Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Two Virulent Phages of Lactobacillus plantarum

ABSTRACT We characterized two Lactobacillus plantarum virulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eight L. plantarum strains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least two L. plantarum strains, LMG9211 and WCSF1. The linear double-stranded DNA genome of the pac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that of Pediococcus damnosus phage clP1 and 77% identity with that of L. plantarum phage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of the cos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those of Bacillus and Lactobacillus strains as well as phages. Some phage B2 genes were similar to ORFs from L. plantarum phage LP65 of the Myoviridae family. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.
Sex differences in skin conductance measures as a function of shock threat.

Investigations of sex differences in various electrodermal measures have yielded inconsistent results. The present investigation attempted to examine sex differences primarily as a function of varied conditions of threat (stated probability of receiving electric shock). Thirty males and 30 females were randomly assigned to three conditions: High Threat Probability (HTP), Moderate Threat Probability (MTP), or No Threat Probability (NTP). All Ss heard, under assigned threat instructions, 2 sets of 11 tones, preceded by a nonstimulation period and followed by 11 tones with shock threat removed. Results indicated that the threat conditions did affect electrodermal measures as expected. In addition, males exhibited higher tonic (basal conductance) levels throughout, while females displayed greater phasic reactivity (GSR magnitude) and a larger number of nonspecific GSRs. In addition, nonspecific frequency was affected by the interaction of sex with treatment (threat), such that females displayed higher frequencies under moderate threat, while males increased linearly with increased threat. Degree of stress or threat, the possibility of differential perceptions, and a theory of differential hormonal functioning were applied in interpreting results.
Role of Oral Proficiency on Reading Comprehension

This longitudinal study examined the role of oral proficiency on English reading comprehension, as measured with elicited narratives using a wordless picture book, Frog Where are You? The sample consisted 102 English language learners, including both Spanish and Cantonese speakers. Narrative samples were collected in the winter of first grade and reading skills were assessed on the same children one year later in second grade. Children were enrolled in either bilingual programs or mainstream programs. Multiple regression results show it was not the quantity and variety of words used in the narratives that predicted English reading comprehension one year later. Instead, the ability to produce a coherent oral narrative, in either the home language or English, explained a small variance in English reading comprehension for both English learner groups. These findings highlight the importance of examining narrative skills, especially as measured by narrative structure. Implications for parents and educators are discussed.
Alignment of a restriction map with the genetic map of bacteriophage T4

A restriction map of the bacteriophage T4 genome was aligned with the T4 genetic map. Included were the cleavage sites for BamHI, BglII, KpnI, PvuI, SalI, and XbaI. The alignment utilized the fact that the T4 genetic map had been oriented previously with respect to a T2/T4 heteroduplex map. DNA fragments from a BglII digestion of cytosine-containing DNA from a T4 dCTPase- denA denB(rIIH23B) alc mutant were hybridized with full-length chromosomal strands of bacteriophage T2, and the heteroduplexes were examined by electron microscopy. From their lengths and patterns of substitution and deletion loops, the heteroduplexes formed with 6 of the 13 BglII fragments could be unambiguously identified and positioned on the T2/T4 heteroduplex map. The ends of the T4 DNA strands in the heteroduplexes directly identified the location of 10 BglII cleavage sites. The remaining three BglII cleavage sites could be assigned to the T2/T4 heteroduplex map based on their relative locations on the restriction map. It was also possible to identify the source of the DNA strands (i.e., T2 or T4) in four previously unassigned deletion loops on the T2/T4 heteroduplex. Among the BglII fragments identified in heteroduplexes was the fragment containing the rIIH23B deletion; this deletion was used as the primary point of reference for alignment of the T4 restriction map with the T2/T4 heteroduplex map and, hence, with the T4 genetic map.
Biophysics of viral infectivity: matching genome length with capsid size

Abstract In this review, we discuss recent advances in biophysical virology, presenting experimental and theoretical studies on the physical properties of viruses. We focus on the double-stranded (ds) DNA bacteriophages as model systems for all of the dsDNA viruses both prokaryotic and eukaryotic. Recent studies demonstrate that the DNA packaged into a viral capsid is highly pressurized, which provides a force for the first step of passive injection of viral DNA into a bacterial cell. Moreover, specific studies on capsid strength show a strong correlation between genome length, and capsid size and robustness. The implications of these newly appreciated physical properties of a viral particle with respect to the infection process are discussed.
Evaluation of estimation algorithms part I: incomprehensive measures of performance

Practical metrics for performance evaluation of estimation algorithms are discussed. A variety of metrics useful for evaluating various aspects of the performance of an estimation algorithm is introduced and justified. They can be classified in two different ways: 1) absolute error measures (without a reference), relative error measures (with a reference), or frequency counts (of some events), and 2) optimistic (i.e., how good the performance is), pessimistic (i.e., how bad the performance is), or balanced (neither optimistic nor pessimistic). Pros and cons of these metrics and the widely-used RMS error are explained. The paper advocates replacing the RMS error in many cases by a measure called average Euclidean error
Using Semantics, Grammar, Phonology, and Rapid Naming Tasks to Predict Word Identification

This study investigated the relative importance of semantic, grammatical, phonological, and rapid naming abilities in predicting word identification in a large, representative sample of children enrolled in first through sixth grade, using correlation, factor analysis, multiple regression, and predictive outcome analysis techniques. Composite measures of these abilities were found to correlate significantly with word identification, even after controlling for the effects of nonverbal intelligence. Factor analysis indicated that the spoken language composites and the word identification composite loaded on one factor, whereas the perceptual speed composites loaded on a second factor. Multiple regression analyses showed that among younger children in the early stages of learning to read and children whose word identifying skills were below average, the phonology and rapid naming composites accounted for the most variance in predicting word identification skills. Among older children and children who were proficient in word identification, the semantics composite accounted for the most variance. The most important analyses in this study (i.e., the calculations of the sensitivity indexes, the specificity indexes, and the positive predictive values) evaluated the practical value of using the composites to predict poor word identification skills in children. To be considered practically useful, all predictive outcome values had to be . 75 or greater. None of the composites studied, including an application of the double-deficit hypothesis, met this criterion. The results from this study question the accuracy and utility of using any of the abilities studied to predict which students are at risk for or have poor word identification skills.
Associations of Posthemodialysis Weights above and below Target Weight with All-Cause and Cardiovascular Mortality.

BACKGROUND AND OBJECTIVES Fluid removal via ultrafiltration is a primary function of hemodialysis, and inadequate volume control is associated with significant morbidity and mortality among chronic dialysis patients. Treatment-to-treatment fluid removal goals are typically calculated on the basis of interdialytic weight gain and prescribed target weight. The clinical effect of frequent missed target weights is unclear. This study was designed to evaluate the associations of postdialysis weights above and below the prescribed target weight (separately) and outcomes. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Data were taken from a national cohort of 10,785 prevalent, thrice-weekly, in-center hemodialysis patients dialyzing from 2005 to 2008 (median time at risk, 2.1 [25th percentile, 75th percentile] years) at a single dialysis organization. Patients were characterized as having an above target weight miss if their postdialysis weight was >2 kg above target weight in at least 30% of baseline treatments (14.6% of cohort), or they were characterized as control otherwise. Below target weight miss characterization was analogous for patients with postdialysis weight >2 kg below target weight (6.6% of cohort). Coprimary endpoints were all-cause and cardiovascular mortality. RESULTS Above target weight miss in at least 30% of treatments (versus not) was associated with greater all-cause mortality (adjusted hazard ratio, 1.28; 95% confidence interval, 1.15 to 1.43); and below target weight miss in at least 30% of treatments (versus not) was associated with greater all-cause mortality (adjusted hazard ratio, 1.22; 95% confidence interval, 1.05 to 1.40). Both above and below target weight misses were also significantly associated with greater cardiovascular mortality. Secondary analyses demonstrated dose-response relationships between target weight misses and mortality. Results from sensitivity analyses considering the difference in postdialysis and target weights as a proportion of body weight were analogous to the primary results. CONCLUSIONS Postdialysis weights >2 kg above and below target weight are associated with higher all-cause and cardiovascular mortality. Consistent target weight achievement is a viable target for improving fluid management.
Prevalence and risk factors of iodine deficiency among schoolchildren.

The aim of this study was to demonstrate the prevalence of iodine deficiency among schoolchildren and the risk factors influencing it. One thousand five hundred and seventy-three schoolchildren were chosen from 14 schools in seven different regions in Istanbul. After all data relating to sociodemographic factors and the use of iodized salt were recorded, iodine contents of urine samples were determined by the Sandell Kolthoff reaction. Chi-squared and multiple regression analysis were used for the investigation of the correlation between iodine deficiency and risk factors. The prevalence of goitre (> or = 2 grade) was 1.9 per cent. The median urine iodine level was in the normal range (10.5 microg/dl). In 46.2 per cent of the students the urine iodine levels were below 10 microg/dl and 13.9 per cent of the students had urine iodine levels below 5 microg/dl. The prevalence of iodine deficiency was significantly higher in younger (< or = 10 years) children, in children with less educated mothers and fathers, and with poorer and more crowded families (p < 0.01, p < 0.01 and p < 0.01, p < 0.001, respectively). The rate of iodine deficiency was significantly higher in females than in males and also higher in children who lived on the European side of Istanbul than on the Anatolian side of Istanbul (p < 0.0001, p < 0.0001, respectively). The rate of use of iodized salt was 44.4 per cent and the iodine deficiency rate was not affected by the use of iodized salt (p > 0.05). Although the median urine iodine level was in the normal range, in 46.2 per cent of the students urine iodine levels were low (< 10 microg/dl). As there seems to be no effect from the use of iodized salt in iodine deficiency, the use of a more stable potassium iodate for the fortification of salt may be required.
Similarities and differences between phrase structure and morphosyntactic violations in Spanish: An event-related potentials study

Event-related potentials (ERPs) were employed to compare word category and verb inflection violations in Spanish. A similar frontal negativity was found between 250-400 ms for both violation types, suggesting that they equally disrupt initial syntactic analyses. Also, word category violations elicited a negativity at posterior electrodes larger than verb inflection anomalies and correct sentences within this time window, probably reflecting difficulties to semantically analyse phrase structure violations. Finally, a centroparietal positivity in the 500-700 ms interval was found for both error types. Both violations did not differ along the first half of this interval (500-600 ms), but larger effects for verb inflection violations were reported along the second half of this period (600-700 ms). These findings suggest that whereas processes dealing with the reanalyses of sentence structure are equally triggered by both anomaly types, further attempts of repairing the structure of sentences occur only with verb inflection violations.
Extended release once a day tacrolimus

Purpose of reviewThis article provides an update of the literature on the use of extended release once-daily tacrolimus in solid organ transplant recipients. Recent findingsMedication nonadherence occurs in a substantial proportion of patients posttransplant and is associated with worse outcomes. Multiple daily dosing is associated with an increased risk for nonadherence. Several studies have indicated once-daily dosing of medications and reduced complexity improve medication adherence. The extended release formulations of tacrolimus have been developed with the potential benefits of improving adherence, and hence safety and outcomes. Astagraf XLTM (Advagraf in Europe) and Envarsus XR. are the two extended release once-daily tacrolimus formulations that have recently become available for clinical use and provide promising alternatives to the treatment choices available for immunosuppression in solid organ transplant recipients. SummaryAlthough extended release tacrolimus shows promise in improving patient adherence to transplant medication therapy, further studies are needed to confirm improved compliance and to assess long-term safety and efficacy.
An Approximation Method of the Quadratic Discriminant Function and Its Application to Estimation of High-Dimensional Distribution

In statistical pattern recognition, it is important to estimate the distribution of patterns precisely to achieve high recognition accuracy. In general, precise estimation of the parameters of the distribution requires a great number of sample patterns, especially when the feature vector obtained from the pattern is high-dimensional. For some pattern recognition problems, such as face recognition or character recognition, very high-dimensional feature vectors are necessary and there are always not enough sample patterns for estimating the parameters. In this paper, we focus on estimating the distribution of high-dimensional feature vectors with small number of sample patterns. First, we define a function, called simplified quadratic discriminant function (SQDF). SQDF can be estimated with small number of sample patterns and approximates the quadratic discriminant function (QDF). SQDF has fewer parameters and requires less computational time than QDF. The effectiveness of SQDF is confirmed by three types of experiments. Next, as an application of SQDF, we propose an algorithm for estimating the parameters of the normal mixture. The proposed algorithm is applied to face recognition and character recognition problems which require high-dimensional feature vectors.
Analysis of CPW for LiNbO/sub 3/ optical modulator by extended spectral-domain approach

A LiNbO/sub 3/ optical modulator using CPW with a SiO/sub 2/ buffer layer is analyzed accurately by incorporating the TW electrode thickness effect as well as anisotropic effect. By introducing a finite electrode thickness, the loss calculation becomes available for the lines with thinner as well as thicker conductors. Numerical computations show that the electrode thickness is as important a parameter as the buffer layer thickness for the line characteristics. The use of thicker electrodes increases the velocity of microwaves in the interaction part and decreases the conductor loss significantly, and it can be utilized advantageously for the modulator's design. <<ETX>>
Association between interleukin-10 gene polymorphism and development of IgA nephropathy in a Chinese population

We carried out a study to investigate the association between three promoter SNPs (-592G/A, -819T/C and -1082A/C) of Interleukin-10 (IL-10) and development of IgA nephropathy. A hospital-based case-control design was taken in this study. The present study consisted of 184 patients with IgA nephropathy and 237 healthy controls. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay was applied to assess IL-10 -592G/A, -819T/C and -1082A/C gene polymorphisms. By Chi-square test, we observed a significant difference in terms of genotype distributions of IL-10 -1082A/C between patients with IgA nephropathy and control subjects (χ2=12.81, P=0.002). Using unconditional logistic regression analysis, the CC genotype of IL-10 -1082A/C was found to have 3.69 folds risk of IgA nephropathy when compared with the AA genotype (adjusted OR=3.69, 95% CI=1.62-8.81) (P<0.001). Also, we found that the C allele of IL-10 -1082A/C was associated with an increased risk of IgA nephropathy risk when compared with the A allele, and the adjusted OR (95%) were 1.65 (1.21-2.25) (P=0.001). In our study, we firstly reported a significant relationship between IL-10 -1082A/C genetic variation and IgA nephropathy in a Chinese population.
A systematic review and meta-analysis of meditative interventions for informal caregivers and health professionals

Background Burnout, stress and anxiety have been identified as areas of concern for informal caregivers and health professionals, particularly in the palliative setting. Meditative interventions are gaining acceptance as tools to improve well-being in a variety of clinical contexts, however, their effectiveness as an intervention for caregivers remains unknown. Aim To explore the effect of meditative interventions on physical and emotional markers of well-being as well as job satisfaction and burnout among informal caregivers and health professionals. Design Systematic review of randomised clinical trials and pre–post intervention studies with meditative interventions for caregivers. Data sources PubMed, EMBASE, CINAHL and PsycINFO were searched up to November 2013. Of 1561 abstracts returned, 68 studies were examined in full text with 27 eligible for systematic review. Results Controlled trials of informal caregivers showed statistically significant improvement in depression (effect size 0.49 (95% CI 0.24 to 0.75)), anxiety (effect size 0.53 (95% CI 0.06 to 0.99)), stress (effect size 0.49 (95% CI 0.21 to 0.77)) and self-efficacy (effect size 0.86 (95% CI 0.5 to 1.23)), at an average of 8 weeks following intervention initiation. Controlled trials of health professionals showed improved emotional exhaustion (effect size 0.37 (95% CI 0.04 to 0.70)), personal accomplishment (effect size 1.18 (95% CI 0.10 to 2.25)) and life satisfaction (effect size 0.48 (95% CI 0.15 to 0.81)) at an average of 8 weeks following intervention initiation. Conclusions Meditation provides a small to moderate benefit for informal caregivers and health professionals for stress reduction, but more research is required to establish effects on burnout and caregiver burden.
Neorustmicin A, a new macrolide antibiotic active against wheat stem rust fungus.

Sir: Stem rust caused by the infection of Puccinia graminis f. sp. tritici is known as one of the several limiting factors of wheat production. We have previously reported the isolation and structural elucidation of rustmicin active against this pathogen with the screening systems using an inhibition assay of spore germination in vitro and plant inoculation test in green housel1). During the course of further screening, a new antibiotic neorustmicin A (I) was found in the cultured broth of Micromonospora chalcea 1302AV2. This communication reports the isolation, structural elucidation and some biological activities of I. Fermentation was carried out at 27°C for 4 days in 500-m1 Erlenmeyer flasks each containing 100 ml of the same medium used for fermentation of rustmicin. The active substance was isolated from the mycelium. The mycelial cake was obtained by centrifugation of the whole broth (ca. 10 liters) and extracted with acetone (10 liters). The extract was evaporated in vacuo to give an aqueous solution which was extracted with three 1.5-liter portions of EtOAc. The combined organic layer was washed successively with 5% NaHCO3, 0.01 N HCl and H2O, dried over anhydrous Na2SO4 and concentrated in vacuo. The oily residue (850 mg) was chromatographed on a silica gel column developing with EtOAcbenzene (1: 3). The active fractions were combined and concentrated in vacuo to give a brownish oil (20 mg). Further purification of the oily material by preparative TLC (EtOAc benzene, 1 : 3, Rf 0.35) gave 5.3 mg of I as a yellowish oily material. Physico-chemical properties of neorustmicin A are as follows: UV AMeOHmax 212 (r 13,700) and 233 nm (11,000); IR vCHCl3max 3540, 1740 (sh) and 1720 cm-1; EI-MS ,n/z 364 (M+); [a]21D -83.1° (c 0.25, MeOH). The molecular formula of I was established to be C21H32O5 by high resolution mass spectral data (obsd 364.2288; calcd 364.2251). Its molecular formula is one less oxygen than that of rustmicin. In addition to the UV and IR spectra, 1H and13C NMR spectral data of I are very close to those of rustmicin (1H NMR data will be given below and 13C NMR data were shown in Table 1). Comparison of 1H and 13C NMR spectral data between rustmicin and I indicated that a methoxy signal at 31, 3.48 and o, 57.0 of rustmicin was lost and a methyl signal at o. 1.64 and o, 17.5 was newly observed in I. This finding suggested that the methoxy group at C-6 of rustmicin has been replaced by a methyl group at C-6 in I. At the same time, a quaternary carbon signal attached to the methyl group and the adjacent carbon signals in 13C NMR spectrum of I must Fig. 1. Structure of neorustmicin A (I).