Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and Functional Characterization of Bluetongue Virus VP5 Protein: Role in Cellular Permeabilization

ABSTRACT Segment 5 of bluetongue virus (BTV) serotype 10, which encodes the outer capsid protein VP5, was tagged with glutathioneS-transferase and expressed by a recombinant baculovirus. The recombinant protein was subsequently purified to homogeneity, and its possible biological role in virus infection was investigated. Purified VP5 was able to bind mammalian cells but was not internalized, which indicates it is not involved in receptor-mediated endocytosis. The purified VP5 protein was shown to be able to permeabilize mammalian and Culicoides insect cells, inducing cytotoxicity. Sequence analysis revealed that VP5 possesses characteristic structural features (including two amino-terminal amphipathic helices) compatible with virus penetration activity. To assess the role of each feature in the observed cytotoxicity, a series of deleted VP5 molecules were generated, and their expression and biological activity was compared with the parental molecule. VP5 derivatives that included the two amphipathic helices exhibited cytotoxicity, while those that omitted these sequences did not. To confirm their role in membrane destabilization two synthetic peptides (amino acids [aa] 1 to 20 and aa 22 to 41) encompassing the two helices and an additional peptide representing the adjacent downstream sequences were also assessed for their effect on the cell membrane. Both helices, but not the downstream VP5 sequence, exhibited cytotoxicity with the most-amino-terminal helix (aa 1 to 20) showing a higher activity than the adjacent peptide (aa 22 to 41). Purified VP5 was shown to readily form trimers in solution, a feature of many proteins involved in membrane penetration. Taken together, these data support a role for VP5 in virus-cell penetration consistent with its revelation in the entry vesicle subsequent to cell binding and endocytosis.
Dynamics of analog decoders for different message representation domains

We study analog decoders in an abstract level and show that their dynamic equations can change with message representation domain. This result, which is in contrast with the behavior of conventional discrete-time iterative decoders, is derived based on continuity requirement for messages that are passed between processing nodes in analog decoders. In this paper, this requirement is met by assigning low-pass filters between processing nodes that remain unchanged for different message representation domains.
Towards Achieving Performance Portability Using Directives for Accelerators

In this paper we explore the performance portability of directives provided by OpenMP 4 and OpenACC to program various types of node architectures with attached accelerators, both self-hosted multicore and offload multicore/GPU. Our goal is to examine how successful OpenACC and the newer offload features of OpenMP 4.5 are for moving codes between architectures, how much tuning might be required and what lessons we can learn from this experience. To do this, we use examples of algorithms with varying computational intensities for our evaluation, as both compute and data access efficiency are important considerations for overall application performance. We implement these kernels using various methods provided by newer OpenACC and OpenMP implementations, and we evaluate their performance on various platforms including both X86_64 with attached NVIDIA GPUs, self-hosted Intel Xeon Phi KNL, as well as an X86_64 host system with Intel Xeon Phi coprocessors. In this paper, we explain what factors affected the performance portability such as how to pick the right programming model, its programming style, its availability on different platforms, and how well compilers can optimize and target to multiple platforms.
Maximum Pressure Policies in Stochastic Processing Networks

Complex systems like semiconductor wafer fabrication facilities (fabs), networks of data switches, and large-scale call centers all demand efficient resource allocation. Deterministic models like linear programs (LP) have been used for capacity planning at both the design and expansion stages of such systems. LP-based planning is critical in setting a medium range or long-term goal for many systems, but it does not translate into a day-to-day operational policy that must deal with discreteness of jobs and the randomness of the processing environment.A stochastic processing network, advanced by J. Michael Harrison (2000, 2002, 2003), is a system that takes inputs of materials of various kinds and uses various processing resources to produce outputs of materials of various kinds. Such a network provides a powerful abstraction of a wide range of real-world systems. It provides high-fidelity stochastic models in diverse economic sectors including manufacturing, service, and information technology.We propose a family of maximum pressure service policies for dynamically allocating service capacities in a stochastic processing network. Under a mild assumption on network structure, we prove that a network operating under a maximum pressure policy achieves maximum throughput predicted by LPs. These policies are semilocal in the sense that each server makes its decision based on the buffer content in its serviceable buffers and their immediately downstream buffers. In particular, their implementation does not use arrival rate information, which is difficult to collect in many applications. We also identify a class of networks for which the nonpreemptive, non-processor-splitting version of a maximum pressure policy is still throughput optimal. Applications to queueing networks with alternate routes and networks of data switches are presented.
Main-Memory Hash Joins on Multi-Core CPUs Tuning to the Underlying Hardware

—The architectural changes introduced with multi-core CPUs have triggered a redesign of main-memory join algorithms. In the last few years, two diverging views have appeared. One approach advocates careful tailoring of the algorithm to the architectural parameters (cache sizes, TLB, and memory bandwidth). The other approach argues that modern hardware is good enough at hiding cache and TLB miss latencies and, consequently, the careful tailoring can be omitted without sacriﬁcing performance. In this paper we demonstrate through experimental analysis of different algorithms and architectures that hardware still matters. Join algorithms that are hardware conscious perform better than hardware-oblivious approaches. The analysis and comparisons in the paper show that many of the claims regarding the behavior of join algorithms that have appeared in literature are due to selection effects (relative table sizes, tuple sizes, the underlying architecture, using sorted data, etc.) and are not supported by experiments run under different parameters settings. Through the analysis, we shed light on how modern hardware affects the implementation of data operators and provide the fastest implementation of radix join to date, reaching close to 200 million tuples per second.
Redshifts and Velocity Dispersions of Galaxy Clusters in the Horologium-Reticulum Supercluster

We present 118 new optical redshifts for galaxies in 12 clusters in the Horologium-Reticulum supercluster (HRS) of galaxies. For 76 galaxies, the data were obtained with the Dual Beam Spectrograph on the 2.3 m telescope of the Australian National University at Siding Spring Observatory. After combining 42 previously unpublished redshifts with our new sample, we determine mean redshifts and velocity dispersions for 13 clusters in which previous observational data were sparse. In 6 of the 13 clusters, the newly determined mean redshifts differ by more than 750 km s-1 from the published values. In three clusters, A3047, A3109, and A3120, the redshift data indicate the presence of multiple components along the line of sight. The new cluster redshifts, when combined with other reliable mean redshifts for clusters in the HRS, are found to be distinctly bimodal. Furthermore, the two redshift components are consistent with the bimodal redshift distribution found for the intercluster galaxies in the HRS by Fleenor and coworkers.
The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling

Mutagenesis and molecular pharmacological analysis of the glucagon-like peptide-1 (GLP-1) receptor highlighted several residues involved in peptide agonist recognition. Coupled with a new molecular model of the full-length agonist-docked receptor, the binding site and a pharmacophore for agonist peptides are described.
Antigen Retrieval Methods and Estrogen Receptor Immunoexpression Using 1D5 Antibody: A Comparative Study

Long-term formalin tissue fixation results in antigen masking, probably through aldehydic linkage between proteins and fixative molecules. Immunohistochemistry results depend on the type of the detection procedure and the type of antibody used for the reaction. Considering the difficulty in working with estrogen receptor (ER) antibodies and the lack of standardization of the antigen retrieval methods, we quantified the immunoexpression of ER using the 1D5 antibody and a standard streptavidin-biotin detection procedure retrieving with microwave oven, steamer, pressure cooker, and water bath in a set of SBR grade 2 invasive breast carcinomas. Pressure-cooking provided the best results. No significant differences were observed in using the other methods. Pressure-cooking should be recommended as the method of choice for standardization of the ER immunohistochemical reaction.
Effects of Angiotensin II on Adipose Conversion and Expression of Genes of the Renin-Angiotensin System in Human Preadipocytes

A complete functional renin-angiotensin system exists in human adipose tissue, but its regulation and the effects of angiotensin II on cells from this tissue are only beginning to be understood. In this study, we examined the effects of angiotensin II on changes in lipid accumulation, specific glycerol-3-phosphate dehydrogenase activity, and the expression of five genes of the renin-angiotensin system during the adipose conversion of human primary cultured preadipocytes. Angiotensin II leads to a distinct reduction in insulin-induced differentiation, but only has a marginal effect on the adipose conversion of cells stimulated with insulin, cortisol, and isobutyl methyl xanthine. During differentiation, angiotensinogen mRNA levels rise, renin mRNA levels decline, whereas renin-binding protein and angiotensin-converting enzyme levels are unaffected. Angiotensin II downregulates angiotensinogen and renin gene expression, but it does not affect renin-binding protein and angiotensin-converting enzyme levels. Angiotensin II thus prevents the development of adipocytes in contact with high insulin levels, while not inhibiting differentiation, which is further stimulated. Therefore, angiotensin II could be a protective factor against uncontrolled expansion of adipose tissue. Further studies are needed to find out whether the effects of angiotensin II on the renin-angiotensin system are direct feedback loops or secondary to changes in the differentiation program.
Three-stage multiconnection networks which are nonblocking in the wide sense

A multiconnection network deals with the connections of pairs {(X, Y)} where X is a subset of the input terminals and Y is a subset of the output terminals. We study the conditions under which a three-stage Clos network is nonblocking for such connections. We show that the number of middle switches needed for nonblocking depends on the routing strategy. Therefore the networks satisfying the conditions are networks nonblocking in the wide sense. We also derive formulas for computing the minimum numbers of crosspoints required by such networks.
Effects of Genotype and Growth Temperature on the Contents of Tannin, Phytate and In Vitro Iron Availability of Sorghum Grains

Background It has been predicted that the global temperature will rise in the future, which means crops including sorghum will likely be grown under higher temperatures, and consequently may affect the nutritional properties. Methods The effects of two growth temperatures (OT, day/night 32/21°C; HT 38/21°C) on tannin, phytate, mineral, and in vitro iron availability of raw and cooked grains (as porridge) of six sorghum genotypes were investigated. Results Tannin content significantly decreased across all sorghum genotypes under high growth temperature (P ≤0.05), while the phytate and mineral contents maintained the same level, increased or decreased significantly, depending on the genotype. The in vitro iron availability in most sorghum genotypes was also significantly reduced under high temperature, except for Ai4, which showed a pronounced increase (P ≤0.05). The cooking process significantly reduced tannin content in all sorghum genotypes (P ≤0.05), while the phytate content and in vitro iron availability were not significantly affected. Conclusions This research provides some new information on sorghum grain nutritional properties when grown under predicted future higher temperatures, which could be important for humans where sorghum grains are consumed as staple food.
Nonpreferred Stimuli Modify the Representation of Faces in the Fusiform Face Area

The ventral visual cortex has a modular organization in which discrete and well-defined regions show a much stronger response to certain object categories (e.g., faces, bodies) than to other categories. The majority of previous studies have examined the response of these category-selective regions to isolated images of preferred or nonpreferred categories. Thus, little is known about the way these category-selective regions represent more complex visual stimuli, which include both preferred and nonpreferred stimuli. Here we examined whether glasses (nonpreferred) modify the representation of simultaneously presented faces (preferred) in the fusiform face area. We used an event-related fMR-adaptation paradigm in which faces were presented with glasses either on or above the face while subjects performed a face or a glasses discrimination task. Our findings show that the sensitivity of the fusiform face area to glasses was maximal when glasses were presented on the face than above the face during a face discrimination task rather than during a glasses discrimination task. These findings suggest that nonpreferred stimuli may significantly modify the representation of preferred stimuli, even when they are task irrelevant. Future studies will determine whether this interaction is specific to faces or may be found for other object categories in category-selective areas.
Knowledge, attitude and practice for cervical cancer prevention and control among women of childbearing age in Hossana Town, Hadiya zone, Southern Ethiopia: Community-based cross-sectional study

Background Cervical cancer is the second most common female cancer which Ethiopia put a strategic goal to reduce its incidence and mortality by 2020. Lack of knowledge and poor attitude towards the disease and risk factors can affect screening practice and development of preventive behavior for cervical cancer. The aim of this study was to assess knowledge, attitude, practices and factors for each domain for cervical cancer among women of child bearing age in Hossana town, Southern, Ethiopia. Methods Community based cross sectional study was carried out in June 2015. A total of 583 participants were selected using systematic random sampling technique. Pretested structured interviewer administered questionnaire was used to gather the data. Data were entered in to Epi Info software version 3.5. 4 and exported to SPSS version 16 for descriptive and logistic regression analysis. Results Two hundred seventy (46.3%) of the respondents had poor comprehensive knowledge. Only 58 (9.9%) of participants had been screed for the cervical cancer before the survey. Two hundred three (34.8%) of participants had negative attitude towards selected proxy variables. Not having health seeking behavior for cervical cancer [AOR: 5.45, 95% CI: (1.18, 30.58), P <0.031], had not ever received information about cervical cancer and its prevention [AOR: 2.63, 95%CI: (1.78,8.84), P < 0.018] and not actively seeking health information about cervical cancer [AOR: 6.25, (95%CI: (1.26, 31.06) P < 0.025] were significantly associated factors with poor knowledge. Poor knowledge score was associated with poor attitude [AOR: 56.51, 95%CI: (23.76, 134.37), P <0.001]. Had not ever received information about the disease from any source [AOR: 45.24, (95%CI: (11.47, 178.54), P <0.001] was significantly associated factor with not to be screened for the disease. Conclusion This study highlighted the importance of awareness creation, increasing knowledge, promoting active searching for health information and experiences of receiving information from any information sources regarding cervical cancer. Therefore, it will be essential to integrate cervical cancer prevention strategies with other reproductive health services at all level of health care delivery system.
Meet and merge: approximation algorithms for confluent flows

In this paper we investigate the problem ofdetermining confluent flows with minimum congestion. A flow of a given commodity is said to be confluent if at any node all the flow of the commodity departs along a single edge. Confluent flows appear in a variety of application areas ranging from wireless communications to evacuations; in fact, most flows in the Internet are confluent since Internet routing is destination based.We consider the single commodity confluent flow problem, in which we are given an n-node directed network G, a sink t and supplies at each node, and the goal is to find a confluent flow that routes all the supplies to the sink while minimizing the maximum edge congestion. Our main result is an approximation algorithm, based on randomized rounding, for the special case when all the supplies are uniform; the algorithm finds a confluent flow with edge congestion O(C2 log3 n) where C is the node congestion of an optimal splittable flow. This implies an Õ(√n) approximation algorithm for the problem. Our result relies on the analysis of a natural probabilistic process defined on directed acyclic graphs, that may be of independent interest.For tree networks, we present an optimal polynomial-time algorithm for a multi-sink generalization of the above confluent flow problem. We show that it is NP-hard to approximate the congestion of the optimal confluent flow for general networks to within a factor of 4/3. We also establish a lower bound on the gap between confluent and splittable flows, and consider multicommodity and fractional versions of confluent flow problems.
Genomic Sequence and Evolution of Marine Cyanophage P60: a New Insight on Lytic and Lysogenic Phages

ABSTRACT The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria.
Comparison of continuity clinic experience by practice setting and postgraduate level.

OBJECTIVE To compare continuity clinic experiences by practice setting and postgraduate level. DESIGN Mailed questionnaire. SETTING Baylor College of Medicine pediatric residents selected 1 of 3 continuity practice settings, including community-based private offices (n = 35) and university-based clinics in a private (n = 71) and a public (n = 12) hospital. SUBJECTS One hundred eighteen pediatric residents, May 1993. OUTCOME MEASURES Patient volume, continuity of care, type of patient visit, and faculty supervision. RESULTS The response rate was 77% (91/118). Pediatric residents in community-based private offices reported seeing more patients per session than those in the university-based private and public clinics (88%, 10%, and 0% residents in the respective practice settings reported > or = 4 patients per session), but were less likely to see patients repeatedly (6%, 68%, and 40% residents in the respective practice settings had seen more than half their patients > 2 times). Residents in private offices provided a smaller percentage of well child care (16%, 61%, and 90% residents in the respective practice settings reported > 50% patients were well) and more acute care (68%, 15% and 0% residents in the respective practice settings reported > 25% patients were acutely ill). Residents in private offices reported a higher percentage of time spent observing only (33%, 0%, and 0% residents in the respective practice settings observed > 25% of the time) and less time managing patients independently (93%, 59%, and 40% residents, respectively, managed < or = 25% of the time). No significant differences among postgraduate levels were found for these variables. CONCLUSIONS Patient volume, continuity of care, type of patient visit, and faculty supervision were significantly different among continuity practice settings. Postgraduate level of training did not affect significantly these measures of continuity clinic experience. These differences need to be considered in curriculum development.
Design and formulation of a topical hydrogel integrating lemongrass-loaded nanosponges with an enhanced antifungal effect: in vitro/in vivo evaluation

Lemongrass oil (LGO) is a volatile oil extracted from the leaves of Cymbopogon citratus that has become one of the most important natural oils in the pharmaceutical industry because of its diverse pharmacologic and clinical effects. However, LGO suffers from low aqueous solubility, which could lead to a reduced effect. Moreover, the instability of its major active constituent, citral, could lead to volatilization, reaction with other formulation ingredients, and consequently, skin irritation. To surmount these problems, this research aims to formulate lemongrass-loaded ethyl cellulose nanosponges with a topical hydrogel with an enhanced antifungal effect and decreased irritation. The minimal inhibitory concentration and minimal fungicidal concentration of LGO against Candida albicans strain ATC 100231, determined using the broth macrodilution method, were found to be 2 and 8 μL/mL, respectively. The emulsion solvent evaporation technique was used for the preparation of the nanosponges. The nanosponge dispersions were then integrated into carbopol hydrogels (0.4%). Nine formulations were prepared based on a 32 full factorial design employing the ethyl cellulose:polyvinyl alcohol ratio and stirring rate as independent variables. The prepared formulations were evaluated for particle size, citral content, and in vitro release. Results revealed that all the nanosponge dispersions were nanosized, with satisfactory citral content and sustained release profiles. Statistical analysis revealed that both ethyl cellulose:polyvinyl alcohol ratio and stirring rate have significant effects on particle size and percentage released after 6 hours; however, the effect of the stirring rate was more prominent on both responses. The selected hydrogel formulation, F9, was subjected to surface morphological investigations, using scanning and transmission electron microscopy, where results showed that the nanosponges possess a spherical uniform shape with a spongy structure, the integrity of which was not affected by integration into the hydrogel. Furthermore, the selected formulation, F9, was tested for skin irritation and antifungal activity against C. albicans, where results confirmed the nonirritancy and the effective antifungal activity of the prepared hydrogel.