Miracle-dz/UniFAR-FTUs huggingface dataset:
An Inducible Operon Is Involved in Inulin Utilization in Lactobacillus plantarum Strains, as Revealed by Comparative Proteogenomics and Metabolic Profiling

ABSTRACT The draft genomes of Lactobacillus plantarum strains isolated from Asian fermented foods, infant feces, and shrimp intestines were sequenced and compared to those of well-studied strains. Among 28 strains of L. plantarum, variations in the genomic features involved in ecological adaptation were elucidated. The genome sizes ranged from approximately 3.1 to 3.5 Mb, of which about 2,932 to 3,345 protein-coding sequences (CDS) were predicted. The food-derived isolates contained a higher number of carbohydrate metabolism-associated genes than those from infant feces. This observation correlated to their phenotypic carbohydrate metabolic profile, indicating their ability to metabolize the largest range of sugars. Surprisingly, two strains (P14 and P76) isolated from fermented fish utilized inulin. β-Fructosidase, the inulin-degrading enzyme, was detected in the supernatants and cell wall extracts of both strains. No activity was observed in the cytoplasmic fraction, indicating that this key enzyme was either membrane-bound or extracellularly secreted. From genomic mining analysis, a predicted inulin operon of fosRABCDXE, which encodes β-fructosidase and many fructose transporting proteins, was found within the genomes of strains P14 and P76. Moreover, pts1BCA genes, encoding sucrose-specific IIBCA components involved in sucrose transport, were also identified. The proteomic analysis revealed the mechanism and functional characteristic of the fosRABCDXE operon involved in the inulin utilization of L. plantarum. The expression levels of the fos operon and pst genes were upregulated at mid-log phase. FosE and the LPXTG-motif cell wall anchored β-fructosidase were induced to a high abundance when inulin was present as a carbon source. IMPORTANCE Inulin is a long-chain carbohydrate that may act as a prebiotic, which provides many health benefits to the host by selectively stimulating the growth and activity of beneficial bacteria in the colon. While certain lactobacilli can catabolize inulin, this has not yet been described for Lactobacillus plantarum, and an associated putative inulin operon has not been reported in this species. By using comparative and functional genomics, we showed that two L. plantarum strains utilized inulin and identified functional inulin operons in their genomes. The proteogenomic data revealed that inulin degradation and uptake routes, which related to the fosRABCDXE operon and pstBCA genes, were widely expressed among L. plantarum strains. The present work provides a novel understanding of gene regulation and mechanisms of inulin utilization in probiotic L. plantarum generating opportunities for synbiotic product development.
Occurrence and Genetic Diversity of Arcobacter butzleri in an Artisanal Dairy Plant in Italy

ABSTRACT The present study aimed to investigate the presence, distribution, and persistence of Arcobacter spp. in an artisanal dairy plant and to test the isolates to determine their different genotypes in the processing plant and in foods. Samples were collected in an artisanal cheese factory on four occasions between October and December 2012. Food samples (raw milk, ricotta cheese, mozzarella cheese, and conditioning liquid), water samples, and environmental samples were analyzed by the culture method; isolates were identified by multiplex PCR and genotyped by pulsed-field gel electrophoresis (PFGE) analysis. Arcobacter butzleri was isolated from 29 out of 59 samples (46.6%), 22 of which were from environmental samples and 7 of which were from food samples. Cluster analysis divided the strains into 47 PFGE patterns: 14 PFGE clusters and 33 unique types. Our findings indicate that the plant harbored numerous A. butzleri pulsotypes and that the manual cleaning and sanitation in the studied dairy plant do not effectively remove Arcobacter. The recurrent isolation of A. butzleri suggests that the environmental conditions in the dairy plant constitute a good ecological niche for the colonization of this microorganism. In some cases, the presence of indistinguishable strains isolated from the same facilities on different sampling days showed that these strains were persistent in the processing environment.
Memes as games: The evolution of a digital discourse online

This study proposes a theoretical framework for understanding how and why certain memes prevail as a form of political discourse online. Since memes are constantly changing as they spread, drawing inferences from a population of memes as concrete digital artifacts is a pressing challenge for researchers. This article argues that meme selection and mutation are driven by a cooperative combination of three types of communication logic: wasteful play online, social media political expression, and cultural evolution. To illustrate this concept, we map Shepard Fairey’s Obama Hope Poster as it spreads online. Employing structural rhetorical analysis, the study categorizes Internet memes on branching diagrams as they evolve. We argue that mapping these variations is a useful tool for organizing memes as an expression of the values and preferences embedded in online communities. The study adds to the growing literature around the subversive nature of memetic diffusion in popular and political culture.
Polyphosphate-Accumulating Bacteria: Potential Contributors to Mineral Dissolution in the Oral Cavity

ABSTRACT Bacteria that accumulate polyphosphates have previously been shown to dynamically influence the solubility of phosphatic minerals in marine settings and wastewater. Here, we show that dental plaque, saliva, and carious lesions all contain abundant polyphosphate-accumulating bacteria. Saturation state modeling results, informed by phosphate uptake experiments using the model organism Lactobacillus rhamnosus, which is known to inhabit advanced carious lesions, suggest that polyphosphate accumulation can lead to undersaturated conditions with respect to hydroxyapatite under some oral cavity conditions. The cell densities of polyphosphate-accumulating bacteria we observed in some regions of oral biofilms are comparable to those that produce undersaturated conditions (i.e., those that thermodynamically favor mineral dissolution) in our phosphate uptake experiments with L. rhamnosus. These results suggest that the localized generation of undersaturated conditions by polyphosphate-accumulating bacteria constitutes a new potential mechanism of tooth dissolution that may augment the effects of metabolic acid production. IMPORTANCE Dental caries is a serious public health issue that can have negative impacts on overall quality of life and oral health. The role of oral bacteria in the dissolution of dental enamel and dentin that can result in carious lesions has long been solely ascribed to metabolic acid production. Here, we show that certain oral bacteria may act as a dynamic shunt for phosphate in dental biofilms via the accumulation of a polymer known as polyphosphate—potentially mediating phosphate-dependent conditions such as caries (dental decay).
Molecular Epidemiology and Characterization of Campylobacter spp. Isolated from Wild Bird Populations in Northern England

ABSTRACT Campylobacter infections have been reported at prevalences ranging from 2 to 50% in a range of wild bird species, although there have been few studies that have investigated the molecular epidemiology of Campylobacter spp. Consequently, whether wild birds are a source of infection in humans or domestic livestock or are mainly recipients of domestic animal strains and whether separate cycles of infection occur remain unknown. To address these questions, serial cross-sectional surveys of wild bird populations in northern England were carried out over a 2-year period. Fecal samples were collected from 2,084 wild bird individuals and screened for the presence of Campylobacter spp. A total of 56 isolates were recovered from 29 birds sampled at 15 of 167 diverse locales. Campylobacter jejuni, Campylobacter lari, and Campylobacter coli were detected by PCR, and the prevalences of different Campylobacter spp. in different avian families ranged from 0% to 33%. Characterization of 36 C. jejuni isolates by multilocus sequence typing revealed that wild birds carry both livestock-associated and unique strains of C. jejuni. However, the apparent absence of unique wild bird strains of C. jejuni in livestock suggests that the direction of infection is predominantly from livestock to wild birds. C. lari was detected mainly in wild birds sampled in an estuarine or coastal habitat. Fifteen C. lari isolates were analyzed by macrorestriction pulsed-field gel electrophoresis, which revealed genetically diverse populations of C. lari in Eurasian oystercatchers (Haematopus ostralegus) and clonal populations in magpies (Pica pica).
Splenic Hemorrhage with Hemoperitoneum Caused by a Snakebite

In Asia, snakebites are estimated to affect 4 million people every year, and of these, 100,000 people are estimated to die. In Korea, snakebites occur frequently from the spring to the fall, but their importance is often overlooked. Fatal complications, including acute respiratory distress and acute kidney injury, can occur, and in some cases, severe hemorrhage results from coagulopathy. There have been only a few cases of snakebite-induced liver or intestinal bleeding, but to our knowledge, spontaneous bleeding from the spleen has not been previously reported. Here, we report the case of a 61-year-old male who visited the emergency room with abrupt abdominal pain due to hemoperitoneum associated with splenic hemorrhage after a snakebite.
Sleep Disordered Breathing in Chronic Obstructive Pulmonary Disease

Sleep depresses ventilation in normal persons, producing an increase in arterial carbon dioxide pressure (PaCO2) and a decrease in arterial oxygen pressure (PaO2). Since many patients with severe chronic obstructive pulmonary disease (COPD) have reduced alveolar ventilation with hypoxemia and hypercapnia while awake, one would predict that they will have more profound alterations in arterial blood gases than normal persons during sleep. In fact, these abnormalities do occur and have been reported by a number of investigators. Since the initial reports of worsening blood gases in patients with COPD during sleep, a great deal more knowledge has been gained about sleep in general and sleep-disordered breathing in particular. The problem of episodic arterial desaturation during sleep in patients with COPD is much more profound than suggested by these earlier studies and its consequences may be of lasting significance. In this review we will describe the nature and prevalence of these episodes, explore their pathophysiology and possible consequences, and discuss their management.
Shared Binding Sites for the Bacillus thuringiensis Proteins Cry3Bb, Cry3Ca, and Cry7Aa in the African Sweet Potato Pest Cylas puncticollis (Brentidae)

ABSTRACT Bacillus thuringiensis Cry3Bb, Cry3Ca, and Cry7Aa have been reported to be toxic against larvae of the genus Cylas, which are important pests of sweet potato worldwide and particularly in sub-Saharan Africa. However, relatively little is known about the processing and binding interactions of these coleopteran-specific Cry proteins. The aim of the present study was to determine whether Cry3Bb, Cry3Ca, and Cry7Aa proteins have shared binding sites in Cylas puncticollis to orient the pest resistance strategy by genetic transformation. Interestingly, processing of the 129-kDa Cry7Aa protoxin using commercial trypsin or chymotrypsin rendered two fragments of about 70 kDa and 65 kDa. N-terminal sequencing of the trypsin-activated Cry7Aa fragments revealed that processing occurs at Glu47 for the 70-kDa form or Ile88 for the 65-kDa form. Homologous binding assays showed specific binding of the two Cry3 proteins and the 65-kDa Cry7Aa fragment to brush border membrane vesicles (BBMV) from C. puncticollis larvae. The 70-kDa fragment did not bind to BBMV. Heterologous-competition assays showed that Cry3Bb, Cry3Ca, and Cry7Aa (65-kDa fragment) competed for the same binding sites. Hence, our results suggest that pest resistance mediated by the alteration of a shared Cry receptor binding site might render all three Cry toxins ineffective.
Probabilistic optimum filtering for robust speech recognition

We present a new mapping algorithm for speech recognition that relates the features of simultaneous recordings of clean and noisy speech. The model is a piecewise linear transformation applied to the noisy speech feature. The transformation is a set of multidimensional linear least-squares filters whose outputs are combined using a conditional Gaussian model. The algorithm was tested using SRI's DECIPHER speech recognition system. Experimental results show how the mapping is used to reduce recognition errors when the training and testing acoustic environments do not match. <<ETX>>
The bradykinin-degrading aminopeptidase P is increased in women taking the oral contraceptive pill

Introduction. The renin-angiotensin and kininogen-kinin hormonal systems are critically involved in regulating blood pressure and are candidates in contributing to oral contraceptive pill (OCP)-induced hypertension.Angiotensin-converting enzyme (ACE) and aminopeptidase P (AP-P) are key enzymes in these systems and are both involved in the degradation of the vasodilator bradykinin. Methods. Circulating ACE and AP-P levels were measured by activity assay using selective fluorogenic peptide substrates in plasma samples from the Leeds Family Study. In addition, the effect of progesterone on the expression of AP-P and ACE was examined in cells. Results. Women on the OCP had higher age-adjusted plasma AP-P (mean [95% confidence interval]) (0.27 [0.23-0.32] nmol/min/ml (n = 53)) compared with women not on the OCP (0.17 [0.16-0.19] nmol/min/ml (n = 133), p < 0.001) or males (0.19 [0.17-0.20] nmol/min/ml (n = 209), p<0.001). There were no differences in the age-adjusted plasma ACE levels among the three groups. In HepG2 cells, progesterone treatment increased the AP-P protein and mRNA expression, whereas no effect of progesterone treatment was observed for ACE. Conclusion. Increased AP-P may result in increased breakdown of bradykinin.These data suggest that progesterone-induced increases in AP-P may contribute to the development of OCP-induced hypertension in susceptible Women.
Up- and down-regulation of angiotensin II AT1-A and AT1-B receptors in afferent and efferent rat kidney arterioles

Introduction. The contractile effect of angiotensin II via AT1 receptors on the kidney arterioles is a crucial element in the kidney microcirculation.Angiotensin II also plays a role as an inhibitor via the AT1 receptors in the renin granulation of the arterioles.We have previously demonstrated that the AT1 receptors are downregulated in the renin-positive smooth muscle cells (SMCs) in contrast to renin-negative SMCs. In this study, we estimated the numbers of the AT1 receptor sub-types separately in the afferent and efferent arterioles and the renin-positive and renin-negative SMCs. Methods. The immunohistochemical signals of theAT1-A and AT1-B receptors were counted by stereological methods.1 Results. The number of AT1-B receptors in the efferent arterioles (expressed in signals/µm 3; mean (CV): 0.32 (0.33)) was significantly higher (78%; p<0.05) as compared with the number in the afferent arterioles (0.18 (0.11)). No differences were found in the AT1-A receptors. In a number ofAT 1-A receptors, significant differences (p<0.01) were detected between the afferent arteriolar renin-positive SMCs (0.13 (0.36)) and the number in renin-negative SMCs (0.25 (0.34)). The AT1-B receptors did not display any differences. Conclusions. These results indicate that the AT1 receptor sub-types are regulated independently in the SMCs of the normal kidney arterioles.
Efficacy in angiotensin receptor blockade: a comparative review of data with olmesartan

A range of angiotensin II receptor blockers (ARB) is available, and analyses suggest there are differences between agents in terms of antihypertensive efficacy and 24-hour blood pressure control.This review assesses the data comparing olmesartan with other ARBs in terms of blood pressure reductions, goal achievement, 24-hour control and speed of onset. Olmesartan seems to have a more favourable efficacy profile relative to standard doses of the ARBs used in comparative studies; results consistent with the high degree of blockade of the angiotensin II type 1 receptor for olmesartan.Taken together, there might be differences between ARBs regarding their blood pressure lowering efficacy, and these results may provide further support of the benefits of olmesartan therapy since choice of an effective agent is crucial in antihypertensive therapy.
Influence of gender and body mass index on autonomic reactivity in adults and middle-aged population

Background and Aim: Studies have reported that both age and gender influences cardiovascular reactivity among adult and elderly. The current study was conducted to assess the effect of body mass index (BMI) on autonomic reactivity tests of different age groups in both sexes. Methods: The present study was conducted on 124 healthy volunteers categorized into adult population aged 20-45 years (male = 32, female = 31) and middle-aged population aged 46-60 years (male = 31, female = 30). Parameters for parasympathetic activity (30:15 ratio, standing to lying ratio, and deep breathing difference) were recorded using electrocardiograph. Sympathetic activity was assessed by cold pressure test (rise in diastolic blood pressure). Pearson's correlation coefficient was used to assess the association of BMI with autonomic reactivity. Results: Adults males had larger positive correlation between BMI and autonomic reactivity than females, but in middle-aged, there is no significant difference between the sexes. Among females, premenopausal subjects have less correlation between BMI and autonomic reactivity compared to postmenopausal subjects. Conclusion: Body mass index is correlated with autonomic reactivity in the younger population compared to the middle-aged population. Gender appears to alter the autonomic reactivity by affecting the BMI. BMI plays an important role in the modulation of autonomic functions.
Influence of GSTT1, GSTM1 and GSTP1 Polymorphisms on the Development of Breast Cancer

Introduction: Every year, more than 10 million women are diagnosed worldwide with breast cancer. Breast cancer remains the leading cause of death from malignancy in women. In Mexico about 12 Mexican women die every day from this disease. Glutathione S-transferase (GST) family consists of a group of isoenzymes involved in Phase II detoxification of xenobiotics by glutathione conjugation. There have been reports showing GST polymorphisms as a risk factor for developing cancer. Objective: Determine if the frequencies of polymorphisms of GSTT1, GSTM1 and GSTP1 are associated with breast cancer development. Materials and Methods: We studied 22 women with breast cancer and a control group of 30 women. DNA was extracted from blood. Polymorphisms of T1 and M1 were identified by multiplex PCR. The identification of GSTP1b (exon 5) and GSTP1c (exon 6), was performed separately by RFLP-PCR, using BsmAI and AciI enzymes respectively. Results: Frequencies of polymorphisms were as follows: for breast cancer group 33% null GSTT1 vs 40% null in the control, 32% null GSTM1 vs 63% of control; 63% heterozygote GSTP1b P1a/P1b and 18% homozygote P1b/P1b, vs 53% heterozygote and 20% homozygote in the control, 41% heterozygote P1a/P1c GSTP1c and 0% homozygote vs 10% heterozygote P1c/P1c and 0% homozygote control. Significant differences were found between GSTM1 and GSTP1c polymorphisms with GSTM1 null percentage higher in the control group and a higher frequency of P1c heterozygotes in the cancer group. Conclusion: As this is a pilot study where the results showed no association with breast cancer, further investigation is required on the involvement of GST genes in neoplasm development.
Macrolide-Resistant Streptococcus pneumoniae and Use of Antimicrobial Agents

common cause of childhood illness. Only 7 children with culture-positive influenza were hospitalized during this study, and many were too young to have received either influenza vaccine or antiviral treatment. Influenzavirus remained, however, associated with a substantial number of symptomatic office visits, cases of acute otitis media, and cases of lower respiratory tract disease in children over 2 years of age. Although
Antibacterial Mechanism of 405-Nanometer Light-Emitting Diode against Salmonella at Refrigeration Temperature

ABSTRACT The aim of this study was to elucidate the antibacterial mechanism of 405 ± 5-nm light-emitting diode (LED) illumination against Salmonella at 4°C in phosphate-buffered saline (PBS) by determining endogenous coproporphyrin content, DNA oxidation, damage to membrane function, and morphological change. Gene expression levels, including of oxyR, recA, rpoS, sodA, and soxR, were also examined to understand the response of Salmonella to LED illumination. The results showed that Salmonella strains responded differently to LED illumination, revealing that S. enterica serovar Enteritidis (ATCC 13076) and S. enterica subsp. enterica serovar Saintpaul (ATCC 9712) were more susceptible and resistant, respectively, than the 16 other strains tested. There was no difference in the amounts of endogenous coproporphyrin in the two strains. Compared with that in nonilluminated cells, the DNA oxidation levels in illuminated cells increased. In illuminated cells, we observed a loss of efflux pump activity, damage to the glucose uptake system, and changes in membrane potential and integrity. Transmission electron microscopy revealed a disorganization of chromosomes and ribosomes due to LED illumination. The levels of the five genes measured in the nonilluminated and illuminated S. Saintpaul cells were upregulated in PBS at a set temperature of 4°C, indicating that increased gene expression levels might be due to a temperature shift and nutrient deficiency rather than to LED illumination. In contrast, only oxyR in S. Enteritidis cells was upregulated. Thus, different sensitivities of the two strains to LED illumination were attributed to differences in gene regulation. IMPORTANCE Bacterial inactivation using visible light has recently received attention as a safe and environmentally friendly technology, in contrast with UV light, which has detrimental effects on human health and the environment. This study was designed to understand how 405 ± 5-nm light-emitting diode (LED) illumination kills Salmonella strains at refrigeration temperature. The data clearly demonstrated that the effectiveness of LED illumination on Salmonella strains depended highly on the serotype and strain. Our findings also revealed that its antibacterial mechanism was mainly attributed to DNA oxidation and a loss of membrane functions rather than membrane lipid peroxidation, which has been proposed by other researchers who studied the antibacterial effect of LED illumination by adding exogenous photosensitizers, such as chlorophyllin and hypericin. Therefore, this study suggests that the detailed antibacterial mechanisms of 405-nm LED illumination without additional photosensitizers may differ from that by exogenous photosensitizers. Furthermore, a change in stress-related gene regulation may alter the susceptibility of Salmonella cells to LED illumination at refrigeration temperature. Thus, our study provides new insights into the antibacterial mechanism of 405 ± 5-nm LED illumination on Salmonella cells.