Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genome analysis of a multidrug-resistant Pseudomonas aeruginosa sequence type 277 clone that harbours two copies of the blaSPM-1 gene and multiple single nucleotide polymorphisms in other resistance-associated genes

Pseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of blaSPM-1 gene, encoding a metallo-beta-lactamase, in addition to other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify physiological key aspects that may lead to the exposure of new targets for therapy. This study was designed to characterize the genome of Pseudomonas aeruginosa CCBH4851 through the detection of genomic features and genome comparison with other Pseudomonas aeruginosa strains. The CCBH4851 closed genome showed features that were consistent with data reported for the specie. However, comparative genomics revealed the absence of genes important for pathogenesis. On the other hand, CCBH4851 genome contained acquired genomic islands that carry additional virulence and antimicrobial resistance-related genes. The presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations could influence the multidrug-resistant behavior of CCBH4851. Overall, the characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed several features that could directly impact the profile of virulence and antibiotic resistance of this pathogen in infectious outbreaks.
CHAAI@SMM4H’22: RoBERTa, GPT-2 and Sampling - An interesting concoction

This paper describes the approaches to the SMM4H 2022 Shared Tasks that were taken by our team for tasks 1 and 6. Task 6 was the “Classification of tweets which indicate self-reported COVID-19 vaccination status (in English)”. The best test F1 score was 0.82 using a CT-BERT model, which exceeded the median test F1 score of 0.77, and was close to the 0.83 F1 score of the SMM4H baseline model. Task 1 was described as the “Classification, detection and normalization of Adverse Events (AE) mentions in tweets (in English)”. We undertook task 1a, and with a RoBERTa-base model achieved an F1 Score of 0.61 on test data, which exceeded the mean test F1 for the task of 0.56.
Guide To Numerical Analysis

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Observational Needs of Sea Surface Temperature

Sea surface temperature (SST) is a fundamental physical variable for understanding, quantifying and predicting complex interactions between the ocean and the atmosphere. Such processes determine how heat from the sun is redistributed across the global oceans, directly impacting large- and small-scale weather and climate patterns. The provision of daily maps of global SST for operational systems, climate modelling and the broader scientific community is now a mature and sustained service coordinated by the Group for High Resolution Sea Surface Temperature (GHRSST) and the CEOS SST Virtual Constellation (CEOS SST-VC). Data streams are shared, indexed, processed, quality controlled, analyzed, and documented within a Regional/Global Task Sharing (R/GTS) framework, which is implemented internationally in a distributed manner. Products rely on a combination of low-Earth orbit infrared and microwave satellite imagery, geostationary orbit infrared satellite imagery, and in situ data from moored and drifting buoys, Argo floats, and a suite of independent, fully characterized and traceable in situ measurements for product validation (Fiducial Reference Measurements, FRM). Research and development continues to tackle problems such as instrument calibration, algorithm development, diurnal variability, derivation of high-quality skin and depth temperatures, and areas of specific interest such as the high latitudes and coastal areas. In this white paper, we review progress versus the challenges we set out 10 years ago in a previous paper, highlight remaining and new research and development challenges for the next 10 years (such as the need for sustained continuity of passive microwave SST using a 6.9 GHz channel), and conclude with needs to achieve an integrated global high-resolution SST observing system, with focus on satellite observations exploited in conjunction with in situ SSTs. The paper directly relates to the theme of Data Information Systems and also contributes to Ocean Observing Governance and Ocean Technology and Networks within the OceanObs2019 objectives. Applications of SST contribute to all the seven societal benefits, covering Discovery; Ecosystem Health & Biodiversity; Climate Variability & Change; Water, Food, & Energy Security; Pollution & Human Health; Hazards and Maritime Safety; and the Blue Economy.
The Testing Method Based on Software Knowledge

In the software testing phase of a software development project, we often use debug testing and operational profile testing methods, and both of them adopts the random testing strategy. In this paper, we advance the software testing method based on knowledge used in the software. The testing method based on software knowledge can be applied to software reliability stable growing test and software safety test, object-oriented software system test, and software system test that adopts reusable components technology.
Production and metabolic consequences of high-energy and low-crude-protein diet fed to 49-wk-old Shaver white leghorn without or with top-dressed organic selenium

Abstract: Production and metabolic consequences of feeding 49-wk-old Shaver white hens a high-energy low-crude-protein (HELP) diet were investigated over 6 wk. The test diets included standard diet [2750 kcal kg-1 apparent metabolizable energy (AME) and 17.5% crude protein (CP)], HELP (3000 kcal kg-1 of AME and 13.0% CP) diet, and HELP top dressed with selenium (HELP + Se). All diets had 0.3 mg Se kg-1 as part of premix. Hens (33) were procured, three birds necropsied for baseline liver samples, and the rest placed in individual cages and allocated diets (n = 10). Feed intake (FI), hen day egg production (HDEP), and egg weight (EW) were monitored weekly. Plasma and liver samples were collected from all birds. Birds fed standard and HELP diets had similar (P > 0.05) FI (with exception of weeks 4 and 5) and HDEP, whereas HELP + Se depressed (P < 0.05) feed and nutrient intake at weeks 5 and 6, HDEP, and EW. There were no (P > 0.05) diet effects on hepatic weight and crude fat content. Birds fed HELP diets had lower (P > 0.05) concentration of plasma total protein, macrominerals, and some enzymes. Overall, HELP diet had minimal impact on production and metabolism; however, addition of Se had negative effects on hen performance.
Spontaneous hypoglycemia: a review

Spontaneous hypoglycemia is an important entity that may affect multiple organs. The differential diagnosis is broad in individuals with hypoglycemia in the absence of diabetes mellitus. Multiple etiologies may be present concurrently. Drugs, critical illnesses, hormone deficiencies, and non-islet cell tumors should be considered in those who are ill or taking medications. In apparently healthy individuals, endogenous hyperinsulinism due to insulinoma, functional β-cell disorders, or insulin autoimmune conditions are possible, as are accidental, surreptitious or factitious causes of hypoglycemia. Investigations should be guided by clinical scenario. Irrespective of the exact cause of the spontaneous hypoglycemia, treatment consists of correcting the glycemic state and preventing recurrence by alleviating underlying pathology. This review discusses the causes, diagnosis and management of spontaneous hypoglycemia. IMC J Med Sci 2019; 13(1): 001
Perennial ryegrass and novel festulolium forage grasses in the tropical highlands of Central Kenya: Preliminary assessment

Two perennial ryegrass (Lolium perenne) varieties and 5 festulolium hybrids (L. perenne × Festuca spp.) were evaluated on-farm for their performance over one growing season on clay loam soils at Ol-joro-Orok in the central highlands of Kenya at about 2,600‒2,800 masl. Seed was sown in May 2015 and fertilizer (90 kg N + 90 kg P/ha) was applied at planting. The study continued for 8 months with harvests after 113, 99 and 32 days (3 growth cycles). Growth attributes assessed included dry matter yield (DMY) and plant height, while forage nutritive value was measured in terms of crude protein (CP), acid detergent fiber (ADF) and neutral detergent fiber (NDF) concentrations. At the end of the first growth cycle, 61 local dairy farmers rated the grasses on criteria they nominated as being important, including DMY, growth rate, height, frost tolerance, disease tolerance and leafiness. Total herbage yields for the whole study period (8 months) ranged from 14.6 to 18.0 t DM/ha for perennial ryegrass and 14.3 to 20.9 t DM/ha for festulolium with very poor growth in the third growth cycle. All perennial ryegrass and festulolium lines contained similar (P>0.05) concentrations of CP (163–190 g/kg DM), ADF (264–281 g/kg DM) and NDF (448–493 g/kg DM). For perennial ryegrass, farmers gave a minimum weighted score of 6.7 and for festulolium, 7.9. Based on herbage production, forage nutritive value and farmers’ assessments, we conclude that all perennial ryegrass and festulolium lines tested have the potential to contribute to improving the forage resource base in this and other similar areas, especially for farmers whose land sizes allow grazing instead of stall-based feeding only. Further studies with N applications after each harvest would determine whether yields can be maintained at high levels for longer than in this study, while grazing and feeding studies would determine how well the pastures support weight gains and milk yields. Studies over a number of years are needed to assess how persistent these varieties/hybrids are in this and other environments.
Evaluation of Strategies to Improve In Vitro Mutagenicity Assessment: Alternative Sources of S9 Exogenous Metabolic Activation and the Development of an In Vitro Assay Based on MutaMouse Primary Hepatocytes

In vitro genetic toxicity tests using cultured bacterial or mammalian cells provide a cost- and time-effective alternative to animal tests. Unfortunately, existing in vitro assays are not always reliable. This is in part due to the limited metabolic capacity of the cells used, which is often critical to accurately assess chemical genotoxicity. This limited metabolic capacity necessitates the use of exogenous sources of mammalian metabolic enzymes that can simulate in vivo mammalian metabolic activation reactions. In response to this, and other limitations, alongside the worldwide trend to reduce animal testing, there is an acute need to consider various strategies to improve in vitro mutagenicity assessment. This thesis first examined the utility of exogenous metabolic activation systems based on human hepatic S9, relative to conventional induced rat liver S9, for routine genetic toxicity assessment. This was accomplished by critically evaluating existing literature, as well as new experimental data. The results revealed the limitations of human liver S9 for assessment of chemical mutagenicity. More specifically, the analyses concluded that, due to the increased risk of false negative results, human liver S9 should not be used as a replacement for induced rat liver S9. To address the limitations of conventional mammalian cell genetic toxicity assays that require exogenous hepatic S9, the thesis next evaluated the utility of an in vitro mutagenicity assay based on metabolically-competent primary hepatocytes (PHs) derived from the transgenic MutaMouse. Cultured MutaMouse PHs were thoroughly characterized, and found to temporarily retain the phenotypic attributes of hepatocytes in vivo; they express hepatocyte-specific proteins, exhibit the karyotype of typical hepatocytes, and maintain metabolic activity for at least the first 24 hours after isolation. Preliminary validation of the in vitro MutaMouse PH gene mutation assay, using a panel of thirteen mutagenic and non-mutagenic chemicals, demonstrated excellent sensitivity and specificity. Moreover, inclusion of substances requiring a diverse array of metabolic activation pathways revealed comprehensive metabolic competence. Finally, the thesis further investigated the applicability domain of the in vitro MutaMouse PH assay by challenging the assay with selected azo compounds. Comparison of these results with those obtained using the in vivo MutaMouse TGR (transgenic rodent) assay revealed that MutaMouse PHs can carry out some forms of reductive metabolism. Overall, this thesis demonstrated that a gene mutation assay based on MutaMouse PHs holds great promise for routine assessments of chemical mutagenicity.
On Biped Walking of Humanoid Robot Based on Movement Similarity

A design method of biped walking actions of humanoid robot based on the movement similarity of human body is proposed.The system of parameter acquiring and similarity matching for human walking trajectory is improved,and the application range of similarity function is extended.The key postures and the sub-stage transformations during biped walking period are defined through the characteristics of mechanic chains of the humanoid robot,the constraint equations of movements are built,and the corresponding problems in the dynamic stabilization when walking are also restricted.The validity of this method is confirmed by simulation and actual robot experiment.
Genetic Variation of Calpastation Gene of Indigenous Bali Cattle (Bos javanicus) in Indonesia

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.
Sequential Operations Revealed by Serendipitous Feature Selectivity in Frontal Eye Field

Neurons in macaque frontal eye field contribute to spatial but typically not feature selection during visual search. Using an innovative visual search task, we report a serendipitous discovery that some frontal eye field neurons can develop rapid selectivity for stimulus orientation that is used to guide gaze during a visual search task with pro-saccade and anti-saccade responses. This feature selectivity occurs simultaneously at multiple locations for all objects sharing that feature and coincides with when neurons select the singleton of a search array. This feature selectivity also reveals the distinct, subsequent operation of selecting the endpoint of the saccade in pro-saccade as well as anti-saccade trials. These results demonstrate that target selection preceding saccade preparation is composed of multiple operations. We conjecture that singleton selection indexes the allocation of attention, which can be divided, to conspicuous items. Consequently, endpoint selection indexes the focused allocation of attention to the endpoint of the saccade. These results demonstrate that saccade target selection is not a unitary process. SIGNIFICANCE STATEMENT Frontal eye field is well known to contribute to spatial selection for attention and eye movements. We discovered that some frontal eye field neurons can acquire selectivity for stimulus orientation when it guides visual search. The chronometry of neurons with and without feature selectivity reveal distinct operations accomplishing visual search.
Expression characterization and transcription regulation analysis of porcine Yip1 domain family member 3 gene

Objective The Yip1 domain family (YIPF) proteins were proposed to function in endoplasmic reticulum (ER) to Golgi transport and maintenance of the morphology of the Golgi, which were homologues of yeast Yip1p and Yif1p. YIPF3, the member 3 of YIPF family was a homolog of Yif1p. The aim of present study was to investigate the expression and regulation mechanism of porcine YIPF3. Methods Quantitative realtime polymerase chain reaction (qPCR) was used to analyze porcine YIPF3 mRNA expression pattern in different tissues and pig kidney epithelial (PK15) cells stimulated by polyinosine-polycytidylic acid (poly [I:C]). Site-directed mutations combined with dual luciferase reporter assays and electrophoretic mobility shift assay (EMSA) were employed to reveal transcription regulation mechanism of porcine YIPF3. Results Results showed that the mRNA of porcine YIPF3 (pYIPF3) was widely expressed with the highest levels in lymph and lung followed by spleen and liver, while weak in heart and skeletal muscle. Subcellular localization results indicated that it expressed in Golgi apparatus and plasma membranes. Upon stimulation with poly (I:C), the level of this gene was dramatically up-regulated in a time- and concentration-dependent manner. pYIPF3 core promoter region harbored three cis-acting elements which were bound by ETS proto-oncogene 2 (ETS2), zinc finger and BTB domain containing 4 (ZBTB4), and zinc finger and BTB domain containing 14 (ZBTB14), respectively. In which, ETS2 and ZBTB4 both promoted pYIPF3 transcription activity while ZBTB14 inhibited it, and these three transcription factors all played important regulation roles in tumorigenesis and apoptosis. Conclusion The pYIPF3 mRNA expression was regulated by ETS2, ZBTB4, and ZBTB14, and its higher expression in immune organs might contribute to enhancing ER to Golgi transport of proteins, thus adapting to the immune response.
Transcriptome profiling in Camellia japonica var. decumbens for the discovery of genes involved in chilling tolerance under cold stress

Camellia japonica var. decumbens is a naturally occurring highly cold resistant variety of Camellia japonica which is suitable for snowy and cold regions. However, the underlying cold-adaptive mechanisms associated with gene regulation have been poorly investigated. We analyzed the transcriptomic changes caused by cold stress in a cold-tolerant accession. Samples were collected at the end of each temperature treatment (T1, T3, T5, T7 and T9 represent the temperatures 25°C, 0°C, -4°C, -8°C and -12°C, respectively). Sample T1 at 25°C was used as control. Based on transcriptome analysis, 2828, 2384, 3099 and 3075 differentially expressed genes (DEGs) were up-regulated, and 3184, 2592, 2373 and 2615 DEGs were down-regulated by analyzing T3/T1, T5/T1, T7/T1 and T9/T1, respectively. A gene ontology (GO) analysis revealed an enrichment of GO terms such as response to stimulus, metabolic process, catalytic activity or binding. Out of the larger number of DEGs, 67 functional and regulatory DEGs stood out, since they were functionally characterized in other models. These genes are cold-responsive transcription factors (26) or involved in cold sensor or signal transduction (17) and in the stabilization of the plasma membrane and osmosensing response (24). These results suggest rapid and multiple molecular mechanisms of perception, transduction and responses to cold stress in cold acclimation of Camellia japonica var. decumbens. They could also serve as a valuable resource for relevant research on cold-tolerance and help to explore cold-related genes to foster the understanding of low-temperature tolerance and plant-environment interactions.
Silage of rehydrated corn grain

ABSTRACT The objective with this study was to evaluate the effect of different levels of water inclusion on the chemical composition and fermentation profiles of reconstituted corn grain silage. The experiment was carried out in a factorial arrangement in a completely randomized design, with three replicates per treatment. Five treatments were evaluated with different levels of water inclusion (% of the natural matter): dry corn grain (control); 90% dry corn grain (DCG) and 10% water; 80% DCG and 20% water; 70% DGC and 30% water; and 60% DCG and 40% water, totaling 45 experimental silos. Inclusion of water in the silage of reconstituted corn grain promoted a reduction in the CP (%) and NDF (%) contents. However, the water increase elevated the NPN/TN contents and the amount of effluent, gas and dry matter (%) losses. The treatment with inclusion of 30% water in the natural matter leads to a better fermentation profile and fewer losses of effluent and dry matter, so it is recommended for ensiling dry ground corn grain.
Evaluation of Scoring Function Performance on DNA-ligand Complexes

DNA has been a pharmacological target for different types of treatment, such as antibiotics and chemotherapy agents, and is still a potential target in many drug discovery processes. However, most docking and scoring approaches were parameterised for protein-ligand interactions; their suitability for modelling DNA-ligand interactions is uncertain. This study investigated the performance of four scoring functions on DNA-ligand complexes. Here, we explored the ability of four docking protocols and scoring functions to discriminate the native pose of 33 DNA-ligand complexes over a compiled set of 200 decoys for each DNA-ligand complexes. The four approaches were the AutoDock, ASP@GOLD, ChemScore@GOLD and GoldScore@GOLD. Our results indicate that AutoDock performed the best when predicting binding mode and that ChemScore@GOLD achieved the best discriminative power. Rescoring of AutoDock-generated decoys with ChemScore@GOLD further enhanced their individual discriminative powers. All four approaches have no discriminative power in some DNA-ligand complexes, including both minor groove binders and intercalators. This study suggests that the evaluation for each DNA-ligand complex should be performed in order to obtain meaningful results for any drug discovery processes. Rescoring with different scoring functions can improve discriminative power.