Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate Analyses Revealed Distinctive Features Differentiating Human and Cattle Isolates of Shiga Toxin-Producing Escherichia coli O157 in Japan

Genotypes of Shiga toxin-producing Escherichia coli (STEC) O157 isolated from humans and cattle were analyzed by uni- and multivariable logistic regression, and population structure methods, to gain insight into transmission and the nature of human infection. Eleven genotyping assays, including PCR typing of ﬁve virulence factors ( stx 1 , stx 2 , stx 2c , eae , and ehxA ) and a lineage-speciﬁc polymorphism assay using six markers (LSPA6), were considered in the analyses. The prevalence of the stx 1 , stx 2 , and stx 2c virulence factors was signiﬁcantly different between human and cattle isolates. However, multivariable regression revealed that the presence of only the stx 2 gene was signiﬁcantly associated with human isolates after controlling for confounding effects. LSPA6 typing demonstrated an apparent difference in the distribution of LSPA6 lineages between human and cattle isolates and a strong association between stx genotypes and LSPA6 genotypes. Population genetics tools identiﬁed three genetically distinct clusters of STEC O157. Each cluster was characterized by stx genotypes and LSPA6 genotypes. The human isolates typically comprised LSPA6 lineage I with stx 1 stx 2 strains and LSPA6 lineage I/II with stx 2 or stx 2 stx 2c strains. In contrast, the cattle isolates comprised LSPA6 lineage II strains with stx 2c or stx 2 stx 2c strains in addition to the clusters identiﬁed for the human isolates. Our analyses provide new evidence that the stx 2 gene is the most distinctive feature in human isolates compared to cattle isolates in Japan, and only a subset of the genetically diverse population isolated from cattle is involved in human illnesses. Our results may contribute to international comparisons and risk assessments of STEC O157. analysis to determine whether our samples could be grouped into genetic clusters and to infer the number of clusters that best ﬁt the data, the Bayesian clustering method implemented in the STRUCTURE program (24) was used. This analysis uses departures from the Hardy-Weinberg equilibrium to detect population structure and begins by classifying individuals of unknown origin into a predeﬁned number of populations ( K s ). A Bayesian approach is used to infer the value of K that provides the best ﬁt to the data, as measured by the estimated log probability of the data [ln P ( D )]. Markov chain Monte Carlo searches consisted of 10,000 “burn-in” steps followed by 100,000 iterations. K values of 1 to 10 were evaluated with 10 replicate runs each, under the admixture model with correlated allele frequencies. A graph of the results was produced using the programs CLUMPP and DISTRUCT (12, 26).
THE RESPONSE OF THE GROWING PIG TO CHANGES IN ENERGY INTAKE ACHIEVED THROUGH CHANGES IN DIETARY ENERGY CONCENTRATION VERSUS RESTRICTION OF FEED INTAKE

This study was undertaken to compare the effects of changing energy intake, either by restricting feed intake or by altering dietary energy concentration, on the growth performance of pigs. The relative abilities of the DE, ME and NE systems to predict pig growth performance were also evaluated. A total of 72 barrows, having initial body-weights of 30 ± 2 kg, were randomly assigned to one of nine dietary treatments. These treatments were organized in a 3 x 3 factorial arrangement consisting of three dietary energy concentrations (2.18, 2.29 and 2.40 Mcal NE/kg) and three levels of feed allowance (80, 90 and 100% of ad libitum). Actual feed allowances of 79, 91 and 100% of ad libitum were achieved. No interactive effects of feeding level and dietary energy concentration were observed (P > 0.10). Increases in feed allowance from 79 to 91 to 100% of ad libitum resulted in increases in daily intakes of feed (P < 0.0001) and energy (P < 0.0001). Improvements in the rate (P < 0.0001) and efficiency (P < 0.0001) of body-weight gain were also noted. Additionally, feeding level affected the amount of energy available for body-weight gain on a daily (P < 0.0001) but not on a total (P > 0.10) basis. The efficiency with which dietary energy was used for weight gain was unaffected by feeding level (P > 0.10). Increases in dietary energy concentration were accompanied by decreases in daily feed intakes (P = 0.0016); however, dietary energy concentration did not affect daily energy intakes (P > 0.10). Neither average daily gains nor feed conversion efficiencies were affected by changes in dietary energy concentration (P > 0.10). Additionally, there were no differences among energy concentration treatments in terms of the amount of dietary energy available for body-weight gain (P > 0.10) or the efficiency with which it was used (P > 0.10). No differences were observed between the DE, ME and NE systems in terms of their abilities to predict the growth performance of pigs. The present study demonstrates that the energy intake of pigs can be
Relationship between Cell Surface Carbohydrates and Intrastrain Variation on Opsonophagocytosis ofStreptococcus pneumoniae

ABSTRACT Streptococcus pneumoniae undergoes spontaneous phase variation between a transparent and an opaque colony phenotype, the latter being more virulent in a murine model of sepsis. Opaque pneumococci have previously been shown to express lower amounts of C polysaccharide (cell wall teichoic acid) and in this study were shown to have a higher content of capsular polysaccharide by immunoelectron microscopy. This report then examined the relationship between expression of these two cell surface carbohydrate structures and their relative contribution to the increased virulence of opaque variants. Comparison of genetically related strains showed that the differential content of capsular polysaccharide did not affect the amount of teichoic acid as measured by a capture enzyme-linked immunosorbent assay (ELISA). In contrast, when the teichoic acid structure was altered by replacing choline in the growth medium with structural analogs, the quantity of capsular polysaccharide as measured by a capture ELISA was decreased, demonstrating a linkage in the expression of the two surface carbohydrate structures. A standardized assay was used to assess the relative contribution of cell surface carbohydrates to opsonophagocytosis. The opaque variants required 1.2- to 30-fold more immune human serum to achieve 50% opsonophagocytic killing than did related transparent variants (types 6B and 9V). The opsonophagocytic titer was proportional to the quantity of capsular polysaccharide rather than teichoic acid. The major factor in binding of the opsonin, C-reactive protein (CRP), was also the amount of capsular polysaccharide rather than the teichoic acid ligand. Only for the transparent variant (type 6B), which bound more CRP, was there enhanced opsonophagocytic killing in the presence of this serum protein. Increased expression of capsular polysaccharide, therefore, appeared to be the major factor in the decreased opsonophagocytic killing of opaque pneumococci.
Bresiliid shrimps from the Red Sea (Crustacea: Decapoda: Caridea) with the description of a new species

ABSTRACT A new species of bresiliid shrimp, Bresilia briankensleyi, from over 700 m in the central Red Sea, is described and illustrated. Another bresiliid shrimp, Discias musicus Holthuis, is reported from the Red Sea, for its third occurrence and for the first time outside the Western Pacific region.
VIEWPOINT: PART OF A SPECIAL ISSUE ON THE PLANT CELL CYCLE A commentary on the G2/M transition of the plant cell cycle

†Background The complex events of mitosis rely on precise timing and on immaculate preparation for their success, but the G2/M transition in the plant cell cycle is currently steeped in controversy and alternative models. †Scope In this brief review, the regulation of the G2/M transition in plants is commented on. The extent to which the G2/M transition is phosphoregulated by WEE1 kinase and CDC25 phosphatase, as exemplified in yeasts and animals, is discussed together with an alternative model that excludes these proteins from this transition. Arabidopsis T-DNA insertional lines for WEE1 and CDC25 that develop normally prompted the latter model. An argument is then presented that environmental stress is the norm for higher plants in temperate conditions. If so, the repressive role that WEE1 has under checkpoint conditions might be part of the normal cell cycle for many proliferative plant cells. Arabidopsis CDC25 can function as either a phosphatase or an arsenate reductase and recent evidence suggests that cdc25 knockouts are hypersensitive to hydroxyurea, a drug that induces the DNA-replication checkpoint. That other data show a null response of these knockouts to hydroxyurea leads to an airing of the controversy surrounding the enigmatic plant CDC25 at the G2/M transition.
Host-parasitoid dynamics in periodic boreal moths

Numerous insect species with fixed multiannual life cycle emerge synchronously in large numbers, mostly with a period of two or three years. Moths in the genus Xestia with a two-year life cycle are strikingly abundant in boreal forests around the Northern Hemisphere every second year but scarce in alternate years. Many hypotheses have been put forward to explain their periodic occurrence, including interaction with natural enemies. Here we present biological, numerical and modelling evidence strongly suggesting that the scarcity of the even-year cohorts of eight coexisting Xestia species in eastern Finnish Lapland is due to regulation by the parasitoid wasp Ophion luteus, possibly reinforced by predation by shrews.
Quality of service based distributed control of wireless networks

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In Vitro Susceptibility of Helicobacter pylori to Several Antimicrobial Combinations

Synergy between metronidazole and its hydroxymetabolite and between each compound and amoxicillin or tetracycline-HCl was determined against Helicobacter pyloni. Metronidazole plus its hydroxymetabolite and either compound combined with amoxicillin showed synergism against all 10 strains of H. pylori tested. Metronidazole plus tetracycline-HCl or the hydroxymetabolite plus tetracycline-HCl acted synergistically against seven and six strains, respectively, acted additively against three strains, and had no additional effect against one strain. These results may help to explain the in vivo efficacies of metronidazole combinations in the treatment of H. pyloni-associated gastritis.
Effects of transgenic maize expressing the Cry1Ab protein (event MON810) on locally adapted earthworms in a sandy loam soil in the Central Eastern Cape, South Africa

This field study investigated effects of growing Bacillus thuringiensis (Bt) maize (MON810) on local earthworms in the Central Eastern Cape, South Africa. Two Bt maize cultivars (DKC61-25B and PAN6Q-321B) and their near-isolines (DKC61-24 and PAN6777) were grown in the 2009/2010 and 2010/2011 summer seasons. Earthworms were sampled after six, nine and eighteen weeks in 2009/2010 and after six, twelve and twenty-one weeks in the 2010/2011 season. The four maize treatments had similar earthworm counts, irrespective of sampling time, in both seasons. Sampling time had no effect in the 2009/2010 season, whereas the earthworm counts at 21 weeks after planting (WAP) were lower than the other two sampling times during the 2010/2011 season. The findings suggested that, at least in the short-term, growing Bt maize does not have negative effects on the numbers of the earthworms in the Central Eastern Cape, South Africa. Key words: Bacillus thuringiensis (Bt) maize, Cry1Ab protein, earthworm counts.
Transforming Growth Factor β-Induced Failure of Resistance to Infection with Blood-Stage Plasmodium chabaudiin Mice

ABSTRACT The role of transforming growth factor β (TGF-β) in infection with Plasmodium chabaudi was investigated with resistant and susceptible mouse models. C57BL/10 mice produced gamma interferon (IFN-γ) and nitric oxide (NO) shortly after infection and cleared the parasite spontaneously. In contrast, BALB/c mice showed a transient enhancement of TGF-β production, followed by a relative lack of IFN-γ and NO production, and succumbed to the infection. However, there was no correlation between levels of serum TGF-β and splenic TGF-β mRNA in both mouse strains before and after infection. Administration of recombinant TGF-β (rTGF-β) rendered resistant mice susceptible because of suppression of subsequent production of IFN-γ and NO. Administration of anti-TGF-β antibody to the infected BALB/c mice resulted in remarkable increases in serum IFN-γ and NO, and the mice resisted the infection. Splenic CD4+ T and CD11b+ cells of C57BL/10 mice were significantly activated after infection, but this was completely abrogated by administration of rTGF-β. These results suggested that, in the P. chabaudi-susceptible but not resistant mice, production of TGF-β was promoted, and subsequent failure of IFN-γ- and NO-dependent resistance to the parasite was induced. This study is the first to indicate that TGF-β production was the key event in failure of resistance to mouse malaria.
Neutralizing Antibody Responses in COVID-19 Convalescent Sera

Passive transfer of antibodies from COVID-19 convalescent patients is being used as an experimental treatment for eligible patients with SARS-CoV-2 infections. The United States Food and Drug Administration's (FDA) guidelines for convalescent plasma recommends target antibody titers of 160. We evaluated SARS-CoV-2 neutralizing antibodies in sera from recovered COVID-19 patients using plaque reduction neutralization tests (PRNT) at low (PRNT50) and high (PRNT90) stringency thresholds. We found that neutralizing activity increased with time post symptom onset (PSO), reaching a peak at 31-35 days PSO. At this point, the number of sera having neutralizing titers of at least 160 was ~93% (PRNT50) and ~54% (PRNT90). Sera with high SARS-CoV-2 antibody levels ([≥]960 ELISA titers) showed maximal activity, but not all high titer sera contained neutralizing antibody at FDA recommended levels, particularly at high stringency. These results underscore the value of serum characterization for neutralization activity.
Stoichiometry of Antibody Neutralization of Human Immunodeficiency Virus Type 1

The human immunodeﬁciency virus envelope glycoproteins function as trimers on the viral surface, where they are targeted by neutralizing antibodies. Different monoclonal antibodies neutralize human immunodeﬁciency virus type 1 (HIV-1) infectivity by binding to structurally and functionally distinct moieties on the envelope glycoprotein trimer. By measuring antibody neutralization of viruses with mixtures of neutralization-sensitive and neutralization-resistant envelope glycoproteins, we demonstrate that the HIV-1 envelope glyco- protein trimer is inactivated by the binding of a single antibody molecule. Virus neutralization requires essentially all of the functional trimers to be occupied by at least one antibody. This model applies to antibodies differing in neutralizing potency and to virus isolates with various neutralization sensitivities. Understanding these requirements for HIV-1 neutralization by antibodies will assist in establishing goals for an effective AIDS vaccine.
The Effect of Simultaneous Aromatherapy and Quran Recitation on Anxiety Level of Patients with Myocardial Infarction

Introduction: Anxiety is one of the most common psychological problems after myocardial infarction. The purpose of the present study is to investigate the effect of simultaneous aromatherapy and Quran recitation on anxiety levels of patients with myocardial infarction hospitalized in CCU in Kashan Shahid Beheshti hospital in 2013. Methods: This clinical trial was conducted on 70 patients with myocardial infarction having been randomly divided into two experimental group (35 participants) and control group (35 participants). Experimental group participants simultaneously received lavender aroma and Quran recitation four times each day for two days. Control group participants received no intervention. The participants’ anxiety level was measured at the beginning ad at the end of each intervention cycle. The data were collected by Spielberger anxiety questionnaire and were then analyzed by SPSS statistical software (version 16) and through using chi-square test, independent t-test, repeated measurements and analysis of covariance. Results: There was no meaningful difference in the anxiety mean score of experimental group (43.74  13.34) and control group (41.31  12.89) at the beginning of the study. There was a statistical meaningful difference regarding the anxiety rate after intervention in every four cycle (first cycle: experimental 33.23  8.91, control 40.89  13.21, second cycle: experimental 30.84  8.42, control 40,63  13,56, third cycle: experimental 29.32  7.45, control 39.51  13.96 and forth cycle: experimental 27.45  7.47, control 38.77  13.95) (P<0.05). Conclusion: Simultaneous aromatherapy and Quran recitation reduces the anxiety level of patients suffering from myocardial infarction; hence, it
Indigenous technological practices followed by mustard grower in Rajasthan

A study was conducted among 120 farmers sampled from four district representing irrigated mustard eco-system, rainfed low land eco-system, dry land and upland eco-system in the Pali district of Rajasthan state. Indigenous practices related to mustard cultivation were documented using openended questions developed in the form of check list. Findings of the study revealed that summer ploughing (79%) and in-situ burning of mustard stable (38.33%); growing green manures in summer (75.00%); placing weight on soaked seed (48.33%) were some of the traditional practices frequently done by the large number of farmers for the activities like land preparation, green manuring and seed treatment respectively. The study further revealed that farmers sowed mustard seed in furrow methods mainly in the barani kheti. Most common practices related to management of insect pest, rodents and birds were dusting of ash (37.50%), tying white flags in the mustard fields to scare rodents (45.83%) and use of polythene cover (65.83%). Similarly, on the aspects of post harvest management it was found that ‘Mara’ was used by number of sampled farmers (95.83%).
Changes in Erythron Organization during Prolonged Cadmium Exposure: An Indicator of Heavy Metal Stress?

Changes in erythron organization were examined in goldfish (Carassius auratus) exposed for 3 wk to 5, 15, and 25% of 240-h Cd LC50. In a subsequent, more extended study, specimens were first rendered acutely anemic by immersion in phenylhydrazine HCl, allowed to recover in Cd-free water or in concentrations equivalent to ~5 or ~11% of LC50, and sampled after 2, 5, 8, and 11 wk. Total, dividing, and degrading or karyorrhectic cell numbers were recorded, as were cell length, one-sided surface area, and form factor, in fish exposed to ~11% LC50, total cell numbers and the incidence of cell division fell, while karyorrhexis increased. Dividing to total cell ratios declined with time; karyorrhectic to total and karyorrhectic to dividing cell ratios increased. Variations in cytomorphology suggested slower cell maturation at both metal concentrations. Detection of heavy metal stress in fishes by this form of hematological assessment appears feasible.
Magnitude and time-course of excess mortality during COVID-19 outbreak: population-based empirical evidence from highly impacted provinces in northern Italy

Background The real impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on overall mortality remains uncertain as surveillance reports have attributed a limited number of deaths to novel coronavirus disease 2019 (COVID-19) during the outbreak. The aim of this study was to assess the excess mortality during the COVID-19 outbreak in highly impacted areas of northern Italy. Methods We analysed data on deaths that occurred in the first 4 months of 2020 provided by the health protection agencies (HPAs) of Bergamo and Brescia (Lombardy), building a time-series of daily number of deaths and predicting the daily standardised mortality ratio (SMR) and cumulative number of excess deaths through a Poisson generalised additive model of the observed counts in 2020, using 2019 data as a reference. Results We estimated that there were 5740 (95% credible set (CS) 5552–5936) excess deaths in the HPA of Bergamo and 3703 (95% CS 3535–3877) in Brescia, corresponding to a 2.55-fold (95% CS 2.50–2.61) and 1.93 (95% CS 1.89–1.98) increase in the number of deaths. The excess death wave started a few days later in Brescia, but the daily estimated SMR peaked at the end of March in both HPAs, roughly 2 weeks after the introduction of lockdown measures, with significantly higher estimates in Bergamo (9.4, 95% CI 9.1–9.7). Conclusion Excess mortality was significantly higher than that officially attributed to COVID-19, disclosing its hidden burden likely due to indirect effects on the health system. Time-series analyses highlighted the impact of lockdown restrictions, with a lower excess mortality in the HPA where there was a smaller delay between the epidemic outbreak and their enforcement. This study identifies another important element to research on #SARSCoV2 and provides actionable strategies to quantify the excess mortality due to #COVID19 spread, which has public health and research implications to minimise the disease impact https://bit.ly/3jbKXAW
Functional Requirements of the Yellow Fever Virus Capsid Protein

ABSTRACT Although it is known that the flavivirus capsid protein is essential for genome packaging and formation of infectious particles, the minimal requirements of the dimeric capsid protein for virus assembly/disassembly have not been characterized. By use of a trans-packaging system that involved packaging a yellow fever virus (YFV) replicon into pseudo-infectious particles by supplying the YFV structural proteins using a Sindbis virus helper construct, the functional elements within the YFV capsid protein (YFC) were characterized. Various N- and C-terminal truncations, internal deletions, and point mutations of YFC were analyzed for their ability to package the YFV replicon. Consistent with previous reports on the tick-borne encephalitis virus capsid protein, YFC demonstrates remarkable functional flexibility. Nearly 40 residues of YFC could be removed from the N terminus while the ability to package replicon RNA was retained. Additionally, YFC containing a deletion of approximately 27 residues of the C terminus, including a complete deletion of C-terminal helix 4, was functional. Internal deletions encompassing the internal hydrophobic sequence in YFC were, in general, tolerated to a lesser extent. Site-directed mutagenesis of helix 4 residues predicted to be involved in intermonomeric interactions were also analyzed, and although single mutations did not affect packaging, a YFC with the double mutation of leucine 81 and valine 88 was nonfunctional. The effects of mutations in YFC on the viability of YFV infection were also analyzed, and these results were similar to those obtained using the replicon packaging system, thus underscoring the flexibility of YFC with respect to the requirements for its functioning.