Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Phylogenetic Analysis of Caprine Arthritis Encephalitis Virus Using TaqMan-based qPCR in Eastern China

Simple Summary Caprine arthritis encephalitis is an infectious disease caused by the caprine arthritis encephalitis virus (CAEV). This virus can impair the quality of goat’s milk, lamb, and other goat products. Most goats are latently infected with this virus and become long-term carriers, so the development of a rapid and accurate diagnostic method is necessary. Therefore, we constructed a TaqMan real-time quantitative polymerase chain reaction (RT-qPCR) assay and used it to detect CAEV in sheep in eastern China. We found that the prevalence of CAEV infection in sheep in eastern China was 0.77%. This method yields positive results when testing positive references and negative results when testing negative controls or other viruses. The consistency of these results was confirmed through repeating the experiment multiple times. It demonstrated excellent sensitivity, specificity, and reproducibility and holds great promise for its potential application in clinical and field samples in the future. Abstract Caprine arthritis encephalitis is an infectious disease caused by the caprine arthritis encephalitis virus that infects goats, sheep, and other small ruminants. An outbreak of CAEV could be extremely harmful to the goat farming industry and could cause severe economic losses. We designed specific primers and probes for the gag gene and established a TaqMan real-time quantitative polymerase chain reaction assay. This method’s correlation coefficient (R2) was >0.999, and the sensitivity of the assay to the plasmid-carried partial gag gene was approximately 10 copies/µL, 1000 times higher than that of conventional PCR. No specific fluorescence was detected for other sheep viruses. Using this method, we tested 776 asymptomatic sheep blood samples and 4 neurodegenerative sheep brain samples from six farms in eastern China, and the positivity rate was 0.77% (6/780). The gag gene was partially sequenced in the three positive samples and compared with the sequences from other representative strains in GenBank. The results revealed that all three strains belonged to the B1 subtype and were most closely related to the strains from Shanxi and Gansu, previously isolated in China, with their homology ranging from 97.7% to 98.9%. These results suggest that the designed RT-qPCR assay can be used to detect subclinical CAEV in sheep and that the virus is still present in eastern China.
This Paper Is Included in the Proceedings of the 12th Usenix Symposium on Operating Systems Design and Implementation (osdi '16). Unobservable Communication over Fully Untrusted Infrastructure Unobservable Communication over Fully Untrusted Infrastructure

Keeping communication private has become increasingly important in an era of mass surveillance and state-sponsored attacks. While hiding the contents of a conversation has well-known solutions, hiding the associated metadata (participants, duration, etc.) remains a challenge, especially if one cannot trust ISPs or proxy servers. This paper describes a communication system called Pung that provably hides all content and metadata while withstanding global adversaries. Pung is a key-value store where clients deposit and retrieve messages without anyone— including Pung's servers—learning of the existence of a conversation. Pung is based on private information retrieval , which we make more practical for our setting with new techniques. These include a private multi-retrieval scheme, an application of the power of two choices, and batch codes. These extensions allow Pung to handle 10 3 × more users than prior systems with a similar threat model.
Phylogeographical Analysis of mtDNA Data Indicates Postglacial Expansion from Multiple Glacial Refugia in Woodland Caribou (Rangifer tarandus caribou)

Glacial refugia considerably shaped the phylogeographical structure of species and may influence intra-specific morphological, genetic, and adaptive differentiation. However, the impact of the Quaternary ice ages on the phylogeographical structure of North American temperate mammalian species is not well-studied. Here, we surveyed ∼1600 individuals of the widely distributed woodland caribou (Rangifer tarandus caribou) using mtDNA control region sequences to investigate if glacial refugia contributed to the phylogeographical structure in this subspecies. Phylogenetic tree reconstruction, a median-joining network, and mismatch distributions supported postglacial expansions of woodland caribou from three glacial refugia dating back to 13544–22005 years. These three lineages consisted almost exclusively of woodland caribou mtDNA haplotypes, indicating that phylogeographical structure was mainly shaped by postglacial expansions. The putative centres of these lineages are geographically separated; indicating disconnected glacial refugia in the Rocky Mountains, east of the Mississippi, and the Appalachian Mountains. This is in congruence with the fossil record that caribou were distributed in these areas during the Pleistocene. Our results suggest that the last glacial maximum substantially shaped the phylogeographical structure of this large mammalian North American species that will be affected by climatic change. Therefore, the presented results will be essential for future conservation planning in woodland caribou.
Development of Mobile Learning (My Repro) Based on Contextual Teaching Learning to Improve Cognitive Understanding Senior High School Student

During the current pandemic, the utilization of technology is needed in teaching and learning activities. It supports the emergence of Android-based learning innovations. Likewise, biology learning is accompanied by contextual learning related to everyday life. This study aimed to develop learning materials based on contextual teaching-learning and analyze the validity of learning media and cognitive understanding. This research used the 4-D model development method by Thiagarajan (Define, Design, Develop, Disseminate). The subjects were media experts and material experts, while the product's effectiveness was tested on 56 students of class XI MIPA at SMAN 1 Semaka. The results showed that the validation scores of material experts and media experts were 92.39% and 92.61%, respectively, with very valid criteria. Analysis of students' cognitive understanding showed high criteria with an average N-gain value of 0.70 (high criterion). Based on the research analysis results, it can be concluded that learning media mobile learning based on contextual teaching-learning have been valid and effectively used as a learning resource for high school students.
Spermatogenesis and the fine structure of the mature spermatozoon of the liver fluke, Fasciola hepatica (Trematoda: Digenea)

SUMMARY Spermatogenesis and the fine structure of the mature spermatozoon of Fasciola hepatica have been studied by transmission electron microscopy. The primary spermatogonia display a typical gonial morphology and occupy the periphery of the testis. They undergo 3 mitotic divisions to give rise to 8 primary spermatocytes forming a rosette of cells connected to a central cytophore. The primary spermatocytes undergo 2 meiotic divisions, resulting in 32 spermatids that develop into spermatozoa. Intranuclear synaptonemal complexes in primary spermatocytes confirm the first meiotic division. The onset of spermiogenesis is marked by the formation of the zone of differentiation which contains 2 basal bodies and a further centriole derivative, the central body. The zone extends away from the spermatid cell to form the median process; into this migrates the differentiated and elongate nucleus. Simultaneously, 2 axonemes develop from the basal bodies. During development, they rotate through 90° to extend parallel to the median process. The migration of the nucleus to the distal end of the median process coincides with the fusion of the axonemes to the latter to form a monopartite spermatozoon. The mature spermatozoon possesses 2 axonemes of the 9 + ‘1’ pattern typical of parasitic platyhelminths, 2 elongate mitochondria and a variable array of peripheral microtubules. The nuclear region of the spermatozoon is immotile. The value of sperm ultrastructure as a taxonomic tool in platyhelminth phylogeny is discussed.
STEREOCHEMICAL ASPECTS OF ITRACONAZOLE METABOLISM IN VITRO AND IN VIVO

Itraconazole (ITZ) has three chiral centers and is administered clinically as a mixture of four stereoisomers. This study evaluated stereoselectivity in ITZ metabolism. In vitro experiments were carried out using heterologously expressed CYP3A4. Only (2R,4S,2′R)-ITZ and (2R,4S,2′S)-ITZ were metabolized by CYP3A4 to hydroxy-ITZ, keto-ITZ, and N-desalkyl-ITZ. When (2S,4R,2′R)-ITZ or (2S,4R,2′S)-ITZ was incubated with CYP3A4, neither metabolites nor substrate depletion were detected. Despite these differences in metabolism, all four ITZ stereoisomers induced a type II binding spectrum with CYP3A4, characteristic of coordination of the triazole nitrogen to the heme iron (Ks 2.2–10.6 nM). All four stereoisomers of ITZ inhibited the CYP3A4-catalyzed hydroxylation of midazolam with high affinity (IC50 3.7–14.8 nM). Stereochemical aspects of ITZ pharmacokinetics were evaluated in six healthy volunteers after single and multiple oral doses. In vivo, after a single dose, ITZ disposition was stereoselective, with a 3-fold difference in Cmax and a 9-fold difference in Cmin between the (2R,4S)-ITZ and the (2S,4R)-ITZ pairs of diastereomers, with the latter reaching higher concentrations. Secondary and tertiary ITZ metabolites (keto-ITZ and N-desalkyl-ITZ) detected in plasma were of the (2R,4S) stereochemistry. After multiple doses of ITZ, the difference in Cmax and Cmin decreased to 1.5- and 3.8-fold, respectively. The initial difference between the stereoisomeric pairs was most likely due to stereoselective metabolism by CYP3A4, including stereoselective first-pass metabolism as well as stereoselective elimination. However, stereoselective elimination was diminished after multiple dosing, presumably as a result of CYP3A4 autoinhibition. In conclusion, the metabolism of ITZ is highly stereoselective in vitro and in vivo.
Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica

ABSTRACT In the oleaginous yeast Yarrowia lipolytica, de novo lipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase in Y. lipolytica. Strains with a Y. lipolytica snf1 (Ylsnf1) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into a Y. lipolytica strain engineered to produce omega-3 eicosapentaenoic acid (EPA), Ylsnf1 deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of the Y. lipolytica SNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of the Ylsnf1 mutant identified significantly differentially expressed genes during de novo lipid synthesis and accumulation in Y. lipolytica. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.
High-Resolution Spectroscopy in Tr 37: Gas Accretion Evolution in Evolved Dusty Disks

Using the Hectochelle multifiber spectrograph, we have obtained high-resolution (R ∼ 34,000) spectra in the Hα region for a large number of stars in the 4 Myr old cluster Tr 37, containing 146 previously known members and 26 newly identified ones. We present the Hα line profiles of all members, compare them to our IR observations of dusty disks (Two Micron All Sky Survey JHK + IRAC + MIPS 24 μm), use the radial velocities as a membership criterion, and calculate the rotational velocities. We find a good correlation between the accretion-broadened profiles and the presence of protoplanetary disks, noting that a small fraction of the accreting stars presents broad profiles with Hα equivalent widths smaller than the canonical limit separating classical T Tauri stars (CTTSs) and weak-lined T Tauri stars (WTTSs). The number of strong accretors appears to be lower than in younger regions, and a large number of CTTSs have very small accretion rates ( ≤ 10-9 M⊙ yr-1). Taking into account that the spectral energy distributions are consistent with dust evolution (grain growth/settling) in the innermost disk, this suggests a parallel evolution of the dusty and gaseous components. We also observe that about half of the "transition objects" (stars with no IR excesses at λ ≤ 6 μm) do not show any signs of active accretion, whereas the other half is accreting with accretion rates ≤10-9 M⊙ yr-1. These zero or very low accretion rates reveal important gas evolution and/or gas depletion in the innermost disk, which could be related to grain growth up to planetesimal or even planet sizes. Finally, we examine the rotational velocities of accreting and nonaccreting stars, finding no significant differences that could indicate disk locking at these ages.
Inducible Membrane-bound L-Lactate Dehydrogenase from Escherichia coZi

Membrane-bound L-lactate dehydrogenase was solubilized from the membranes ofEscherichia coli and purified to homogeneity using conventional procedures. The enzyme had a pH optimum of 8 to 9 and was specific for L-lactate. Its apparent K, for L-lactate and maximal velocity were 1.2 x lo-’ M and 31 pmol of tetrazolium dye reducedlminlmg of protein, respectively. It had a polypeptide molecular weight of 43,000 determined by polyacrylamide gel electrophoresis in sodium dodecyl sulfate. The average molecular weight of the purified enzyme after removal of detergent was estimated to be 480,000 by sucrose gradient centrifugation, suggesting that the enzyme was an oligomer in detergent-free solution. The purified enzyme was also an oligomer in the presence of Tween SO or cholate. It contained about 1 mol of flavin mononucleotidelmol of polypeptide with molecular weight of 43,000. The fluorescence of the flavin in the purified enzyme was 5.3% quantum yield of that of FMN. Specific antibody for this enzyme inhibited the enzyme activity and L-lactate-dependent uptake of oxygen in inverted membrane vesicles, suggesting that the purified enzyme was a primary dehydrogenase of the respiratory chain and was localizing on the inner surface of the cytoplasmic membranes. This enzyme was induced by growing the cells on
Mitigating the stochastic effects of fading in mobile wireless ad-hoc networks

This research considers the impact of fast fading effects on the discovery and maintenance of communication routes in mobile wireless ad-hoc networks. Moreover, it is a upon this consideration that fast fading directly impacts the performance of the underlying communication protocols for such networks. It is illustrated herein that protocol design should be based upon the consideration of the operating environments to which such networks are deployed. This research provides a statistical interpretation of link quality based on the instantaneous received power under various multi-path fading models, for which associated Type 1 and 2 errors are defined. Based on this viewpoint, this document proposes the embedding GPS information into a protocol in order to block the inclusion of unreliable links within the route of communication. This implementation results in a dramatic enhancement of the end-to-end performance of the mobile wireless ad-hoc communication network. Thus, this dissertation presents a general introduction to wireless communication networks and their inherent issues, and elaborates in detail this new statistical interpretation of fast fading and the results obtained from employing GPS information to realize an efficient protocol design methodology.
Vibration Analysis of Gearbox Top Cover

Gearbox top cover is a vital component of horizontally split integrally geared centrifugal compressor. Reliability of top cover is directly related to the structural rigidity and structural integrity of compressor. Assuming that the top cover is designed within the mechanical limits of its construction material, one of the most common causes of top cover failure is resonance. The aim of the designer while designing top cover is to have minimum weight and still have sufficient rigidity to avoid resonance. It is imperative; however, that rigorous engineering analysis is applied in the initial design phase to prevent resonance that will result in failure of gearbox top cover. To meet the objectives of designing a reliable integrally geared centrifugal compressor, gearbox top cover modal analysis is of utmost importance. Numerical modal analysis, usually based on Finite Element Method, is commonly used to determine the vibration characteristics, such as natural frequencies and the associated mode shapes of a structure. This paper addresses finite element analysis and modal testing of gearbox top cover of an integrally geared centrifugal compressor. The goal is to determine, verify and validate the vibration characteristics of the gearbox top cover using both analytical and experimental techniques. The 3-D solid model of the gearbox top cover was built using Autodesk Inventor®. ANSYS workbench 13® was used for preprocessing, solving and post processing. Modal analysis involved extraction of mode shapes and natural frequencies. Impact testing using hammer excitation was used to experimentally determine the vibration properties of the gearbox top cover. The results obtained by FEA modal analysis are compared and validated against modal test data. The results indicate that the natural frequencies of gearbox top cover predicted by FEA are within 8 percent of the measured natural frequencies of the modal test data, thus confirming the close agreement between FEA and experimental data. Finally a parametric study was conducted using FEA, to study the effect of wall thickness and rib thickness of gearbox top cover on its natural frequencies and associated mode shapes. It was found that the effect of varying casing wall thickness on the natural frequencies of the gearbox top cover was not significant, as compared to increase in the weight of the gearbox top cover. However, the effect of addition of rib on the natural frequencies of the gearbox top cover was significant, as compared to increase in the weight of the gearbox top cover.
Personal health records and hypertension control: a randomized trial

PURPOSE To examine the impact of a personal health record (PHR) in patients with hypertension measured by changes in biological outcomes, patient empowerment, patient perception of quality of care, and use of medical services. METHODS A cluster-randomized effectiveness trial with PHR and no PHR groups was conducted in two ambulatory clinics. 453 of 1686 (26.4%) patients approached were included in the analyses. A PHR tethered to the patient's electronic medical record (EMR) was the primary intervention and included security measures, patient control of access, limited transmission of EMR data, blood pressure (BP) tracking, and appointment assistance. BP was the main outcome measure. Patient empowerment was assessed using the Patient Activation Measure and Patient Empowerment Scale. Quality of care was assessed using the Clinician and Group Assessment Score (CAHPS) and the Patient Assessment of Chronic Illness Care. Frequency of use of medical services was self-reported. RESULTS No impact of the PHR was observed on BP, patient activation, patient perceived quality, or medical utilization in the intention-to-treat analysis. Sub-analysis of intervention patients self-identified as active PHR users (25.7% of those with available information) showed a 5.25-point reduction in diastolic BP. Younger age, self-reported computer skills, and more positive provider communication ratings were associated with frequency of PHR use. CONCLUSIONS Few patients provided with a PHR actually used the PHR with any frequency. Thus simply providing a PHR may have limited impact on patient BP, empowerment, satisfaction with care, or use of health services without additional education or clinical intervention designed to increase PHR use. CLINICAL TRIAL REGISTRATION NUMBER http://ClinicalTrials.gov Identifier: NCT01317537.
Surface Charge Regulation of Osteogenic Differentiation of Mesenchymal Stem Cell on Polarized Ferroelectric Crystal Substrate

Polarized ferroelectric crystal lithium niobate wafers with different cuts are selected to offer differently charged surfaces. By induction of the mesenchymal stem cells differentiation into osteoblasts on different charged surfaces, the specific osteogenic-associated markers are assessed and the results illustrate that the positively charged wafer surface enhances rBMMSCs osteogenic differentiation.
Improving the scalability of fault-tolerant database clusters

Replication has become a central element in modem information systems playing a dual role: increase availability and enhance scalability. Unfortunately, most existing protocols increase availability at the cost of scalability; This paper presents architecture, implementation and performance of a middleware based replication tool that provides both availability and better scalability than existing systems. Main characteristics are the usage of specialized broadcast primitives and efficient data propagation.