Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of methylated neutral amino acids from Escherichia coli ribosomes

The methylated neutral amino acids from both 30S and 50S ribosomal subunits of an Escherichia coli K strain were characterized. The 50S ribosomal subunit contains three methylated neutral amino acids: N-monomethylalanine, N-monomethylmethionine, and an as yet unidentified methylated amino acid found in protein L11. Both N-monomethylalanine and N-monomethylmethionine were found in protein L33. The amount of N-monomethylmethionine in this protein, however, is variable but not more than 0.25 molecules per protein. Thus protein L33 from this E. coli K strain has heterogeneity in its N-terminal amino acid and can start with either N-monomethylalanine or N-monomethylmethionine. The N-monomethylmethionine residue was not derived from the reduction of N-formylmethionine in the protein. The 30S ribosomal subunit contains only one methylated neutral amino acid: N-monomethylalanine.
Maternal anemia and risk of adverse birth and health outcomes in low- and middle-income countries: systematic review and meta-analysis.

BACKGROUND Anemia is a leading cause of maternal deaths and adverse pregnancy outcomes in developing countries. OBJECTIVES We conducted a systematic review and meta-analysis to estimate the pooled prevalence of anemia, the association between maternal anemia and pregnancy outcomes, and the population-attributable fraction (PAF) of these outcomes that are due to anemia in low- and middle-income countries. DESIGN PubMed, EMBASE, CINAHL, and the British Nursing Index were searched from inception to May 2015 to identify cohort studies of the association between maternal anemia and pregnancy outcomes. The anemic group was defined as having hemoglobin concentrations <10 or <11 g/dL or hematocrit values <33% or <34% depending on the study. A metaregression and stratified analysis were performed to assess the effects of study and participant characteristics on adverse pregnancy risk. The pooled prevalence of anemia in pregnant women by region and country-income category was calculated with the use of a random-effects meta-analysis. RESULTS Of 8182 articles reviewed, 29 studies were included in the systematic review, and 26 studies were included in the meta-analysis. Overall, 42.7% (95% CI: 37.0%, 48.4%) of women experienced anemia during pregnancy in low- and middle-income countries. There were significantly higher risks of low birth weight (RR: 1.31; 95% CI: 1.13, 1.51), preterm birth (RR: 1.63; 95% CI: 1.33, 2.01), perinatal mortality (RR: 1.51; 95% CI: 1.30, 1.76), and neonatal mortality (RR: 2.72; 95% CI: 1.19, 6.25) in pregnant women with anemia. South Asian, African, and low-income countries had a higher pooled anemia prevalence than did other Asian and upper-middle-income countries. Overall, in low- and middle-income countries, 12% of low birth weight, 19% of preterm births, and 18% of perinatal mortality were attributable to maternal anemia. The proportion of adverse pregnancy outcomes attributable to anemia was higher in low-income countries and in the South Asian region. CONCLUSION Maternal anemia remains a significant health problem in low- and middle-income countries.
The Structure of Prediction Market Research: Important Publications and Research Clusters

This research paper identifies the most important publications and research clusters in the field of prediction markets. Two literature reviews in 2007 and 2014 have already shown a rising number of publications and classified them into several classes. However, the a priori selection of classes limited the analysis. Furthermore, it is still not quantitatively measured which publications have influenced prediction market research most. This research paper extends the existing literature based on the analysis of more than 18,000 citations. Thus, it identifies the most important publications and relevant research topics. It indicates that prediction market research relies primarily on publications within its own field. This paper concludes that some publications have already become “classic” and four main research clusters have emerged: Efficient information aggregation, manipulation, innovation markets and forecasting elections.
Aplicación del Procesamiento de Lenguaje Natural en la Recuperación de Información

In this paper, a novel model for monolingual Information Retrieval in English and Spanish language is proposed. This model uses Natural Language Processing techniques (a POStagger, a Partial Parser, and an Anaphora Resolver) in order to improve the precision of traditional IR systems, by means of indexing the ? entities? and the ? relations? between these entities in the documents. This model is evaluated on the Spanish and English CLEF corpora. For the English queries, there is a maximum increase of 35.11% in the average precision. For the Spanish queries, the maximum increase is 37.18%
Pathogenic Aspergillus species recovered from a hospital water system: a 3-year prospective study.

Nosocomial aspergillosis, a life-threatening infection in immunocompromised patients, is thought to be caused primarily by Aspergillus organisms in the air. A 3-year prospective study of the air, environmental surfaces, and water distribution system of a hospital in which there were known cases of aspergillosis was conducted to determine other possible sources of infection. Aspergillus species were found in the hospital water system. Significantly higher concentrations of airborne aspergillus propagules were found in bathrooms, where water use was highest (2.95 colony-forming units [cfu]/m(3)) than in patient rooms (0.78 cfu/m(3); P=. 05) and in hallways (0.61 cfu/m(3); P=. 03). A correlation was found between the rank orders of Aspergillus species recovered from hospital water and air. Water from tanks yielded higher counts of colony-forming units than did municipal water. An isolate of Aspergillus fumigatus recovered from a patient with aspergillosis was genotypically identical to an isolate recovered from the shower wall in the patient's room. In addition to the air, hospital water systems may be a source of nosocomial aspergillosis.
Additive effects of trastuzumab and genistein on human breast cancer cells

Soy isoflavone genistein, a tyrosine kinase inhibitor and agonist of estrogen receptor-&bgr; (ER&bgr;), is known to have antitumoral properties. Given that ER&bgr; often is coexpressed with HER2 in breast cancer, both functions of genistein might be able to enhance the antitumoral action of trastuzumab. In this in-vitro study, we tested whether combined treatment with genistein and trastuzumab exerts additive effects on breast cancer cells. HER2-overexpressing breast cancer cell lines were treated with genistein alone and in combination with trastuzumab. The effects of this treatment on proliferation and gene expression were analyzed. Treatment with high-dose genistein (10 &mgr;mol/l) significantly increased the growth-inhibitory effect of trastuzumab on HER2-overexpressing, ER&agr;/&bgr;-positive BT-474 breast cancer cells. Combinatory treatment using lower doses of trastuzumab exerted similar effects as a single treatment with standard doses of this drug. In contrast, this effect was absent in ER&agr;-negative SK-BR-3 cells. Similar results were obtained after cotreatment with the ER&bgr; agonist, 2,3-bis(4-hydroxyphenyl)propionitrile. The growth-inhibitory effect of both drugs was accompanied by an increased expression of the putative tumor suppressor ER&bgr; variant, cx, and their combination further elevated mRNA levels of this receptor. In conclusion, genistein significantly enhanced the antitumoral effect of trastuzumab on BT-474 breast cancer cells in vitro. The relevance of these data particularly for women with HER2-overexpressing and ER&agr;/&bgr;-positive breast cancer has to be verified in animal or clinical studies.
NEM Relay-Based Sequential Logic Circuits for Low-Power Design

Nanoelectromechanical (NEM) relays are a promising class of emerging devices that offer zero off-state leakage and behaves like an ideal switch. The zero leakage operation has generated lot of interest in low power logic design using these relays <citerefgrp><citeref refid="ref1"/></citerefgrp>, <citerefgrp><citeref refid="ref2"> </citeref></citerefgrp>. This paper presents various sequential circuit topologies using NEM relays and analyzes their power, performance, and area tradeoffs. The mechanical delay is inversely proportional to the gate-base voltage <formula formulatype="inline"><tex Notation="TeX">$V_{gb}$</tex></formula>. This paper also presents an integrated voltage doubler-based flip-flop that improves the performance by 2<formula formulatype="inline"><tex Notation="TeX">$\times$</tex></formula> by overdriving <formula formulatype="inline"><tex Notation="TeX">$V_{gb}$</tex></formula>. An electromechanical model which accounts for the mechanical, electrical, and dispersion effects of the suspended gate relay operating at 1 V with a nominal air gap of 5–10 nm has been developed based on published fabrication results in <citerefgrp> <citeref refid="ref1"/></citerefgrp>. Three sequential logic benchmark circuits were designed using NEM relays to verify the correctness of operation of the proposed circuits. This study explores different relay-based latch and flip-flop topologies, proposes fast sequential circuits that can operate at a frequency of <formula formulatype="inline"><tex Notation="TeX">$1/2t_{m}$</tex></formula> (theoretical fastest frequency for NEM relay logic circuits) and further improves speed of sequential circuits by distributed charge boosting.
Molecular cloning and characterization of a novel mRNA present in the squid giant axon

Previously, we reported the presence of a heterogeneous population of mRNAs in the squid giant axon. The construction of a cDNA library to this mRNA population has facilitated the identification of several of the constituent mRNAs which encode several cytoskeletal and motor proteins as well as enolase, a glycolytic enzyme. In this communication, we report the isolation of a novel mRNA species (pA6) from the axonal cDNA library. The pA6 mRNA is relatively small (550 nucleotides in length) and is expressed in both nervous tissue and skeletal muscle. The axonal localization of pA6 mRNA was unequivocally established by in situ hybridization histochemistry. The results of quantitative RT‐PCR analysis indicate that there are 1.8 × 106 molecules of pA6 mRNA (≈0.45 pg) in the analyzed segment of the giant axon and suggest that the level of pA6 mRNA in the axonal domain of the giant fiber system might be equal to or greater than the level present in the parental cell soma. Sequence analysis of pA6 suggests that the mRNA encodes an integral membrane protein comprising 84 amino acids. The putative protein contains a single transmembrane domain located in the middle of the molecule and a phosphate‐binding loop situated near the N terminus. The C‐terminal region of the protein contains two potential phosphorylation sites. These four structural motifs manifest striking similarity to domains present in the ryanodine receptor, raising the possibility that pA6 represents a cephalopod intracellular calcium release channel protein. J. Neurosci. Res. 49:144–153, 1997. © 1997 Wiley‐Liss, Inc.
A Novel Splice Variant of the Cell Death-promoting Protein BAX*

Cell death plays an important role in a number of physiological processes in all complex multicellular organisms. One of the molecules that regulates this process is BAX, an integral membrane protein, that promotes apoptosis. The function of BAX is countered by BCL-2 and BCL-XL. The differential expression of these proteins can influence the ability of the cell to die or survive. In this paper, we describe the cloning, biochemical, and functional characterization of a novel splice isoform of BAX, called BAX-ω. Transient overexpression of BAX-ω protein potentiates cell death at levels comparable to that of BAX-α overexpression.
Mouse Sir2 Homolog SIRT6 Is a Nuclear ADP-ribosyltransferase*

Members of the Sir2 family of NAD-dependent protein deacetylases regulate diverse cellular processes including aging, gene silencing, and cellular differentiation. Here, we report that the distant mammalian Sir2 homolog SIRT6 is a broadly expressed, predominantly nuclear protein. Northern analysis of embryonic samples and multiple adult tissues revealed mouse SIRT6 (mSIRT6) mRNA peaks at day E11, persisting into adulthood in all eight tissues examined. At the protein level, mSIRT6 was readily detectable in the same eight tissue types, with the highest levels in muscle, brain, and heart. Subcellular localization studies using both C- and N-terminal green fluorescent protein fusion proteins showed mSIRT6-green fluorescent protein to be a predominantly nuclear protein. Indirect immunofluorescence using antibodies to two different mSIRT6 epitopes confirmed that endogenous mSIRT6 is also largely nuclear. Consistent with previous findings, we did not observe any NAD+-dependent protein deacetylase activity in preparations of mSIRT6. However, purified recombinant mSIRT6 did catalyze the robust transfer of radiolabel from [32P]NAD to mSIRT6. Two highly conserved residues within the catalytic core of the protein were required for this reaction. This reaction is most likely mono-ADP-ribosylation because only the modified form of the protein was recognized by an antibody specific to mono-ADP-ribose. Surprisingly, we observed that the catalytic mechanism of this reaction is intra-molecular, with individual molecules of mSIRT6 directing their own modification. These results provide the first characterization of a Sir2 protein from phylogenetic class IV.
K-3 Soil-Root-Microbe Interactions in the Rhizosphere-A Key to Understanding and Predicting Nutrient Bioavailability to Plants

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Soil-Root-Microbe Interactions in the Rhizosphere A Key to Understanding and Predicting Nutrient Bioavailability to Plants Philippe Hinsinger, Matthieu Bravin, Nicolas Devau, Frederic Gerard, Edith Le Cadre, Benoît Jaillard
A graphics tracing framework for exploring CPU+GPU memory systems

Modern SoCs contain CPU and GPU cores to execute both general purpose and highly-parallel graphics workloads. While the primary use of the GPU is for rendering graphics, the effects of graphics workloads on the overall system have received little attention. The primary reason for this is the lack of efficient tools and simulators for modern graphics applications. In this work, we present GLTraceSim, a new graphics memory tracing and replay framework for studying the memory behavior of graphics workloads and how they interact in heterogeneous CPU/GPU memory systems. GLTraceSim efficiently generates GPU memory access traces and their corresponding, synchronized, CPU render thread memory traces. The resulting traces can then be replayed in both high-level models and detailed full-system simulators. We evaluate GLTraceSim on a range of graphics workloads from browsers to games. Our results show that GLTraceSim can efficiently generate graphics memory traces, and use these traces to study graphics performance in heterogeneous CPU/GPU memory systems. We show that understanding the impact of graphics workloads is essential, as they can cause slowdowns in co-running CPU applications of 26–59%, depending on the memory technology.
Dynamics and efficacy of saccade-facilitated vergence eye movements in monkeys.

1. Four macaque monkeys were trained to fixate visual targets. Eye movements were recorded binocularly using the search coil technique. Saccades, vergence movements, and combinations of the two were elicited by training the monkeys to alternate the gaze between real visual targets that differed in viewing distance and eccentricity with respect to the monkeys' heads. 2. When they shifted the gaze between targets that were at different viewing distances, the monkeys made vergence eye movements. For targets placed along the midsagittal plane, the monkeys often made binocularly symmetric vergence movements. The peak speed of symmetric divergence movements increased linearly with vergence amplitude by 5.7 deg/s per degree of vergence. The peak speed of symmetric convergence movements increased linearly with vergence amplitude by 7.9 deg/s per degree of vergence. 3. For gaze shifts between targets placed eccentrically with respect to the midsagittal plane and at different viewing distances, the monkeys made saccades in combination with vergence eye movements. When a saccade occurred during a vergence movement, peak vergence eye speed increased abruptly and reached a peak that was proportional to the speed of the saccade. For four monkeys, peak divergence speed ranged from 242 to 315 deg/s and peak convergence speed ranged from 257 to 340 deg/s for 16-deg vergence and 20-deg saccadic eye movements. 4. For gaze shifts between far targets at the same viewing distance but different eccentricities, saccadic eye movements were transiently disjunctive even though there was no vergence requirement. Initially, the eyes diverged and then converged to restore fixation to the correct depth plane. Divergence was followed by convergence regardless of the direction of the saccade. 5. The presence of transient saccade-related disjunctive eye movements suggested that the abrupt increase in peak vergence speed during combined saccadic and vergence eye movements was produced by the linear addition of a vergence eye movement and the saccade-related transients. Consistent with this hypothesis, the rate of change in peak vergence speed during various-sized saccades between far targets (no vergence required) was similar to the rate of change in peak vergence speed during combined saccadic and vergence movements. However, the peak vergence speeds during the combined movements were higher than predicted by the linear addition hypothesis, suggesting the presence of an additional mechanism. 6. The saccade-related increase in peak vergence speed during combined saccades and vergences led to a significant decrease in the amount of time required to complete vergence movements. (ABSTRACT TRUNCATED AT 400 WORDS)
Candida albicans strain delineation

Candida albicans is a major opportunistic pathogen causing a wide spectrum of disease in human beings. Methods for strain delineation of this species to assess or predict virulence or to conduct epidemiologic or pathogenetic investigations have been developed. Although factors associated with virulence have been identified, there is no rapid system to quantitate them in a clinical laboratory. Therefore, many typing methods are based on variable phenotypic characteristics within this species including morphotyping, serotyping, antibiogram, resistogram typing, biotyping, biotyping based on commercial carbon assimilation patterns, enzyme profiles, sensitivity to yeast killer toxins, and typing based on protein variability. Phenotypically defined strains generally do not correlate with the pathogenic potential of a strain with the exception of morphotyping. However, these methods can be useful in epidemiologic investigations; for example, they have revealed that most individuals harbor one strain and that infections are frequently due to an endogenous strain. Problems with these methods usually relate to their discriminatory power. When this is maximized, reproducibility (especially between laboratories) suffers. Recently, methods based on differences in DNA structure (genotyping) for strain delineation have been developed, including electrophoretic karyotyping and restriction enzyme fragment length polymorphisms. The development of a computer-assisted data bank and analysis for these genotypic strain delineators will open investigations into the pathogenesis of this infection and permit epidemiologic studies previously not possible with this important human pathogen.
Auditory event‐related potentials (ERP) reflect temporal changes in speech stimuli

WE studied the brain's reactions to deviations in the duration of a stop consonant using event-related potentials in an oddball paradigm. A naturally produced nonsense word was used as a frequent standard stimulus which differed from two infrequently presented deviant stimuli only by the duration of the silence period inside the stop, making the consonant sound longer. Evoked responses to the deviant stimuli showed sharply rising negativity after the unexpected prolongation of the silence and a later negativity, the duration of which was related to the timing of the beginning of the second part of the deviant sound. This later negativity is, at least partly, elicited by a mismatch process to the omission of a sound at the expected latency.
Persistent and bilateral choroidal vascular abnormalities in central serous chorioretinopathy.

BACKGROUND To clarify the role of choroidal vascular abnormalities in central serous chorioretinopathy (CSC) in active stage, remission, and recurrence. METHODS Indocyanine green angiography and fluorescein angiography were performed in 105 eyes (104 patients) with active CSC. Forty-six patients were followed up for 6 to 48 months (mean +/- standard deviation, 22.5 +/- 8.9 months) with repeated angiography (mean +/- standard deviation, 3.5 +/- 1.5 times). Indocyanine green angiography and fluorescein angiography also were performed during remission in all 46 eyes with CSC and during recurrent CSC in 6 eyes. Unaffected fellow eyes underwent angiographic examinations in all patients. RESULTS In active CSC, indocyanine green angiography showed a choroidal filling delay (71%), venous dilation (61%), and focal choroidal hyperfluorescence (96%) surrounding leakage from the retinal pigment epithelium. Focal choroidal hyperfluorescence was present in unaffected areas of affected eyes (55%). The choroidal venous dilation (36%) and choroidal hyperfluorescence (62%) were noted even in unaffected fellow eyes. These choroidal abnormalities persisted during remission after leakage ceased throughout the follow-up period. In the six patients with recurrent CSC, new leakage developed in the areas of persistent choroidal hyperfluorescence. Central serous chorioretinopathy developed in the unaffected fellow eye in one of these six patients. CONCLUSION Choroidal vascular abnormalities persist in both eyes even after leakage from the retinal pigment epithelium ceases. Central serous chorioretinopathy may recur in areas of choroidal vascular abnormalities.
Total anti‐oxidant status: a biochemical predictor of human male fertility

The objective of the study was to assess whether seminal plasma total antioxidant status (TAS) can be used as a biochemical predictor of male fertility and its variation in different categories of infertile male subjects in our population. The study population consisted of 28 fertile and 127 infertile [teratozoospermic (30), asthenoteratozoospermic (30), azoospermic (21), oligoastheno‐teratozoospermic (20), polyzoospermic (15) and oligozoospermic (11)] male subjects. Seminal plasma was separated by centrifugation and stored at minus 80 degree Celsius. Semen was analysed using computer‐assisted semen analysis according to WHO criteria. Seminal plasma TAS was estimated by colorimetric method using Randox total antioxidant status kit. TAS of fertile male subjects was significantly (P < 0.001) higher than that of infertile patients. In whole studied population, seminal plasma TAS showed a significant positive correlation with sperm concentration (P < 0.001), sperm motility (P < 0.0001), and spermatozoa with normal morphology (P < 0.0001). In conclusion, this study suggests that TAS of seminal plasma is one of the important factors contributing to male infertility, and it can be used as a biochemical predictor for male fertility.