Miracle-dz/UniFAR-FTUs huggingface dataset:
Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL

The bacterial pheL gene encodes the leader peptide for the phenylalanine biosynthetic operon. Translation of pheL mRNA controls transcription attenuation and, consequently, expression of the downstream pheA gene. Fifty-three unique pheL genes have been identified in sequenced genomes of the gamma subdivision. There are two groups of pheL genes, both of which are short and contain a run(s) of phenylalanine codons at an internal position. One group is somewhat diverse and features different termination and 5′-flanking codons. The other group, mostly restricted to Enterobacteria and including Escherichia coli pheL, has a conserved nucleotide sequence that ends with UUC_CCC_UGA. When these three codons in E. coli pheL mRNA are in the ribosomal E-, P- and A-sites, there is an unusually high level, 15%, of +1 ribosomal frameshifting due to features of the nascent peptide sequence that include the penultimate phenylalanine. This level increases to 60% with a natural, heterologous, nascent peptide stimulator. Nevertheless, studies with different tRNAPro mutants in Salmonella enterica suggest that frameshifting at the end of pheL does not influence expression of the downstream pheA. This finding of incidental, rather than utilized, frameshifting is cautionary for other studies of programmed frameshifting.
Long-Term Control of Human Immunodeficiency Virus-1 Replication Despite Extensive Resistance to Current Antiretroviral Regimens: Clonal Analysis of Resistance Mutations in Proviral Deoxyribonucleic Acid

Archived resistance mutations compromise antiretroviral treatment. We have investigated 3 selected aviremic patients who had extensive historical resistance to their current regimen. All 3 patients underwent unstructured treatment interruptions associated to the re-emergence of wild-type virus before starting their current suppressive regimes. Almost all historical resistance mutations detected in plasma were found in circulating proviral deoxyribonucleic acid. None of the clones analyzed was fully resistant to the current antiretroviral regimen.
Short-Term Safety and Tolerability of an Antimalarial Herbal Medicine, CoBaT-Y017 in Healthy Volunteers

Background Malaria is the most prevalent parasitic disease in Benin and the main cause of morbidity and mortality. To fight this disease, a large proportion of the population resorts to herbal drugs. However, for most of these herbal preparations, no scientific evidence of their safety or efficacy has yet been established. The aim of this study was to evaluate the short-term safety and tolerability of CoBaT-Y017 and collect some data on its antimalarial efficacy. Material and Methods CoBaT-Y017 was formulated into syrup accommodated in 70 mL bottles. The trial involved a sample of 10 male volunteers, selected using the Lot Quality Assurance Sampling (LQAS) method and declared apparently healthy by a physician through clinical examination. During the baseline analysis, two cases of parasitaemia were detected. The volunteers were hospitalized for 5 days and orally given 35 mL of CoBaT-Y017 diluted in 1.5 L of mineral water, for four consecutive days. Safety and tolerability were monitored clinically, haematologically, biochemically, and parasitologically on days 0 to 5, 7, and 14. Adverse events were recorded by self-reporting or by a physician through clinical examinations and biological investigations. Results 60% of the volunteers experienced no adverse events; appetite increase (40%) and drowsiness (20%) were adverse events noted. There were no changes in physical characteristics or vital signs and haematological and biochemical parameters. The two initial positive cases of parasitaemia became negative 24 hours after administration. Conclusion CoBaT-Y017 presented a significant safety and tolerability in healthy volunteers to allow its further development by starting a phase II clinical study.
Thesaurus-based query and document expansion in conceptual indexing with UMLS: Application in medical information retrieval

UMLS is known as largest thesaurus in biomedical domain constructed by Library National of Medicine. In this paper, we aim to evaluate effect of the exploration of UMLS knowledge in medical domain information retrieval by mapping large text of collection ImageCLEFMed to UMLS concepts, and expanding queries and documents automatically base on semantic relations in the UMLS hierarchy. We get the encouraging result with the best enhancement on MAP of 66% compared to text only retrieval, and 34% compared to conceptual indexing baseline.
CO(J = 1→0) IN z > 2 QUASAR HOST GALAXIES: NO EVIDENCE FOR EXTENDED MOLECULAR GAS RESERVOIRS

We report the detection of CO(J = 1→0) emission in the strongly lensed high-redshift quasars IRAS F10214+4724 (z = 2.286), the Cloverleaf (z = 2.558), RX J0911+0551 (z = 2.796), SMM J04135+10277 (z = 2.846), and MG 0751+2716 (z = 3.200), using the Expanded Very Large Array and the Green Bank Telescope. We report lensing-corrected CO(J = 1→0) line luminosities of L′CO = (0.34–18.4) × 1010 K km s−1 pc2 and total molecular gas masses of M(H2) = (0.27–14.7) × 1010 M☉ for the sources in our sample. Based on CO line ratios relative to previously reported observations in J ⩾ 3 rotational transitions and line excitation modeling, we find that the CO(J = 1→0) line strengths in our targets are consistent with single, highly excited gas components with constant brightness temperature up to mid-J levels. We thus do not find any evidence for luminous-extended, low-excitation, low surface brightness molecular gas components. These properties are comparable to those found in z > 4 quasars with existing CO(J = 1→0) observations. These findings stand in contrast to recent CO(J = 1→0) observations of z ≃ 2–4 submillimeter galaxies (SMGs), which have lower CO excitation and show evidence for multiple excitation components, including some low-excitation gas. These findings are consistent with the picture that gas-rich quasars and SMGs represent different stages in the early evolution of massive galaxies.
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae

Protein phosphorylation plays a central role in cellular regulation. Recent proteomics strategies for identifying phosphopeptides have been developed using the model organism Saccharomyces cerevisiae, and consequently, when combined with studies of individual gene products, the number of reported specific phosphorylation sites for this organism has expanded enormously. In order to systematically document and integrate these various data types, we have developed a database of experimentally verified in vivo phosphorylation sites curated from the S. cerevisiae primary literature. PhosphoGRID (www.phosphogrid.org) records the positions of over 5000 specific phosphorylated residues on 1495 gene products. Nearly 900 phosphorylated residues are reported from detailed studies of individual proteins; these in vivo phosphorylation sites are documented by a hierarchy of experimental evidence codes. Where available for specific sites, we have also noted the relevant protein kinases and/or phosphatases, the specific condition(s) under which phosphorylation occurs, and the effect(s) that phosphorylation has on protein function. The unique features of PhosphoGRID that assign both function and specific physiological conditions to each phosphorylated residue will provide a valuable benchmark for proteome-level studies and will facilitate bioinformatic analysis of cellular signal transduction networks. Database URL: http://phosphogrid.org/
Relative Morse indices, Fredholm indices, and group velocities

We discuss Fredholm properties of the linearization of partial differential equations on cylindrical domains about travelling and modulated waves. We show that the Fredholm index of each such linearization is given by a relative Morse index which depends only on the asymptotic coefficients. Several strategies are outlined that help to compute relative Morse indices using crossing numbers of spatial eigenvalues, and the results are applied to prove the existence of small viscous shock waves in hyperbolic conservation laws upon adding small localized time-periodic source terms.
Microglia and cytokines in neurological disease, with special reference to AIDS and Alzheimer's disease

Microglia are associated with central nervous system (CNS) pathology of both Alzheimer's disease (AD) and the acquired immunodeficiency syndrome (AIDS). In AD, microglia, especially those associated with amyloid deposits, have a phenotype that is consistent with a state of activation, including immunoreactivity with antibodies to class II major histocompatibility antigens and to inflammatory cytokines (interleukin‐1‐β and tumor necrosis factor‐α). Evidence from other studies in rodents indicate that microglia can be activated by neuronal degeneration. These results suggest that microglial activation in AD may be secondary to neurodegeneration and that, once activated, microglia may participate in a local inflammatory cascade that promotes tissue damage and contributes to amyloid formation. In AIDS, microglia are the primary target of retroviral infection. Both ramified and ameboid microglia, in addition to multinucleated giant cells, are infected by the human immunodeficiency virus (HIV‐1). The mechanism of microglial infection is not known since microglia lack CD4, the HIV‐1 receptor. Microglia display high affinity receptors for immunoglobulins, which makes antibody‐mediated viral uptake a possible mechanism of infection. In AIDS, the extent of active viral infection and cytokine production may be critically dependent upon other factors, such as the presence of coinfecting agents. In the latter circumstance, very severe CNS pathology may emerge, including necrotizing lesions. In other circumstances, HIV infection microglia probably leads to CNS pathology by indirect mechanisms, including release of viral proteins (gp120) and toxic cytokines. Such a mechanism is the best hypothesis for the pathogenesis of vacuolar myelopathy in adults and the diffuse gliosis that characterizes pediatric AIDS, in which very little viral antigen can be detected.
Architecture and performance of runtime environments for data intensive scalable computing

In a world of data deluge, considerable computational power is necessary to derive knowledge from the mountains of raw data which surround us. This trend mandates the use of various parallelization techniques and runtimes to perform such analyses in a meaningful period of time. The information retrieval community has introduced a programming model and associated runtime architecture under the name of MapReduce, and it has demonstrated its applicability to several major operations performed by and within this community. Our initial research demonstrated that, although the applicability of MapReduce is limited to applications with fairly simple parallel topologies, with a careful set of extensions, the programming model can be extended to support more classes of parallel applications; in particular, this holds true for the class of Composable Applications. This thesis presents our experiences in identifying a set of extensions for the MapReduce programming model, which expands its applicability to more classes of applications, including the iterative MapReduce computations; we have also developed an efficient runtime architecture, named Twister, that supports this new programming model. The thesis also includes a detailed discussion about mapping applications and their algorithms to MapReduce and its extensions, as well as performance analyses of those applications which compare different MapReduce runtimes. The discussions of applications demonstrates the applicability of the Twister runtime for large scale data analyses, while the empirical evaluations prove the scalability and the performance advantages one can gain from using Twister.
Cytoskeletal composition of attaching and effacing lesions associated with enteropathogenic Escherichia coli adherence to HeLa cells

The cytoskeletal lesions associated with enteropathogenic Escherichia coli adhering to cultured HeLa epithelial cells were examined by immunofluorescence microscopy. The microfilament-associated proteins actin, alpha-actinin, talin, and ezrin were localized with adherent enteropathogenic E. coli, whereas tropomyosin, keratin and vimentin (intermediate filaments), tubulin (microtubules), and vinculin were not localized. These cytoskeletal structures differed significantly from those associated with Salmonella typhimurium internalization (invasion).
The integration of idioms of distress into mental health assessments and interventions: a systematic review

Background. Psychiatric diagnostic manuals recognise the importance of local expressions of distress in culturally diverse settings [i.e. idioms/cultural concepts of distress (CCDs)], yet there is a lack of consensus on how these should be incorporated into mental health related research. Aims. To perform a narrative synthesis and critical review of research exploring how idioms/CCDs have been integrated into assessment measures and interventions. Method. A systematic review was conducted in accordance with PRISMA guidelines. An adapted version of the COSMIN checklist was used to assess the quality of the linguistic translation of the idioms/CCDs. Results. Twenty-nine papers were included in the final review. Primary qualitative research was the most common method of gathering information about idioms/CCDs. The majority of studies described integrating idioms/CCDs into assessment measures as opposed to interventions. Some studies used information relating to idioms/CCDs to develop novel assessment measures, while others adapted pre-existing assessment measures. The measures generated moderate to high levels of validity. Information relating to the linguistic translation conducted in the completion of the studies tended to be inadequately reported. Conclusions. Integrating information about idioms/CCDs into assessment measures can enhance the validity of these assessments. Allocating greater research attention to idioms/CCDs can also promote more equitable exchanges of knowledge about mental health and wellbeing between the Global North and the Global South.
Alcohol drinking and the risk of colorectal cancer death: a meta-analysis

A causal link between alcohol consumption and colorectal cancer (CRC) was established only recently by the International Agency for Research on Cancer. However, the quantitative association between alcohol drinking and CRC mortality is still an open question. We performed a systemic review and meta-analysis on epidemiological studies to quantify the risk for CRC mortality at different levels of alcohol consumption. A literature search was carried out in PubMed and Web of Science to identify all relevant studies published from January 1966 to June 2013. The pooled relative risk (RR) and the corresponding 95% confidence interval (CI) were estimated by categorical meta-analysis. A dose–risk relation was also analyzed. Nine cohort studies exploring the association between CRC mortality and alcohol drinking were identified. Compared with non/occasional drinkers, the pooled RR was 1.03 (95% CI, 0.93–1.15) for any, 0.97 (95% CI, 0.86–1.10) for light (⩽12.5 g/day of ethanol), 1.04 (95% CI, 0.94–1.16) for moderate (12.6–49.9 g/day of ethanol), and 1.21 (1.01–1.46) for heavy drinkers (≥50 g/day of ethanol). For heavy drinkers, the pooled estimate was apparently higher for men (RR=1.28; 95% CI, 1.13–1.46) than for women (RR=0.79; 95% CI, 0.40–1.54; Pheterogeneity=0.007). The dose–response analysis showed a J-shaped relationship between alcohol consumption and CRC mortality. The present meta-analysis provides the evidence for an association between heavy alcohol drinking (≥50 g/day of ethanol) and CRC mortality.
Transition from traditional to LMS supported examining: A case study in computer engineering

Modern education is hard to imagine without the use of e‐learning tools, but still the transition from traditional “paper‐and‐pencil” examining to electronic exams is to some extent cautious. Although course administration and exam evaluation are much easier with learning management systems, there are concerns among teaching staff, that electronic tests simplify examination process compared to paper tests and classic examining. At the University of Belgrade, School of Electrical Engineering, e‐learning tools are used at several exams, mostly as a secondary tool to aid with laboratory exercises. In this paper, we show our experience with four courses from the computer engineering study program that are to various extent moved to Moodle LMS, and electronic examining. We mostly concentrate on certain aspects of transition from paper tests to electronic exams. We present 12 different transformations needed to conform to electronic examining and automated evaluation, and discuss benefits and drawbacks of such a transition. © 2016 Wiley Periodicals, Inc. Comput Appl Eng Educ 24:775–786, 2016; View this article online at wileyonlinelibrary.com/journal/cae; DOI 10.1002/cae.21750
FISH CONSUMPTION AND THE 30-YEAR RISK OF FATAL MYOCARDIAL INFARCTION

A BSTRACT Background Epidemiologic data on the possible benefit of eating fish to reduce the risk of coronary heart disease have been inconsistent. We used data from the Chicago Western Electric Study to examine the relation between base-line fish consumption and the 30-year risk of death from coronary heart disease. Methods The study participants were 1822 men who were 40 to 55 years old and free of cardiovascular disease at base line. Fish consumption, as determined from a detailed dietary history, was stratified (0, 1 to 17, 18 to 34, and 35 g per day). Mortality from coronary heart disease, ascertained from death certificates, was classified as death from myocardial infarction (sudden or nonsudden) or death from other coronary causes. Results During 47,153 person-years of follow-up, there were 430 deaths from coronary heart disease; 293 were due to myocardial infarctions (196 were sudden, 94 were nonsudden, and 3 were not classifiable). Cox proportional-hazards regression showed that for men who consumed 35 g or more of fish daily as compared with those who consumed none, the relative risks of death from coronary heart disease and from sudden or nonsudden myocardial infarction were 0.62 (95 percent confidence interval, 0.40 to 0.94) and 0.56 (95 percent confidence interval, 0.33 to 0.93), respectively, with a graded relation between the relative risks and the strata of fish consumption (P for trend 0.04 and 0.02, respectively). These findings were accounted for by the relation of fish consumption to nonsudden death from myocardial infarction (relative risk, 0.33; 95 percent confidence interval, 0.12 to 0.91; P for trend 0.007). Conclusions These data show an inverse association between fish consumption and death from coronary heart disease, especially nonsudden death from myocardial infarction. (N Engl J Med 1997;336: 1046-53.)
Exploring Data Compression in Distributed File Systems

The ever-growing imbalance between computation and I/O is one of the fundamental challenges for current petascale and future exascale systems. As these large systems become more compute heavy by design, it is becoming harder to support dataintensive applications with adequate performance. To narrow the gap between computation and I/O, parallel and distributed file systems have been introduced. A popular approach to further ameliorate the I/O pressure is data compression, which aims to reduce the data size and stress on the network. However, it unsurprisingly brings new challenges such as computational overhead, programmability, and co-design with other components in the orchestra of large systems. In order to reduce the computation overhead of data compression in these large scale systems, this paper proposes a new compression mechanism, namely multireference compression (MRC), by introducing multiple references to the underlying physical chunks. These multiple references across the physical chunks enable an efficient decompression of requested chunk subsets, thus bypassing the overhead on decompressing the data outside of the requested range. To make MRC easy to use by scientific computing applications, we have adopted the FUSE kernel module to support POSIX. The MRC system can be used in conjunction with parallel file systems (e.g. GPFS) with no modifications needed to either the application or the high level I/O libraries (e.g. netCDF, HDF5). Towards achieving even higher I/O performance, we have proposed and executed a tight integration of MRC with the FusionFS distributed file system, and explored MRC’s impact on basic file system components such as metadata management and data movement. We show how MRC is able to improve parallel and distributed file system performance by up to 2X over these file systems without compression. Keywords-data compression; parallel file systems; distributed file systems
Ecohydrological analysis of a groundwater influenced blanket bog : Occurrence of schoenus nigricans in roundstone bog, Connemara, Ireland

Since the late 1960s, the occurrence of Schoenus nigricans in Irish blanket bogs has been attributed to inputs of salt spray to the blanket bogs, due to their proximity to the coast and the predominant westerly winds from the Atlantic Ocean. To test this hypothesis we carried out an ecohydrological field study at a large blanket bog in the western part of Connemara, Ireland. We described peat profiles in two transects and sampled pore water from peat at different depths. The water samples were analysed and their macro-ionic composition was used to locate possible inputs of calcareous groundwater to the system. We found clear evidence for inflow of calcareous groundwater at various sites and depths. Inflow of rather base-rich groundwater was indicated by high values of electrical conductivity (EC), high contents of calcium and bicarbonate, and high pH of the pore water. The peat profiles contained macro-remains of reed (Phragmites australis), in most cases only in deeper layers of peat, but at one location throughout the profile. This is another indication that the blanket bog was a groundwater-fed fen for quite some time. We conclude that the occurrence of S. nigricans in the blanket bog studied could be well explained by the hypothesis that S. nigricans is a relic from former more base-rich conditions. Relatively high base saturation could have persisted due to the prevailing groundwater flow in the upper layers preventing decalcification or other loss of cations from the whole soil profile including the topsoil.