Miracle-dz/UniFAR-FTUs huggingface dataset:
Speciation network in Laurasiatheria: retrophylogenomic signals

Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods—too short to fix polymorphic alleles—is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla–Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.
Prevalence of ischaemia in patients with a chronic total occlusion and preserved left ventricular ejection fraction

Aims Previous studies on invasive assessment of collateral function in patients with a chronic total occlusion (CTO) have displayed only a limited increase in collateral flow and high occurrence of coronary steal during pharmacological stress. This could question the necessity for ischaemia testing prior to revascularization of CTOs in the presence of myocardial viability. The purpose of the present study was to determine the prevalence of perfusion impairments in patients with a CTO as assessed by [15O]H2O positron emission tomography (PET). Methods and results Seventy-six consecutive patients (60 men, 62 ± 10 years) with a documented CTO and preserved left ventricular ejection fraction (LVEF) were included. All patients underwent PET to assess (hyperaemic) myocardial blood flow (MBF) and coronary flow reserve (CFR). Collateral connection score was 0 in 7 (9%), 1 in 13 (17%), and 2 in 56 (74%) of the cases, with predominantly a high Rentrop grade (96% ≥2). MBF of the target area during hyperaemia was significantly lower when compared with the remote area (1.37 ± 0.37 vs. 2.63 ± 0.71 mL min-1 g-1, P < 0.001). Target to remote ratio during hyperaemia was on average 0.54 ± 0.13, and 73 (96%) patients demonstrated a significantly impaired target to remote ratio (≤0.75). Only 7 (9%) patients displayed a preserved CFR of ≥2.50, whereas coronary steal (CFR <1.0) was observed in 10 (13%) patients. Conclusions Even in the presence of angiographically well-developed collateral arteries, the vast majority of CTO patients with a preserved LVEF showed significantly impaired perfusion. These results suggest that collateral function during increased blood flow demand in viable myocardium is predominantly insufficient.
Characteristics of Cases With Repeated Sexually Transmitted Infections, Massachusetts, 2014–2016

Background Persons with prior sexually transmitted infections (STIs) are at high risk for reinfection. No recent studies have examined frequency with which persons are diagnosed and reported with multiple bacterial STIs over time. Methods We conducted a retrospective, of confirmed syphilis, gonorrhea, and chlamydial infections reported to Massachusetts state surveillance system within a 2-year period, 28 July 2014-27 July 2016. Results Among Massachusetts population aged 13-65 years (4847510), 49142 (1.0%) were reported with ≥1 STIs; 6999 (14.2% of those with ≥1 STI) had ≥2 STIs, accounting for 27.7% of STIs. Of cases with ≥5 or more STIs (high-volume repeaters), 118 (74%) were men and 42 (26%) were women. Men spanned the age spectrum and were predominantly non-Hispanic white; 87% reported same-sex contacts. Women were younger, predominantly nonwhite, and without known same-sex contacts. Women were reinfected with gonorrhea and chlamydia or chlamydia alone; none had syphilis or human immunodeficiency virus (HIV) infection. All men with syphilis also had gonorrhea and/or chlamydia; 35% were diagnosed with HIV before, during, or within 10 months after study period. The majority (56%) of high-volume repeaters were seen at more than 1 care site/system. Conclusions In Massachusetts, a large proportion of bacterial STIs are reported from a small subpopulation, many of whom have repeated infections and are likely to have higher impact on STI and HIV rates. Public health can play a crucial role in reaching high-volume repeaters whose STI histories may be hidden from clinicians due to fragmented care.
Comparing the effects of different individualized music interventions for elderly individuals with severe dementia

ABSTRACT Background: Individuals with dementia often experience poor quality of life (QOL) due to behavioral and psychological symptoms of dementia (BPSD). Music therapy can reduce BPSD, but most studies have focused on patients with mild to moderate dementia. We hypothesized that music intervention would have beneficial effects compared with a no-music control condition, and that interactive music intervention would have stronger effects than passive music intervention. Methods: Thirty-nine individuals with severe Alzheimer's disease were randomly and blindly assigned to two music intervention groups (passive or interactive) and a no-music Control group. Music intervention involved individualized music. Short-term effects were evaluated via emotional response and stress levels measured with the autonomic nerve index and the Faces Scale. Long-term effects were evaluated by BPSD changes using the Behavioral Pathology in Alzheimer's Disease (BEHAVE-AD) Rating Scale. Results: Passive and interactive music interventions caused short-term parasympathetic dominance. Interactive intervention caused the greatest improvement in emotional state. Greater long-term reduction in BPSD was observed following interactive intervention, compared with passive music intervention and a no-music control condition. Conclusion: Music intervention can reduce stress in individuals with severe dementia, with interactive interventions exhibiting the strongest beneficial effects. Since interactive music intervention can restore residual cognitive and emotional function, this approach may be useful for aiding severe dementia patients’ relationships with others and improving QOL. The registration number of the trial and the name of the trial registry are UMIN000008801 and “Examination of Effective Nursing Intervention for Music Therapy for Severe Dementia Elderly Person” respectively.
Mycoplasma Superantigen Is a CDR3-dependent Ligand for the T Cell Antigen Receptor

Superantigens are defined as proteins that activate a large number of T cells through interaction with the Vβ region of the T cell antigen receptor (TCR). Here we demonstrate that the superantigen produced by Mycoplasma arthritidis (MAM), unlike six bacterial superantigens tested, interacts not only with the Vβ region but also with the CDR3 (third complementarity-determining region) of TCR-β. Although MAM shares typical features with other superantigens, direct interaction with CDR3-β is a feature of nominal peptide antigens situated in the antigen groove of major histocompatibility complex (MHC) molecules rather than superantigens. During peptide recognition, Vβ and Vα domains of the TCR form contacts with MHC and the complex is stabilized by CDR3–peptide interactions. Similarly, recognition of MAM is Vβ-dependent and is apparently stabilized by direct contacts with the CDR3-β region. Thus, MAM represents a new type of ligand for TCR, distinct from both conventional peptide antigens and other known superantigens.
Ammonia excretion in mytilid mussels is facilitated by ciliary beating

ABSTRACT The excretion of nitrogenous waste products in the form of ammonia (NH3) and ammonium (NH4+) is a fundamental process in aquatic organisms. For mytilid bivalves, little is known about the mechanisms and sites of excretion. This study investigated the localization and the mechanisms of ammonia excretion in mytilid mussels. An Rh protein was found to be abundantly expressed in the apical cell membrane of the plicate organ, which was previously described as a solely respiratory organ. The Rh protein was also expressed in the gill, although at significantly lower concentrations, but was not detectable in mussel kidney. Furthermore, NH3/NH4+ was not enriched in the urine, suggesting that kidneys are not involved in active NH3/NH4+ excretion. Exposure to elevated seawater pH of 8.5 transiently reduced NH3/NH4+ excretion rates, but they returned to control values following 24 h acclimation. These mussels had increased abundance of V-type H+-ATPase in the apical membranes of plicate organ cells; however, NH3/NH4+ excretion rates were not affected by the V-type H+-ATPase specific inhibitor concanamycin A (100 nmol l−1). In contrast, inhibition of ciliary beating with dopamine and increased seawater viscosity significantly reduced NH3 excretion rates under control pH (8.0). These results suggest that NH3/NH4+ excretion in mytilid mussels takes place by passive NH3 diffusion across respiratory epithelia via the Rh protein, facilitated by the water current produced for filter feeding, which prevents accumulation of NH3 in the boundary layer. This mechanism would be energy efficient for sessile organisms, as they already generate water currents for filter feeding. Highlighted Article: The plicate organ of mytilid mussels is a main site for ammonia excretion, which is facilitated by Rh channels and ciliary beating.
Molecular autopsy of sudden unexplained deaths reveals genetic predispositions for cardiac diseases among young forensic cases

Aims Coronary artery disease accounts for the majority of sudden cardiac deaths (SCD) in the older population whereas cardiomyopathies and arrhythmogenic abnormalities predominate in younger SCD victims (<35 years) with a significant genetic component. The elucidation of the pathogenetic cause of death might be relevant for the prevention of further deaths within affected families. Aim of this study was to determine the portion of underlying genetic heart diseases among unexplained putative SCD cases from a large German forensic department. Methods and results We included 10 forensic cases of sudden unexplained death (SUD) victims aged 19-40 years, who died by SCD due to forensic autopsy. DNA was analysed by next generation panel sequencing of 174 candidate genes for channelopathies and cardiomyopathies. Cardiological examinations, genetic counselling, and subsequent genetic testing were offered to all affected families. We identified within 1 year 10 cases of SUD among 172 forensic cases. Evidence for a genetic disposition was found in 8 of 10 (80%) cases, with pathogenic mutations in 3 and variants of uncertain significance in 5 of SCD cases. Subsequent selective screening of family members revealed two additional mutation carriers. Conclusion The study provides strong evidence that molecular genetics improves the post mortem diagnosis of fatal genetic heart diseases among SUD victims. Molecular genetics should be integrated in forensic and pathological routine practice.
Safety of surgery in patients with rheumatoid arthritis treated by abatacept: data from the French Orencia in Rheumatoid Arthritis Registry

Objective. To investigate the frequency and risk factors of postoperative complications in RA patients treated with abatacept (ABA). Methods. The Orencia RA registry recruited 1012 patients receiving ABA for RA in routine care. Data from patients treated with ABA who underwent surgery were reviewed to describe the frequency of postoperative complications. Characteristics of patients and surgeries with and without complications were compared to identify factors associated with complications. Results. We identified 205 (20.3%) patients who underwent 263 surgeries, including 176 (66.9%) orthopaedic surgeries. Nineteen (7.2%) surgeries, in 19 patients (9.3%), entailed complications, including 7 delayed wound healing (2.7% of surgeries) and 6 surgical site infections (2.3% of surgeries). The median time between the last infusion of ABA and surgery was 5.9 weeks (range: 0.3‐12.0 weeks), with no significant difference between patients with and without complications. The median corticosteroids daily dosage was higher in the group with complications [10.0 (6.25‐15.0) vs 6.0 (5.0‐10.0) mg/day, P = 0.042]. In multivariate analysis, only the duration of ABA treatment was significantly associated with postoperative complications [adjusted odds ratio (aOR) = 0.94 (95% CI: 0.89, 0.99) for each month of treatment], as were orthopaedic surgeries compared with other kinds of surgery [aOR = 4.45 (95% CI: 1.01, 20.2)]. Conclusion. In RA patients treated with ABA, the rate of surgical complications was low: 7.2% and higher in case of orthopaedic procedure and a more recent initiation of ABA. The median time between surgery and the last infusion of ABA was short and did not influence the rate of postoperative complications.
MicroRNA-100 suppresses human osteosarcoma cell proliferation and chemo-resistance via ZNRF2

Osteosarcoma (OS) is a prevalent cancer worldwide. MicroRNAs (miRNAs) play critical roles in the growth, invasion and carcinogenesis of OS, whereas the underlying mechanisms remain ill-defined. Here, we addressed these questions. We detected significantly higher levels of ZNRF2, a ubiquitin ligase of the RING superfamily, and significantly lower levels of miR-100 in the OS specimens, compared to the paired normal bone tissues. The levels of ZNRF2 and miR-100 inversely correlated in the OS specimens. In addition, low miR-100 levels are associated with poor prognosis of the OS patients. Either ZNRF2 overexpression or miR-100 depletion increased in vitro OS cell growth and improved cell survival at the presence of Doxorubicin. Mechanistically, with the help of bioinformatics analysis and luciferase-reporter assay, we found that miR-100 might bind to the 3’-UTR of ZNRF2 mRNA to prevent its protein translation. Thus, our data suggest that re-expression of miR-100 may inhibit OS cell growth and decrease OS cell chemo-resistance.
Reducing Stomatal Density in Barley Improves Drought Tolerance without Impacting on Yield1[CC-BY]

Manipulation of a gene involved in the suppression of stomatal development in barley can reduce stomatal density, leading to improved drought tolerance without deleterious effects on yield. The epidermal patterning factor (EPF) family of secreted signaling peptides regulate the frequency of stomatal development in model dicot and basal land plant species. Here, we identify and manipulate the expression of a barley (Hordeum vulgare) ortholog and demonstrate that when overexpressed HvEPF1 limits entry to, and progression through, the stomatal development pathway. Despite substantial reductions in leaf gas exchange, barley plants with significantly reduced stomatal density show no reductions in grain yield. In addition, HvEPF1OE barley lines exhibit significantly enhanced water use efficiency, drought tolerance, and soil water conservation properties. Our results demonstrate the potential of manipulating stomatal frequency for the protection and optimization of cereal crop yields under future drier environments.
Specific Appetite for Carotenoids in a Colorful Bird

Background Since carotenoids have physiological functions necessary for maintaining health, individuals should be selected to actively seek and develop a specific appetite for these compounds. Methodology/Principal Findings Great tits Parus major in a diet choice experiment, both in captivity and the field, preferred carotenoid-enriched diets to control diets. The food items did not differ in any other aspects measured besides carotenoid content. Conclusions/Significance Specific appetite for carotenoids is here demonstrated for the first time, placing these compounds on a par with essential nutrients as sodium or calcium.
Changes in Puffing Topography and Nicotine Consumption Depending on the Power Setting of Electronic Cigarettes

Introduction The study purpose was to evaluate changes in puffing topography of experienced electronic cigarette users (vapers) when changing power settings in electronic cigarette battery devices. Methods Experienced adult vapers (n = 21) were recruited. Participants used their own liquids and an atomizer and battery provided by the researchers. Two 30-minute sessions were performed, with the device power set at 6 W and 10 W, in a randomized, crossover, participant-blinded design. Puff number and duration (mean [SD]) were recorded in the provided electronic cigarette battery device, whereas the atomizers were weighted before and after use to determine liquid and nicotine consumption. Results Puff number and puff duration were lower at 10 W (46 [16] puffs and 3.8 [0.8] s) compared with 6 W (57 [20] puffs and 4.6 [1.0] s). Liquid and nicotine consumption was higher at 10 W (373 [176] mg and 4.2 [2.4] mg, respectively) compared with 6 W (308 [165] mg and 3.5 [2.3] mg, respectively). Vapers reported more aerosol volume and ease of use at 10 W compared with 6 W. Conclusions The study identified an attempt for compensatory puffing patterns and nicotine self-titration, with a change in puffing patterns (puff number and duration) observed when changing the power settings of an e-cigarette device. Implications Compensatory smoking behavior and nicotine self-titration is a well-established phenomenon. In electronic cigarettes, changing nicotine concentration in the liquid has been shown to trigger a compensatory puffing pattern. Herein, power setting of the electronic cigarette device was found to be a parameter associated with changes in puffing behavior, whereas higher power was preferable for the participants. These findings could contribute to the understanding of patterns of electronic cigarette use and could explain the preference of dedicated vapers to higher power devices. Additionally, laboratory studies evaluating aerosol emissions should consider using different puffing patterns according to the power settings tested.
Evaluating Precipitation Estimates from Eta, TRMM and CHRIPS Data in the South-Southeast Region of Minas Gerais State - Brazil

Precipitation estimates derived from the Eta model and from TRMM (Tropical Rainfall Measuring Mission) and CHIRPS (Climate Hazards Group InfraRed Precipitation with Station data) remotely sensed data were compared to the precipitation data of the INMET (National Institute of Meteorology) meteorological stations in the south-southeast region of Minas Gerais state, Brazil, in the period between July 2009 and June 2015. Then, information about evapotranspiration (ETR), water deficit (DEF), and water surplus (EXC) was obtained from the precipitation data, using the sequential water balance (SWB) separately for each type of precipitation data (INMET, TRMM, Eta, and CHIRPS). Subsequently, the components of the SWB were comparatively analyzed. The results indicate that all three products overestimate rainfall. The strongest relationships between the INMET data and the estimated data were observed for the TRMM, in terms of precipitation estimates, as well as DEF, EXC, and ETR components. The Eta precipitation estimates are overestimated relative to those from INMET, resulting in underestimation of the water deficit (DEFETA) and overestimation of evapotranspiration (ETRETA). In general, the CHIRPS data presented a pattern similar to the station data, though statistical analyses were lower than those of the TRMM data.
Newborn Screening of Genetic Mutations in Common Deafness Genes With Bloodspot-Based Gene Chip Array.

Purpose This study screens for deafness gene mutations in newborns in the Northwest China population. Method The 9 sites of 4 common deafness genes (GJB2, GJB3, SLC26A4, and mt 12S rRNA) were detected by bloodspot-based gene chip array in 2,500 newborns. Results We detected mutations of the 4 genes in 101 (4.04%) newborns; particularly, 0.20% detected the double mutations. In the Hui population, 4.58% of the newborns tested positive for mutations, whereas 4.01% of Han newborns tested positive for mutations. The detective rates are as follows: 1.44% for GJB2 235delC, 1.08% for SLC26A4 IVS7-2A>G, 0.48% for GJB2 299_300delAT, 0.28% for SLC26A4 2168A>G, 0.2% for mt 12S rRNA 1555A>G, and 0.16% for GJB3 538C>T. The 31.25% (5/16) of infants with GJB2 235delC, 50% (3/6) with GJB2 299_300delAT, and 25% (3/12) with SLC26A4 IVS7-2A>G showed abnormal hearing when tested; only 1 double mutation case received the hearing test, and this infant showed abnormality in both ears on the hearing test. Conclusions High mutation rates in the common deafness genes were detected in newborns in Northwest China. Our study is helpful in understanding the deafness genomic epidemiology and also provides evidence for prenatal and postnatal care as well as policy making on population health in the region.
Hawthorne effect reporting in orthodontic randomized controlled trials: truth or myth? Blessing or curse?

Objective To investigate in 10 orthodontic journals how many randomized controlled trials (RCTs) considered the Hawthorne effect, and if considered, to determine whether it was related to the patients or the therapists involved in the trial and, finally, to discuss the Hawthorne effect in an educational way. Materials and methods A search was performed on the Medline database, via PubMed, for publication type 'randomized controlled trial' published for each journal between 1 August 2007 and 31 July 2017. The American Journal of Orthodontics and Dentofacial Orthopedics, Angle Orthodontist, Australian Orthodontic Journal, Dental Press Journal of Orthodontics, European Journal of Orthodontics, Journal of Orthodontics, Journal of Orofacial Orthopedics, Korean Journal of Orthodontics, Orthodontics and Craniofacial Research and Progress in Orthodontics were assessed. Two independent reviewers extracted the data and identified whether the Hawthorne effect was considered or discussed in the articles and whether the Hawthorne effect was related to the behaviour of the patients, the therapists, or both. Results The initial search generated 502 possible trials. After applying the inclusion and exclusion criteria, 290 RCTs were included and assessed. The Hawthorne effect was considered or discussed in 10 of 290 RCTs (3.4%), and all were related to the patients' and none to the therapists' behaviour. Conclusions The Hawthorne effect reported in orthodontic RCTs was suboptimal. The researchers' lack of knowledge about this phenomenon is evident, despite evidence that the Hawthorne effect may cause over-optimistic results or false-positive bias.