Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of aPasteurella multocidaPlasmid and Its Use to Express Recombinant Proteins inP. multocida

Abstract The complete nucleotide sequence of a naturally occurring 5.36-kb streptomycin and sulphonamide resistance plasmid, designated pIG1, isolated from type D Pasteurella multocida was determined. A 1.6-kb noncoding region and a 1.4-kb region encoding three putative proteins were shown by sequence homologies and functional characterizations to be involved in the replication and mobilization of pIG1, respectively. The remaining sequence carried an unusual arrangement of streptomycin- and sulphonamide-resistant genes when compared to various other plasmids. It appears that the antibiotic resistance region of pIG1 may have evolved by recombination between three different short direct repeat DNA sequences. A 4.5-kb recombinant plasmid was constructed by replacing the antibiotic resistance genes of pIG1 with a kanamycin resistance gene and seven unique restriction sites. The resulting plasmid, designated pIG112, stably replicates in P. multocida, Pasteurella haemolytica, Actinobacillus pleuropneumoniae, and Escherichia coli and can be introduced into these organisms by either transformation or conjugation. This vector exists at approximately 70 copies per cell in P. multocida and approximately 20 copies per cell in E. coli. To demonstrate plasmid-borne gene expression in P. multocida, the P. multocida dermonecrotic toxin gene, toxA, and a genetically modified form of this gene were cloned into pIG112 and expressed in high amounts in a nontoxigenic P. multocida strain. Cell culture assays demonstrated that nontoxigenic P. multocida expressing toxA was cytopathic, whereas a strain expressing the modified toxA derivative was not.
New Unsaturated Biodegradable Poly(ester amide)s Composed of Fumaric Acid, L-leucine and α,ω-Alkylene Diols

The synthesis of α-amino acid L-leucine (Leu) based high-molecular-weight and biodegradable unsaturated poly(ester-amide)s (PEAs) was reported. Amino acid L-phenylalanine (Phe) was used to synthesize some copolymers for a comparative study. The syntheses of three types of new unsaturated PEA polymers were explored – (i) Unsaturated PEA homopolymers (UPEAs) composed of fumaric acid, aliphatic diol and one alpha-amino acid: L-Leu or L-Phe; (ii) L-Leu-based unsaturated-saturated copolymers (USPEAs) composed of aliphatic diol, fumaric and saturated fatty diacid, and (iii) L-Leu- and L-Phe-based copolymers (co-UPEAs) composed of 100% fumaric acid, aliphatic diol and combinations of both amino acids. Many of the targeted unsaturated polymers were soluble in common organic solvents and showed good film-forming property. The unsaturated PEA polymers were further chemically modified into functional derivatives and subjected to thermal and photochemical transformations (curing) that substantially expand material properties and, hence, the scopes of potential applications as absorbable surgical devices and drug carriers.
Peanut resistance to Sclerotinia minor and S. sclerotiorum

The fungi Sclerotinia minor and S. sclerotiorum are the causal agents of two similar diseases of peanut (Arachis hypogaea L.). Both diseases cause significant losses in the Australian peanut industry. Development of cultivars with resistance to Sclerotinia will be an important component of integrated control. The aims of this project are to generate information that will assist in breeding for Sclerotinia resistance in peanut: to identify Sclerotinia-resistant peanut germplasm, to understand the inheritance and estimate heritability of resistance, and to test the effectiveness of identified sources of resistance against both S. minor and S. sclerotiorum. This study has clearly established that material that shows resistance to S. minor in the USA is resistant to S. minor and likely to be resistant to S. sclerotiorum in Australia. The high level of resistance to both S. minor and S. sclerotiorum in germplasm from Texas, particularly TxAG-4, was confirmed. VA 93B showed good resistance in the field, which is primarily due to the open bush type rather than physiological resistance. Physiological resistance to S. minor was also identified in a cultivar and a landrace from Indonesia and a rust-resistant line from Queensland. All germplasm found to have high physiological resistance to S. minor belonged to the Spanish type. Inheritance of physiological resistance to S. minor was studied using a Generation Means Analysis (GMA) of the cross TxAG-4/VA 93B and its reciprocal. The broad-sense heritability of physiological resistance on a single plant basis was estimated at 47%, much higher than earlier estimates obtained in field studies. The average gene action of Sclerotinia resistance genes from TxAG-4 was found to be additive. No dominance effects were detected in the GMA. A small but significant reciprocal effect between TxAG-4 and VA 93B indicated that VA 93B passed on some physiological resistance maternally. An experiment was conducted to confirm the value of resistance against both S. minor and S. sclerotiorum. TxAG-4 was found to have physiological resistance to both S. minor and S. sclerotiorum. This resistance was expressed against both Sclerotinia species by progeny that were selected for resistance to S. minor. On the basis of the information obtained, the comparative advantages of 3 strategies for Sclerotinia-resistant cultivar development are discussed: (1) introduction of germplasm; (2) recurrent backcrossing with screening and crossing in the BCnF1 generation; and (3) pedigree selection. At present, introduction and backcrossing are recommended as the preferred strategies.
The Determination of the Readily Available Phosphorus of Soils1

(3), and Shedd (6). The N/5 nitric acid method, developed in this country largely by Peter and Averitt (4), by Stoddart (7), and by Fraps (2), and ~% citric acid method, developed in England by Dyer (~), have probably been the most successful of the methods proposed. Until recently, investigators have been handicapped in working on this problem by a lack of. a satisfactory method for determining small amounts of phosphorus quick, ly and accurately. The development of the Denig~ colorimetrie method for phosphorus in recent years has entirely eliminated this handicap. The perfected method is, undoubtedly, one of the most satisfactory colorirnetric methods in existence. For a detailed discussion of this method the reader is referred to the paper by Truog and Meyer (8).
Difficulties of Identifying the Early HIV Antibody Seroconversion Period Depending on the Confirmatory Assay

Abstract Background Identification of HIV infection at the early stage is valuable for patient management, for prevention, and for research purposes. In practice, identification of a recent HIV infection at diagnosis proves challenging after HIV antibody seroconversion but can be suspected using Western blots (WBs) or immunoblots (IBs) as confirmatory assays. Methods Five commercially available confirmatory assays were compared using 43 samples from recently infected individuals. This included 2 WBs (New LAV Blot I, Biorad, and HIV Blot 2.2, MP Biomedicals), 2 IBs (INNO-LIA HIV I/II, Fujirebio, and RecomLine HIV-1 & HIV-2, Mikrogen Diagnostik), and 1 immunochromatographic single-use assay (Geenius HIV1/2 supplemental assay, Biorad). Results Following the manufacturer’s recommendations for interpretation, the 2 WBs led to indeterminate results for 30% and 42% of the samples, suggesting recent infection, compared with 2%–7% for the 3 other assays. When interpreted based on the Fiebig classification, concordant stages were observed in 42% of samples, and only 49% were classified as early seroconversion by all 5 assays. For the remaining specimens, the distinction with chronic infection was highly variable depending on the assay (5%–100%). Conclusions Clinical laboratories must consider this variability, which must be kept in mind both for initial diagnosis and for multicenter studies for which inclusion criteria refer to serological profiles by confirmatory assays.
The effects of knee arthroplasty on plasma vitamin C concentrations and cognitive function: a case study

Abstract Post-operative neurocognitive disorders are becoming well-documented conditions, with their pathogenesis remaining unclear. Vitamin C is a molecule that has recently demonstrated both a potential link with cognitive function and a significant post-operative decline. Here, we present a case study of a 72-year-old male who underwent total knee replacement surgery. The patient demonstrated a substantial decline in plasma vitamin C concentrations, indicative of a severe deficiency, during the first post-operative week (post-operative Days 3 and 7). Similarly, at these time points, a number of validated paper and pen tests revealed a substantial decline in cognition on tasks relating to total recall, delayed recall, motor speed, recognition and motor speed, with no signs of delirium. These results provide the justification for larger, cohort studies to determine whether post-operative plasma vitamin C depletions could contribute to cognitive deficits post-operatively.
Epstein–Barr Virus Nuclear Antigen 2–Estrogen Receptor Fusion Proteins Transactivate Viral and Cellular Genes and Interact with RBP-Jκ in a Conditional Fashion

Abstract Epstein–Barr virus nuclear antigen 2 (EBNA2) is a transcriptional activator of viral and cellular genes involved in B cell transformation by EBV and is targeted to EBV responsive promoters through interaction with cellular DNA binding proteins such as RBP-Jκ. To develop a conditional system in which the function of EBNA2 can be switched on and off, we have fused the hormone binding domain of the estrogen receptor to the N- or C-terminus of EBNA2. Here we show that after transient or stable transfer of these chimerical EBNA2 genes into human B cell lymphoma lines, transactivation of LMP1, TP1, and TP2 promoter constructs, expression of the cell surface markers CD21 and CD23, and binding of EBNA2 to its cellular partner RBP-Jκ are dependent on the presence of estrogen. The EBNA2 fusion proteins proved to be virtually inactive in the absence of hormone.
Effect of Linseed Oil Calcium Salt on the Methane Emission and Carcass Characteristics of Beef Cattle.

褐毛和種去勢牛12頭を，アマニ油脂肪酸カルシウムを4%添加した濃厚飼料を給与する油脂区（6頭）と無添加の濃厚飼料を給与する対照区（6頭）に分け，14ヵ月齢から10ヵ月間肥育を行い，この間のメタン発生と肥育成績を比較検討した．乾物摂取量（DMI）あたりのメタン発生量は，有意な差ではなったが，試験期間を通じて対照区よりも油脂区で小さな値を示した．また，アマニ油脂肪酸カルシウム添加によるメタン発生の減少量は不飽和脂肪酸摂取量から計算される減少量の7割程度であったことから，アマニ油脂肪酸カルシウムはメタン発生抑制に効果があったと考えられた．油脂区は対照区よりも増体成績が優れ，日増体量あたりのメタン発生量は，有意な差ではないものの13%低い値を示した．以上の結果からアマニ油脂肪酸カルシウムの添加は，DMIあたりのメタン発生を抑制し，増体成績を改善することにより，増体あたりのメタン発生量を削減する可能性が示唆された．
The carotenoid-labeling method: measuring specific rates of carotenoid synthesis in natural phytoplankton communities

The physiological basis of the carotenoid-I4C-labeling method for the determination of growth rates ( p , d-') of specific groups of microalgae was established in the laboratory and the method was tested in the subarctic Paclfic and in Chesapeake Bay (USA). '%labelin9 patterns of carotenoids in a variety of algal species grown in batch cultures were descnbed successfully with a s~mple precursor-pigment model whose free parameters, the specific rate of carotenoid synthesis (p,,,,, d-') and the precursor and the pigment turnover rates (d-l), were determined by least squares analysis. AU xanthophylls except peridinin had turnover rates that did not differ significantly from zero; the turnover rate of peridinin was 0.7 p. Precursor turnover rates varied from about 5 p for fucoxanthin to 36 p for lutein. We propose to use the precursor-pigment model to calculate p,, from the amount of I4C incorporated into carotenoids and values of carotenoid precursor turnover rates, which are assumed to be known a priori. A well-constrained estimate of the fucoxanthin precursor turnover rate is presented here. It was shown for laboratory cultures that the carotenoid-labeling method is capable of measuring specific rates of carotenoid synthesis and that these rates equal rates of cell growth only when growth is balanced. We demonstrated that pigment synthesis and carbon flxation can be unbalanced in natural phytoplankton populations due to the effects of light perturbations and growth under a natural photocycle. We recommend that labeling experiments last 24 h to average rates of synthesis over the die1 photoperiod since rates of carotenoid synthesis and cell growth can be unbalanced at any time during the photoperiod. The field experiments also demonstrated that the carotenoid-labeling method is a powerful tool to study the physiological ecology of natural populations of phytoplankton.
H2BR: an HTTP/2-based retransmission technique to improve the QoE of adaptive video streaming

HTTP-based Adaptive Streaming (HAS) plays a key role in over-the-top video streaming. It contributes towards reducing the rebuffering duration of video playout by adapting the video quality to the current network conditions. However, it incurs variations of video quality in a streaming session because of the throughput fluctuation, which impacts the user's Quality of Experience (QoE). Besides, many adaptive bitrate (ABR) algorithms choose the lowest-quality segments at the beginning of the streaming session to ramp up the playout buffer as soon as possible. Although this strategy decreases the startup time, the users can be annoyed as they have to watch a low-quality video initially. In this paper, we propose an efficient retransmission technique, namely H2BR, to replace low-quality segments being stored in the playout buffer with higher-quality versions by using features of HTTP/2 including (i) stream priority, (ii) server push, and (iii) stream termination. The experimental results show that H2BR helps users avoid watching low video quality during video playback and improves the user's QoE. H2BR can decrease by up to more than 70% the time when the users suffer the lowest-quality video as well as benefits the QoE by up to 13%
Genome-wide identification and expression analysis of SnRK2 gene family in mungbean (Vigna radiata) in response to drought stress

Abstract. Drought stress causes lower crop production globally. Plants have acquired many adaptations to overcome drought stress. Mungbean (Vigna radiata (L.) R.Wilczek) is a legume crop widely cultivated in South, East and Southeast Asia. It is grown in high-temperature areas where drought is the main cause of reduced plant growth and productivity. Plants cope with drought stress by activating different signalling mechanisms. The sucrose non-fermenting-1-related protein kinase 2 family (SnRK2s) is known to play vital roles in osmotic stress and in abscisic acid (ABA) signalling pathways by phosphorylating downstream targets. The genes encoding SnRK2s in mungbean and their detailed characterisation remain unexplored. We have conducted extensive genome-wide analysis for gene prediction, in silico gene analysis, evolutionary analysis and gene-expression profiling under drought-stress conditions by quantitative real-time PCR. Through genome-wide analysis, eight SnRK2 genes were predicted in the mungbean genome and were assigned the names VrSnRK2.1–VrSnRK2.8, according to their order on the chromosomes. The VrSnRK2 genes identified were classified into three clusters based on their phylogenetic relationship with those of Arabidopsis thaliana. Drought stress was imposed on 11-day-old mungbean plants by completely withholding water for 3 days. According to real-time qPCR data, the expression of most of the VrSnRK2 genes was induced by drought stress, indicating their role in the drought-stress response. One of the genes, namely SnRK2.6c, showed highest expression level (12-fold) under drought stress, possibly indicating a critical role under water-deficit conditions. These data provide important information about the VrSnRK2 gene family in mungbean. The results will help in future functional characterisation of VrSnRK2 genes.
Parallel Space Traveling: A Security Analysis of App-Level Virtualization in Android

App-level virtualization becomes increasingly popular. It allows multiple instances of an application to run simultaneously on the same Android system, without requiring modification of the Android firmware. These virtualization-capable apps are used by more than 100 million users worldwide. We conduct a systematic study of the implementation of app-level virtualization and the security threats that their users may face. First, we survey more than 160 apps collected from several popular app markets which can provide application virtualization capability. We find that these apps are implemented based on a similar design, and apps running in such a virtual environment are not completely isolated from each other. Second, we analyze malicious virtualized guest apps, and identify several areas of potential attack vectors, including privilege escalation, code injection, ransomware, etc. Malicious virtualized guest apps can launch reference hijacking attacks. Once a legitimate app is running in the virtual context, all of its sensitive data will be exposed to the host app. Third, we find a new type of repackaging attack. In our collection of 2 million app data set, we find that 68 apps pack and load malwares by using the virtualization technology to evade antivirus detection, 91 apps pack some legal apps for the purpose of wide distribution, and insert screen ads to gain profits at its startup. Finally, we discuss a variety of mitigation solutions for users, developers and vendors.
Monitoring and forecasting the number of reported and unreported cases of the COVID-19 epidemic in Brazil using Particle Filter

In this paper, we combine algorithm of Liu & West for the Particle Filter (PF) with SIRU-type epidemic model to monitor and forecast cases of Covid-19 in Brazil from February up to September. We filter the number of cumulative reported cases and estimate model parameters and more importantly unreported infectious cases (asymptomatic and symptomatic infectious individuals). The parameters under study are related to the attenuation factor of the transmission rate and the fraction of asymptomatic infectious becoming reported as symptomatic infectious. Initially, the problem is analysed through Particle Swarm Optimization (PSO) based simulations to provide initial guesses, which are then refined by means of PF simulations. Subsequently, two additional steps are performed to verify the capability of the adjusted model to predict and forecast new cases. According to the results, the pandemic peak is expected to take place in mid-June 2020 with about 25,000 news cases per day. As medical and hospital resources are limited, this result shows that public health interventions are essential and should not be relaxed prematurely, so that the coronavirus pandemic is controlled and conditions are available for the treatment of the most severe cases.
MR Imaging Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer

Tumor hypoxia levels range from mild to severe and have different biological and therapeutical consequences, but are not easily assessable in patients. We present a method based on diagnostic dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) that visualizes a continuous range of hypoxia levels in tumors of cervical cancer patients. Hypoxia images were generated using an established approach based on pixel-wise combination of the DCE-MRI parameters Ve and Ktrans, reflecting oxygen consumption and supply, respectively. An algorithm to retrieve hypoxia levels from the images was developed and validated in 28 xenograft tumors, by comparing the MRI-defined levels with hypoxia levels derived from pimonidazole stained histological sections. We further established an indicator of hypoxia levels in patient tumors based on expression of nine hypoxia responsive genes. A strong correlation was found between these indicator values and the MRI-defined hypoxia levels in 63 patients. Chemoradiotherapy outcome of 74 patients was most strongly predicted by moderate hypoxia levels, whereas more severe or milder levels were less predictive. By combining gene expression profiles and MRI-defined hypoxia levels in cancer hallmark analysis, we identified a distribution of levels associated with each hallmark; oxidative phosphorylation and G2/M checkpoint were associated with moderate hypoxia, and epithelial-to-mesenchymal transition and inflammatory responses with significantly more severe levels. At the mildest levels, interferon response hallmarks, together with stabilization of HIF1A protein by immunohistochemistry, appearred significant. Thus, our method visualizes the distribution of hypoxia levels within patient tumors and has potential to distinguish levels of different prognostic and biological significance.
Modelling the thermal inactivation of viruses from the Coronaviridae family in suspensions or on surfaces with various relative humidities.

Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-values (time to obtain a log10 reduction of virus infectivity), including values for SARS-CoV-2, were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global dataset of D-values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points or new coronavirus strains.
Clonality of Mycobacterium ulcerans by Using VNTR-MIRU Typing in Ivory Coast (Côte d’Ivoire), West Africa

Background: Buruli ulcer (BU) is neglected skin disease caused by Mycobacterium ulcerans. The lack of early diagnosis and treatment causes severe disability. In Central and in West Africa, BU is endemic and its control is difficult because the most cases occur in rural regions. The molecular particularity of M. ulcerans was the acquisition of the virulence plasmid pMUM001. Genetic analyses have demonstrated the high diversity with variable number tandem repeats (VNTR) and Mycobacterial Interspersed Repetitive Units (MIRU) in M. ulcerans and in mycolactone producing Mycobacteria (MPMs). Original Research Article Solange et al.; IJTDH, 7(4): 163-171, 2015; Article no.IJTDH. 2015.069 164 Objective: The objective of this study was to investigate the molecular diversity by using MIRUVNTR method in clinical samples of BU patients in Cote d’Ivoire. Study Design: 21 clinical samples were collected from BU patients in different sites and were first analyzed in molecular diagnosis of BU using two targets insertion sequence IS2404 and keto reductase-B-domain (KR). In a second step, we have analyzed the strains by PCR typing for four specific and sensitive markers MIRU1, VNTR6, ST-1 and VNTR19. Results and Conclusion: 100% of clinical samples were positive in molecular tests for IS2404 and 95% for KR and confirm M. ulcerans in the samples. By PCR typing, we have found 61.9 % positive for MIRU1 and 52%, 85.7%, and 61.9% for VNTR6, ST-1 and VNTR19 respectively. One of sample was negative for all genotyping markers. Two different genetic profiles were identified by MIRU1 and ST-1 loci by gel-analyzed of the amplified products. The VNTR profile C (3,1,1) corresponding of 3 copies MIRU1, 1 copy VNTR6 and 1 copy ST-1 was detected in 28.5% of samples and confirms the West African genotype in Cote d’Ivoire. Different genetic strains of M. ulcerans were co-circulated in the same endemic region in the country. This study has described first the circulating of different genetic strains of M. ulcerans in Cote d’Ivoire.