Miracle-dz/UniFAR-FTUs huggingface dataset:
Cereulide synthetase acquisition and loss events within the evolutionary history of Group III Bacillus cereus sensu lato facilitate the transition between emetic and diarrheal foodborne pathogen

Cereulide-producing members of Bacillus cereus sensu lato (B. cereus s.l.) Group III, also known as “emetic B. cereus”, possess cereulide synthetase, a plasmid-encoded, non-ribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by “emetic B. cereus” has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize Group III B. cereus s.l. genomes which possess ces (ces-positive) alongside their closely related ces-negative counterparts to (i) assess the genomic diversity encompassed by “emetic B. cereus”, and (ii) identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive Group III B. cereus s.l. genomes and the ces-negative genomes interspersed among them (n = 150), we show that “emetic B. cereus” is not clonal; rather, multiple lineages within Group III harbor cereulide-producing strains, all of which share a common ancestor incapable of producing cereulide (posterior probability [PP] 0.86-0.89). The ST 26 common ancestor was predicted to have emerged as ces-negative (PP 0.60-0.93) circa 1904 (95% highest posterior density [HPD] interval 1837.1-1957.8) and first acquired the ability to produce cereulide before 1931 (95% HPD 1893.2-1959.0). Three subsequent ces loss events within ST 26 were observed, including among isolates responsible for B. cereus s.l. toxicoinfection (i.e., “diarrheal” illness). Importance “B. cereus” is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., “emetic” syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., “diarrheal” syndrome). Here, we show that “emetic B. cereus” is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some Group III B. cereus s.l. populations to oscillate between diarrheal and emetic foodborne pathogen over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus s.l. outbreaks, as some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.
Identification of antigen-specific TCR sequences using a strategy based on biological and statistical enrichment in unselected subjects

Recent advances in high-throughput T cell receptor (TCR) sequencing have allowed for new insights into the TCR repertoire. However, methods for capturing antigen-specific repertoires remain an area of development. Here, we describe a novel approach that utilizes both a biological and statistical enrichment to define putatively antigen-specific complementarity-determining region 3 (CDR3) repertoires in unrelated individuals. The biological enrichment entails fluorescence-activated cell sorting of in vitro antigen-activated memory CD4+ T cells followed by TCRβ sequencing. The resulting TCRβ sequences are then filtered by selecting those that are statistically enriched when compared to their frequency in the autologous resting T cell compartment. Applying this method to define putatively peanut protein-specific repertoires in 27 peanut-allergic individuals resulted in a library of 7345 unique CDR3 amino acid sequences that had similar characteristics to validated antigen-specific repertoires in terms of homology and diversity. In-depth analysis of these CDR3s revealed 36 public sequences that demonstrated high levels of convergent recombination. In a network analysis, the public CDR3s unveiled themselves as core sequences with more edges than their private counterparts. This method has the potential to be applied to a wide range of T cell mediated disorders, and to yield new biomarkers and biological insights.
Morphology and Metrics, Isotopes and Dates: Determining the Validity of Equus laurentius Hay, 1913

ABSTRACT Direct radiocarbon dating and stable isotope and biometric analyses are evidence that the holotype of Equus laurentius Hay, 1913 comprises the skull and jaw of two different horses that are less than 500 years old. The size and morphology of the specimens fall within the range of like elements of modern Equus caballus Linnaeus, 1758. The mandibular cheek teeth exhibit bit wear, demonstrating that the mandible is that of a domestic animal. The taxonomy of the purportedly late Pleistocene species is therefore resolved, and Equus laurentius Hay is a junior synonym of Equus caballus Linnaeus. Equus laurentius and its holotype are neither taxonomically nor phylogenetically pertinent to studies of North American Pleistocene Equus.
Nailfold Capillaroscopy and Retinal Findings in Patients with Systemic Sclerosis: Is There An Association?

Introduction: Systemic sclerosis (SSc) is characterized by fibrosis and intimal proliferation of cutaneous and visceral small vessels. These architectural abnormalities can be visualized with nailfold capillaroscopy (NFC); the changes being quite characteristic. At the same time, morphological alterations in retinal vascular bed are expected but sparsely described. Aim: We aimed to characterize the frequency and type of retinal microvascular changes in patients with SSc and to analyze any association with NFC changes. Patients and Methods: With institutional ethical committee approval, we recruited 45 consecutive patients with SSc (diagnosed based on American College of Rheumatology and European League against Rheumatism [ACR/EULAR-2013] criteria). NFC was done for all of them with a Universal Serial Bus (USB) dermatoscope; additionally, fundoscopy, fundus photography, and optical coherence tomography (OCT) were analyzed. Disease characteristics in patients with and without retinal disease were compared. Results: Among the 45 SSc patients, 12 (26.67%) had limited cutaneous SSc (lSSc) while 33 (73.33%) had diffuse cutaneous disease (dSSc). Retinal microvascular changes seen as mild arteriolar alteration and arteriovenous crossing changes were recorded in 13 patients (28.89%); mostly in those with dSSc (12/13). The NFC architectural changes were more severe in patients with retinal disease, though the difference was not statistically significant. Conclusion: Patients with SSc can often have retinal microvascular abnormalities commensurate with the vascular changes characteristic of SSc. The severity of retinal changes correlates with changes in NFC. NFC, which is now an essential tool for the management of SSc, could be a surrogate marker for retinal involvement in these patients.
Casting a Genetic Light on the Evolution of Eyes

Light has been exploited for information by organisms through the evolution of photoreceptors and, ultimately, eyes in animals. Only a handful of eye types exist because the physics of light constrains photodetection. In the past few years, genetic tools have revealed several parallel pathways through which light guides behavior and have provided insights into the convergent evolution of eyes. The gene encoding opsin (the primary phototransduction protein) and some developmental genes had very early origins and were recruited repeatedly during eye evolution. Eye lens proteins arose separately and make up a diverse group, many of which were co-opted from other functions. A major challenge now is understanding how newly discovered pathways for processing light evolved and how they collaborate with eyes to harvest information from light.
POPULATION GENETIC STRUCTURE OF BALDCYPRESS (TAXODIUM DISTICHUM [L.] RICH. VAR. DISTICHUM) AND PONDCYPRESS (T. DISTICHUM VAR. IMBRICARIUM [NUTTALL] CROOM): BIOGEOGRAPHIC AND TAXONOMIC IMPLICATIONS

Abstract An allozyme analysis was conducted to determine the population genetic structure of baldcypress (Taxodium distichum [L.] Rich. var. distichum) and pondcypress (Taxodium distichum var. imbricarium [Nuttall] Croom) and the level of genetic differentiation between these two taxa. Approximately 400 individuals of both varieties and apparent morphological intermediates were sampled from 21 locations across the geographic range of Taxodium distichum and 11 enzyme loci assayed by starch gel electrophoresis. Although baldcypress populations contain higher levels of genetic variation among sub-populations, populations of both varieties have approximately the same levels of heterozygosity. Populations of baldcypress and pondcypress were found to differ on the basis of varying allele frequencies of one locus, PGI-2, which appears to be semi-diagnostic as a varietal indicator. A correlation was observed between the allele frequencies of this locus and a ratio of bark thickness to diameter (BT/D). Baldcypress exhibits higher frequencies of PGI-2 allele “1” and lower BT/D ratios, whereas pondcypress has higher frequencies of PGI-2 allele “3” and higher BT/D ratios. An apparent clinal gradient was observed in the spatial distribution of both BT/D ratios and PGI-2 phenotypes within a few populations. The apparent existence of gene flow (whether it is presently occurring or has occurred in the recent past) and the possibility of clinal variation within populations suggest that these two taxa are best regarded as varieties of the same species.
Effects of Dietary Fish Oil during the Fetal and Postnatal Periods on the Learning Ability of Postnatal Rats

The effects of a diet containing fish oil with a low level of docosahexaenoic acid fed during the fetal to newborn stage on the learning ability of postnatal rats were evaluated.Learning ability estimated by the swimming test was superior with the fish oil group of 6-wk-old rats to that with the non-fish oil group. These findings suggest that the ingestion of fish oil, and especially of docosahexaenoic acid, during the period from the fetal to newborn stage, but not during the weaning period, and the accumulation of a large amount of dietary docosahexaenoic acid in the brain of fetal and newborn rats may be related to an improved cerebral function of postnatal rats.
Tree replacement in a cove hardwood forest of the southern Appalachians

To determine whether non-random tree replacement occurs in a diverse southern Appalachian cove hardwood forest, the species of each fallen canopy tree and its successor were determined in 100 single-tree gaps. No strong intraspecific inhibition or interspecific mutualism was detected. Although non-random relations among species are weak or absent, cove hardwood forests maintain a high diversity (1/1pi = 6.5) both in species richness and evenness through tree replacement in single-tree gaps created by endogenous disturbances.
Laboratory and greenhouse assessment of plant-available N in organic materials

Laboratory indices (KCl extraction, thermal fractionation, pepsin extraction, C:N ratio and N mineralization) of organic materials were compared with plant availability of mineral-N produced from organic-N in a greenhouse experiment. Six types of organic materials [farmyard manure (FYM), pig manure (PG), poultry manure (PL), sewage sludge (SS), pressmud (PM) and compost (CP)] were compared with urea as a chemical reference fertilizer. Relative effectiveness of organic N (REo) was used to compare the fraction of N extracted with different N availability laboratory indices. REo values of organic materials ranged from 0.14 to 0.77 and decreased in the following order: PL > PG > SS > PM > CP > FYM. The KCl-extracted inorganic N, pepsin-extracted organic N and N mineralized during 42 days gave a positive relationship with REo, and the C:N ratio a negative relationship with REo. Among the different N availability laboratory indices, pepsin extraction of organic N, C:N ratio and N mineralization can be recommended for determining mineralizable organic N in organic materials. KCl-extracted inorganic N proved to be a useful index for organic materials having a low inorganic N fraction. Thermal fractionation did not provide a suitable index of plant-available N in organic materials.
Sarcopenia and Adverse Post-Surgical Outcomes in Geriatric Patients: A Scoping Review

Background Sarcopenia is associated with adverse outcomes in cancer, chemotherapy, solid organ transplants, intensive care and medical patients. It has also been proven to increase perioperative mortality, hospital length of stay and complications in patients of various age groups. However, a limited number of studies have examined the association of post-surgical outcomes and sarcopenia inclusively in patients aged 65 years and older. Objective This scoping review aimed to examine the relationship between adverse postsurgical outcomes and sarcopenia in patients aged 65 years and older. Methodology EMBASE and Medline databases were searched for sarcopenia, perioperative period and post-surgical outcomes. The articles were screened based on exclusion and inclusion criteria and were reviewed systematically as per the Joanna Briggs Institute (JBI) Methodology for Scoping Reviews. Results After duplicates removal and application of the inclusion and exclusion criteria, eight articles were included for this study from a total of nine hundred initially identified articles. All studies defined sarcopenia as low muscle mass but did not include physical function or muscle strength as the parameter of sarcopenia. Low muscle mass was associated with higher mortality in emergency surgeries, reduced long term survival in open elective surgeries, and increased length of hospital stay in endoscopic surgeries. Conclusion The current review suggests that low muscle mass is associated with higher mortality and various adverse post-surgical outcomes in the elderly. It remains to be determined if applying the definition of sarcopenia as per the international consensus/guidelines will affect the association of adverse postsurgical outcomes and sarcopenia.
Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota

The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo. GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro. GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo. This study thus describes an alternative antimicrobial therapy for dental caries. ABSTRACT Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo. In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions. IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo. GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro. GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo. This study thus describes an alternative antimicrobial therapy for dental caries.
Variations saisonnières comparées de l’activité sexuelle (données pondérales) chez deux espèces de Rongeurs (Psammomys obesus et Gerbillus gerbillus) du Sahara occidental algérien

Lc Rat des sables (Psammomys obesus) et la Gerbille (Gerbillus gerbillus) presentent, dans la m£me region du Sahara occidental algerien, d'importantes variations saisonnieres ponderales de leur appareil reproducteur ; mais ces variations sont differentes pour les 2 especes de Rongeurs desertiques. Le plus grand developpement des testicules et des vesicules seminales se situe en automnehiver et au debut du printemps chez Psammomys obesus. II est limits au printemps chez Gerbillus gerbillus. La regression ponderale de ces organes commence plus precocement chez le Rat des sables (mars-avril) que chez la Gerbille (mai-juin). Si le poids minimal s'observe en juillet pour Psammomys, I'lnvolution^ bien que tres importante cette παβΊηβ epoque, se poursuit jusqu'au dobut novembre chez quelques trds rares Gerbilles. La reprise ponderale est sensible des septembre chez le Rat des sables alors qu'elle ne depute qu'en fovrier chez la Gerbille. La p^rzWe de gestation s'etend d'octobre mai chez Psammomys obesus et de la mifevrier la mi-juillet chez Gerbillus gerbillus. La difference essentielle entre ces deux especes vivant dans une meme region geographique mais dont le rythme d'activito et le rdgime alimentaire sont difforents, concerne la p^riode de l'automne au debut du printemps au cours de laquelle Psammomys obesus est en activito sexuelle alors que, pour Gerbillus gerbillus, c'est une periode de rogression ou d'atrophie de Tappareil reproducteur.
Recent Trends of Infectious Complications Following Heart Transplantation

Background. Heart transplantation is a life-saving procedure that has seen improvements in transplant and patient outcomes due to advances in immunosuppression and prevention of posttransplantation infectious episodes (IEps). This study systematically evaluates IEps in the modern era of heart transplantation at Stanford University Medical Center. Methods. This is a single-center retrospective review that includes 279 consecutive adult heart transplantation recipients from January 2008 to September 2017. Baseline demographic, clinical, serological, and outcomes information were collected. Kaplan-Meier estimator was used to assess survival stratified by IEp occurrence within the first year. Results. A total of 600 IEps occurred in 279 patients (2.15 IEps per patient) during a median follow-up period of 3 years. Overall survival was 83.3% (95% confidence interval [CI], 76.2-88.4) at 1 year posttransplantation for those with any IEp compared with 93.0% (95% CI, 87.2-96.4) in those without IEp (P = 0.07). Bacterial IEps were the most common (n = 375; 62.5%), followed by viral (n = 180; 30.0%), fungal (n = 40; 6.7%), and parasitic (n = 5; 0.8%). IEps by Gram-negative bacteria (n = 210) outnumbered those by Gram-positive bacteria (n = 142). Compared with prior studies from our center, there was a decreased proportion of viral (including cytomegalovirus), fungal (including Aspergillus spp. and non-Aspergillus spp. molds), and Nocardia infections. There were no IEps due to Mycobacterium tuberculosis, Pneumocystis jirovecii, or Toxoplasma gondii. Conclusions. A significant reduction in viral, fungal, and Nocardia IEps after heart transplantation was observed, most likely due to advancements in immunosuppression and preventive strategies, including pretransplant infectious diseases screening and antimicrobial prophylaxis.
Influence of Culture Conditions on Growth and Physicochemical Properties of Carrageenans in Gigartina teedii (Rhodophyceae — Gigartinales)

Female gametophytes of Gigartina teedii collected on the coasts of Brittany (France) contain in equal proportion kappa- and iota-carrageenans. In order to increase exploitable quantities of G. teedii, by keeping high the yield of carrageenan, without modifying qualities of gelification or viscosity, we have studied in controlled culture the action of some factors: light, temperature and nitrogen on the growth rate of G. teedii as well their effect on physicochemical caracteristics of the polymer. Temperatures of 20 to 25 °C and light intensities of 500 μE m −2 s −1 give active growth. On the other hand, high light intensities induce active synthesis of rhodamylon at the expense of the yield of colloid. A medium without nitrate decreases growth, but increases yields of carrageenans
Neuropsychological functions, sleep, and mental health in adults with Klinefelter syndrome

A few studies have examined neuropsychological functions, sleep, and mental health combined in Klinefelter syndrome (KS; 47,XXY). We investigated neuropsychological functions with standard tests, sleep with actigraphy, and self‐reported mental health in 30 men with KS (Mean age = 36.7 years) compared to 21 controls (Mean age = 36.8 years). Men with KS scored significantly lower on mental speed, attention span, working memory, inhibition, and set‐shifting tests, as well as overall IQ (mean effect size difference Cohen's d = 0.79). Men with KS had significantly longer night wakes, with no differences in other sleep variables (mean d = 0.34). Men with KS reported poorer mental health than controls (mean d = 1.16). Regression analyses showed neuropsychological functions explained variance in some sleep domains for men with KS but not for controls. Neuropsychological functions explained variance in some mental health domains for controls. For men with KS, however, verbal IQ was the only significant predictor of mental health. Altogether, men with KS display problems in neuropsychological functions and mental health but do not appear different from controls on most sleep parameters. Our findings indicate that relations between neuropsychological functions, sleep, and mental health differ between men with KS and controls.