Miracle-dz/UniFAR-FTUs huggingface dataset:
H nuclear magnetic resonance spectroscopy supports larger amplitude fast motion and interference with lipid chain ordering for membrane that contains β sheet human immunodeficiency virus gp41 fusion peptide or helical hairpin influenza virus hemagglutinin fusion peptide at fusogenic pH

Enveloped viruses are surrounded by a membrane which is obtained from an infected host cell during budding. Infection of a new cell requires joining (fusion) of the virus and cell membranes. This process is mediated by a monotopic viral fusion protein with a large ectodomain outside the virus. The ectodomains of class I enveloped viruses have a N-terminal “fusion peptide” (fp) domain that is critical for fusion and binds to the cell membrane. In this study, H NMR spectra are analyzed for deuterated membrane with fp from either HIV gp41 (GP) or influenza hemagglutinin (HA) fusion proteins. In addition, the HAfp samples are studied at more fusogenic pH 5 and less fusogenic pH 7. GPfp adopts intermolecular antiparallel β sheet structure whereas HAfp is a monomeric helical hairpin. The data are obtained for a set of temperatures between 35 and 0 °C using DMPC-d54 lipid with perdeuterated acyl chains. The DMPC has liquid-crystalline (Lα) phase with disordered chains at higher temperature and rippled gel (Pβ′) or gel phase (Lβ′) with ordered chains at lower temperature. At given temperature T, the no peptide and HAfp, pH 7 samples exhibit similar spectral lineshapes. Spectral broadening with reduced temperature correlates with the transition from Lα to Pβ′ and then Lβ′ phases. At given T, the lineshapes are narrower for HAfp, pH 5 vs. no peptide and HAfp, pH 7 samples, and even narrower for the GPfp sample. These data support larger-amplitude fast (> 10 Hz) lipid acyl chain motion for samples with fusogenic peptides, and peptide interference with chain ordering. The NMR data of the present paper correlate with insertion of these peptides into the hydrocarbon core of the membrane and support a significant fusion contribution from the resultant lipid acyl chain disorder, perhaps because of reduced barriers between the different membrane topologies in the fusion pathway. Membrane insertion and lipid perturbation appear common to both β sheet and helical hairpin peptides.
The new monotypic genus Bardotia (Orobanchaceae) from Madagascar and remarks on the phylogenetic relationships of the African and Madagascan genera Parastriga , Radamaea , Rhamphicarpa and Sieversandreas

The newly described monotypic genus Bardotia, with the new species B. ankaranensis from limestone tsingy in Northern Madagascar, and its differences from Radamaea and Sieversandreas are discussed. The phylogenetic positions of the genera Radamaea , Rhamphicarpa and Sieversandreas are investigated. Bardotia , Radamaea , Rhamphicarpa, and Sieversandreas form a clade. The monotypic Parastriga alectroides nests within Harveya. The new combination Harveya alectroides is made.
Positive attitudes towards feline obesity are strongly associated with ownership of obese cats

Overweight and obesity (O&O) is a risk factor for several health conditions and can result in a shorter lifespan for cats. The objectives of this study were to investigate (a) cat owners’ attitudes towards feline O&O and their associations with O&O in their cats; and (b) the risk factors for feline O&O and underweight, particularly those involving owner practice. An online survey comprising questions related to cat owners’ attitudes towards feline O&O, owner-reported body weight and body condition of their cat, and potential risk factors for feline O&O was conducted. Primarily targeting the Australian population, the survey attracted 1,390 valid responses. In response to ten attitude-related questions, more participants (percentage range among the ten questions: 39.1–76.6%) held a disapproving attitude towards feline O&O than a neutral (17.1–31.9%) or approving attitude (3.9–27.7%). A greater proportion of participants had a more disapproving attitude towards obesity than towards overweight. Cats belonging to owners with an approving attitude towards O&O were more likely to be overweight or obese than cats belonging to owners with a disapproving attitude towards O&O. The cats had particularly high odds of overweight or obesity if their owner agreed that ‘being chubby says that the cat has a quality life’ (OR: 3.75, 95% CI: 2.41–5.82) and ‘being fat says that the cat has a quality life’ (OR: 4.98, 95%CI: 2.79–8.91). This study revealed, for the first time, that begging for food was a risk factor for O&O in cats. Other important feline risk factors for O&O identified included being middle-aged, being mixed-breed, dry food as the major diet, the amount of feed not being quantified, and frequently spending time indoors. Being over 11 years, receiving no dry food and receiving measured amounts of feed were associated with an increased odds of underweight in cats. As specific attitudes often lead to certain behaviours, reducing approving attitudes towards feline O&O may potentially reduce the frequency of O&O and the risks of O&O-related disorders in cats.
Draft Genome Sequence of Erysipelothrix rhusiopathiae, Isolated from a Canine Case of Diskospondylitis

This is the draft genome of an Erysipelothrix rhusiopathiae strain isolated from the blood of a canine. Initial 16S ribosomal DNA amplification identified the isolate as belonging to the Erysipelothrix genus but could not elucidate the species due to previous misidentification of E. rhusiopathiae and E. tonsillarum. The species identification was confirmed by whole-genome sequencing. ABSTRACT This is the draft genome of an Erysipelothrix rhusiopathiae strain isolated from the blood of a canine. Initial 16S ribosomal DNA amplification identified the isolate as belonging to the Erysipelothrix genus but could not elucidate the species due to previous misidentification of E. rhusiopathiae and E. tonsillarum. The species identification was confirmed by whole-genome sequencing.
C-terminal phosphorylation modulates ERM-1 localization and dynamics to control cortical actin organization and support lumen formation during Caenorhabditis elegans development

ABSTRACT ERM proteins are conserved regulators of cortical membrane specialization that function as membrane-actin linkers and molecular hubs. The activity of ERM proteins requires a conformational switch from an inactive cytoplasmic form into an active membrane- and actin-bound form, which is thought to be mediated by sequential PIP2 binding and phosphorylation of a conserved C-terminal threonine residue. Here, we use the single Caenorhabditis elegans ERM ortholog, ERM-1, to study the contribution of these regulatory events to ERM activity and tissue formation in vivo. Using CRISPR/Cas9-generated erm-1 mutant alleles, we demonstrate that a PIP2-binding site is crucially required for ERM-1 function. By contrast, dynamic regulation of C-terminal T544 phosphorylation is not essential but modulates ERM-1 apical localization and dynamics in a tissue-specific manner, to control cortical actin organization and support lumen formation in epithelial tubes. Our work highlights the dynamic nature of ERM protein regulation during tissue morphogenesis and the importance of C-terminal phosphorylation in fine-tuning ERM activity in a tissue-specific context. Summary: CRISPR/Cas9-generated erm-1 mutant alleles reveal that a PIP2-binding site is crucial for ERM-1 function, and phosphorylation of a C-terminal regulatory threonine modulates its localization and dynamics to control actin organization and support lumen formation in development.
Femoral neck fracture detection in X-ray images using deep learning and genetic algorithm approaches

Objectives This study aims to detect frontal pelvic radiograph femoral neck fracture using deep learning techniques. Patients and methods This retrospective study was conducted between January 2013 and January 2018. A total of 234 frontal pelvic X-ray images collected from 65 patients (32 males, 33 females; mean age 74.9 years; range, 33 to 89 years) were augmented to 2106 images to achieve a satisfactory dataset. A total of 1,341 images were fractured femoral necks while 765 were non-fractured ones. The proposed convolutional neural network (CNN) architecture contained five blocks, each containing a convolutional layer, batch normalization layer, rectified linear unit, and maximum pooling layer. After the last block, a dropout layer existed with a probability of 0.5. The last three layers of the architecture were a fully connected layer of two classes, a softmax layer and a classification layer that computes cross entropy loss. The training process was terminated after 50 epochs and an Adam Optimizer was used. Learning rate was dropped by a factor of 0.5 on every five epochs. To reduce overfitting, regularization term was added to the weights of the loss function. The training process was repeated for pixel sizes 50x50, 100x100, 200x200, and 400x400. The genetic algorithm (GA) approach was employed to optimize the hyperparameters of the CNN architecture and to minimize the error after testing the model created by the CNN architecture in the training phase. Results Performance in terms of sensitivity, specificity, accuracy, F1 score, and Cohen’s kappa coefficient were evaluated using five- fold cross validation tests. Best performance was obtained when cropped images were rescaled to 50x50 pixels. The kappa metric showed more reliable classifier performance when 50x50 pixels image size was used to feed the CNN. The classifier performance was more reliable according to other image sizes. Sensitivity and specificity rates were computed to be 83% and 73%, respectively. With the inclusion of the GA, this rate increased by 1.6%. The detection rate of fractured bones was found to be 83%. A kappa coefficient of 55% was obtained, indicating an acceptable agreement. Conclusion This experimental study utilized deep learning techniques in the detection of bone fractures in radiography. Although the dataset was unbalanced, the results can be considered promising. It was observed that use of smaller image size decreases computational cost and provides better results according to evaluation metrics.
Germination behaviour of Italian ryegrass in flooding pampa rangelands

Abstract Lolium multiflorum Lam. , a winter annual grass species originating from the Mediterranean region, has become widespread in native grasslands of the flooding pampa (Argentina). The dynamics of dormancy release of L. multiflorum seeds in simulated natural conditions was studied. Dormancy was overcome by exposing imbibed seeds to mild cool temperatures (15°C or below) for brief periods (pre-chilling). After-ripening progressively released dormancy, at a higher rate in seeds that remained under the canopy (30/20°C) than those that were dry-stored (20°C). Germination was promoted by red light only when the after-ripening requirement was partially fulfilled or after pre-chilling treatment. These results provide useful knowledge for designing grazing strategies aimed at obtaining well-developed ryegrass canopy of high forage quality during winter and spring.
Improved Performance of Flow rate Tracking in a Ventilator using Iterative Learning Control

This paper considers the performance improvement of an artificial ventilator machine in controlling breathing rate actively during the inspiratory cycle and passively in expiratory cycle. Respiratory issues pose a great threat to mankind and may lead to immediate death if proper intervention is not made. Artificial ventilator machine acts like a magic wand which revives a person by spontaneous breathing, reducing the work load of the respiratory muscles. For this purpose, Iterative Learning Control (ILC) can be applied to control the volumetric flow rate of a ventilator machine. As a medical device demands high performance, so ILC alone may not give desired output. Hence a feedback PID controller along with ILC is proposed to improve the control effort and track the error performance of the ventilator. Simulation results are obtained and presented for illustration.
Role of age with some physiological and biochemical parameters in local female buffaloes.

The study included 90 buffalo from Yarimjah in the southern of Mosul city, divided in to three groups, the first group (30) buffalo (1-1.5 years), second group (30) buffalo (5-8) years and the third group (30) buffalo (15-20) years to study the effect of the age progress on some physiological and biochemical parameters as indicator of oxidative stress. The results showed that all of the red blood cells, hemoglobin, packed cell volume increased significantly in the middle ages compared with other groups of the study and the lowest value in the older age group, while platelets increased gradually and significantly with age increase. In addition, white blood cells increases significantly in the middle-aged compared with the study groups, and significantly decreased in older age group while the percentage of eosinophils and neutrophils showed the highest significant value in the older age groups and the lowest value at the small ages , lymphocytes showed a gradual significant decline with increasing age compare with other study groups. monocytes appeared in the highest significant value in the middle ages and the lowest value in the older and small ages groups, there was no significant difference in basophils between the studied groups. On the other hand glutathione appeared with the highest significant value in the middle ages and the lowest value in the older ages, while malondialdehyde increased significantly with gradual age progress, this is due to an increase in free radical production and دلجملا ،ةيرطيبلا مولعلل ةيقارعلا ةلجملا ٢٦ يفاضإ ددع ، ٣ ، ٢٠١٢ ) ٢١٩ ٢٢٣ ( عئاقو ملا ةعماج ،يرطيبلا بطلا ةيلك ،سداسلا يملعلا رمتؤملا لصو
Modeling Chilling Requirement and Diurnal Temperature Differences on Flowering and Yield Performance in Strawberry Crown Production

In North America, over 800 million strawberry crowns are produced by nurseries each year for the strawberry fruit industry. A modeling approach is a quantifiable method to help nurseries predict optimal crown harvest date and potential fruit yield associated with the annual strawberry crown growing environment. Most available models that quantify growth conditions, e.g., chilling effects, use controlled environment chambers and target prediction of time of strawberry flowering, not fruit yield. This study used commercial field fruit yield data over a 6-year period and five geographically distinct locations to construct models to predict the effects of chilling, diurnal temperature difference, and their interaction with daylength on fruit yield and time to flower. Accumulative chilling unit (ACU) was estimated by using nonweighted (simple, M0) and weighted (Mu (Utah Model), M1, M2) accumulation of effective temperature units. The results showed that flowering time correlated with accumulative chilling hours using either a simple (M0) accumulation model or a weighted accumu- lation model (Mu, M1, M2). The best correlation of flowering time with ACU was a quadratic function (y= 82.27 -0.049x +1.74e -5 x 2 ,where y=flowering time,x= ACU) and effective temperatures were from -2 to 15 8C. By contrast, fruit yield was only correlated with ACU using specific weighted accumulation models. The correlation was influenced by weighting factors and effective or inhibitive temperatures involved in the model. Therefore, temperatures have differential effects on fruit yield and on flowering time. Whenpooledacrossregionsandyears,fruit yieldcouldbepredicted onlybytheweighted accumulation Model 2 (M2), a quadratic function (y = -72.15 + 0.98x + 0.0022x 2 ) of the ACU accumulated from 45 d before crown harvest. Fruit yield response to ACU had an optimal level with yield reduction at other values. By contrast, fruit yield linearly increased with increasing difference in diurnal temperature across years and locations. However, the days to first flower were affected interactively by the diurnal temperature difference and daylength when geographically distinct locations are compared. The greater the difference in diurnal temperature at 2 to 3 months before crown harvest, the higher the subsequent fruit yield and the shorter the flowering time. An accumulative diurnal temperature unit of 180 degree-days resulted in 30% yield enhancement of Saskatchewan-grown crowns over California-sourced crowns. The greater diurnal temperature difference may be the major contributor to the Northern Vigour response of strawberry crowns produced in northern latitudes such as Saskatchewan.
An Old Cytokine Against a New Virus?

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. An Old Cytokine Against a New Virus? Sandra Pellegrini, Gilles Uzé
Detection of Human papillomavirus and the role of p16INK4a in colorectal carcinomas

Introduction Human papillomavirus (HPV) infection is associated with the development of anogenital and head and neck cancers. In recent years a potential role of HPV in colorectal cancer (CRC) has been suggested. Objective To investigate the presence of HPV in colorectal carcinomas and to study the role of p16INK4a as a marker of transcriptionally active HPV infection. In addition, to investigate the correlation between these findings and the CRC prognostic factors. Methods Case control study with 92 cases of colorectal cancers, 75 controls of normal tissue adjacent to the tumor, and 30 controls of precursor lesions, including polyps and colorectal adenomas. Paraffinized samples were used, HPV detection and genotyping were performed by PCR and reverse hybridization by using the INNO LIPA kit, with SPF10 plus primers. The expression of the p16INK4a protein was investigated using immunohistochemistry. Data analysis was performed using descriptive, univariate statistics and survival curves were calculated by using the Kaplan Meier and log-rank method. Results HPV was detected in 13% of the cases and the most prevalent genotype was HPV 16. HPV DNA was not detected in either control groups. The high expression of p16INK4a was observed in 30% of the cases, but it was not associated to the presence of HPV. The overall survival was 53.3% and was influenced by prognostic factors such as later stage, lymph node and distant metastasis. Conclusions Based on these results, HPV is unlikely to be involved in colorectal carcinogenesis and p16INK4a expression is not a relevant marker of transcriptionally active HPV infection in CRC.
A Novel lncRNA-Disease Association Prediction Model Using Laplacian Regularized Least Squares and Space Projection-Federated Method

Recent studies indicated that numerous long noncoding RNAs (lncRNAs) are closely related to human diseases and can serve as potential biomarkers and drug targets for complex diseases. Therefore, identifying lncRNAs associated with diseases through computational methods is conducive to the exploration of disease pathogenesis. Most previous studies had shortcomings, such as low prediction accuracy, the need for negative samples, and weak generalization. Such studies established shallow prediction models and failed to fully capture the complex relationships among lncRNA–disease associations, lncRNA similarity, and disease similarity. LRLSSP, a new computational method based on Laplacian regularized least squares (LRLS) and space projection was used to predict candidate disease lncRNAs in this study. LRLSSP deeply integrates information on lncRNA similarity, disease similarity, and known lncRNA–disease associations. The estimated score of lncRNA–disease association was obtained through LRLS, and network projection was utilized to reliably predict disease-related lncRNAs. Leave-one-out cross validation(LOOCV) was implemented to evaluate the prediction performance of LRLSSP. Results showed that LRLSSP performed was better than other state-of-the-art methods in predicting lncRNA–disease associations. In addition, case studies conducted on melanoma,cervical cancer, ovarian cancer and breast cancer indicated that LRLSSP can discover potential and novel lncRNA–disease associations. Overall, the results demonstrated that LRLSSP may serve as a reliable and effective computational tool for disease-related lncRNAs prediction.
A phase I study of toripalimab, an anti‐PD‐1 antibody, in patients with refractory malignant solid tumors

Abstract Background Several programmed cell death ligand 1 (PD‐L1)/programmed cell death protein 1 (PD‐1) antibodies have been approved for cancer treatment worldwide. Their pharmacokinetic and pharmacodynamic characteristics have been reported mainly in western countries, but related data in Chinese patients are limited. This study was conducted to investigate the safety, efficacy, pharmacokinetics, and pharmacodynamics of an anti‐PD‐1 antibody, toripalimab, in Chinese patients. Methods A single‐center phase I study was conducted in Sun Yat‐sen University Cancer Center. Eligible patients were adults with histologically confirmed, treatment‐refractory, advanced, solitary malignant tumors. Toripalimab was intravenously infused every 2 weeks in dose‐escalating cohorts at 0.3 mg/kg, 1 mg/kg, 3 mg/kg, 10 mg/kg, and 240 mg. The study followed standard 3 + 3 design. Results Between 15th March 2016 and 27th September 2016, 25 patients were enrolled, of whom 3 (12.0%), 7 (28.0%), 6 (24.0%), 6 (24.0%), 3 (12.0%) received 0.3 mg/kg, 1 mg/kg, 3 mg/kg, 10 mg/kg, and 240 mg toripalimab, respectively. After a median follow‐up time of 5.0 months (range: 1.5‐19.8 months), we observed that the commonest treatment‐related adverse events (TRAEs) were fatigue (64.0%) and rash (24.0%). No grade 3 or higher TRAEs were observed. No dose‐limiting toxicity, treatment‐related serious adverse events (SAEs), or treatment‐related death occurred. Objective response rate was 12.5%. The half‐life of toripalimab was 150‐222 h after a single dose infusion. Most patients, including those from the 0.3 mg/kg group, maintained complete PD‐1 receptor occupancy (> 80%) on activated T cells since receiving the first dose of toripalimab. Conclusions Toripalimab is a promising anti‐PD‐1 antibody, which was well tolerated and demonstrated anti‐tumor activity in treatment‐refractory advanced solitary malignant tumors. Further exploration in various tumors and combination therapies is warranted.
Waveguide Quadruplet Diplexer for Multi-Beam Satellite Applications

The objective of this paper is to describe the design of an innovative and low-cost diplexer for Ka-band multi-beam satellite applications. The device is based on the use of two quadruplets to implement a number of transmission zeros (TZs) thus obtaining high-selectivity quasi-elliptic transfer functions. The resulting diplexer structure is particularly flexible in terms of layout, does not require tuning and has an excellent high-power behavior. In addition to theory, we compare the results of our simulations with the measurements obtained with a manufactured breadboard. The comparison shows excellent agreement thereby fully validating both the design procedure, and the new diplexer structure.