Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-genome data reveal the complex history of a diverse ecological community

Significance Widespread biological communities are common, but little is known about how they assemble. A key question is how sets of trophically linked species (predators and their prey, hosts and parasites) spread to occupy current distributions. Do they disperse together, preserving ecological interactions, or separately, such that interactions are interrupted? This is central to assessing the potential for coevolution in a system and requires inference of species associations both over space and through time. Here, we use de novo genomic data and likelihood-based approaches to infer the assembly history of a multispecies community of Western Palearctic insect herbivores and parasitoid natural enemies—the two trophic groups that together comprise 50% of all animal species. How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of “enemy-free space. ” The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.
Long-Term In Vitro Culture of the Syphilis Spirochete Treponema pallidum subsp. pallidum

ABSTRACT Investigation of Treponema pallidum subsp. pallidum, the spirochete that causes syphilis, has been hindered by an inability to culture the organism continuously in vitro despite more than a century of effort. In this study, long-term logarithmic multiplication of T. pallidum was attained through subculture every 6 to 7 days and periodic feeding using a modified medium (T. pallidum culture medium 2 [TpCM-2]) with a previously described microaerobic, rabbit epithelial cell coincubation system. Currently, cultures have maintained continuous growth for over 6 months with full retention of viability as measured by motility and rabbit infectivity. This system has been applied successfully to the well-studied Nichols strain of T. pallidum, as well as to two recent syphilis isolates, UW231B and UW249B. Light microscopy and cryo-electron microscopy showed that in vitro-cultured T. pallidum retains wild-type morphology. Further refinement of this long-term subculture system is expected to facilitate study of the physiological, genetic, pathological, immunologic, and antimicrobial susceptibility properties of T. pallidum subsp. pallidum and closely related pathogenic Treponema species and subspecies. IMPORTANCE Syphilis, a sexually transmitted disease with a global distribution, is caused by a spiral-shaped bacterium called Treponema pallidum subspecies pallidum. Previously, T. pallidum was one of the few major bacterial pathogens that had not been cultured long-term in vitro (in a test tube), greatly hindering efforts to better understand this organism and the disease that it causes. In this article, we report the successful long-term cultivation of T. pallidum in a tissue culture system, a finding that is likely to enhance our ability to obtain new information applicable to the diagnosis, treatment, and prevention of syphilis. Syphilis, a sexually transmitted disease with a global distribution, is caused by a spiral-shaped bacterium called Treponema pallidum subspecies pallidum. Previously, T. pallidum was one of the few major bacterial pathogens that had not been cultured long-term in vitro (in a test tube), greatly hindering efforts to better understand this organism and the disease that it causes. In this article, we report the successful long-term cultivation of T. pallidum in a tissue culture system, a finding that is likely to enhance our ability to obtain new information applicable to the diagnosis, treatment, and prevention of syphilis.
Head-to-head comparison of 1-year aripiprazole long-acting injectable (LAI) versus paliperidone LAI in comorbid psychosis and substance use disorder: impact on clinical status, substance craving, and quality of life

Background To overcome nonadherence in patients with psychosis switch to long-acting injectable (LAI) antipsychotic formulations is adopted. Most oral versus LAI comparisons showed similar antipsychotic responses. Psychoses often overlap with substance use disorder (SUD). Head-to-head LAI comparisons have hitherto focused only on non-comorbid populations. Objective The objective of this study was to compare two LAIs, administered for 12 months, in initially hospitalized patients with psychosis comorbid with SUD in their clinical and quality of life (QoL) outcomes. Patients and methods Inpatients were recruited during 2016 and switched randomly to 400 mg intramuscular aripiprazole monohydrate (AM) (N=50) or to 100 mg intramuscular paliperidone palmitate (PP) once-monthly (N=51); patients were discharged and followed up for 12 months. Patients were rated at baseline and after 1 year through the Clinical Global Impression scale – severity (CGIs), substance craving intensity was rated through a visual analog scale for substance craving, and QoL through the World Health Organization (WHOQOL-BREF) scale. We addressed confounders with backward stepwise logistic regression and three-way analysis of variance. Results PP were older and had more cases of schizophrenia spectrum and less bipolar disorders than AM, but AM had a stronger craving for substances at baseline. Both LAIs were associated with significant improvements in all outcomes, with AM displaying stronger effect sizes than PP. The two groups did not differ on baseline WHOQOL-BREF scores in any domain, but at the 1-year follow-up, AM fared better on all domains. The two groups did not differ in final severity, but PP scored higher than AM in craving at the 1-year endpoint. Limitation: The CGIs is not a refined tool for severity and the substance craving may be subject to recall bias. Conclusion 1-year AM and PP was followed by improved clinical status and QoL and reduced substance craving in a population with psychosis and SUD comorbidity. AM, compared to PP, improved craving and QoL at the 1-year follow-up.
How Can Additives Control the Early Stages of Mineralisation

The interactions between additives and mineral precursors and intermediates are at the heart of additive-controlled crystallisation, which is of high importance for various fields. In this commentary, we reflect on potential modes of additive control according to classical nucleation theory on one hand, and from the viewpoint of the so-called pre-nucleation cluster pathway on the other. This includes a brief review of the corresponding literature. While the roles of additives are discussed generally, i.e., without specific chemical or structural details, corresponding properties are outlined where possible. Altogether, our discussion illustrates that “non-classical” nucleation pathways promise an improved understanding of additive-controlled scenarios, which could be utilised in targeted applications in various fields, ranging from scale inhibition to materials chemistry.
Early Pulmonary Vascular Disease in Young Adults Born Preterm

Rationale: Premature birth affects 10% of live births in the United States and is associated with alveolar simplification and altered pulmonary microvascular development. However, little is known about the long‐term impact prematurity has on the pulmonary vasculature. Objectives: Determine the long‐term effects of prematurity on right ventricular and pulmonary vascular hemodynamics. Methods: Preterm subjects (n = 11) were recruited from the Newborn Lung Project, a prospectively followed cohort at the University of Wisconsin‐Madison, born preterm with very low birth weight (≤1,500 g; average gestational age, 28 wk) between 1988 and 1991. Control subjects (n = 10) from the same birth years were recruited from the general population. All subjects had no known adult cardiopulmonary disease. Right heart catheterization was performed to assess right ventricular and pulmonary vascular hemodynamics at rest and during hypoxic and exercise stress. Measurements and Main Results: Preterm subjects had higher mean pulmonary arterial pressures (mPAPs), with 27% (3 of 11) meeting criteria for borderline pulmonary hypertension (mPAP, 19‐24 mm Hg) and 18% (2 of 11) meeting criteria for overt pulmonary hypertension (mPAP ≥ 25 mm Hg). Pulmonary vascular resistance and elastance were higher at rest and during exercise, suggesting a stiffer vascular bed. Preterm subjects were significantly less able to augment cardiac index or right ventricular stroke work during exercise. Among neonatal characteristics, total ventilatory support days was the strongest predictor of adult pulmonary pressure. Conclusions: Young adults born preterm demonstrate early pulmonary vascular disease, characterized by elevated pulmonary pressures, a stiffer pulmonary vascular bed, and right ventricular dysfunction, consistent with an increased risk of developing pulmonary hypertension.
Evaluation of three pain assessment scales used for ventilated neonates

AIMS AND OBJECTIVES To compare and evaluate the reliability, validity, feasibility, clinical utility, and nurses' preference of the Premature Infant Pain Profile-Revised, the Neonatal Pain, Agitation, and Sedation Scale, and the Neonatal Infant Acute Pain Assessment Scale used for procedural pain in ventilated neonates. BACKGROUND Procedural pain is a common phenomenon but is undermanaged and underassessed in hospitalised neonates. Information for clinician selecting pain measurements to improve neonatal care and outcomes is still limited. DESIGN A prospective observational study was used. METHODS A total of 1,080 pain assessments were made at 90 neonates by two nurses independently, using three scales viewing three phases of videotaped painful (arterial blood sampling) and nonpainful procedures (diaper change). Internal consistency, inter-rater reliability, discriminant validity, concurrent validity and convergent validity of scales were analysed. Feasibility, clinical utility and nurses' preference of scales were also investigated. RESULTS All three scales showed excellent inter-rater coefficients (from 0.991-0.992) and good internal consistency (0.733 for the Premature Infant Pain Profile-Revised, 0.837 for the Neonatal Pain, Agitation, and Sedation Scale and 0.836 for the Neonatal Infant Acute Pain Assessment Scale, respectively). Scores of painful and nonpainful procedures on the three scales changed significantly across the phases. There was a strong correlation between the three scales with adequate limits of agreement. The mean scores of the Neonatal Pain, Agitation, and Sedation Scale for feasibility and utility were significantly higher than those of the Neonatal Infant Acute Pain Assessment Scale, but not significantly higher than those of the Premature Infant Pain Profile-Revised. The Neonatal Pain, Agitation, and Sedation Scale was mostly preferred by 55.9% of the nurses, followed by the Neonatal Infant Acute Pain Assessment Scale (23.5%) and the Premature Infant Pain Profile-Revised (20.6%). CONCLUSIONS The three scales are all reliable and valid, but the Neonatal Pain, Agitation, and Sedation Scale and the Neonatal Infant Acute Pain Assessment Scale perform better in reliability. The Neonatal Pain, Agitation, and Sedation Scale appears to be a better choice for frontier nurses to assess procedural pain in ventilated neonates based on its good feasibility, utility and nurses' preference. RELEVANCE TO CLINICAL PRACTICE Choosing a valid, reliable, feasible and practical measurement is the key step for better management of procedural pain for ventilated newborns. Using the right and suitable tool is helpful to accurately identify pain, ultimately improve the neonatal care and outcomes.
Biocompatibility and antibacterial properties of zirconium nitride coating on titanium abutments: An in vitro study

Improving soft tissue attachment and reducing bacterial colonization on titanium abutments are key factors for the long-term maintenance of healthy soft and hard peri-implant tissues. This in vitro study was conducted to compare the biocompatibility and antibacterial activity of four different surfaces: uncoated Ti6Al4V, anodized, and coated with titanium nitride or zirconium nitride. Surface topography was investigated with a high-resolution system for measuring surface finishes. Human gingival fibroblast (HGF) adhesion and proliferation were examined using MTT assay, Scanning Electron Microscopy (SEM) imaging, immunofluorescence analysis and real-time PCR for selected target genes. The hemolysis and AMES tests were performed to assess the chemical compounds’ blood compatibility and mutagenic potential, respectively. Antibacterial activity was tested against five bacterial strains isolated from the oral cavity (Streptococcus salivarius, S. sanguinis, S. mutans, S. sobrinus, S. oralis), and the percentage of dead bacteria was calculated. Roughness measurements confirmed a substantial similarity between the surfaces and their compatibility with clinical applications. MTT assay, SEM analysis and immunofluorescence staining showed adhesion and proliferation of HGFs cultured on all the examined surfaces. PCR confirmed that HGFs produced extracellular matrix components efficiently on all the surfaces. No hemolytic activity was detected, and the AMES test confirmed the surfaces’ clinical safety. For all tested bacterial strains, biofilms grown on the zirconium nitride surface showed a higher percentage of dead bacteria than on the other disks. The titanium nitride surface inactivated bacterial biofilms, too, but to a lesser extent.
Fate of the tributaries of sapheno femoral junction following endovenous thermal ablation of incompetent axial vein – A review article

Sapheno femoral junctional tributaries are usually left untreated at the time of endovenous ablation of axial vein. The long-term clinical significance of these untreated tributaries remains elusive and there is very little research done into this area. This article reviews the fate of untreated tributaries at sapheno femoral junction following ablation of incompetent axial vein. A literature search and analysis of evidence reveal that the junctional tributaries are one of the commonest (ranges between 8% and 31%) cause for recurrence following endovenous ablation of the axial veins. Follow up of this subset of patients after their axial vein treatment should be considered to identify neoreflux in side branches at sapheno femoral junction and plan treatment.
Preliminary Empirical Validation of the “Basic Needs Satisfaction in Sport Scale” With a Sample of Spanish Athletes

The theory of self-determination establishes the existence of three basic psychological needs (autonomy, competence, and relationship). If these needs are satisfied, optimal personal well-being will be achieved. The Basic Needs Satisfactions in Sport Scale (BNSSS) is a measurement developed to evaluate these needs within the sporting context. The BNSSS measures the satisfaction of the three basic psychological needs through 20 items distributed in five dimensions: autonomy-choice, autonomy-volition, autonomy-perceived locus of internal causality, competence, and relatedness. The purpose of this study is to validate a Spanish version of the BNSSS. The sample were 441 team athletes with a mean age of 17.46 (SD = 3.59), which 46.5% were men and the remaining percentage (53.5%) were women. After a standardised data collection, confirmatory factor analysis and invariance analyses were performed, as well as composite reliability. The obtained version showed a good overall fit of the model and values of composite reliability higher to 0.70. Therefore, a useful tool for assessing basic psychological needs in team sports was obtained.
Probiotics improve insulin resistance status in an experimental model of Alzheimer’s disease

Background: Nowadays, Alzheimer’s disease (AD) is considered as Type 3 diabetes in which insulin resistance is the common cause of both diseases. Disruption of insulin signaling cascade and insulin resistance can induce AD; and central insulin resistance causes systemic alterations in serum insulin, FBS levels, and lipid profile. Studies have shown that probiotics (Lactobacillus and Bifidobacterium species) can be used as a nutritional approach to improve these metabolic changes. We assessed the probiotic effect (4 species of Lactobacillus and Bifidobacterium) on insulin resistance biomarkers in an experimental model of AD. Methods: A total of 60 rats were divided into 5 groups: (1) a control group without surgical and dietary intervention; (2) a controlprobiotics group receiving probiotics for 8 weeks, but not receiving any surgical intervention; (3) a group receiving a sham operation in which PBS was injected intrahippocampus but without dietary intervention; (4) an Alzheimer group for which Amyloid-ß (Aß) 1- 42 was injected intrahippocampus but without dietary intervention; (5) and an Alzheimer-probiotics group for which Aß1-42 was injected intrahippocampus and given 2g probiotics for 8 weeks. The FBS levels and lipid profile were measured by a calorimetric method, insulin levels were detected by an ELISA kit, and HOMA-IR was calculated using a formula. ANOVA (one way analysis of variance followed by Bonferroni comparisons post hoc) was used to compare all the variables between groups. Results: Serum glucose, insulin levels, and HOMA-IR index increased in the Alzheimer group compared to the control (p<0.001), while probiotics decreased only insulin level and HOMA-IR index in AP group compared to Alzheimer group (p<0.001). Also, TG levels increased in the Alzheimer group (p<0.001), but no significant difference was detected between Alzheimer and Alzheimerprobiotics group. Conclusion: It seems that probiotics play an effective role in controlling glycemic status of Alzheimer’s disease.
Ischaemia, healing and outcomes in proximal humeral fractures

Interfragmental ischaemia is a prerequisite for the initiation of the inflammatory and immunological response to fracturing of bone. Intrafragmental ischaemia is inevitable: the extent of the initial ischaemic insult does not, however, directly relate to the outcome for healing of the fracture zones and avascular necrosis of the humeral head. The survival of distal regions of fragments with critical perfusion may be the result of a type of inosculation (blood vessel contact), which establishes reperfusion before either revascularization or neo-angiogenesis has occurred. Periosteum has a poorly defined role in fracture healing in the proximal humerus. The metaphyseal periosteal perfusion may have a profound effect, as yet undefined, on the healing of most metaphyseal fractures of the proximal humerus, and may be disturbed further by inadvertent surgical manipulation. The metaphysis can be considered as a ‘torus’ or ring of bone, its surface covered by periosteum antero- and posterolaterally, through which the tuberosity segments gain perfusion and capsular reflections antero- and posteromedially, through which the humeral head (articular) fragment gains perfusion. The torus is broken in relatively simple primary patterns: a fracture line at the upper surface of the torus is an anatomical ‘neck’ fracture; a fracture line at the lower surface of the torus is the surgical ‘neck’ fracture. Secondary fragmentation (through compression and/or distraction) of the torus itself creates complexity for analysis (classification), alters the capacity and outcome for healing (by variable interruption of the fragmental blood supply) and influences interfragmental stability. Cite this article: EFORT Open Rev 2018;3 DOI: 10.1302/2058-5241.3. 180005
Early Childhood Caries: Epidemiology, Aetiology, and Prevention

Early childhood caries (ECC) is one of the most prevalent diseases in children worldwide. ECC is driven by a dysbiotic state of oral microorganisms mainly caused by a sugar-rich diet. Additionally, poor oral hygiene or insufficient dental plaque removal leads to the rapid progression of ECC. ECC leads not only to dental destruction and pain with children, but also affects the quality of life of the caregivers. Children with extensive ECC are at high risk to develop caries with the permanent dentition or will have other problems with speaking and/or eating. To prevent ECC, several strategies should be taken into account. Children should brush their teeth with toothpastes containing gentle ingredients, such as mild surfactants and agents showing antiadherent properties regarding oral microorganisms. Parents/caregivers have to help their children with brushing the teeth. Furthermore, remineralizing and nontoxic agents should be included into the toothpaste formulation. Two promising biomimetic agents for children's oral care are amorphous calcium phosphate [Cax(PO4)yn H2O] and hydroxyapatite [Ca5(PO4)3(OH)].
Modulation of caveolae by insulin/IGF‐1 signaling regulates aging of Caenorhabditis elegans

Reducing insulin/IGF‐1 signaling (IIS) extends lifespan, promotes protein homeostasis (proteostasis), and elevates stress resistance of worms, flies, and mammals. How these functions are orchestrated across the organism is only partially understood. Here, we report that in the nematode Caenorhabditis elegans, the IIS positively regulates the expression of caveolin‐1 (cav‐1), a gene which is primarily expressed in neurons of the adult worm and underlies the formation of caveolae, a subtype of lipid microdomains that serve as platforms for signaling complexes. Accordingly, IIS reduction lowers cav‐1 expression and lessens the quantity of neuronal caveolae. Reduced cav‐1 expression extends lifespan and mitigates toxic protein aggregation by modulating the expression of aging‐regulating and signaling‐promoting genes. Our findings define caveolae as aging‐governing signaling centers and underscore the potential for cav‐1 as a novel therapeutic target for the promotion of healthy aging.