Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity of drug and multidrug-resistant Mycobacterium tuberculosis circulating in Veracruz, Mexico

Background Mexico is one of the most important contributors of drug and multidrug-resistant tuberculosis in Latin America; however, knowledge of the genetic diversity of drug-resistant tuberculosis isolates is limited. Methods In this study, the genetic structure of 112 Mycobacterium tuberculosis strains from the southeastern Mexico was determined by spoligotyping and 24-loci MIRU-VNTRs. Findings The results show eight major lineages, the most of which was T1 (24%), followed by LAM (16%) and H (15%). A total of 29 (25%) isolates were identified as orphan. The most abundant SITs were SIT53/T1 and SIT42/LAM9 with 10 isolates each and SIT50/H3 with eight isolates. Fifty-two spoligotype patterns, twenty-seven clusters and ten clonal complexes were observed, demonstrating an important genetic diversity of drug and multidrug-resistant tuberculosis isolates in circulation and transmission level of these aggravated forms of tuberculosis. Being defined as orphan or as part of an orphan cluster, was a risk factor for multidrug resistant-tuberculosis (OR 2.5, IC 1.05–5.86 and OR 3.3, IC 1–11.03, respectively). Multiple correspondence analyses showed association of some clusters and SITs with specific geographical locations. Conclusions Our study provides one of the most detailed description of the genetic structure of drug and multidrug-resistant tuberculosis strains in southeast Mexico, establishing for the first time a baseline of the genotypes observed in resistant isolates circulating, however further studies are required to better elucidate the genetic structure of tuberculosis in region and the factors that could be participating in their dispersion.
Reducing mutans streptococci and caries development by Lactobacillus paracasei SD1 in preschool children: a randomized placebo-controlled trial

Abstract Objective: To examine a reducing effect of Lactobacillus paracasei SD1 on MS and caries in preschool children. Materials and methods: A total of 124 children, aged 1.5–5 years old, participated and were randomly assigned to the probiotic or control group. The probiotic group received L. paracasei SD1-milk and the control group received standard-milk once daily for 3 months. MS/lactobacilli were enumerated and the caries score was examined. Association between probiotic consumption and bacterial level, or caries progression was assessed by a multivariate logistic regression. This study was registered at the Thai-Clinical-Trials-Registry (TCTR20140903001). Results: Probiotic was found to be a factor associated with the MS level. Children in the probiotic group had a significantly lower risk of an increase in the MS level than in the control group after receiving the probiotic milk at 3- and 4-months with p < . 001 and p = . 040, respectively. Probiotic significantly reduced the risk for caries compared to the control group (p = .016). There were no adverse effects or non-compliance reported in either group. Conclusions: Consumption of milk powder containing L. paracasei SD1 resulted in a reduction of both salivary MS and delayed new caries development, and the strain is safe for use in young children. Results suggest that L. paracasei SD1 may be an alternative way for caries prevention in young children.
Lithium in drinking water and suicide rates across the East of England

Summary Lithium can be found naturally in drinking water. In clinical practice, it is widely used in pharmacological doses for the treatment of bipolar disorder; and may also prevent suicidal behaviour in people with mood disorders. In two studies, lithium levels in tap water have been significantly and negatively correlated with suicide. We measured lithium levels in tap water in the 47 subdivisions of the East of England and correlated these with the respective suicide standardised mortality ratio in each subdivision. We found no association between lithium in drinking water and suicide rates across the East of England from 2006 to 2008.
Birds in the playground: Evaluating the effectiveness of an urban environmental education project in enhancing school children’s awareness, knowledge and attitudes towards local wildlife

Children nowadays, particularly in urban areas, are more disconnected from nature than ever before, leading to a large-scale “extinction of experience” with the natural world. Yet there are many potential benefits from children interacting with nature first-hand, including via outdoor learning opportunities. Urban environmental education programmes typically aim to increase awareness and knowledge of local biodiversity and to promote positive attitudes and behaviour towards the environment. However, limited research has been conducted evaluating to what extent these interventions achieve their goals. Here, we explore and assess the influence of a six-week bird-feeding and monitoring project conducted within school grounds (“Bird Buddies”) on individual awareness, knowledge and attitudes towards birds by primary school children. This initiative was conducted across eight (sub-)urban primary schools within Brighton and Hove (UK), with 220 participating children (aged 7 to 10). Via pre- and post-project questionnaires, we found evidence for enhanced awareness of local biodiversity, alongside significant gains in both bird identification knowledge and attitudes, which were greatest for children with little prior exposure to nature. Many children expressed a keenness to continue improving the environmental value of their school grounds and to apply elements of the project at home. Student project evaluation scores were consistently positive. Mirroring this, participating teachers endorsed the project as a positive learning experience for their students. One year after the project, several schools were continuing to feed and watch birds. Collectively, the findings from this study highlight the multiple benefits that can be derived from engagement with a relatively short outdoor environmental activity. We therefore believe that such interventions, if repeated locally/longer term, could enhance children’s experience with nature in urban settings with combined positive environmental impact.
FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects

Motivation: In genetic association studies, meta‐analyses are widely used to increase the statistical power by aggregating information from multiple studies. In meta‐analyses, participating studies often share the same individuals due to the shared use of publicly available control data or accidental recruiting of the same subjects. As such overlapping can inflate false positive rate, overlapping subjects are traditionally split in the studies prior to meta‐analysis, which requires access to genotype data and is not always possible. Fortunately, recently developed meta‐analysis methods can systematically account for overlapping subjects at the summary statistics level. Results: We identify and report a phenomenon that these methods for overlapping subjects can yield low power. For instance, in our simulation involving a meta‐analysis of five studies that share 20% of individuals, whereas the traditional splitting method achieved 80% power, none of the new methods exceeded 32% power. We found that this low power resulted from the unaccounted differences between shared and unshared individuals in terms of their contributions towards the final statistic. Here, we propose an optimal summary‐statistic‐based method termed as FOLD that increases the power of meta‐analysis involving studies with overlapping subjects. Availability and implementation: Our method is available at http://software.buhmhan. com/FOLD. Contact: mail: buhm.han@amc.seoul. kr Supplementary information: Supplementary data are available at Bioinformatics online.
Vicarious pain responders and emotion: Evidence for distress rather than mimicry.

Up to a third of the population experiences pain when seeing another in pain. The mechanisms underlying such vicarious sensory experiences are thought to reflect hyperactive mirror systems (threshold theory) or dysfunctional processing and representation of oneself versus others (self/other theory). This study investigated whether the tendency to experience vicarious pain corresponds to disinhibited physiological reactivity toward other's emotions, and/or greater empathic mimicry of other's physiological state (respiratory behavior) during fear, pain, and positive emotion. Fifty healthy individuals aged 18-55 years (23 vicarious pain responders) completed empathy- and anxiety-related questionnaires, and a film task. Respiration was measured noninvasively with piezoelectric respiration belts while participants viewed emotional film clips depicting three emotions (fear/pain/positive) interspersed with neutral clips. The emotional stimuli depicted scenes in which the characters showed increases or decreases in respiration. The results suggest that vicarious pain responders do not mimic emotional respiratory behavior. Rather, vicarious pain responders had a significantly slower respiration rate for all emotional stimuli (MDiff = 1.40 respiratory cycles, SE = .68), compared to nonresponders. However, this was associated with heightened trait anxiety. The findings suggest vicarious pain is associated with acute distress, rather than empathic mimicry of the emotional states of another.
Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles

&NA; Distillers dried grains with solubles (DDGS) have increasingly been used in poultry diets as a consequence of rising grain costs. Some, but not all, sources of DDGS have a variable compositional value, and a high inclusion of this by‐product could be considered a risk factor for presentation of enteric diseases. Presently, 2 experiments were conducted using a starter corn‐soybean diet (zero to 7 d) and a corn‐DDGS‐soybean grower diet (8 to 28 d) with or without inclusion of a Bacillus‐direct‐fed microbial (DFM). In both experiments, day‐of‐hatch chicks were randomly assigned to 2 different groups: control group without DFM or Bacillus‐DFM group, containing 106 spores/g of feed. In each experiment, 8 pens of 20 chicks (n = 160/group) were used. Performance parameters of BW, BW gain (BWG), feed intake (FI), and feed conversion (FCR) were evaluated in each growth phase. Additionally, in experiment 2, intestinal samples were collected to determine duodenal and ileal morphology (n = 8/group), as well as the microbiota population of total lactic acid bacteria (TLAB), total Gram‐negative bacteria (TGNB), and total anaerobic bacteria (TAB) on d 28 (n = 16/group). Furthermore, both tibias were evaluated for bone strength and bone composition (n = 16/group). In both experiments BW, BWG, and FCR were improved by the DFM when compared to the control group (P < 0.05). In experiment 2, chickens supplemented with the DFM had less TGNB in the foregut intestinal segment and higher TLAB counts in both foregut and hindgut sections (P < 0.05). In addition significant increases in tibia breaking strength and bone mineralization were observed in the DFM group when compared with the control. In the case of intestinal morphology, DFM dietary inclusion increased villus height (VH), villus width, villus area, muscular thickness, and the VH to crypt depth ratio (VH:CD) in both duodenum and ileum sections. Results of the present study suggest that consumption of a selected Bacillus‐DFM producing a variable set of enzymes could contribute to enhanced performance, intestinal microbial balance, and bone quality in broiler chickens consuming a grower diet that contains corn‐DDGS.
Wonderful Life Revisited: Chance and contingency in the Ediacaran-Cambrian radiation

In his 1989 book Wonderful Life Stephen Jay Gould employed the fossils of the middle Cambrian Burgess Shale to argue for a pervasive role of contingency in the history of life. But Gould wrote at the advent of an explosion of research in the Ediacaran-Cambrian diversification of animals, before ‘tree-thinking’ had made great inroads into the reconstruction of phylogeny, and with just the first glimmer of data on the remarkable conservation of developmental genes across major animal clades. More than twenty years on, not only have views of the Burgess Shale fossils undergone considerable change, but the role of contingency has become more widely accepted among paleobiologists. Yet much of Gould’s argument that if one ‘played the tape again’ the outcome would differ is difficult to accept. In this contribution I review new views of the Ediacaran-Cambrian explosion relevant to the role of chance in evolution as an example of a larger tension between historicity and laws in evolution. Introduction Although the importance of determinism versus chance was not one of the ‘eternal metaphors’ in Stephen Jay Gould’s essay of the same name (Gould, 1977), but it might well have been, for the debate over how much of the history of life is deterministic, the result of physical processes, scaling laws or various biological constraints, versus how much of it reflects either chance or just one of many possible evolutionary histories (contingency) dates at least to Darwin (Beatty, 2008). Although the topic became less prominent with the Modern Synthesis, chance and necessity served as the title of Monod’s eponymous book (Monod, 1972), arose as ‘frozen accidents’ in Crick’s early discussion of the structure of the genetic code (Crick, 1968), and played a significant role in Kauffman arguments that many aspects of evolution may be ‘frozen accidents’, preserved not for their adaptive value but rather because they generate complexity which is subsequently preserved (Kauffman, 1993). The tension between determinism and chance continues today (Carroll, 2001). It appears in discussions over the ubiquity of allometric scaling relationships (Brown et al., 2004) and in structuralist arguments for the importance of physical forces (Salazar-Ciudad et al., 2003). In astrobiology a fundamental assumption is that sufficient regularities exist in the history of life that studies on Earth will have implications for life elsewhere in the Universe. The ubiquity of convergence of morphological form has often been used as evidence against contingency (Conway Morris 2003, McGhee, 2011), generating a suite of issues. But chance and contingency are different issues. Since 1989 the much of focus of this tension over chance,
Transformations of volatile methylated selenium in soil Dean

Microbial volatilization of selenium as dimethylselenide (DMSe) and dimethyldiselenide (DMDSe) from soil is an important part of the Se cycle in nature, but little is known about the stability and transformations of these gases during residence in the soil environment before dissipation to the atmosphere. Experiments monitored by gas chromatography and atomic absorption spectroscopy were made with various clay mineral standards, charcoal, commercial humic substances and soils to determine the sorption and transformations of DMSe and DMDSe injected into the headspace or passed through soil materials. Batch experiments conducted with 2±5 g materials placed into 40 mL Te ̄on centrifuge tubes equipped with Mininert 2 gas sampling valves showed that DMSe was slowly sorbed by soil materials and most of the DMSe de®cit in the headspace was recovered as SeO3 and SeO = 4 . In contrast, DMDSe was rapidly partitioned from the gas phase and resulted in an increased recovery of less soluble elemental and selenide-Se forms. These results were con®rmed during ̄ow-through soil column studies with both little DMSe sorption and sorption of the majority of DMDSe addition. Additions of selenomethionine (SeMet) to soil to produce DMSe and DMDSe in sealed ̄asks resulted in an increased partitioning of Se into inorganic Se when compared with a ̄owthrough system designed to limit the contact of Se gases with soil. These results suggest that soil Se volatilization as DMSe and DMDSe results in Se loss to the atmosphere as DMSe with concomitant soil Se immobilization due to the instability of DMDSe. # 1999 Elsevier Science Ltd. All rights reserved.
Could specialization to cold‐water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue‐footed booby, Sula nebouxii

Aim We assessed population differentiation and gene flow across the range of the blue‐footed booby (Sula nebouxii) (1) to test the generality of the hypothesis that tropical seabirds exhibit higher levels of population genetic differentiation than their northern temperate counterparts, and (2) to determine if specialization to cold‐water upwelling systems increases dispersal, and thus gene flow, in blue‐footed boobies compared with other tropical sulids.
Cathelicidins: a history and current knowledge with experimental data on the antimicrobial and cytotoxic activities of SMAP29 and congeners

Recommended Citation Weistroffer, Paula L. "Cathelicidins: a history and current knowledge with experimental data on the antimicrobial and cytotoxic activities of SMAP29 and congeners. " MS ii ACKNOWLEDGEMENTS I would like to thank Dr. Georgia Johnson for being a great department head and giving feedback on many presentations; Dr. Kim Brogden for his vast knowledge of antimicrobials and willingness to teach me about them; Dr. Sophie Joly and Tina Srikantha for their excellent laboratory skills, their help in answering all of my technical questions, and for being great people to work with; Connie Maze for her excellent organizational skills and lab support; Dr. Tim Starner for helping lyophilize our peptides; and Dr. Brian Tack for the development and synthesis of our peptides. And finally and most importantly, I thank Dr. Janet Guthmiller, without whom this project could not have been done. Thank you for taking me in so early in your Iowa career, for trusting me with this project, and for working on it with me these 9 years. Your knowledge, ability to teach, problem solve, think critically, and write are unsurpassed. And a final thanks for your inspiration and encouragement to begin my teaching career. Figure A3. Proposed model of how a cathelicidin-like peptide, such as SMAP29, might incorporate into the lipid bilayer of bacterial cell by means of the carpet theory. Blue and red colors represent the hydrophilic and hydrophobic residues, respectively. Figure A8. SEM of ovine cathelicidin SMAP29 a) within bacterial membrane of Pseudomonas aeruginosa PAO1 using specific antibody and protein A colloidal gold labeling; b) blebs start to form and protrude from the microbial surface; c) blebs in cross section appear as electron-dense material attached to the microbial surface (arrow) after a 3 hour timeframe . Figure A11. Agar plate poured, solidified, and punched with 3mm diameter wells. Figure A12. Agar plate with A. actinomycetemcomitans Y4 stained with Coomassie blue with visible zones of inhibition after incubations with Figure A13. Calculation of MIC – Inhibition zone measurements were converted to radial diffusion units (zone of inhibition (mm) − well diameter (3 mm) × 10). The MIC was calculated by determining the x intercept obtained from the relationship between radial diffusion units versus log 10 peptide concentration after regression. The following example shows the determination of MICs of SMAP28 for three periodontal pathogens. vii Figure A14. Susceptibility of aerobic and anaerobic oral bacteria to SMAP29 and congeners. MICs, …
Effects of long-term high-load exercise on the anatomy of the hip joints: a preliminary report

The aim of this study was to assess the impact of different sports on hip joint anatomic parameters in athletes. This was a cross-sectional study of eight male trampolinists, eight male weightlifters, and eight male volunteers enrolled in July 2014. Hip joint anatomic parameters were measured from plain radiographs taken at the level of the lesser trochanter center. Data were compared between groups using the &khgr;2-test or one-way analysis of variance with the Bonferroni post-hoc test. There were no significant differences among groups in age, height, or weight. Compared with the controls, trampolinists showed higher pelvic width, femoral neck length, metaphyseal width (T0), width 20 mm above T0 (T+20), width 20 mm below T0 (T−20) and center edge (CE) angle, and lower head–trochanter ratio, joint space, neck-shaft angle, and articular cartilage angle (P<0.05). Compared with the controls, weightlifters showed lower pelvic femoral index, joint space, length of femoral neck, eccentricity, neck-shaft, and AC angle, and higher pelvic width, femoral head radius, and CE angle (P<0.05). Compared with trampolinists, weightlifters showed higher head–trochanter ratio and femoral head radius, and lower pelvic femoral index, femoral neck length, eccentricity, T0, T+20, T−20, neck-shaft angle, CE angle, and articular cartilage angle (P<0.05). Long-term high-intensity training causes adaptive changes in the hip joint structure that differ between trampolinists and weightlifters.
Evaluating the Recovery Curve for Clinically Assessed Reaction Time After Concussion.

CONTEXT A change in reaction time is one of various clinical measures of neurocognitive function that can be monitored after concussion and has been reported to be among the most sensitive indicators of cognitive impairment. OBJECTIVE To determine the timeline for clinically assessed simple reaction time to return to baseline after a concussion in high school athletes. DESIGN Observational study. SETTING Athletic training room. PATIENTS OR OTHER PARTICIPANTS Twenty-one high school-aged volunteers. INTERVENTION(S) Participants completed 8 trials of the ruler-drop test during each session. Along with baseline measures, a total of 6 additional test sessions were completed over the course of 4 weeks after a concussion (days 3, 7, 10, 14, 21, and 28). MAIN OUTCOME MEASURE(S) The mean reaction times calculated for all participants from each of the 7 test sessions were analyzed to assess the change in reaction time over the 7 time intervals. RESULTS After a concussion and compared with baseline, simple reaction time was, on average, 26 milliseconds slower at 48 to 72 hours postinjury (P < .001), almost 18 milliseconds slower on day 7 (P < .001), and about 9 milliseconds slower on day 10 (P < .001). Simple reaction time did not return to baseline levels until day 14 postinjury. CONCLUSIONS Clinically assessed simple reaction time appeared to return to baseline levels within a timeframe that mirrors other measures of cognitive performance (approximately 14 days).