Miracle-dz/UniFAR-FTUs huggingface dataset:
A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples

A colorimetric isothermal RNA amplification method was shown to detect SARS-CoV-2 RNA in clinical samples with excellent sensitivity and specificity. A colorful test for SARS-CoV-2 RNA detection We need simple methods to rapidly test large numbers of people for infection with the SARS-CoV-2 coronavirus. Quantitative PCR (qPCR) after reverse transcription (RT), the standard method, is very sensitive but requires expensive instrumentation. Loop-mediated isothermal amplification (LAMP) is an alternative to qPCR that is faster and requires fewer resources. Dao Thi et al. tested the RT-LAMP assay on several hundred clinical RNA samples isolated from pharyngeal swabs collected from individuals being tested for COVID-19. They confirmed that the RT-LAMP assay was a simpler albeit less sensitive option compared to RT-qPCR for large-scale testing for SARS-CoV-2 RNA. These investigators also developed a simplified version of this method (direct swab–to–RT-LAMP assay) that did not require a prior RNA isolation step as well as a method for highly multiplexed sequencing of RT-LAMP reactions (LAMP-sequencing). The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.
Modelling fertility traits under natural mating conditions in beef cattle

Fertility traits are the most economically important traits in beef cattle and in spite of having low heritabilities they ought to be included in breeding programs. The genetic selection programs in Spain are based on improving growth traits, neglecting the fertility traits up to now. In this study, a first analysis of the calving interval between first and second parities (CI 12 ) was carried out to establish a suitable selection criterion. The selected breeds were two local breeds Avilena-Negra Iberica (ANI) and Retinta (RT), raised in extensive production with natural mating. Two models including cow and bull effects were studied. –Systematic effects were herd-year-season of first calving, age of cow at first calving and age of bull at second calving and regressions on inbreeding coefficients for cows and bulls. Then, a full model (FULL) included additive genetic and permanent environmental components for bull and an additive genetic effect for cows. A reduced model (RED) was the same as FULL but with the additive genetic component for bull excluded. Both models provided similar estimates of systematic and cow additive genetic components. Inbreeding depression was found for bulls (0.79 and 0.83 days/% inbreeding in ANI and RT, respectively) but nearly null regression coefficients on inbreeding were obtained for cows. In both breeds, heritability estimates were 0.05 for cows. For FULL, heritability estimates for bull effects were larger than the cows heritability, 0.08 for ANI and 0.10 for RT. The bull permanent component was large, with values of 0.20 and 0.31 for ANI and RT, respectively. Herd fertility in these populations can be substantially improved by bulls screening. Genetic selection can be practiced but with low efficiency, as it is commonly the case for fertility traits
Defoliation effects on carbon and nitrogen substrate import and tissue‐bound efflux in leaf growth zones of grasses

Grassland plants suffer regular defoliation, causing loss of photosynthetic activity and internal resources. Consequently, re-foliation may be substrate-limited. The present study was undertaken to test the hypothesis that decreased C import in leaf growth zones is (partially) compensated by: (i) mobilization of substrate within growth zones; and (ii) increased efficiency of substrate use in leaf area expansion; but (iii) that these processes depend on the C status of growth zones at defoliation. Mixtures of a C3 (Lolium perenne L.) and a C4 grass (Paspalum dilatatum Poir.) were grown at 15 °C (C3 dominance) and 23 °C (C4 dominance). Individual plants thus grew in contrasting (light and temperature) environments before being defoliated. Defoliation caused a drastic and immediate decrease in C import, but effects on leaf area expansion were buffered by biomass mobilization in the growth zone and increases in specific leaf area of produced tissue. Thus, over the first 2 d post-defoliation, the amount of leaf area produced per unit imported C increased by 39 to 102% depending on treatment. The magnitude of these buffering responses was correlated with the concentration of water soluble carbohydrates in the growth zone at defoliation. Similar responses were observed for N, although defoliation effects were smaller and delayed relative to those on C import. This study demonstrates refoliation is sustained by short-term mobilization of reserves within the growth zone and reduced costs of produced leaf area, but that these mechanisms depend on growth zone C status at defoliation.
Evaluation of wound healing activity of leaf extract of Alstonia scholaris Linn. In rats

Alstonia scholaris Linn. (Apocynaceae) is a medium sized tree known for its pharmacological activities like antimicrobial, antimalarial, anticholeric properties etc. The present study was aimed to assess the wound healing potential of crude methanol extract of A. scholaris (leaf) using three types of wound models in rats as incision wound, excision wound and dead space wound. The results were obtained with respect to the parameters such as wound contraction, epithelialization time, tensile strength, hydroxyproline content and granuloma weight. Enhanced wound contraction and decreased epithelialization time were observed in extract-treated animals in excision wound model. The tensile strength of the incision wound was significantly increased in comparison to control group. The granulation tissue weight and hydroxyproline content in the dead space wounds were also increased significantly in treated animals compared with control.
Responses of white spruce (Picea glauca) to experimental warming at a subarctic alpine treeline

From 2001 to 2004 we experimentally warmed 40 large, naturally established, white spruce [Picea glauca (Moench) Voss] seedlings at alpine treeline in southwest Yukon, Canada, using passive open‐top chambers (OTCs) distributed equally between opposing north and south‐facing slopes. Our goal was to test the hypothesis that an increase in temperature consistent with global climate warming would elicit a positive growth response. OTCs increased growing season air temperatures by 1.8°C and annual growing degree‐days by one‐third. In response, warmed seedlings grew significantly taller and had higher photosynthetic rates compared with control seedlings. On the south aspect, soil temperatures averaged 1.0°C warmer and the snow‐free period was nearly 1 month longer. These seedlings grew longer branches and wider annual rings than seedlings on the north aspect, but had reduced Photosystem‐II efficiency and experienced higher winter needle mortality. The presence of OTCs tended to reduce winter dieback over the course of the experiment. These results indicate that climate warming will enhance vertical growth rates of young conifers, with implications for future changes to the structure and elevation of treeline contingent upon exposure‐related differences. Our results suggest that the growth of seedlings on north‐facing slopes is limited by low soil temperature in the presence of permafrost, while growth on south‐facing slopes appears limited by winter desiccation and cold‐induced photoinhibition.
High-risk Human Papillomavirus Testing in Young Japanese Women with Atypical Squamous Cells of Undetermined Significance

Introduction: The mortality due to uterine cervical cancer has been gradually increasing in women under 40 years of age (U40) in Japan. We investigated the effect of high-risk human papillomavirus (HR-HPV) on U40 subjects without any overt cytological abnormalities. Materials and Methods: We retrospectively examined the clinical data, including the findings of a cobas 4800 HPV test that was approved in Japan in 2013 to triage women with atypical squamous cells of undetermined significance (ASC-US) and a histological examination in 589 Japanese women. Results: The overall prevalence rate of HR-HPV was 34.5%. Biopsy-confirmed cervical intraepithelial neoplasia (CIN) 2, or worse (CIN2+) was identified in 45.1% (23/51) of HR-HPV-positive women with ASC-US, who underwent colposcopy immediately. The mean period from the HPV test to the diagnosis of CIN2+ was 3.7 months. CIN2+ was more common (69.6%) in U40 patients. The rates of single or multiple infections of HPV-16, HPV-18, and 12 other HR-HPV (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) in CIN2+ U40 patients were 31.3%, 0%, and 81.3%, respectively. The relative risk for CIN 2+ among U40 women with HPV-16 was not significantly different from that of the patients with infection of any of the 12 other HR-HPVs. Conclusion: The results of this study suggest that the 12 other HR-HPVs have a potential to generate high-grade cervical lesions among young women, and the examination rate of colposcopy should be increased.
Why Chain Length of Hyaluronan in Eye Drops Matters

The chain length of hyaluronan (HA) determines its physical as well as its physiological properties. Results of clinical research on HA eye drops are not comparable without this parameter. In this article methods for the assessment of the average molecular weight of HA in eye drops and a terminology for molecular weight ranges are proposed. The classification of HA eye drops according to their zero shear viscosity and viscosity at 1000 s−1 shear rate is presented. Based on the gradient of mucin MUC5AC concentration within the mucoaqueous layer of the tear film a hypothesis on the consequences of this gradient on the rheological properties of the tear film is provided. The mucoadhesive properties of HA and their dependence on chain length are explained. The ability of HA to bind to receptors on the ocular epithelial cells, and in particular the potential consequences of the interaction between HA and the receptor HARE, responsible for HA endocytosis by corneal epithelial cells is discussed. The physiological function of HA in the framework of ocular surface homeostasis and wound healing are outlined, and the influence of the chain length of HA on the clinical performance of HA eye drops is illustrated. The use of very high molecular weight HA (hylan A) eye drops as drug vehicle for the next generation of ophthalmic drugs with minimized side effects is proposed and its advantages elucidated. Consequences of the diagnosis and treatment of ocular surface disease are discussed.
Flavonoid and Non-Flavonoid Compounds of Autumn Royal and Egnatia Grape Skin Extracts Affect Membrane PUFA’s Profile and Cell Morphology in Human Colon Cancer Cell Lines

Grapes contain many flavonoid and non-flavonoid compounds with anticancer effects. In this work we fully characterized the polyphenolic profile of two grape skin extracts (GSEs), Autumn Royal and Egnatia, and assessed their effects on Polyunsaturated Fatty Acid (PUFA) membrane levels of Caco2 and SW480 human colon cancer cell lines. Gene expression of 15-lipoxygenase-1 (15-LOX-1), and peroxisome proliferator-activated receptor gamma (PPAR-γ), as well as cell morphology, were evaluated. The polyphenolic composition was analyzed by Ultra-High-Performance Liquid Chromatography/Quadrupole-Time of Flight mass spectrometry (UHPLC/QTOF) analysis. PUFA levels were evaluated by gas chromatography, and gene expression levels of 15-LOX-1 and PPAR-γ were analyzed by real-time Polymerase Chain Reaction (PCR). Morphological cell changes caused by GSEs were identified by field emission scanning electron microscope (FE-SEM) and photomicrograph examination. We detected a different profile of flavonoid and non-flavonoid compounds in Autumn Royal and Egnatia GSEs. Cultured cells showed an increase of total PUFA levels mainly after treatment with Autumn Royal grape, and were richer in flavonoids when compared with the Egnatia variety. Both GSEs were able to affect 15-LOX-1 and PPAR-γ gene expression and cell morphology. Our results highlighted a new antitumor mechanism of GSEs that involves membrane PUFAs and their downstream pathways.
Biodiversité des mouches des fruits (Diptera : Tephritidae) en vergers de manguiers de l’ouest du Burkina Faso : structure et comparaison des communautés de différents sites

Introduction . Un inventaire des especes de Tephritidae dans des vergers de l’ouest du Burkina Faso a ete effectue entre decembre 2007 et decembre 2009. Materiel et methodes . Un piegeage de detection a ete mene dans sept vergers de manguiers en utilisant comme appât de la levure de Torula placee dans des pieges Mac Phail. Resultats et discussion . L’identification et le denombrement des Tephritidae capturees a permis de recenser 18 especes : neuf du genre Ceratitis , sept du genre Dacus et deux du genre Bactrocera . Ceratitis cosyra et Bactrocera invadens (respectivement 53,02 % et 36,19 % de l’ensemble des captures) se sont revelees etre les especes dominantes. Nous avons mis en evidence une forte similarite des communautes de Tephritidae au niveau des differents sites etudies (coefficients de similitude entre 42,86 % et 100 %); cette similarite pourrait etre expliquee d’une part par l’homogeneite des conditions climatiques, d’autre part par celle de la vegetation de la zone d’etude. La proximite des parcelles de cultures maraicheres et la diversite des fruitiers locaux hotes des Tephritidae autour des vergers de manguiers pourraient etre a l’origine de la richesse specifique elevee que nous avons constatee. Conclusion . Notre etude a revele une diversite de Tephritidae dans la zone d’investigation qui presente des communautes d’especes homogenes. Ces resultats seront completes par l’identification des especes associees aux degâts sur manguier et a l’evaluation de leur importance. Ils suggerent des a present la possibilite de developper, contre ces ravageurs, une strategie de lutte commune a toutes les localites de la zone d’etude de l’ouest du Burkina Faso.
Do women’s preferences for men’s facial hair change with reproductive status?

Women’s preferences for masculine traits are reported to be greater among young reproductively capable women, particularly just prior to ovulation, than among pregnant and postmenopausal women. This study is the first to investigate whether women’s preferences for men’s facial hair follow this pattern. We conducted surveys quantifying reproductive status and attractiveness ratings for facial hair (clean-shaven, light stubble, heavy stubble, and full beards) among 426 women from Wellington City, New Zealand. Results showed that pregnant, pre- and postmenopausal women rated faces that were clean-shaven, or with light and heavy stubble, as more attractive than full beards. Postmenopausal women gave higher scores for all degrees of facial hair, including full beards, than premenopausal and pregnant women. Premenopausal women at the high fertility phases of the menstrual cycle gave higher ratings for heavy stubble than participants at the low fertility phase or who were using contraceptives. However, these differences were not statistically significant, and the main effects were driven primarily by the low ratings ascribed to full beards. Women with partners that were clean-shaven judged clean-shaven faces as most attractive, whereas women with partners with heavy stubble or full beards judged heavy stubble as most attractive. Although women’s current partner and father’s degree of beardedness were positively correlated, their fathers’ beardedness showed little relationship to attractiveness judgments of facial hair. These results demonstrate that all women by no means consider beards unattractive. However, preferences vary only subtly with respect to hormonal, reproductive, and relationship status.
Predicting Online Travel Adoption Intention of an Indian Consumer: A SEM-Neural Network Approach

Online channel has redefined the way businesses were conducted and many e-travel firms were the first to exemplify. The purpose of this paper is to determine the key factors that influence consumers’ intention to adopt online channel for train travel. The extended model incorporates the basic ingredients of TAM, TPB and Shim’s model along with several external variables such as trust, convenience and involvement. Data were collected from 514 online travel customers. In the first phase, structural equation modeling was employed to determine the significant variables and in the second phase, the neural network model was used to rank the relative importance of the significant predictors identified by SEM. The results indicated that Trust, Perceived Usefulness, Convenience and Website as significant factors. Among significant ones, neural networks suggested “convenience” as the highest importance. The study indicates few marketing approaches that can help travel service providers to formulate optimal marketing strategies.
High prevalence of SARS‐CoV‐2 and influenza A virus (H1N1) coinfection in dead patients in Northeastern Iran

In the last months of 2019, an outbreak of fatal respiratory disease started in Wuhan, China, and quickly spread to other parts of the world. It was named COVID‐19, and to date, thousands of cases of infection and death are reported worldwide. This disease is associated with a wide range of symptoms, which makes accurate diagnosis of it difficult. During previous severe acute respiratory syndrome (SARS) pandemic in 2003, researchers found that the patients with fever, cough, or sore throat had a 5% influenza virus‐positive rate. This finding made us think that the wide range of symptoms and also relatively high prevalence of death in our patients may be due to the coinfection with other viruses. Thus, we evaluated the coinfection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) with other respiratory viruses in dead patients in North Khorasan. We evaluated the presence of influenza A/B virus, human metapneumovirus, bocavirus, adenovirus, respiratory syncytial virus (RSV), and parainfluenza viruses in 105 SARS‐CoV‐2 positive dead patients, using polymerase chain reaction (PCR) and reverse transcription PCR tests. We found coinfection with influenza virus in 22.3%, RSV, and bocavirus in 9.7%, parainfluenza viruses in 3.9%, human metapneumovirus in 2.9%, and finally adenovirus in 1.9% of SARS‐CoV‐2 positive dead cases. Our findings highlight a high prevalence of coinfection with influenza A virus and the monopoly of coinfection with Human metapneumovirus in children.
Recommendations for the Development and Reform of Microtia and Atresia Services.

BACKGROUND The initial step in setting up standardized microtia-atresia service is investigating the current status of the service and comparing this to internationally recognized guidelines or care standards. In many countries, documented information about microtia care is lacking. This study is an initiative to guide reform efforts of national microtia service in any country. The UK care standards for microtia-atresia can be a useful model to help set up a comprehensive microtia-atresia service. METHODS The authors conducted a survey to investigate different aspects of microtia service in Egypt. The major plastic surgery centers (n = 22) were surveyed by a structured questionnaire. The results were compared with the UK care standards for microtia-atresia to identify the aspects that need improvement. Thorough analysis of the main problems in microtia-atresia service is presented. RESULTS The authors found that microtia service is fragmented between the surveyed centers with 65% of the centers treating less than 10 microtia cases annually. Multiple surgeons are responsible for ear reconstruction in 90% of centers and only 25% of them practise a multidisciplinary team approach. None of the centers uses validated tools of aesthetic or psychological patient-reported outcome measures. RECOMMENDATIONS These 5 recommendations are the keys to reforming microtia service in any country:(1) Establishing nationally designated centers to concentrate the required expertise. (2) Assigning fewer high-volume surgeons to optimize the surgical outcomes. (3) Providing treatment by experienced multidisciplinary teams. (4) Using validated tools of patient-reported outcome measures. (5) Collecting and keeping standardized records for regular audit and intercenter studies.