells play an important role in T. cruzi infection control.
Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

Abstract The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C–S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma
ANTIOXIDANT AND ANTICANDIDAL ACTIVITY STUDIES ON PHYLLANTHIN COMPOUND FROM PHYLLANTHUS NIRURI

Objective: The present study was to investigate the phyllanthin present in Phyllanthus niruri which belongs to the family, Euphorbiaceae. The vital aim was to evaluate the antioxidant and to determine the anticandidal efficacies against Candida albicans. Methods: Phyllanthin, is one of the active lignan which was isolated from Phyllanthus niruri by silica gel column chromatography employing gradient elution with hexane–ethyl acetate solvent mixture. The eluted samples were further identified and estimated using HPTLC. Free radical scavenging activity of phyllanthin was examined using DPPH assay. Anticandidal activity was studied by analysing the growth inhibition and Minimum Fungicidal Concentration (MFC) rate. Results: The retention time of phyllanthin is 23.4 and its total run time was 45 min. Phyllanthin exhibited very high antioxidative property by its low IC50=7.5 µmol/mL. The isolated phyllanthin alters the growth of C. albicans and showed significant results in vitro. Among the various concentrations of phyllanthin, 250 µl/L concentration revealed the high rate of inhibition. Conclusion: The phyllanthin compound from the medicinal plant, Phyllanthus niruri confirmed as an effective antifungal agent to prevent the candidiasis and the secondary infections caused in various diseases.
EVALUATION OF ANTI-PYRETIC POTENTIAL OF FICUS CARICA LEAVES

ABSTARCT A study was carried out to evaluate the anti-pyretic effect of an ethanol extract of leaves, of Ficus carica Linn. belonging to the family of Moraceae, at normal body temperature and yeast-induced pyrexia, in albino rats. A yeast suspension (10 ml/kg body wt.) increased rectal temperature 19 hours after the subcutaneous injection. The ethanol extract of Ficus carica, at doses of 100, 200 and 300 mg/kg body wt. p.o. , showed significant dose-dependent reduction in normal body temperature and yeast-provoked elevated temperature. The effect extended up to five hours after drug administration. The anti-pyretic effect of the ethanol extract of Ficus carica was comparable to that of Paracetamol (150 mg/kg body wt., p.o.), a standard anti-pyretic agent.
Livestock and Poultry Production in Nepal and Current Status of Vaccine Development

The livestock and poultry sectors are an integral part of Nepalese economy and lifestyle. Livestock and poultry populations have continuously been increasing in the last decade in Nepal and are likely to follow that trend as the interests in this field is growing. Infectious diseases such as Foot and Mouth Disease (FMD), Peste des Petits Ruminants (PPR), hemorrhagic septicemia (HS), black quarter (BQ), swine fever, avian influenza, and Newcastle disease (ND) constitute one of the major health challenges to the Nepalese livestock and poultry industry. Vaccinations are an efficient means of preventing the occurrence and spread of several diseases in animals and birds. Considering this fact, the government of Nepal began the production of veterinary vaccines in the 1960s. Nepal is self-reliant in producing several vaccines for cattle and buffaloes, sheep and goats, pigs, and poultry. Despite these efforts, the demand for vaccines is not met, especially in the commercial poultry sector, as Nepal spends billions of rupees in vaccine imports each year. There is a need of strengthening laboratory facilities for the isolation and characterization of field strains of pathogens and capacity building for the production of different types of vaccines using the latest technologies to be self-reliant in veterinary vaccine production in the future in Nepal.
Larval Fish Community in the Missouri River below Garrison Dam, North Dakota

ABSTRACT The abundance and species composition of larval fishes in the Missouri River below Garrison Dam, North Dakota, was assessed during May-August of 1993 and 1994. Only Catostomus spp. , Ictiobus spp. , Moxostoma spp. , Stizostedion spp. , Osmerus mordax, and Perca flavescens were collected during the course of the study. Larval fish species diversity and abundance were lower than expected given the number of adult fish species found in the tailwaters and numbers of larval fishes collected in other studies on the Missouri and Mississippi rivers. The low abundance and diversity likely were due to the hypolimnetic discharge of cold water from Lake Sakakawea. Larval fish species also appeared later in the season than expected.
Lycopus lucidus Turcz. ex Benth. var. hirtus Regel (Lamiaceae) in Italy: a new naturalized alien species for the European flora

Abstract Lycopus lucidus Turcz. ex Benth. var. hirtus Regel (Lamiaceae), a neophyte native to Asia, is recorded for the first time in Europe. A naturalized population was discovered in the Milan railway area (Italy). Diagnostic characters and an updated identification key for the genus Lycopus in Europe are presented. Furthermore, the invasive status and the possible means of introduction are discussed.
Survival Benefits Based on the Number of Lymph Nodes Removed during Radical Nephroureterectomy for Upper Tract Urothelial Carcinoma: Systematic Review and Meta-Analysis

The role of lymph node dissection (LND) is still controversial for upper tract urothelial carcinoma (UTUC), and there are no guidelines regarding its use. This study was conducted to find a higher level of evidence for the survival benefits based on the number of LNs removed during radical nephroureterectomy (RNUx) through a systematic review and meta-analysis. We included studies comparing patients who underwent LND during RNUx for UTUC. We searched the major electronic databases (Pubmed, Embase®, and Scopus®) and conducted manual searches of the electronically available abstracts of the major international urology cancer meetings [American Society of Clinical Oncology (ASCO), American Urological Association (AUA), and Eropean Association of Urology (EAU)] prior to April 2019 using grouped terms of nephroureterectomy (nephroureterectom*) and lymph node excision (lymphadenectomy; lymph + node*; lymph* + metasta*) with variations in the terms. Study selection, data collection, and risk of bias assessment were performed by two independent authors (A and B). Six retrospective case-control studies included a total of 33,944 patients who underwent RNUx for UTUC, 5071 of whom underwent LND and were finally included in the meta-analysis. The pooled hazard ratio (HR) in these studies revealed that an increased number of LNs removed during RNUx was associated with improved cancer-specific survival (CSS) in patients with UTUC (HR = 0.95, 95% CI: 0.91–0.99; p = 0.07). In addition, increased numbers of LNs removed were associated with improved overall survival (OS) in pN0 patients. However, in pN+ patients, the number of LNs removed showed no survival benefit on CSS, overall survival (OS), or progression-free survival (PFS). Higher numbers of LNs removed during RNUx were associated with improved survival outcomes in patients with UTUC. This study confirmed that LND also has oncological benefits in UTUC patients. Although still a controversial topic, meticulous LND must be considered, and efforts should be made to eliminate as many LNs as possible when administering RNUx for UTUC, especially in patients without clear evidence of LN metastasis.
Electro-mechanics or mechano-electrics, an intricate interplay

Excitation–contraction coupling, describing how electrical signals translate to mechanical activity, is extensively studied both in animal models and in patients with electrical diseases, cardiomyopathies, and heart failure. However, translation to clinical practice is not straight-forward. Lessons learnt from imaging studies in cardiac resynchronization therapy (CRT) candidates have highlighted that understanding the field of electro-mechanical interactions is complicated. Typical measures of myocardial electrical delay and inhomogeneity are increased QRS duration and QT duration on electrocardiogram (ECG), representing delay in intraventricular conduction and electrical repolarization. Prolonged QRS duration affects the electromechanical interplay, as clearly illustrated in patients with left bundle branch block and echocardiographic finding of dyssynchronous contractions. Strain echocardiography
Targeting the Heme-Heme Oxygenase System to Prevent Severe Complications Following COVID-19 Infections

SARS-CoV-2 is causing a pandemic resulting in high morbidity and mortality. COVID-19 patients suffering from acute respiratory distress syndrome (ARDS) are often critically ill and show lung injury and hemolysis. Heme is a prosthetic moiety crucial for the function of a wide variety of heme-proteins, including hemoglobin and cytochromes. However, injury-derived free heme promotes adhesion molecule expression, leukocyte recruitment, vascular permeabilization, platelet activation, complement activation, thrombosis, and fibrosis. Heme can be degraded by the anti-inflammatory enzyme heme oxygenase (HO) generating biliverdin/bilirubin, iron/ferritin, and carbon monoxide. We therefore postulate that free heme contributes to many of the inflammatory phenomena witnessed in critically ill COVID-19 patients, whilst induction of HO-1 or harnessing heme may provide protection. HO-activity not only degrades injurious heme, but its effector molecules possess also potent salutary anti-oxidative and anti-inflammatory properties. Until a vaccine against SARS-CoV-2 becomes available, we need to explore novel strategies to attenuate the pro-inflammatory, pro-thrombotic, and pro-fibrotic consequences of SARS-CoV-2 leading to morbidity and mortality. The heme-HO system represents an interesting target for novel “proof of concept” studies in the context of COVID-19.
Behavioral adaptation of Pallas's squirrels to germination schedule and tannins in acorns

Using acorns from Castanea henryi (CH) and Quercus variabilis (QV) with contrasting germination schedule (related to food perishability) and tannin levels, we conducted field experiments in a subtropical forest in Southwest China to investigate how free-ranging Pallas's squirrels (Callosciurus erythraeus) utilize acorns as long-term storage based on the food perishability and high-tannin hypotheses. Though QV acorns germinated much earlier than CH ones, we found that Pallas's squirrels hoarded more high-tannin QV acorns over low-tannin CH ones, supporting the high-tannin hypothesis (but not the food perishability hypothesis). However, several other predictions derived from the food perishability hypothesis received sound support: nondormant QV acorns had their embryos removed with a higher probability (68.5%) than dormant CH ones (8.8%) and embryo-removed acorns had a much lower germination success but had a higher probability surviving as long-term storage. During the caching-recovery process, hoarding animals actively detected acorn state (dormant or not) and removed acorn embryos with an increasing probability in subsequent hoarding events. In addition, embryo-removed acorns could serve as long-term storage because they had a very low probability being infested by fungi as intact acorns did during the time of storage. We conclude that tree squirrels can differentially respond to acorn germination and remove the embryos of nondormant acorns more frequently as long-term storage, but tannin level is more important in determining whether a given acorn is hoarded or not. Combined with the studies from North America, our results suggest convergent evolution of acorn hoarding behavior in tree squirrels across different continents. Copyright 2009, Oxford University Press.