Miracle-dz/UniFAR-FTUs huggingface dataset:
Eukaryotic coupled translation of tandem cistrons: identification of the influenza B virus BM2 polypeptide.

Previous nucleotide sequence analysis of RNA segment 7 of influenza B virus indicated that, in addition to the reading frame encoding the 248 amino acid M1 protein, there is a second overlapping reading frame (BM2ORF) of 585 nucleotides that has the coding capacity for 195 amino acids. To search for a polypeptide product derived from BM2ORF, a genetically engineered beta‐galactosidase‐BM2ORF fusion protein was expressed in Escherichia coli and a polyclonal rabbit antiserum was raised to the purified fusion protein. This antiserum was used to identify a polypeptide, designated BM2 protein (Mr approximately equal to 12,000), that is synthesized in influenza B virus‐infected cells. To understand the mechanism by which the BM2 protein is generated from influenza B virus RNA segment 7, a mutational analysis of the cloned DNA was performed and the altered DNAs were expressed in eukaryotic cells. The expression patterns of the M1 and BM2 proteins from the altered DNAs indicate that the BM2 protein initiation codon overlaps with the termination codon of the M1 protein in an overlapping translational stop‐start pentanucleotide, TAATG, and that the expression of the BM2 protein requires 5′‐adjacent termination of M1 synthesis. Our data suggest that a termination‐reinitiation scheme is used in translation of a bicistronic mRNA derived from influenza B virus RNA segment 7, and this strategy has some analogy to prokaryotic coupled stop‐start translation of tandem cistrons.
On the locality of bounded growth

Many large-scale networks such as ad hoc and sensor networks, peer-to-peer networks, or the Internet have the property that the number of independent nodes does not grow arbitrarily when looking at neighborhoods of increasing size. Due to this bounded "volume growth," one could expect that distributed algorithms are able to solve many problems more efficiently than on general graphs. The goal of this paper is to help understanding the distributed complexity of problems on "bounded growth" graphs. We show that on the widely used unit disk graph, covering and packing linear programs can be approximated by constant factors in constant time. For a more general network model which is based on the assumption that nodes are in a metric space of constant doubling dimension, we show that in O(log*! n) rounds it is possible to construct a (O(1), O(1))-network decomposition. This results in asymptotically optimal O(log*! n) time algorithms for many important problems.
An association between the level of oxidative stress and the concentrations of NEFA and BHBA in the plasma of ketotic dairy cows.

The aim of this study was to evaluate the oxidative status in ketotic cows. We observed changes in the oxidative status and correlations between the oxidative and metabolic status in non-ketotic (n = 10), subclinical ketotic (n = 10) and ketotic cows (n = 10). Plasma samples were analysed by standard biochemical techniques and ELISA to determine traditional metabolic parameters: triglyceride (TG), phosphonium (P), calcium (Ca), aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), total protein (TP), albumin (ALB), immune globulin (Ig), total cholesterol (TC), high-density lipoprotein (HDL), very low-density lipoprotein (VLDL) and lactate dehydrogenase (LDH); energy metabolism indices: glucose, β-hydroxybutyrate (BHBA) and non-esterified fatty acids (NEFA); and indices of oxidative status: malondialdehyde (MDA), hydrogen peroxide (H2 O2 ), vitamin C, vitamin E, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), xanthine oxidase (XOD) and total antioxidant capacity (TAOC). The results of this study showed that plasma glucose levels were lower in ketotic and subclinical ketotic cows than in non-ketotic cows; however, the plasma NEFA and BHBA concentrations were higher. In addition, significant decreases in TC, HDL and VLDL and significant increases in AST, ALT and LDH were observed in the plasma of the ketotic cows. The ketotic cows showed decreased plasma SOD, CAT, vitamin C and vitamin E, inhibited hydroxyl radical capacity and increased plasma H2 O2 and MDA. There were positive correlations between the plasma NEFA and ALT, AST, LDH and MDA and negative correlations between the plasma NEFA and TC, HDL, VLDL, SOD, vitamin C, vitamin E, 1542280 uric acid and inhibited hydroxyl radical capacity. In addition, there were positive correlations between BHBA concentrations and ALT, AST and LDH and negative correlations between plasma BHBA concentrations and TC, HDL, VLDL, vitamin E and inhibited hydroxyl radical capacity. Overall, ketotic dairy cows experience oxidative stress, which is presumably associated with hyperketonemia and higher NEFA.
Correlating Shape and Functional Properties Using Decomposition Approaches

In this paper, we propose the application of standard decomposition approaches to find local correlations in multimodal data. In a test scenario, we apply these methods to correlate the local shape of turbine blades with their associated aerodynamic flow fields. We compare several decomposition algorithms, i.e., k-Means, Principal Component Analysis, Non-negative Matrix Factorization and Uni-orthogonal Non-negative Matrix Factorization, with regards to their efficiency at finding local, relevant correlations and their ability to predict one modality from another.
Response Time Analysis of Parallel Computer and Storage Systems

Fork-join structures have gained increased importance in recent years as a means of modeling parallelism in computer and storage systems. The basic fork-join model is one in which a job arriving at a parallel system splits into K independent tasks that are assigned to K unique, homogeneous servers. In the paper, a simple response time approximation is derived for parallel systems with exponential service time distributions. The approximation holds for networks modeling several devices, both parallel and nonparallel. (In the case of closed networks containing a stand-alone parallel system, a mean response time bound is derived.) In addition, the response time approximation is extended to cover the more realistic case wherein a job splits into an arbitrary number of tasks upon arrival at a parallel system. Simulation results for closed networks with stand-alone parallel subsystems and exponential service time distributions indicate that the response time approximation is, on average, within 3 percent of the seeded response times. Similarly, simulation results with nonexponential distributions also indicate that the response time approximation is close to the seeded values. Potential applications of our results include the modeling of data placement in disk arrays and the execution of parallel programs in multiprocessor and distributed systems.
Inferring Gene Dependency Network Specific to Phenotypic Alteration Based on Gene Expression Data and Clinical Information of Breast Cancer

Although many methods have been proposed to reconstruct gene regulatory network, most of them, when applied in the sample-based data, can not reveal the gene regulatory relations underlying the phenotypic change (e.g. normal versus cancer). In this paper, we adopt phenotype as a variable when constructing the gene regulatory network, while former researches either neglected it or only used it to select the differentially expressed genes as the inputs to construct the gene regulatory network. To be specific, we integrate phenotype information with gene expression data to identify the gene dependency pairs by using the method of conditional mutual information. A gene dependency pair (A,B) means that the influence of gene A on the phenotype depends on gene B. All identified gene dependency pairs constitute a directed network underlying the phenotype, namely gene dependency network. By this way, we have constructed gene dependency network of breast cancer from gene expression data along with two different phenotype states (metastasis and non-metastasis). Moreover, we have found the network scale free, indicating that its hub genes with high out-degrees may play critical roles in the network. After functional investigation, these hub genes are found to be biologically significant and specially related to breast cancer, which suggests that our gene dependency network is meaningful. The validity has also been justified by literature investigation. From the network, we have selected 43 discriminative hubs as signature to build the classification model for distinguishing the distant metastasis risks of breast cancer patients, and the result outperforms those classification models with published signatures. In conclusion, we have proposed a promising way to construct the gene regulatory network by using sample-based data, which has been shown to be effective and accurate in uncovering the hidden mechanism of the biological process and identifying the gene signature for phenotypic change.
Cloning and expression of intercellular adhesion molecule 3 reveals strong homology to other immunoglobulin family counter-receptors for lymphocyte function-associated antigen 1

Based on protein sequence, we have isolated a cDNA for intercellular adhesion molecule 3 (ICAM-3), the most recently defined counter- receptor for lymphocyte function-associated antigen 1 (LFA-1). Expression of the cDNA yields a product that reacts with monoclonal antibody to ICAM-3 and functions as a ligand for LFA-1. The deduced 518- amino acid sequence of the predicted mature protein defines a highly glycosylated type I integral membrane protein with five immunoglobulin (Ig)-like domains. The five Ig-like domains of ICAM-3 are highly homologous with those of human ICAM-1 (52% identity) and human ICAM-2 (37% identity).
Determining How Functionally Diverse Intertidal Sediment Species Preserve Mudflat Ecosystem Properties After Abrupt Biodiversity Loss

ABSTRACT Hale, H. ; Jacques, R.O. , and Tolhurst, T.J., 2019. Determining how functionally diverse intertidal sediment species preserve mudflat ecosystem properties after abrupt biodiversity loss. Journal of Coastal Research, 35(2), 389–396. Coconut Creek (Florida), ISSN 0749-0208. As a result of anthropogenic climate change, extreme climatic events have increased in frequency, severity, and longevity. The consequences for community structure after a catastrophic event have been well studied. However, changes in ecosystem functioning that occur after such an event, including ecosystem recovery, are still uncertain. A catastrophic event was simulated in an intertidal sedimentary habitat. Postevent sediment replicates were assigned to one of four recovery scenarios: (1) no recovery, (2) migration recovery, and recovery by differential opportunistic colonisation by (3) the polychaete worm Hediste diversicolor and (4) the mud snail Peringia ulvae, two locally dominant infauna species. These are compared with a control scenario not subjected to the event. The simulated extreme event caused a shift in habitat state due to a reduction in mobile macrofauna abundance and an increase in microphytobenthos biomass. Migratory recovery of species and the simulated opportunistic expansion of a single species ameliorated this shift and, for some metrics, functional compensation for the loss of other species and the preservation of certain ecosystem functions was observed. The dominant species identity during postevent habitat recovery can have considerable effects on important ecosystem processes and functions with consequences that may result in functional regime shifts in a habitat and alter coastal stability.
Modeling Corticosteroid Effects in a Rat Model of Rheumatoid Arthritis I: Mechanistic Disease Progression Model for the Time Course of Collagen-Induced Arthritis in Lewis Rats

A mechanism-based model was developed to describe the time course of arthritis progression in the rat. Arthritis was induced in male Lewis rats with type II porcine collagen into the base of the tail. Disease progression was monitored by paw swelling, bone mineral density (BMD), body weights, plasma corticosterone (CST) concentrations, and tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and glucocorticoid receptor (GR) mRNA expression in paw tissue. Bone mineral density was determined by PIXImus II dual energy X-ray densitometry. Plasma CST was assayed by high-performance liquid chromatography. Cytokine and GR mRNA were determined by quantitative real-time polymerase chain reaction. Disease progression models were constructed from transduction and indirect response models and applied using S-ADAPT software. A delay in the onset of increased paw TNF-α and IL-6 mRNA concentrations was successfully characterized by simple transduction. This rise was closely followed by an up-regulation of GR mRNA and CST concentrations. Paw swelling and body weight responses peaked approximately 21 days after induction, whereas bone mineral density changes were greatest at 23 days after induction. After peak response, the time course in IL-1β, IL-6 mRNA, and paw edema slowly declined toward a disease steady state. Model parameters indicate TNF-α and IL-1β mRNA most significantly induce paw edema, whereas IL-6 mRNA exerted the most influence on BMD. The model for bone mineral density captures rates of turnover of cancellous and cortical bone and the fraction of each in the different regions analyzed. This small systems model integrates and quantitates multiple factors contributing to arthritis in rats.
Automatic Discovery of Non-Compositional Compounds in Parallel Data

Automatic segmentation of text into minimal content-bearing units is an unsolved problem even for languages like English. Spaces between words offer an easy first approximation, but this approximation is not good enough for machine translation (MT), where many word sequences are not translated word-for-word. This paper presents an efficient automatic method for discovering sequences of words that are translated as a unit. The method proceeds by comparing pairs of statistical translation models induced from parallel texts in two languages. It can discover hundreds of non-compositional compounds on each iteration, and constructs longer compounds out of shorter ones. Objective evaluation on a simple machine translation task has shown the method's potential to improve the quality of MT output. The method makes few assumptions about the data, so it can be applied to parallel data other than parallel texts, such as word spellings and pronunciations.
An Intelligent Mobile Advertising System (iMAS): Location-Based Advertising to Individuals and Business

Rapid expansion of wireless technologies has provided a platform to support intelligent systems in the domain of mobile marketing. Utilizing Location Based Services (LBS) and Global Navigational Satellite Systems (GNSS) infrastructure provides the transport of real-time, scheduled, location-based advertising to individuals and business. In this paper a distributed synchronous platform is proposed called iMAS. iMAS proposes to use an open source platform independent approach to provide the services and interaction with the iMAS system. Intelligent advertising services (IAS) is an integral component of the system and uses a global positioning system (GPS) to enable information to be received depending on the longitude and latitude coordinates of the iMAS device. This allows for contextual information to be used as a means to provide intelligent context-aware location-centric targeted marketing advertisements to the general public. At this stage iMAS is a proof of concept and subsequent research is already under way to test the device in a controlled environment.
Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry

Abstract Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positively with their efficacy in stabilizing the enzyme-mediated DNA breaks. Structural analysis of hTop2α and hTop2β revealed the presence of methionine residues in the drug-binding pocket, we therefore tested whether a tighter Top2-drug association may be accomplished by introducing a methionine-reactive Pt2+ into a drug to further stabilize the DNA break. Herein, we synthesized an organoplatinum compound, etoplatin-N2β, by replacing the methionine-juxtaposing group of the drug etoposide with a cis-dichlorodiammineplatinum(II) moiety. Compared to etoposide, etoplatin-N2β more potently inhibits both human Top2s. While the DNA breaks arrested by etoposide can be rejoined, those captured by etoplatin-N2β are practically irreversible. Crystallographic analyses of hTop2β complexed with DNA and etoplatin-N2β demonstrate coordinate bond formation between Pt2+ and a flanking methionine. Notably, this stable coordinate tether can be loosened by disrupting the structural integrity of drug-binding pocket, suggesting that Pt2+ coordination chemistry may allow for the development of potent inhibitors with protein conformation-dependent reversibility. This approach may be exploited to achieve isoform-specific targeting of human Top2s.
The minor salivary gland proteome in Sjögren's syndrome.

OBJECTIVE To identify the global protein expression (the proteome) in the minor salivary glands from primary Sjögren's syndrome (pSS) patients and non-SS controls. MATERIALS AND METHODS Minor labial salivary glands were obtained from six pSS patients and from six age-matched non-SS controls, lysed in SDS buffer and pooled into two groups, respectively. The lysates were analysed by liquid chromatography electrospray ionization combined with tandem mass spectrometry. Also, the proteins were separated by two-dimensional polyacrylamide gel electrophoresis and protein spots were subjected to mass spectrometry. RESULTS Heat shock proteins, mucins, carbonic anhydrases, enolase, vimentin and cyclophilin B were among the proteins identified. The differences in the proteomes of minor salivary glands from pSS patients and non-SS controls were mainly related to ribosomal proteins, immunity and stress. Alpha-defensin-1 and calmodulin were among six proteins exclusively identified in pSS patients. CONCLUSION We have identified several minor salivary gland proteins that may have implications for clarifying the SS pathophysiology. This experiment adds to the knowledge of proteins produced in salivary glands in health and disease, and may form the basis of further studies on biomarkers of prognostic and diagnostic value.
The Change of Land Cover and Biocapacity of CO2 Gas Emission Absorption in Gresik Urban Area

Gresik urban area is dominated by industrial, housing, trade and services activities. The growth of activities contributes to the land use change from green open spaces into built-up areas. The impact of land use change influence the level of air pollution and CO2 gas emission in Gresik urban area. The previous study briefly shows that this urban area produces 50.37% of the total CO2 gas emissions. The production of CO2 gas emissions should be controlled to reduce the impact of climate change in urban areas such as increasing urban temperature, hydrological cycle anomaly, drought, land degradation and other social and environmental issues. The green open space can recycle the CO2 gas emissions and can increase the absorption capacity of the CO2 gas emissions (bio-capacity). The land cover change for built-up area potentially reduces the absorption of CO2 gas emissions in Gresik urban area. Therefore the identification of the land cover change on CO2 emission absorption becomes an objective of this study. The preliminary study can formulate the strategic steps in the development of Gresik urban area that supports urban greenery and adaptive effort to respond the climate change. The study is conducted in two steps. The first step is to analysis the land cover change based on the Landsat satellite imagery analysis. The second step is to measure the dynamic change of the region's ability (bio-capacity) to absorb CO2 emissions by using ecological footprint analysis. The results show that Gresik urban area has a high development of developed land to the North area, Manyar Sub District. The growth of the developed land is more converting the fishpond land. The green areas in this region tend to be influenced by farming activities which also convert into fishpond land. Bio-capacity of CO2 gas emission absorption increases from 2003 of 3.548 gha to 5.656 gha but the comparison between bio-capacity of CO2 gas emission absorption and developed land shows the declining tendency in each year. In 2003, the comparison score is 1.59 gha/ha of developed land. In 2014, the score is declining into 1.48 gha/ha or developed land.
Use of blood tests in general practice: a collaborative study in eight European countries. Eurosentinel Study Group.

BACKGROUND Laboratory tests are routine examinations in general practice and are associated with increasing costs in industrialized countries. AIM The objective of this collaborative study was to determine the differences in general practitioners' use of blood tests in different European countries and to evaluate the relationship between these differences and organizational aspects of the health care system and also characteristics of the participating general practices. METHOD A descriptive study was conducted by eight European sentinel networks. Voluntary participating general practitioners registered all blood tests requested for four weeks, specifying the type of test, and age group and sex of patients. Details of all face-to-face encounters with patients by age group and sex were collected for the same period. Information on the participating practices and general practitioners was collected by questionnaire. RESULTS The request rate for blood tests varied considerably between countries. The characteristics of general practitioners and practice were only slightly or were not associated with the use of blood tests while dummy 'country' variables were strongly associated. The number of general practitioners per 1000 inhabitants was the most positively associated variable partly explaining the intercountry variation. CONCLUSION This European study suggests that some national characteristics of the health system could determine the use of blood tests in general practice and underlines the need for further investigation in order to develop successful strategies for promoting the optimal use of diagnostic technology.
A Survey of BGP Security

The Border Gateway Protocol (BGP) is the de facto interdomain routing protocol of the Internet. Although the performance BGP has been historically acceptable, there are mounting concerns about its ability to meet the needs of the rapidly evolving Internet. A central limitation of BGP is its failure to adequately address security. Recent outages and security analyses clearly indicate that the Internet routing infrastructure is highly vulnerable. Moreover, the design and ubiquity of BGP has frustrated past e! orts at securing interdomain routing. This paper considers the vulnerabilities of existing interdomain routing and surveys works relating to BGP security. The limitations and advantages of proposed solutions are explored, and the systemic and operational implications of their design considered. We centrally note that no current solution has yet found an adequate balance between comprehensive security and deployment cost. This work calls not only for the application of ideas described within this paper, but also for further introspection on the problems and solutions of BGP security.