Miracle-dz/UniFAR-FTUs huggingface dataset:
The Hemiparasitic Plant Phtheirospermum (Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China

Phtheirospermum (Orobanchaceae), a hemiparasitic genus of Eastern Asia, is characterized by having long and viscous glandular hairs on stems and leaves. Despite this unifying character, previous phylogenetic analyses indicate that Phtheirospermum is polyphyletic, with Phtheirospermum japonicum allied with tribe Pedicularideae and members of the Ph. tenuisectum complex allied with members of tribe Rhinantheae. However, no analyses to date have included broad phylogenetic sampling necessary to test the monophyly of Phtheirospermum species, and to place these species into the existing subfamiliar taxonomic organization of Orobanchaceae. Two other genera of uncertain phylogenetic placement are Brandisia and Pterygiella, also both of Eastern Asia. In this study, broadly sampled phylogenetic analyses of nrITS and plastid DNA revealed hard incongruence between these datasets in the placement of Brandisia. However, both nrITS and the plastid datasets supported the placement of Ph. japonicum within tribe Pedicularideae, and a separate clade consisting of the Ph. tenuisectum complex and a monophyletic Pterygiella. Analyses were largely in agreement that Pterygiella, the Ptheirospermum complex, and Xizangia form a clade not nested within any of the monophyletic tribes of Orobanchaceae recognized to date. Ph. japonicum, a model species for parasitic plant research, is widely distributed in Eastern Asia. Despite this broad distribution, both nrITS and plastid DNA regions from a wide sampling of this species showed high genetic identity, suggesting that the wide species range is likely due to a recent population expansion. The Ph. tenuisectum complex is mainly distributed in the Hengduan Mountains region. Two cryptic species were identified by both phylogenetic analyses and morphological characters. Relationships among species of the Ph. tenuisectum complex and Pterygiella remain uncertain. Estimated divergence ages of the Ph. tenuisectum complex corresponding to the last two uplifts of the Qinghai–Tibet Plateau at around 8.0–7.0 Mya and 3.6–1.5 Mya indicated that the development of a hot-dry valley climate during these uplifts may have driven species diversification in the Ph. tenuisectum complex.
Comparisons of indices of movement discrimination: Psychometric function, information theory, and signal detection analysis

Quantitative assessments of movement discrimination ability are used in sport and rehabilitation to gain insights into the mechanisms of neural function, skill performance under different conditions and recovery after injury. Here, we have for the first time compared three psychophysical measures of discrimination of extent of ankle movements. The movement discrimination sensitivity indices were; the just noticeable difference (JND) derived from the psychometric function, the amount of transmitted information (TI) from information theory, and the area under the ROC curve (AUC) from non-parametric signal detection analysis. Absolute judgements were obtained from 25 participants for the extents of active ankle inversion movements made to physical stops at different depths. Only the AUC showed a significant difference in discrimination scores with depth and a downwards linear trend of lesser scores with greater movement extents. These results are consistent with the previous findings of Cattell and Fullerton (1892) and Magill and Parks (1983).
Size-dependent acute toxicity of silver nanoparticles in mice

In this study, we aimed to evaluate changes in the acute toxicity of intraperitoneally administered silver nanoparticles (AgNPs) of varying sizes in BALB/c mice. Seven-week-old female BALB/c mice were intraperitoneally administered AgNPs measuring 10, 60, or 100 nm in diameter (0.2 mg/mouse) and then sacrificed 1, 3, or 6 h after treatment. In mice administered 10 nm AgNPs, reduced activity and piloerection were observed at 5 h post administration, and lowered body temperature was observed at 6 h post administration, with histopathological changes of congestion, vacuolation, single cell necrosis, and focal necrosis in the liver; congestion in the spleen; and apoptosis in the thymus cortex. These histopathological changes were not evident following administration of either 60 or 100 nm AgNPs. These results suggested that smaller AgNPs, e.g., those measuring 10 nm in diameter, had higher acute toxicity in mice.
Risk for injuries and accidents in epilepsy

Objective To study the risk for injuries/accidents in people with newly diagnosed epileptic seizures in relation to comorbidities. Methods Between September 1, 2001, and August 31, 2008, individuals in northern Stockholm with incident unprovoked seizures (epilepsy; n = 2,130) were included in a registry. For every epilepsy patient, 8 individuals matched for sex and inclusion year (n = 16,992) were randomly selected as references from the population of the catchment area. Occurrence of injuries/accidents was monitored through the national patient and cause of death registers until December 31, 2013. These registers also provided information on comorbidities (e.g., brain tumor, stroke, psychiatric disease, diabetes mellitus). Results Injury/accident was demonstrated in 1,033 epilepsy cases and 6,202 references (hazard ratio [HR] 1.71, 95% confidence interval 1.60–1.83). The excess risk was seen mainly during the first 2 years after diagnosis. Sex and educational status had no significant effect on HR. The risk was normal in children but increased in adults. Highest HR was seen for drowning, poisoning, adverse effect of medication, and severe traumatic brain injury. Compared to references without comorbidities, HR was 1.17 (1.07–1.28) in epilepsy without comorbidities, 4.52 (4.18–4.88) in references with comorbidities, and 7.15 (6.49–7.87) in epilepsy with comorbidities. Conclusion Presence of comorbidities should be considered when counseling patients with newly diagnosed epilepsy concerning risk for injuries/accidents. Early information is important, as the risk is highest during the first 2 years following seizure onset.
Observational Study of Infective Endocarditis at a Community-based Hospital: Dominance of Elderly Patients with Comorbidity

Objective The purpose of this study was to present the recent clinical profiles and the real-world management of infective endocarditis (IE). Methods All medical records of patients with IE were reviewed retrospectively for their clinical data, including clinical presentation, laboratory results, blood cultures, echocardiographic findings, treatments and complications. Using the clinical data collected, we calculated the EuroSCORE II, the European risk score for adult cardiac surgery, the Charlson Comorbidity Index as a surrogate of comordibity, and the Katz Index as a surrogate of frailty. Results Thirty-eight patients were identified as having IE (24 men, age: 71.8±13.1 years). Congestive heart failure occurred in 16 patients (42%), stroke in 14 (50%), and systemic embolism in 5 (13%). The EuroSCORE II and Charlson Comorbidity Index were high (7.7±5.8% and 5.5±2.8%, respectively). The Katz Index was fair (5.5±1.4) before the onset but deteriorated to 2.8±2.7 at the time of establishing the diagnosis of IE (p<0.001). Early surgery was performed in 22 cases (61%). In-hospital death occurred in 10 cases (26%). A EuroSCORE II ≥9%, Staphylococcus aureus etiology, and a Charlson Comorbidity Index were suggested as determinants of in-hospital death (hazard ratios: 173.60, 9.31, 1.57, respectively). In contrast, early surgery was suggested as a determinant of the survival (hazard ratio: 0.04). The Charlson Comorbidity Index was also suggested as a determinant for selecting conservative management (odds ratio: 1.40). Conclusion Comorbidity may influence the treatment selection and outcome of elderly patients with IE.
Child Work Safety on the Farms of Local Agricultural Market Producers: Parent and Child Perspectives

ABSTRACT Agriculture is a hazardous industry, yet there are few regulations on the ages at which children may engage in farm work. Local agricultural market producers (LAMPs) are a growing subset of farmers within “sustainable agriculture” who engage in direct-to-consumer and direct-to-retailer enterprises. This study explores the occupational health and safety perceptions of parents and children for children who work on their families’ LAMP farms. In-depth interviews were conducted with 12 parent–child dyads from LAMP farms in Illinois and North Carolina. Four themes emerged from these 24 interviews; parents and children perceived that: (1) the nature of small farms makes them safer than industrial agricultural operations; (2) child safety on farms is common sense; (3) avoiding hazardous tasks keeps children safe; and (4) parents know best (compared to regulations) about ways to keep their children safe. Some of these themes echo the results of earlier studies conducted with more conventional farms. Further research is needed to develop programs to improve child occupational safety on LAMP farms.
A longitudinal assessment of myoelectric activity, postural sway, and low-back pain during pregnancy.

PURPOSE The present study aimed at investigating the control of upright quiet standing in pregnant women throughout pregnancy, and whether low-back pain exerts influence on this motor task. METHODS Myoelectric signals from postural muscles and stabilometric data were collected from 15 non-pregnant and 15 pregnant women during upright quiet standing. Electromyogram envelopes and center of pressure metrics were evaluated in the control group, as well as in pregnant women in their first and third trimester of pregnancy. A correlation analysis was performed between the measured variables and a low-back pain disability index. RESULTS Pregnant women exhibited a decreased maximum voluntary isometric activity for all postural muscles evaluated. Additionally, the activity of lumbar muscles during the postural task was significantly higher in the pregnant women in comparison to the non-pregnant controls. The soleus muscle maintained its activity at the same level as the gestation progressed. Higher postural oscillations were observed in the anteroposterior direction while mediolateral sway was reduced in the third trimester of pregnancy. No correlation was detected between the lowback pain disability index and neuromechanical variables. CONCLUSION This study provides additional data regarding the functioning and adaptations of the postural control system during pregnancy. Also, we provide further evidence that postural control during quiet standing cannot be used to predict the occurrence of low-back pain. We hypothesize that the modifications in the neural drive to the muscles, as well as in postural sway may be related to changes in the biomechanics and hormonal levels experienced by the pregnant women.
Distribution of Rotavirus Genotypes Circulating in Ahvaz, Iran in 2016

Background: Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and will provide a strategy for the development of appropriate vaccines. Methods: A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping. Results: Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non typeable] (3.1%). Conclusion: A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
Characterization of Welding Induced Anisotropy in Steel by Magnetic Barkhausen Noise

Residual stress continues to be important issues in shipbuilding. This paper demonstrates how the heat affected zone that results from welding could be identified nondestructively using MBN (magnetic Barkhausen noise) technique. A stress concentration region was created by placing a weld bead on a marine steel plate used in ship construction. MBN measurements were made on the back surface of the welded plate along the weld direction and perpendicular to it in a line that crosses the weld bead. The stress distribution as deduced from the MBN measurements was found to be anisotropic in the material of the heat affected zone. The heat induced anisotropy was completely eliminated by shot peening the HAZ material as revealed by MBN intensity. It was concluded that the directional MBN measurements could be used to characterize the induced anisotropy and hence assess the thermal residual stresses distribution near a localized stresses concentration regions imposed by welding.
Early activation of the hypothalamic-pituitary-adrenal-axis in very-low-birth-weight infants with small thymus at birth

Background. An acute thymic involution in human fetuses and newborns has been described in very-low-birth-weight (VLBW) infants with histological chorioamnionitis. However, the mechanisms of thymic involution remain to be clarified. Here, we tested the hypothesis that an activation of the hypothalamic-pituitary-adrenal (HPA) axis occurs in VLBW infants with acute thymic involution at birth. Methods. A total of 180 randomly selected VLBW newborns (28.8 ± 3.15 wk gestation; 1093 ± 305 g) entered the study. Thymic size was measured on standard chest radiographs at birth, and expressed as the ratio between the transverse diameter of the cardiothymic image at the level of the carina (CT) and that of the thorax (T). CT/T < 0.28 was considered to indicate a small thymic size. Plasma cortisol and adrenocorticotropic hormone (ACTH) concentrations were determined on days 1 (d-1) and 7 (d-7), and at 1 month (mo-1). Results. A total of 66 (36.7%) newborns had CT/T < 0.28. Infants with small thymus had significantly increased cortisol on d-1 (∼5.2-folds) [median: 18.95 (95% CI: 11.20–39.4) μg/dl vs. 3.66 (1.94–6.82) μg/dl, p < 0.0001)] and d-7(∼1.7-folds) [12.0 (4.39–22.97) μg/dl vs. 7.8 (3.63–12.8) μg/dl, p = 0.0384)], as compared with those with normal thymic size, together with higher adrenocorticotropic hormone (ACTH) concentrations on d-1 (∼1.9-folds) [28 (15.6–61.07) pg/ml vs. 14.9 (9.0–23.42) pg/ml, p = 0.0005)], while no significant differences for cortisol at mo-1 or ACTH concentrations on d-7 and mo-1 were evidenced (p > 0.50). From a multivariate logistic regression analysis, a small thymus at birth was a significant independent predictor of plasma cortisol concentrations in the top-quartile (OR = 14.4; 95% CI: 6.079–34.11), and plasma ACTH concentrations in the top-quartile (OR = 4.40 (95% CI: 1.99–9.74) on d-1 (results adjusted for variables significant at univariate analysis). Conclusions. Our data indicated the presence of a previously unrecognized, early activation of the HPA axis in VLBW newborns with a small thymus at birth.
Self‐assembled liver organoids recapitulate hepatobiliary organogenesis in vitro

Several three‐dimensional cell culture systems are currently available to create liver organoids. In gneral, these systems display better physiologic and metabolic aspects of intact liver tissue compared with two‐dimensional culture systems. However, none reliably mimic human liver development, including parallel formation of hepatocyte and cholangiocyte anatomical structures. Here, we show that human fetal liver progenitor cells self‐assembled inside acellular liver extracellular matrix scaffolds to form three‐dimensional liver organoids that recapitulated several aspects of hepatobiliary organogenesis and resulted in concomitant formation of progressively more differentiated hepatocytes and bile duct structures. The duct morphogenesis process was interrupted by inhibiting Notch signaling, in an attempt to create a liver developmental disease model with a similar phenotype to Alagille syndrome. Conclusion: In the current study, we created an in vitro model of human liver development and disease, physiology, and metabolism, supported by liver extracellular matrix substrata; we envision that it will be used in the future to study mechanisms of hepatic and biliary development and for disease modeling and drug screening. (Hepatology 2018;67:750‐761).
Efficacy and safety of glecaprevir/pibrentasvir in Japanese patients with chronic genotype 2 hepatitis C virus infection

Glecaprevir (nonstructural protein 3/4A protease inhibitor) and pibrentasvir (nonstructural protein 5A inhibitor) (G/P), a coformulated once‐daily, all oral, ribavirin (RBV)‐free, direct‐acting antiviral regimen, was evaluated for safety and efficacy in hepatitis C virus genotype 2 (GT2)–infected Japanese patients, including those with compensated cirrhosis. CERTAIN‐2 is a phase 3, open‐label, multicenter study assessing the safety and efficacy of G/P (300/120 mg) once daily in treatment‐naive and interferon ± RBV treatment–experienced Japanese patients without cirrhosis but with GT2 infection. Patients were randomized 2:1 to receive 8 weeks of G/P (arm A) or 12 weeks of sofosbuvir (400 mg once daily) + RBV (600‐1000 mg weight‐based, twice daily) (arm B). The primary endpoint was noninferiority of G/P compared to sofosbuvir + RBV by assessing sustained virologic response at posttreatment week 12 (SVR12) among patients in the intent‐to‐treat population. SVR12 was also assessed in treatment‐naive and interferon ± RBV treatment‐experienced patients with GT2 infection and compensated cirrhosis who received G/P for 12 weeks in the CERTAIN‐1 study. A total of 136 patients were enrolled in CERTAIN‐2. SVR12 was achieved by 88/90 (97.8%) patients in arm A and 43/46 (93.5%) patients in arm B. No patient in arm A experienced virologic failure, while 2 did in arm B. The primary endpoint was achieved. In CERTAIN‐1, 100% (18/18) of GT2‐infected patients with compensated cirrhosis achieved SVR12. Treatment‐emergent serious adverse events were experienced by 2 patients without cirrhosis in each arm and no patient with cirrhosis. Conclusion: The results demonstrate high efficacy and favorable tolerability of G/P in GT2‐infected Japanese patients. (Hepatology 2018;67:505‐513).
A signaling cascade including ARID1A, GADD45B and DUSP1 induces apoptosis and affects the cell cycle of germ cell cancers after romidepsin treatment

In Western countries, the incidence of testicular germ cell cancers (GCC) is steadily rising over the last decades. Mostly, men between 20 and 40 years of age are affected. In general, patients suffering from GCCs are treated by orchiectomy and radio- or chemotherapy. Due to resistance mechanisms, intolerance to the therapy or denial of chemo- / radiotherapy by the patients, GCCs are still a lethal threat, highlighting the need for alternative treatment strategies. In this study, we revealed that germ cell cancer cell lines are highly sensitive to the histone deacetylase inhibitor romidepsin in vitro and in vivo, highlighting romidepsin as a potential therapeutic option for GCC patients. Romidepsin-mediated inhibition of histone deacetylases led to disturbances of the chromatin landscape. This resulted in locus-specific histone-hyper- or hypoacetylation. We found that hypoacetylation at the ARID1A promotor caused repression of the SWI/SNF-complex member ARID1A. In consequence, this resulted in upregulation of the stress-sensors and apoptosis-regulators GADD45B, DUSP1 and CDKN1A. RNAi-driven knock down of ARID1A mimicked in parts the effects of romidepsin, while CRISPR/Cas9-mediated deletion of GADD45B attenuated the romidepsin-provoked induction of apoptosis and cell cycle alterations. We propose a signaling cascade involving ARID1A, GADD45B and DUSP1 as mediators of the romidepsin effects in GCC cells.
Department of Applied Mathematics and Statistics

As recent advances in calcium sensing technologies enable us to simultaneously image many neurons, complementary analytical tools must also be developed to maximize the utility of this experimental paradigm. While the observations are fluorescence movies, the signals of interest are the spike trains and/or time-varying intracellular calcium concentrations, [Ca++]. Inferring the value of these “hidden states” is often problematic for a number of reasons: (i) observations are inherently both noisy and intermittent; (ii) the relationship between fluorescence, [Ca++], and spike trains is nonlinear; and (iii) the parameters governing the dynamics of these states are typically unknown. We develop a sequential Monte Carlo Expectation Maximization algorithm designed to optimally infer precise spike times and [Ca++] dynamics, given the above properties. This framework confers several advantages over standard signal processing approaches. First, we can often infer the expected timing of spikes at a temporal resolution greater than that of the image frames. Second, we provide both the expected value of [Ca++] and spike trains, and their variances. Third, the parameters governing these dynamics are automatically recovered, obviating additional calibration experiments. Fourth, this framework facilitates incorporating stimulus information, potentially improving the inference fidelity. We close by discussing some possible applications for these tools.