Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth

ABSTRACT Psychrobacter arcticus strain 273-4, which grows at temperatures as low as −10°C, is the first cold-adapted bacterium from a terrestrial environment whose genome was sequenced. Analysis of the 2.65-Mb genome suggested that some of the strategies employed by P. arcticus 273-4 for survival under cold and stress conditions are changes in membrane composition, synthesis of cold shock proteins, and the use of acetate as an energy source. Comparative genome analysis indicated that in a significant portion of the P. arcticus proteome there is reduced use of the acidic amino acids and proline and arginine, which is consistent with increased protein flexibility at low temperatures. Differential amino acid usage occurred in all gene categories, but it was more common in gene categories essential for cell growth and reproduction, suggesting that P. arcticus evolved to grow at low temperatures. Amino acid adaptations and the gene content likely evolved in response to the long-term freezing temperatures (−10°C to −12°C) of the Kolyma (Siberia) permafrost soil from which this strain was isolated. Intracellular water likely does not freeze at these in situ temperatures, which allows P. arcticus to live at subzero temperatures.
Group code equivalence and optimum codes

This paper describes a search for optimum group codes using the IBM 704 computer. Some theory of the relation. ship between equivalent codes used in narrowing the search is described, and the method of searching is outlined. The newly found optimum codes are listed, along with a number of counter-examples to typical conjectures on binary group codes.
Calcium-Enhanced Twitching Motility in Xylella fastidiosa Is Linked to a Single PilY1 Homolog

ABSTRACT The plant-pathogenic bacterium Xylella fastidiosa is restricted to the xylem vessel environment, where mineral nutrients are transported through the plant host; therefore, changes in the concentrations of these elements likely impact the growth and virulence of this bacterium. Twitching motility, dependent on type IV pili (TFP), is required for movement against the transpiration stream that results in basipetal colonization. We previously demonstrated that calcium (Ca) increases the motility of X. fastidiosa, although the mechanism was unknown. PilY1 is a TFP structural protein recently shown to bind Ca and to regulate twitching and adhesion in bacterial pathogens of humans. Sequence analysis identified three pilY1 homologs in X. fastidiosa (PD0023, PD0502, and PD1611), one of which (PD1611) contains a Ca-binding motif. Separate deletions of PD0023 and PD1611 resulted in mutants that still showed twitching motility and were not impaired in attachment or biofilm formation. However, the response of increased twitching at higher Ca concentrations was lost in the pilY1-1611 mutant. Ca does not modulate the expression of any of the X. fastidiosa PilY1 homologs, although it increases the expression of the retraction ATPase pilT during active movement. The evidence presented here suggests functional differences between the PilY1 homologs, which may provide X. fastidiosa with an adaptive advantage in environments with high Ca concentrations, such as xylem sap.
Insulin resistance is associated with chronic hepatitis C and virus infection fibrosis progression

Abstract Background & Aims: Chronic hepatitis C virus infection is associated with an increased prevalence of type 2 diabetes. We hypothesized that virus-induced insulin resistance may be a mechanism for fibrogenesis in chronic hepatitis C virus infection. Methods: In 260 hepatitis C virus-infected subjects, we examined the relationship between histological findings and anthropometric and biochemical data, including insulin resistance determined by the homeostasis model assessment (HOMA-IR). We also compared fasting serum insulin, C peptide, and HOMA-IR levels between the subset of 121 hepatitis C virus patients with stage 0 or 1 hepatic fibrosis and 137 healthy volunteers matched by sex, body mass index, and waist-hip ratio. Results: Hepatitis C virus-infected subjects with stage 0 or 1 hepatic fibrosis had higher levels of insulin, C peptide, and HOMA-IR (all P ≤ 0.01) compared with matched healthy controls. In the 250 hepatitis C virus patients (fibrosis stage 0 to 4), viral genotype and portal, but not lobular, inflammation were univariate predictors of HOMA-IR. By multiple linear regression analysis, independent predictors of HOMA-IR included body mass index ( P P P P = 0.01). Genotype 3 had significantly lower HOMA-IR than other genotypes (which were comparable when adjusted for effects of the remaining independent predictors). HOMA-IR was an independent predictor for the degree of fibrosis ( P P = 0.03). Conclusions: Hepatitis C virus may induce insulin resistance irrespective of the severity of liver disease, and this effect seems to be genotype specific. Further, our findings support the hypothesis that insulin resistance may contribute to fibrotic progression in chronic hepatitis C virus infection.
Is mild cognitive impairment a distinct clinical entity

Mild cognitive impairment is a syndrome characterized by significant cognitive deficits in the absence of dementia. Persons with mild cognitive impairment have a high risk of developing Alzheimer’s disease and other dementias. However, opinion on whether mild cognitive impairment is a prodromal phase of Alzheimer’s disease and should be treated is divided. The first part of this article will address some of the controversies in mild cognitive impairment on which most researchers have now reached an agreement. Second, we will discuss some of the remaining major controversies in the field, and suggest some avenues for future research. The article will focus around two questions: Is mild cognitive impairment a distinct clinical entity and should it be treated as Alzheimer’s disease?
Analysis of recurrent codes

A definition of a recurrent code is given in a framework which renders it amenable to mathematical analysis. Recurrent codes for both independent and burst errors are considered, and a necessary and sufficient condition for either type of error correction is established. For burst-error-correcting codes, the problem treated is (for a fixed burst length and redundancy) the minimization of the error-free distance ("guard space") required between bursts. A lower bound is obtained on the guard space, and in certain cases, codes which realize this bound are given. A general code which is close to the lower bound in many cases is also given. For independent errors, a code which will correct any error, provided that no consecutive " n " positions have more than " e " digits in error, is discussed. For e = 1 , a necessary and sufficient condition on n is derived; for e > 1 , a lower bound on n is obtained, and for the case of redundancy 1/2 , an upper bound on n is also derived.
Molecular Structure and Transferability of Tn1546-Like Elements in Enterococcus faecium Isolates from Clinical, Sewage, and Surface Water Samples in Iran

ABSTRACT The molecular structure and transferability of Tn1546 in 143 vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from patients (n = 49), surface water (n = 28), and urban and hospital sewage (n = 66) in Tehran, Iran, were investigated. Molecular characterization of Tn1546 elements in vanA VREF was performed using a combination of restriction fragment length polymorphism analysis and DNA sequencing of the internal PCR fragments of vanA transposons. Long-PCR amplification showed that the molecular size of Tn1546 elements varied from 10.8 to 12.8 kb. The molecular analysis of Tn1546 showed that 45 isolates (31.5%) harbored a deletion/mutation upstream from nucleotide 170. No horizontal transfer of Tn1546 was observed following filter-mating conjugation with these isolates. Nevertheless, the rates of transferability for other isolates were 10−5 to 10−6 per donor. Insertion sequences IS1216V and IS1542 were present in 103 (72%) and 138 (96.5%) of the isolates, respectively. The molecular analysis of Tn1546 elements resulted in three genomic organizations. The genomic organization lineage 1 was dominated by the isolates from clinical samples (3.4%), lineage 2 was dominated mostly by sewage isolates (24.5%), and lineage 3 contained isolates obtained from all sources (72.1%). The genetic diversity determined using pulsed-field gel electrophoresis (PFGE) revealed a single E. faecium clone, designated 44, which was common to the samples obtained from clinical specimens and hospital and municipal sewage. Furthermore, the results suggest that lineage 3 Tn1546 was highly disseminated among our enterococcal isolates in different PFGE patterns.
Phase I Trial of Panobinostat (LBH589) in Combination with Trastuzumab in Pretreated HER2-Positive Metastatic Breast Cancer (mBC): Preliminary Safety, Efficacy and Pharmacokinetic Results.

Background : Panobinostat (LBH589), a potent inhibitor of histone deacetylases (HDACs), has demonstrated single-agent activity and synergistic effects when administered in combination with trastuzumab or docetaxel in HER2-positive breast cancer xenografts. Methods : This multicenter study is enrolling patients with metastatic breast cancer (mBC) who have progressed on or within 6 months of trastuzumab-based therapy. Patients receive panobinostat either intravenously (i.v.) (Day 1+8 every 3 weeks) or orally (three times per week, continuously) in combination with trastuzumab 2 mg/kg weekly. Phase Ib of the study evaluates the maximum tolerated dose (MTD) for each formulation, three i.v. dose cohorts (10, 15 and 20 mg/m 2 ) and four oral dose cohorts (15, 20, 30 and 40 mg) are planned. Once the MTDs are established, Phase IIa of the study will assess the efficacy of these doses. The pharmacokinetic (PK) profile is also being determined. Results : In this ongoing trial, 33 patients have received treatment. At baseline these patients had a median age of 52 y (33–65). All breast cancers were HER2-positive and 16 (48%) were ER and PR negative. Lung (45%), liver (33%) and the central nervous system (21%) were the most common sites of metastatic disease. Most patients had received prior taxanes and/or anthracyclines. For the i.v. arm, the 10 mg/m 2 (n=7) and 15 mg/m 2 (n=7) cohorts completed with no dose-limiting toxicity (DLT), while two out of six patients experienced DLTs in the 20 mg/m 2 cohort. One patient experienced Grade (G) 4 thrombocytopenia, and one patient had G4 nausea, vomiting and diarrhea. The 20 mg/m 2 cohort is currently being expanded to a total of 12 patients to confirm the MTD. For the oral arm, one of six patients experienced a DLT in the 15 mg cohort (uncomplicated G4 thrombocytopenia) and two of eight patients experienced DLTs in the 20 mg cohort. One patient had G3 unstable angina and G3 thrombocytopenia, and the second patient experienced G3 thrombocytopenia and G3 anorexia. The 20 mg cohort has been expanded to 12 patients. Overall the most frequent adverse events reported included gastrointestinal events of nausea, vomiting and diarrhea, and hematologic events of thrombocytopenia and neutropenia. To date, no clinically significant ECG changes have been observed from the 820 ECGs performed. Two patients experienced tumor reduction of 29% (one patient each in the i.v. 10 mg/m 2 and oral 20 mg cohorts); both patients had liver metastasis. Eight of the 25 patients (32%) with tumor measurements had a best response of stable disease, across all cohorts. Five of these patients received over 18 weeks of treatment with the combination. Conclusions : These preliminary results demonstrate that the combination of panobinostat and trastuzumab is well tolerated and shows promising activity. Additional patient safety, efficacy and PK data will be presented. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6101.
Sequential Use of Nitrogen Compounds by Saccharomyces cerevisiae during Wine Fermentation: a Model Based on Kinetic and Regulation Characteristics of Nitrogen Permeases

ABSTRACT The efficiency of nitrogen use is a key determinant of the completion of alcoholic fermentation. We analyzed the kinetics of consumption of 18 nitrogen compounds by 14 Saccharomyces cerevisiae strains of various origins in a synthetic medium that mimicked a grape must. The kinetic profiles of total nitrogen consumption were diverse, but the order of nitrogen source consumption was similar for all strains. The nitrogen compounds could be classified into three groups, according to their order of use: prematurely consumed (Lys), early consumed (Asp, Thr, Glu, Leu, His, Met, Ile, Ser, Gln, and Phe), and late consumed (ammonium, Val, Arg, Ala, Trp, and Tyr). The initial concentrations of these compounds did not alter the order in which they were consumed, except for arginine and ammonium. Early consumed amino acids are transported by specific permeases under Ssy1p-Ptr3p-Ssy5 (SPS)-mediated control that are expressed at the beginning of consumption. Most nitrogen compounds consumed late are transported by permeases under nitrogen catabolite repression (NCR), and others (Val, Trp, and Tyr) are transported by SPS-regulated low-affinity permeases. Therefore, the kinetic characteristics of transporters, as well as SPS and NCR, are likely key factors controlling the temporal sequence of consumption of nitrogen compounds and constitute a system highly conserved in S. cerevisiae species. This work sheds new light on the mechanistic basis of the sequential use of different nitrogen compounds in complex environments.
Quantification of Human Polyomaviruses JC Virus and BK Virus by TaqMan Quantitative PCR and Comparison to Other Water Quality Indicators in Water and Fecal Samples

ABSTRACT In the United States, total maximum daily load standards for bodies of water that do not meet bacterial water quality standards are set by each state. The presence of human polyomaviruses (HPyVs) can be used as an indicator of human-associated sewage pollution in these waters. We have developed and optimized a TaqMan quantitative PCR (QPCR) assay based on the conserved T antigen to both quantify and simultaneously detect two HPyVs; JC virus and BK virus. The QPCR assay was able to consistently quantify ≥10 gene copies per reaction and is linear over 5 orders of magnitude. HPyVs were consistently detected in human waste samples (57 of 64) and environmental waters with known human fecal contamination (5 of 5) and were not amplified in DNA extracted from 127 animal waste samples from 14 species. HPyV concentrations in sewage decreased 81.2 and 84.2% over 28 days incubation at 25 and 35°C, respectively. HPyVs results were compared to Escherichia coli, fecal coliform, and enterococci concentrations and the presence of three other human-associated microbes: Bacteroidetes, Methanobrevibacter smithii, and adenovirus. HPyVs were the most frequently detected of these in human and contaminated environmental samples and were more human specific than the Bacteroidetes (HF183) or M. smithii. HPyVs and M. smithii more closely mimicked the persistence of adenovirus in sewage than the other microbes. The use of this rapid and quantitative assay in water quality research could help regulatory agencies to identify sources of water pollution for improved remediation of contaminated waters and ultimately protect humans from exposure to pathogens.
Accidental exposure to politics on social media as online participation equalizer in Germany, Italy, and the United Kingdom

We assess whether and how accidental exposure to political information on social media contributes to citizens’ online political participation in comparative perspective. Based on three online surveys of samples representative of German, Italian, and British Internet users in the aftermath of the 2014 European Parliament elections, we find that accidental exposure to political information on social media is positively and significantly correlated with online participation in all three countries, particularly so in Germany where overall levels of participation were lower. We also find that interest in politics moderates this relationship so that the correlation is stronger among the less interested than among the highly interested. These findings suggest that inadvertent encounters with political content on social media are likely to reduce the gap in online engagement between citizens with high and low interest in politics, potentially broadening the range of voices that make themselves heard.
γ-Resorcylate Catabolic-Pathway Genes in the Soil Actinomycete Rhodococcus jostii RHA1

ABSTRACT The Rhodococcus jostii RHA1 gene cluster required for γ-resorcylate (GRA) catabolism was characterized. The cluster includes tsdA, tsdB, tsdC, tsdD, tsdR, tsdT, and tsdX, which encode GRA decarboxylase, resorcinol 4-hydroxylase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, an IclR-type regulator, a major facilitator superfamily transporter, and a putative hydrolase, respectively. The tsdA gene conferred GRA decarboxylase activity on Escherichia coli. Purified TsdB oxidized NADH in the presence of resorcinol, suggesting that tsdB encodes a unique NADH-specific single-component resorcinol 4-hydroxylase. Mutations in either tsdA or tsdB resulted in growth deficiency on GRA. The tsdC and tsdD genes conferred hydroxyquinol 1,2-dioxygenase and maleylacetate reductase activities, respectively, on E. coli. Inactivation of tsdT significantly retarded the growth of RHA1 on GRA. The growth retardation was partially suppressed under acidic conditions, suggesting the involvement of tsdT in GRA uptake. Reverse transcription-PCR analysis revealed that the tsd genes constitute three transcriptional units, the tsdBADC and tsdTX operons and tsdR. Transcription of the tsdBADC and tsdTX operons was induced during growth on GRA. Inactivation of tsdR derepressed transcription of the tsdBADC and tsdTX operons in the absence of GRA, suggesting that tsd gene transcription is negatively regulated by the tsdR-encoded regulator. Binding of TsdR to the tsdR-tsdB and tsdT-tsdR intergenic regions was inhibited by the addition of GRA, indicating that GRA interacts with TsdR as an effector molecule.
Characterization of Newcastle Disease Viruses in Wild and Domestic Birds in Luxembourg from 2006 to 2008

ABSTRACT Newcastle disease virus (NDV) is one of the most important viral diseases of birds. Wild birds constitute a natural reservoir of low-virulence viruses, while poultry are the main reservoir of virulent strains. Exchange of virus between these reservoirs represents a risk for both bird populations. Samples from wild and domestic birds collected between 2006 and 2010 in Luxembourg were analyzed for NDV. Three similar avirulent genotype I strains were found in ducks during consecutive years, suggesting that the virus may have survived and spread locally. However, separate introductions cannot be excluded, because no recent complete F gene sequences of genotype I from other European countries are available. Detection of vaccine-like strains in wild waterbirds suggested the spread of vaccine strains, despite the nonvaccination policy in Luxembourg. Among domestic birds, only one chicken was positive for a genotype II strain differing from the LaSota vaccine and exhibiting a so-far-unrecognized fusion protein cleavage site of predicted low virulence. Three genotype VI strains from pigeons were the only virulent strains found. The circulation of NDV in wild and free-ranging domestic birds warrants continuous surveillance because of increased concern that low-virulence wild-bird viruses could become more virulent in domestic populations.
Exponential error bounds for incoherent orthogonal signals (Corresp.)

It is well known that arbitrarily small error probabilities can be obtained at any source rate less than capacity for the band-infinite Gaussian channel by block coding binary digits into either coherent or incoherent orthogonal signals. In this correspondence it is shown that the exponential rate at which the error probability approaches zero with increasing block length is the same for the coherent and incoherent orthogonal signals for any source rate less than channel capacity.
Foundation for the Future: Meeting the Psychosocial Needs of Children Living With HIV in South Africa and Uganda

Successes in diagnosing and treating pediatric HIV have necessitated care that extends beyond basic medical needs. However, capacity for providing childhood psychosocial support (PSS) remains limited. Programmatic research with young PLHIV, care providers and parents in Uganda and South Africa explored challenges in meeting the psychosocial needs of HIV-positive children. Three areas for childhood PSS were examined: disclosure, stigma, and grief/bereavement. This research identified programming gaps, strategies and good practices in five focal areas: providing immediate postdiagnosis support, stigma reduction, capacity building, addressing grief, and promoting peer support. Recommendations are presented for enhancing PSS for HIV-positive children in resource-limited settings.
Does protein binding modulate the effect of angiotensin II receptor antagonists?

Introduction Angiotensin II AT 1-receptor antagonists are highly bound to plasma proteins (≥ 99%). With some antagonists, such as DuP-532, the protein binding was such that no efficacy of the drug could be demonstrated clinically. Whether protein binding interferes with the efficacy of other antagonists is not known. We have therefore investigated in vitro how plasma proteins may affect the antagonistic effect of different AT1-receptor antagonists. Methods A radio-receptor binding assay was used to analyse the interaction between proteins and the ability of various angiotensin II (Ang II) antagonists to block AT1-receptors. In addition, the Biacore technology, a new technique which enables the real-time monitoring of binding events between two molecules, was used to evaluate the dissociation rate constants of five AT1-receptor antagonists from human serum albumin. Results The in vitro AT 1-antagonistic effects of different Ang II receptor antagonists were differentially affected by the presence of human plasma, with rightward shifts of the IC50 ranging from one to several orders of magnitude. The importance of the shift correlates with the dissociation rate constants of these drugs from albumin. Our experiments also show that the way that AT1-receptor antagonists bind to proteins differs from one compound to another. These results suggest that the interaction with plasma proteins appears to modulate the efficacy of some Ang II antagonists. Conclusion Although the high binding level of Ang II receptor antagonist to plasma proteins appears to be a feature common to this class of compounds, the kinetics and characteristics of this binding is of great importance. With some antagonists, protein binding interferes markedly with their efficacy to block AT1-receptors.
Measurement of random time-variant linear channels

This paper concerns the problems of the measurability and measurement of random time-variant linear channels. With regard to measurability, a new, less stringent channel measurability criterion is proposed to supersede the BL product introduced by Kailath. This criterion involves the area of occupancy of the Doppler-delay spread function (or its dual). By using time and bandwidth constraints on the input and output of a channel, channel measurement is reduced to the measurement of a discrete set of finite parameters. Optimal measurement techniques are described and their performances determined for both known and unknown channel correlation functions.