Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens

Background Non-typhoidal Salmonella enterica serovars, associated with different foods including poultry products, are important causes of bacterial gastroenteritis worldwide. The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain. The aim of this study was to compare the genomes of 25 S. enterica serovars isolated from broiler chicken farms to assess their intra- and inter-genetic variability, with a focus on virulence and antibiotic resistance characteristics. Methodology/Principal Finding The genomes of 25 S. enterica isolates covering five serovars (ten Typhimurium including three monophasic 4,[5],12:i:, four Enteritidis, three Hadar, four Heidelberg and four Kentucky) were sequenced. Most serovars were clustered in strongly supported phylogenetic clades, except for isolates of serovar Enteritidis that were scattered throughout the tree. Plasmids of varying sizes were detected in several isolates independently of serovars. Genes associated with the IncF plasmid and the IncI1 plasmid were identified in twelve and four isolates, respectively, while genes associated with the IncQ plasmid were found in one isolate. The presence of numerous genes associated with Salmonella pathogenicity islands (SPIs) was also confirmed. Components of the type III and IV secretion systems (T3SS and T4SS) varied in different isolates, which could explain in part, differences of their pathogenicity in humans and/or persistence in broilers. Conserved clusters of genes in the T3SS were detected that could be used in designing effective strategies (diagnostic, vaccination or treatments) to combat Salmonella. Antibiotic resistance genes (CMY, aadA, ampC, florR, sul1, sulI, tetAB, and srtA) and class I integrons were detected in resistant isolates while all isolates carried multidrug efflux pump systems regardless of their antibiotic susceptibility profile. Conclusions/Significance This study showed that the predominant Salmonella serovars in broiler chickens harbor genes encoding adhesins, flagellar proteins, T3SS, iron acquisition systems, and antibiotic and metal resistance genes that may explain their pathogenicity, colonization ability and persistence in chicken. The existence of mobile genetic elements indicates that isolates from a given serovar could acquire and transfer genetic material. Conserved genes in the T3SS and T4SS that we have identified are promising candidates for identification of diagnostic, antimicrobial or vaccine targets for the control of Salmonella in broiler chickens.
An epidemiological study of hyperdontia in American blacks and whites.

OBJECTIVE To test the null hypothesis that American blacks do not have a higher frequency of extra permanent teeth than whites. MATERIALS AND METHODS Panoramic radiographs of adolescent orthodontic patients, either American whites (n = 1100) or American blacks (n = 600), were reviewed systematically. RESULTS The frequencies of supernumerary incisors, premolars, and molars were each significantly more common in blacks. While incisors are the most common extra teeth in whites (and extra molars are least common), just the opposite ranking occurs in blacks. Overall, the odds ratio was 8.8 (95% confidence limits = 3.9, 20.0), confirming that American blacks are significantly more likely (almost 9 times more likely) to possess extra permanent teeth than American whites. CONCLUSIONS The hypothesis is rejected. Both the frequencies and the patterns of extra permanent teeth are significantly different in blacks and whites, suggesting different frequencies of the relevant (but unidentified) factors governing the developmental mechanisms that result in hyperdontia.
Robust Performance of Marginal Pacific Coral Reef Habitats in Future Climate Scenarios

Coral reef ecosystems are under dual threat from climate change. Increasing sea surface temperatures and thermal stress create environmental limits at low latitudes, and decreasing aragonite saturation state creates environmental limits at high latitudes. This study examines the response of unique coral reef habitats to climate change in the remote Pacific, using the National Center for Atmospheric Research Community Earth System Model version 1 alongside the species distribution algorithm Maxent. Narrow ranges of physico-chemical variables are used to define unique coral habitats and their performance is tested in future climate scenarios. General loss of coral reef habitat is expected in future climate scenarios and has been shown in previous studies. This study found exactly that for most of the predominant physico-chemical environments. However, certain coral reef habitats considered marginal today at high latitude, along the equator and in the eastern tropical Pacific were found to be quite robust in climate change scenarios. Furthermore, an environmental coral reef refuge previously identified in the central south Pacific near French Polynesia was further reinforced. Studying the response of specific habitats showed that the prevailing conditions of this refuge during the 20th century shift to a new set of conditions, more characteristic of higher latitude coral reefs in the 20th century, in future climate scenarios projected to 2100.
Nonsurgical treatment of skeletal anterior open bite in adult patients: Posterior build-ups.

OBJECTIVE To (1) evaluate the efficacy of build-ups in the correction of anterior open bite in adults, (2) evaluate their efficacy in producing molar intrusion, (3) analyze skeletal and dental changes, and (4) assess the long-term stability. MATERIALS AND METHODS The sample consisted of 93 lateral cephalograms from 31 patients with skeletal and dental anterior open bite. The patients had received orthodontic treatment consisting of bonded resin blocks on the maxillary molars combined with Tip-Edge Plus bracket appliances. Cephalometric measurements were performed on radiographs taken before treatment (T1), after treatment (T2), and after a retention period (T3), which were analyzed and compared. RESULTS Significant dental and skeletal changes were observed after treatment. Molar intrusion averaging 1 mm; 1.44 and 1.57 mm extrusion of mandibular and maxillary incisors, respectively; and a mean of 3.98 mm overbite increase were observed. The mandibular plane angle showed a mean closure of 1.19°, and there was a mean decrease in anterior facial height of 0.7 mm. A mild relapse tendency was observed, but long-term stability was acceptable. CONCLUSIONS Build-ups are an effective treatment alternative for anterior open bite in adults. Outcomes remain significantly stable during the retention period.
Factors influencing patient-reported quality of life in pretreatment orthognathic surgery patients.

OBJECTIVE To investigate the relationship between condition-specific quality of life (QoL) and occlusal/skeletal traits of pretreatment orthognathic surgery patients. MATERIALS AND METHODS Patients referred for orthognathic surgery during the 2012-2014 period were asked to complete the Orthognathic Quality of Life Questionnaire (OQLQ) at consultation. Patient demographics, indices of treatment need, occlusal traits, and cephalometric variables were also recorded. Bivariate analyses were carried out between the OQLQ scores and the clinical measurements. Significant variables were added to a multivariate regression model to determine the effect of these predictive factors on OQLQ. RESULTS One hundred and two patients were recruited. Initial analyses showed that gender and overjet were significantly associated with the overall OQLQ score. Being female increased the overall OQLQ score by 15.6 points when compared to males (95% confidence interval [CI], 7.4-23.8). Females also had significant associations in the social and awareness domains of the OQLQ. The magnitude of overjet away from normal values was associated with poorer overall QoL, with significant relationships in the esthetic and functional domains. The Index of Orthognathic Functional Treatment Need was significantly associated with the functional domain of OQLQ, with patients in category 5 scoring a mean of 10.0 points more than patients in category 4 (95% CI, 2.1-17.8). The Index of Complexity, Outcome and Need and other cephalometric variables were not associated with the OQLQ. CONCLUSIONS Females are more aware of their facial deformity and report a greater social detriment when compared to males. Patients with a higher orthognathic treatment need report greater functional disadvantage.
Diagnosis and management of Cushing's syndrome : Results of an Italian multicentre study

The past 45 yr’ experience with Cushing’s syndrome (CS) has led to the awareness of its complex nature and, by the same token, brought about an increase in the diagnostic and therapeutic dilemmas. We carried out a retrospective multicentre study on the diagnostic work-up and treatment in 426 patients with CS, subdivided as follows: 288 with Cushing’s disease (CD), 80 with an adrenal adenoma, 24 with an adrenal carcinoma, 25 with ectopic ACTH and/or CRH secretion, and 9 with ACTH-independent nodular adrenal hyperplasia. Normal urinary free cortisol (UFC) values among multiple collections were recorded in about 10% of patients with CS. In 28% of patients with ACTH-independent CS, basal ACTH concentrations were within the normal range but did not respond to CRH stimulation. Measurement of ACTH levels by immunoradiometric assay, rather than by RIA, offered a greater chance of recognizing patients with ACTH-independent CS or ectopic secretion. A 50% increase in ACTH or cortisol levels after CRH yielded a diagn.
High Prevalence of Hepatitis C Virus (HCV) RNA in Dialysis Patients: Failure of Commercially Available Antibody Tests to Identify a Significant Number of Patients with HCV Infection

Results of serologic tests were correlated with hepatitis C virus (HCV) viremia, determined by a cDNA polymerase chain reaction assay to detect HCV RNA, in 340 Danish dialysis patients; of these, 28 (8.2%) were positive for antibodies to HCV (anti-HCV) with second-generation ELI-SAs. HCV RNA was found in sera from 27 of these 28 anti-HCV-positive patients. However, 8 dialysis patients had detectable levels of HCV RNA but were anti-HCV-negative with second-generation ELISAs. Among the 35 HCV-infected dialysis patients 16 were positive, 7 indeterminate, and 12 negative with the second-generation RIBA. More than 60% of patients with evidence of ongoing liver disease had HCV infection. Thus, current commercially available antibody tests did not accurately reflect the HCV status in dialysis patients. A relatively high prevalence (> 10%) of HCV RNA, closely associated with liver disease, was found among dialysis patients in a low-prevalence area of the world.
12-Week Vitamin D Supplementation Trial Does Not Significantly Influence Seasonal 25(OH)D Status in Male Collegiate Athletes

Vitamin D insufficiency is widespread in the general population and supplementation is often necessary. Recent research has examined prevalence of vitamin D insufficiency in various athletic groups. The purpose of this study was to examine male, outdoor athletes for vitamin D insufficiency and to test the efficacy of a 12-week, seasonal supplementation trial using an oral vitamin D spray. It was hypothesized that participants would have lower rates of vitamin D insufficiency compared to existing data from the general population and that vitamin D supplementation would be beneficial in maintaining optimal 25(OH)D status from fall to winter. Outdoor, male athletes ( n = 27) were randomly assigned to the control ("CON", daily placebo spray) or treatment ("VITD", 1000 IU vitamin D/day) group for a 12-week supplementation trial. Participants were examined in the fall and winter on 25(OH)D concentrations, body composition, as well as dietary and lifestyle factors. Initially, 25% of participants displayed vitamin D insufficiency. Following the 12-week supplementation trial, no significant difference was observed between the VITD and CON groups. Overall, 25(OH)D levels significantly declined (p < 0.001) from fall to winter, regardless of treatment group. Results suggest that supplementation with 1000 IU/day of vitamin D may not be adequate to prevent the seasonal decline of 25(OH)D in male athletes. In support of the hypothesis, vitamin D insufficiency appears to be lower among male, outdoor athletes compared to the general population; however, the common supplementation recommendation of 1000 IU/day was not adequate to prevent seasonal decline from fall to winter. Consequently, research continues to be warranted regarding vitamin D intake recommendations and supplementation in athletes.
Recollection-Based Retrieval Is Influenced by Contextual Variation at Encoding but Not at Retrieval

In this article, we investigated the effects of variations at encoding and retrieval on recollection. We argue that recollection is more likely to be affected by the processing that information undergoes at encoding than at retrieval. To date, manipulations shown to affect recollection were typically carried out at encoding. Therefore, an open question is whether these same manipulations would also affect recollection when carried out at retrieval, or whether there is an inherent connection between their effects on recollection and the encoding stage. We therefore manipulated, at either encoding or retrieval, fluency of processing (Experiment 1)—typically found not to affect recollection—and the amount of attentional resources available for processing (Experiments 2 and 3)—typically reported to affect recollection. We found that regardless of the type of manipulation, recollection was affected more by manipulations carried out at encoding and was essentially unaffected when these manipulations were carried out at retrieval. These findings suggest an inherent dependency between recollection-based retrieval and the encoding stage. It seems that because recollection is a contextual-based retrieval process, it is determined by the processing information undergoes at encoding—at the time when context is bound with the items—but not at retrieval—when context is only recovered.
Apical root resorption due to orthodontic treatment detected by cone beam computed tomography.

OBJECTIVE To determine the frequency of apical root resorption (ARR) due to orthodontic treatment using cone beam computed tomography (CBCT) in a sample of 1256 roots from 30 patients. MATERIALS AND METHODS All patients had Class I malocclusion with crowding. Of the 30 patients evaluated, 11 were boys and 19 were girls; their mean age was 13 years (11 to 16 years). Orthodontic treatment followed the nonextraction treatment. CBCT images were obtained before and after orthodontic treatment, and ARR was determined using Axial Guided Navigation of CBCT images. RESULTS All patients had ARR. No statistically significant association was found between resorption frequency, gender, and age. ARR was detected using CBCT in 46% of all roots that underwent orthodontic treatment. CONCLUSIONS CBCT was effective for detecting in vivo even minimal degrees of ARR due to orthodontic treatment and allowed three-dimensional evaluation of dental roots and visualization of palatine roots of maxillary molars. The highest frequencies and the most significant ARR occurred in incisors and distal roots of first maxillary and mandibular molars.
Repeated sets or single set of resistance training – A systematic review

The aim of the study was to review studies concerning single-set and multiple-set resistance training. Twenty-six articles were found, 19 randomized controlled trials and seven studies without randomization process. Out of the 26 articles, 11 showed similar increases in strength when comparing number of sets, mostly one set compared with three sets. Eight of the articles showed a greater increase when training with multiple sets. In four of the articles, the comparison was made between single-set training programmes, multiple-set programmes and periodized multiple-set programmes, showing superior results with periodized training. None of the articles reported superior strength gain in the single-set training group. There was no difference in outcome when comparing articles with trained subjects to articles with untrained subjects. It seems that in order to be physically active and staying fit, the use of single-set training is sufficient. However, to gain the greatest possible strength, the use of multiple-set training seems to be appropriate.
Comparison of stepwise vs single-step advancement with the Functional Mandibular Advancer in Class II division 1 treatment.

OBJECTIVE To compare two groups of subjects at the peak of the pubertal growth period treated with the Functional Mandibular Advancer (FMA; Forestadent, Pforzheim, Germany) appliance using either single-step or stepwise mandibular advancement. MATERIALS AND METHODS This study was conducted on 34 Class II division 1 malocclusion subjects at or just before the peak phase of pubertal growth as assessed by hand-wrist radiographs. Subjects were assigned to two groups of mandibular advancement, using matched randomization. Both groups were treated with the FMA. While the mandible was advanced to a super Class I molar relation in the single-step advancement group (SSG), patients in the stepwise mandibular advancement group (SWG) had a 4-mm initial bite advancement and subsequent 2-mm advancements at bimonthly intervals. The material consisted of lateral cephalograms taken before treatment and after 10 months of FMA treatment. Data were analyzed by means paired t-tests and an independent t-test. RESULTS There were statistically significant changes in SNB, Pg horizontal, ANB, Co-Gn, and Co-Go measurements in both groups (P < .001); these changes were greater in the SWG with the exception of Co-Go (P < .05). While significant differences were found in U1-SN, IMPA, L6 horizontal, overjet, and overbite appraisals in each group (P < .001), these changes were comparable (P > .05). CONCLUSION Because of the higher rates of sagittal mandibular skeletal changes, FMA using stepwise advancement of the mandible might be the appliance of choice for treating Class II division 1 malocclusions.
A finite element study on the effects of midsymphyseal distraction osteogenesis on the mandible and articular disc.

OBJECTIVE To evaluate the biomechanical effect of midsymphyseal distraction osteogenesis with three types of distractors on the mandible and articular disc using a three-dimensional finite element model analysis. MATERIALS AND METHODS A virtual model of the mandible was produced from computed tomography scan images of a healthy 27-year-old man. On the finite element model of the mandible, expansion of the bone-borne, tooth-borne, and hybrid type distractors were simulated with the jaw-closing muscles. The displacement and stress distribution of the mandible and articular disc were analyzed. RESULTS With the bone-borne appliance the alveolar process area was displaced more than the basal bone area. The tooth-borne appliance displaced the mandibular body in a parallel manner and showed high level of the von Mises stress in the alveolar process and the ramal region as well as in the condylar neck area. The hybrid type showed medium amount of displacement and stress distribution compared with the bone-borne and tooth-borne type. At the articular disc the compressive stress was concentrated in the anteromedial and posterolateral area, and it was highest in the tooth-borne distractor, followed by hybrid appliance and bone-borne appliance. CONCLUSIONS The tooth-borne distractor produced more parallel bony widening in the midsymphyseal area and larger expansion in the molar region; however, it induced higher stress concentration on the articular disc than the hybrid appliance and bone-borne appliance. Whether any long-term side effects on the temporomandibular joint are anticipated, especially in tooth-borne distractor, remains to be investigated.
Correction: Phylogeography of the Rock Shell Thais clavigera (Mollusca): Evidence for Long-Distance Dispersal in the Northwestern Pacific

The present-day genetic structure of a species reflects both historical demography and patterns of contemporary gene flow among populations. To precisely understand how these factors shape current population structure of the northwestern (NW) Pacific marine gastropod, Thais clavigera, we determined the partial nucleotide sequences of the mitochondrial COI gene for 602 individuals sampled from 29 localities spanning almost the whole distribution of T. clavigera in the NW Pacific Ocean (~3,700 km). Results from population genetic and demographic analyses (AMOVA, ΦST-statistics, haplotype networks, Tajima’s D, Fu’s FS, mismatch distribution, and Bayesian skyline plots) revealed a lack of genealogical branches or geographical clusters, and a high level of genetic (haplotype) diversity within each of studied population. Nevertheless, low but significant genetic structuring was detected among some geographical populations separated by the Changjiang River, suggesting the presence of geographical barriers to larval dispersal around this region. Several lines of evidence including significant negative Tajima’s D and Fu’s FS statistics values, the unimodally shaped mismatch distribution, and Bayesian skyline plots suggest a population expansion at marine isotope stage 11 (MIS 11; 400 ka), the longest and warmest interglacial interval during the Pleistocene epoch. The lack of genetic structure among the great majority of the NW Pacific T. clavigera populations may be attributable to high gene flow by current-driven long-distance dispersal of prolonged planktonic larval phase of this species.