Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt

ABSTRACT The nutritional status of pregnant women is vital for healthy outcomes and is a concern for a large proportion of the world's population. The role of the microbiota in pregnancy and nutrition is a promising new area of study with potential health ramifications. In many African countries, maternal and infant death and morbidity are associated with malnutrition. Here, we assess the influence of probiotic yogurt containing Lactobacillus rhamnosus GR-1, supplemented with Moringa plant as a source of micronutrients, on the health and oral, gut, vaginal, and milk microbiotas of 56 pregnant women in Tanzania. In an open-label study design, 26 subjects received yogurt daily, and 30 were untreated during the last two trimesters and for 1 month after birth. Samples were analyzed using 16S rRNA gene sequencing, and dietary recalls were recorded. Women initially categorized as nourished or undernourished consumed similar calories and macronutrients, which may explain why there was no difference in the microbiota at any body site. Consumption of yogurt increased the relative abundance of Bifidobacterium and decreased Enterobacteriaceae in the newborn feces but had no effect on the mother's microbiota at any body site. The microbiota of the oral cavity and GI tract remained stable over pregnancy, but the vaginal microbiota showed a significant increase in diversity leading up to and after birth. In summary, daily micronutrient-supplemented probiotic yogurt provides a safe, affordable food for pregnant women in rural Tanzania, and the resultant improvement in the gut microbial profile of infants is worthy of further study.
Patterns of tobacco use: A 10-year follow-up study of smoking and snus habits in a middle-aged Swedish population

Aims: To study longitudinal patterns of tobacco use over a 10-year period among middle-aged men and women in Vaösterbotten County, Northern Sweden. Methods: The study is based on data from the 16,486 (8800 women and 7686 men) in the Vaösterbotten Intervention Programme (VIP) where people were invited to a health screening and counselling programme at 30, 40, 50 and 60 years of age. Results: Smoking decreased from 22.3% to 15.6% among women and from 18.5% to 12.7% among men. Use of snus (Swedish moist snuff) increased from 3.1% to 6.0% among women and from 24.6% to 26.3% among men. The number of people who used both snus and cigarettes was stable: 0.5% to 0.8% from baseline to follow-up for women, and 4.1% to 3.3% for men. The number of tobacco-free adults increased from 75.2% to 79.2% for women and from 61.1% to 64.3% for men. Of those who became smoke-free during the 10-year follow-up period, 80% of the women and 66% of the men quit smoking without transitioning to snus use. Conclusions: The majority of middle-aged Swedish men and women in this cohort that quit smoking did so without becoming snus dependent. In spite of an increasing use of snus, overall there was a decline in the number of people using tobacco products.
Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay

ABSTRACT Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This report introduces a multiplex PCR assay for differentiating members of C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Coding region sequences unique to each of the four species/subgroups were identified by in silico analyses of thousands of genome assemblies, and PCR primers were designed to amplify each marker. The resulting multiplex PCR assay correctly assigned 41 tested isolates to the appropriate species or subgroup. A separate PCR assay to determine the presence of the ntnh gene (a gene associated with the botulinum neurotoxin gene cluster) was developed and validated. The ntnh gene PCR assay provides information about the presence or absence of the botulinum neurotoxin gene cluster and the type of gene cluster present (ha positive [ha+] or orfX+). The increased availability of whole-genome sequence data and comparative genomic tools enabled the design of these assays, which provide valuable information for characterizing BoNT-producing clostridia. The PCR assays are rapid, inexpensive tests that can be applied to a variety of sample types to assign isolates to species/subgroups and to detect clostridia with botulinum neurotoxin gene (bont) clusters. IMPORTANCE Diverse clostridia produce the botulinum neurotoxin, one of the most potent known neurotoxins. In this study, a multiplex PCR assay was developed to differentiate clostridia that are most commonly isolated in connection with human botulism cases: C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Since BoNT-producing and nontoxigenic isolates can be found in each species, a PCR assay to determine the presence of the ntnh gene, which is a universally present component of bont gene clusters, and to provide information about the type (ha+ or orfX+) of bont gene cluster present in a sample was also developed. The PCR assays provide simple, rapid, and inexpensive tools for screening uncharacterized isolates from clinical or environmental samples. The information provided by these assays can inform epidemiological studies, aid with identifying mixtures of isolates and unknown isolates in culture collections, and confirm the presence of bacteria of interest.
Disability pensioning: The gender divide can be explained by occupation, income, mental distress and health

Background: We aimed to test the hypothesis that gender divide in disability pensioning is attributable to differences in health, mental distress, occupation, and income. Methods: In a health survey between 2000 and 2001, a total of 11,072 (48.7%) of all Oslo inhabitants aged 40, 45, 59, and 60 years participated. Survey data were linked to data from the National Insurance Administration and Statistics Norway for 10,421 of the participants, and 9,195 of those were eligible to receive disability pension at the end of 2000. Occupation, general health, and mental distress were self-reported, while income was obtained from official statistics. Results: Approximately 5% of the eligible sample received a disability pension during the four years following the health survey. The age-adjusted odds of receiving disability pension for women was greater (odds ratio = 1.41) than for men. Self-reported health significantly contributed to the risk of receiving a pension, and seemed to reduce the imbalance in disability rates between the genders, as did adjusting for level of mental distress. Further adjustment for occupation and working conditions reduced the gender divide to an insignificant level, and the inclusion of income level (income three years prior to pensioning) completely eliminated any gender difference in risk of receiving a pension. Conclusions: Gender differences in disability pensioning in Oslo are attributable to women’s poorer self-reported health, greater levels of mental distress, lower wages, and more unfavourable working conditions such as job strain and less control over work.
All-cause and cause-specific mortality of social assistance recipients in Norway: A register-based follow-up study

Aims: To investigate the mortality among social assistance recipients, who are among the most marginalized people in Norway. Cause-specific mortality was analysed in an attempt to explain the excess mortality. Previous research has suggested that social disadvantage leads to higher mortality from all causes, whereas others have found substantial variation when studying separate causes. The impact of the various causes will influence policy recommendations. Methods: Data were compiled through linking between Norwegian administrative records. The entire population born between 1935 and 1974 (2,297,621 people) was followed with respect to social assistance and death from 1993 to 2003. Cause-specific, age-standardized mortality rates for social assistance recipients and the rest of the population were calculated, and both the absolute (rate difference) and relative (rate ratio) rates were measured. Results: The rate ratio for total mortality was 3.1 for men and 2.5 for women for the comparison between social assistance recipients and the general population. The mortality among social assistance recipients was higher for all causes, but the magnitude differed considerably, depending on the cause. The rate ratio for men ranged from 1.2 for non-smoking-related cancer to 18.8 for alcohol- and drug-related causes. Alcohol-and drug-related and violent causes together contributed to half of the excess mortality for men and one-third for women. Conclusions: The mortality of this socially disadvantaged group was considerably higher than that of the general population, and this difference reflected mainly drug-related causes.
Psychosocial work environment and its association with socioeconomic status. A comparison of Spain and Denmark

Aims: The purpose of this study was to describe psychosocial work environment inequalities among wage earners in Spain and Denmark. Methods: Data came from the Spanish COPSOQ (ISTAS 21) and the Danish COPSOQ II surveys both performed in 2004—05 and based on national representative samples of employees with a 60% response rate. Study population was 3,359 Danish and 6,685 Spanish women and men. Only identical items from both surveys were included to construct 18 psychosocial scales. Socioeconomic status was categorized according to the European Socioeconomic Classification System. Analysis included ordinal logistic regression and multiple correspondence analysis after categorizing all scales. Results: A relationship between socioeconomic status and psychosocial work environment in both Denmark and Spain was observed, with wider social inequalities in Spain for many scales, describing a strong interaction effect between socioeconomic status and country. Conclusions: Socioeconomic status is related to psychosocial work environment and some adverse psychosocial conditions tend to cluster in lower socioeconomic status groups in both Spain and Denmark. This effect could be modified by a country’s characteristics, such as economic and labour market structures, normative regulations and industrial relations including work organization. Hence, preventive strategies to reduce social inequalities in working conditions should consider the combination of actions at the macro and micro levels.
rhs Genes Are Potential Markers for Multilocus Sequence Typing of Escherichia coli O157:H7 Strains

ABSTRACT DNA sequence-based molecular subtyping methods such as multilocus sequence typing (MLST) are commonly used to generate phylogenetic inferences for monomorphic pathogens. The development of an effective MLST scheme for subtyping Escherichia coli O157:H7 has been hindered in the past due to the lack of sequence variation found within analyzed housekeeping and virulence genes. A recent study suggested that rhs genes are under strong positive selection pressure, and therefore in this study we analyzed these genes within a diverse collection of E. coli O157:H7 strains for sequence variability. Eighteen O157:H7 strains from lineages I and II and 15 O157:H7 strains from eight clades were included. Examination of these rhs genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage strains and 280 PL and 12 STs among the 15 clade strains. Phylogenetic analysis using rhs genes generally grouped strains according to their known lineage and clade classifications. These findings also suggested that O157:H7 strains from clades 6 and 8 fall into lineage I/II and that strains of clades 1, 2, 3, and 4 fall into lineage I. Additionally, unique markers were found in rhsA and rhsJ that might be used to define clade 8 and clade 6. Therefore, rhs genes may be useful markers for phylogenetic analysis of E. coli O157:H7.
Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

ABSTRACT Many marine sponges, hereafter termed high-microbial-abundance (HMA) sponges, harbor large and complex microbial consortia, including bacteria and archaea, within their mesohyl matrices. To investigate vertical microbial transmission as a strategy to maintain these complex associations, an extensive phylogenetic analysis was carried out with the 16S rRNA gene sequences of reproductive (n = 136) and adult (n = 88) material from five different Caribbean species, as well as all published 16S rRNA gene sequences from sponge offspring (n = 116). The overall microbial diversity, including members of at least 13 bacterial phyla and one archaeal phylum, in sponge reproductive stages is high. In total, 28 vertical-transmission clusters, defined as clusters of phylotypes that are found both in adult sponges and their offspring, were identified. They are distributed among at least 10 bacterial phyla and one archaeal phylum, demonstrating that the complex adult microbial community is collectively transmitted through reproductive stages. Indications of host-species specificity and cospeciation were not observed. Mechanistic insights were provided using a combined electron microscopy and fluorescence in situ hybridization analysis, and an indirect mechanism of vertical transmission via nurse cells is proposed for the oviparous sponge Ectyoplasia ferox. Based on these phylogenetic and mechanistic results, we suggest the following symbiont transmission model: entire microbial consortia are vertically transmitted in sponges. While vertical transmission is clearly present, additional environmental transfer between adult individuals of the same and even different species might obscure possible signals of cospeciation. We propose that associations of HMA sponges with highly sponge-specific microbial communities are maintained by this combination of vertical and horizontal symbiont transmission.
Improving Biocatalyst Performance by Integrating Statistical Methods into Protein Engineering

ABSTRACT Directed evolution and rational design were used to generate active variants of toluene-4-monooxygenase (T4MO) on 2-phenylethanol (PEA), with the aim of producing hydroxytyrosol, a potent antioxidant. Due to the complexity of the enzymatic system—four proteins encoded by six genes—mutagenesis is labor-intensive and time-consuming. Therefore, the statistical model of Nov and Wein (J. Comput. Biol. 12:247-282) was used to reduce the number of variants produced and evaluated in a lab. From an initial data set of 24 variants, with mutations at nine positions, seven double or triple mutants were identified through statistical analysis. The average activity of these mutants was 4.6-fold higher than the average activity of the initial data set. In an attempt to further improve the enzyme activity to obtain PEA hydroxylation, a second round of statistical analysis was performed. Nine variants were considered, with 3, 4, and 5 point mutations. The average activity of the variants obtained in the second statistical round was 1.6-fold higher than in the first round and 7.3-fold higher than that of the initial data set. The best variant discovered, TmoA I100A E214G D285Q, exhibited an initial oxidation rate of 4.4 ± 0.3 nmol/min/mg protein, which is 190-fold higher than the rate obtained by the wild type. This rate was also 2.6-fold higher than the activity of the wild type on the natural substrate toluene. By considering only 16 preselected mutants (out of ∼13,000 possible combinations), a highly active variant was discovered with minimum time and effort.
Prevalence of Treponema pallidum Infection among Human Immunodeficiency Virus Seropositive Persons and Their Corresponding CD4 Counts in a Nigerian Cohort

Background: Sexually transmitted infections are a major public health problem especially with the advent of HIV/AIDS. This study was conducted to determine the prevalence of Syphilis among HIV seropositive persons. The study population was seropositive persons accessing antiretroviral therapy (ART) at the Federal Medical Center Keffi. Methodology: Venous blood (5ml) was collected from each of the 200 consenting participants between February and August 2010. Their syphilis serostatus was determined using Rapid Plasma Reagin test and confirmed by an immunochromatographic rapid syphilis test kit. The CD4 count of the positive sample was also determined. Results: Of the 200 persons screened, 56 were males and 144 were females. The prevalence of Treponema pallidum in this study population was 0.5% (1/200). The HIVsyphilis positive was a married man aged 35 years and with a CD4 cell count of ≥ 200 cells/uL. Conclusion: This study reported a very low prevalence of syphilis among HIV positive persons. It is recommended that the sexual partner(s) of the study index case should be traced and also treated to prevent reinfection and/or continued spread of the infection. Despite the low prevalence in this study, syphilis screening among those with HIV should be advocated routinely to avoid the complications associated with the dual infection.
Functional Heterologous Production of Reductive Dehalogenases from Desulfitobacterium hafniense Strains

ABSTRACT The anaerobic dehalogenation of organohalides is catalyzed by the reductive dehalogenase (RdhA) enzymes produced in phylogenetically diverse bacteria. These enzymes contain a cobamide cofactor at the active site and two iron-sulfur clusters. In this study, the tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram-positive Desulfitobacterium hafniense strain Y51 was produced in a catalytically active form in the nondechlorinating, cobamide-producing bacterium Shimwellia blattae (ATCC 33430), a Gram-negative gammaproteobacterium. The formation of recombinant catalytically active PceA enzyme was significantly enhanced when its dedicated PceT chaperone was coproduced and when 5,6-dimethylbenzimidazole and hydroxocobalamin were added to the S. blattae cultures. The experiments were extended to D. hafniense DCB-2, a reductively dehalogenating bacterium harboring multiple rdhA genes. To elucidate the substrate spectrum of the rdhA3 gene product of this organism, the recombinant enzyme was tested for the conversion of different dichlorophenols (DCP) in crude extracts of an RdhA3-producing S. blattae strain. 3,5-DCP, 2,3-DCP, and 2,4-DCP, but not 2,6-DCP and 3,4-DCP, were reductively dechlorinated by the recombinant RdhA3. In addition, this enzyme dechlorinated PCE to trichloroethene at low rates.
Global Transcriptional Response of the Alkali-Tolerant Cyanobacterium Synechocystis sp. Strain PCC 6803 to a pH 10 Environment

ABSTRACT Many cyanobacterial strains are able to grow at a pH range from neutral to pH 10 or 11. Such alkaline conditions favor cyanobacterial growth (e.g., bloom formation), and cyanobacteria must have developed strategies to adjust to changes in CO2 concentration and ion availability. Synechocystis sp. strain PCC 6803 exhibits similar photoautotrophic growth characteristics at pH 10 and pH 7.5, and we examined global gene expression following transfer from pH 7.5 to pH 10 to determine cellular adaptations at an elevated pH. The strategies used to develop homeostasis at alkaline pH had elements similar to those of many bacteria, as well as components unique to phototrophic microbes. Some of the response mechanisms previously identified in other bacteria included upregulation of Na+/H+ antiporters, deaminases, and ATP synthase. In addition, upregulated genes encoded transporters with the potential to contribute to osmotic, pH, and ion homeostasis (e.g., a water channel protein, a large-conductance mechanosensitive channel, a putative anion efflux transporter, a hexose/proton symporter, and ABC transporters of unidentified substrates). Transcriptional changes specific to photosynthetic microbes involved NADH dehydrogenases and CO2 fixation. The pH transition altered the CO2/HCO3− ratio within the cell, and the upregulation of three inducible bicarbonate transporters (BCT1, SbtA, and NDH-1S) likely reflected a response to this perturbed ratio. Consistent with this was increased transcript abundance of genes encoding carboxysome structural proteins and carbonic anhydrase. Interestingly, the transition to pH 10 resulted in increased abundance of transcripts of photosystem II genes encoding extrinsic and low-molecular-weight polypeptides, although there was little change in photosystem I gene transcripts.
Primary Endometriosis of Umbilical Scar: Case Report and Review of Literature

We report a case of umbilical endometriosis and review the literature about the finding. The patient was a 39-year-old woman who presented with 6 months of umbilical bleeding and pain during the first day of her period. A soft tissue ultrasound scan showed 2 superficial solid masses within the periumbilical subcutaneous adipose tissue, suggestive for ectopic endometriosis localization. We decided to remove the umbilical nodules, excising 1 cm of the surrounding tissue. Reports in the literature indicate cases of umbilical endometriosis in about 0.5%-1% of women with endometriosis.
Laypeople's Understanding of Radioactivity and Radiation

It may be argued that the population should have sufficient understanding of radiation phenomena to secure individual safety as well as democratic decisions. To attain this, it is necessary for the communicators of radiation information to be familiar with the lay person's perceptions of these phenomena. A questionnaire survey was conducted to examine non-experts' conceptions of radiation phenomena. The survey revealed incomplete understanding of concepts such as radioactive decay, half-life and absorption of radiation and a lack of differentiation between radiation and radioactive material. Many respondents did not distinguish between sources of ionising radiation and other environmental hazards. Nuclear power plants and submarines were the most feared sources of radiation. There are indications that the lay understanding of radiation phenomena and risk is to a large extent formed by mass media and that 'school knowledge' of these phenomena is not applied in situations belonging to the real world'. To resolve this problem, new teaching and information procedures are needed. These should take into account the learners' preconceptions and should integrate 'school knowledge' with considerations belonging to the 'real world'.