Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological and evolutionary strategies of archaeal, bacterial, and viral communities in deep-sea hydrothermal vents

Ecological and evolutionary strategies of archaeal, bacterial, and viral communities in deep-sea hydrothermal vents Rika Elizabeth Anderson Chair of the Supervisory Committee: Professor John A. Baross School of Oceanography The deep-sea hydrothermal vent habitat, formed by subsurface water-rock reactions that create high-temperature hydrothermal fluid, is dominated by physical, chemical, and mineralogical gradients. The mixing of cold, oxidized seawater with hot, reduced hydrothermal fluid produces environments that span a range of temperatures, pH, redox potential, chemical composition, and mineralogy, with constant fluid flux between these regions. Communities of archaea, bacteria, and viruses live across the gradients within these systems and are both exposed to and transported by these fluids. Since these conditions can push the boundaries of the limits for life, may represent conditions found on other planetary bodies, and are thought to have been important for the early evolution of life on this planet, the study of microbial adaptation to hydrothermal vents is of great astrobiological importance. This dissertation explores how these extreme gradients structure hydrothermal vent microbial and viral communities, and what evolutionary strategies are used by both cells and viruses in hydrothermal systems to adapt to these extremes. The first part of this dissertation address adaptation on the community level by examining microbial community structuring in various niches within the vent environment. First, I explore microbial niche partitioning across diffuse flow and plumes in hydrothermal vent systems, using a combination of microbial community profiling techniques and qPCR to demonstrate that certain microbial lineages are found in high abundance in particular conditions, but are far less abundant in other regions of the gradient. Second, I use 16S pyrotag sequencing to compare the structures of the rare and abundant biospheres across several hydrothermal vent systems worldwide. Through this I demonstrate that archaeal communities exhibit fundamentally different biogeographic patterning compared to bacterial communities. Whereas bacterial rare and abundant groups show similar biogeographic patterning, abundant archaeal groups are generally cosmopolitan and abundant everywhere but rare archaeal groups are biogeographically
Utility of the Rapid Antigen Detection Test E. histolytica Quik Chek for the Diagnosis of Entamoeba histolytica Infection in Nonendemic Situations

Entamoeba histolytica infection is an increasingly common sexually transmitted infection in Japan. Currently, stool ova and parasite examination (O&P) is the only approved diagnostic method. Here, we assessed the utility of the commercially available rapid antigen detection test (Quik Chek) for E. histolytica. A multicenter cross-sectional study was conducted. Stool samples that had been submitted for O&P were included. The samples were subjected to both Quik Chek and PCR, and the Quik Chek results were assessed in comparison with PCR as the reference standard. ABSTRACT Entamoeba histolytica infection is an increasingly common sexually transmitted infection in Japan. Currently, stool ova and parasite examination (O&P) is the only approved diagnostic method. Here, we assessed the utility of the commercially available rapid antigen detection test (Quik Chek) for E. histolytica. A multicenter cross-sectional study was conducted. Stool samples that had been submitted for O&P were included. The samples were subjected to both Quik Chek and PCR, and the Quik Chek results were assessed in comparison with PCR as the reference standard. E. histolytica infection was confirmed in 5.8% (38/657) of the samples and comprised 20 diarrheal and 18 nondiarrheal cases. The overall sensitivity and specificity of Quik Chek were 44.7% (95% confidence interval, 30.1 to 60.3) and 99.8% (99.1 to 100), respectively. The sensitivity of Quik Chek was higher for diarrheal cases (60.0%) than for nondiarrheal cases (27.8%). Furthermore, the combined use of Quik Chek with O&P increased the sensitivity (78.9%), especially for diarrheal cases (up to 90%). The E. histolytica burden assessed by quantitative PCR was similar between Quik Chek-positive and -negative samples. The Quik Chek assay sensitivity was lower for cyst-containing stools than for trophozoite-containing stools, although it was shown that cultured E. histolytica clinical strains from Quik Chek-negative cyst-containing stools exhibited antigenicity in vitro. The present study confirmed the high specificity of Quik Chek for E. histolytica infection. Combined use with O&P increased the sensitivity of detection, facilitating the use of Quik Chek in point-of-care settings in nonendemic situations.
Nicotine dependence, socioeconomic status, lifestyle behaviours and lifetime quit attempts among adult smokers in South Africa.

BACKGROUND Smoking cessation is a complex process influenced by factors such as smokers' nicotine dependence levels, socioeconomic status (SES) and other lifestyle behaviours. Little is known about these relationships in South Africa (SA). OBJECTIVES To explore the relationship between nicotine dependence, SES, lifestyle behaviours and lifetime quit attempts among adult smokers in SA. METHODS This study used data from 2 651 participants aged ≥16 years in the 2011 South African Social Attitudes Survey. Information on SES (measured by asset ownership), binge drinking, physical activity, fruit and vegetable intake, intention to quit smoking and lifetime quit attempts was extracted. Nicotine dependence was measured using the Heaviness of Smoking Index (HSI). All data were weighted to account for the complex survey design and to yield nationally representative estimates. Data analysis included binary logistic regression with high nicotine dependence (HND) defined as HSI ≥4 and lifetime quit attempts as separate outcomes. RESULTS The prevalence of smoking was 20.1% (31.6% for males and 9.5% for females), and was highest in the mixed-ancestry group (37.0%). Overall, 14.5% of smokers had HND, with a higher proportion in the high-SES group. The odds of HND increased with every 10 years of smoking history (odds ratio (OR) 2.05; 95% confidence interval (CI) 1.40 - 3.00) but decreased among participants who reported frequent physical activity (OR 0.4; 95% CI 0.18 - 0.86) and those who planned to quit (OR 0.37; 95% CI 0.19 - 0.75). Quit attempts were more likely among participants who reported frequent fruit and vegetable intake (OR 1.8; 95% CI 1.07 - 2.98) and less likely among those reporting binge drinking (OR 0.31; 95% CI 0.16 - 0.59) or assessed as having HND (OR 0.32; 95% CI 0.17 - 0.58). CONCLUSIONS Most adult smokers in SA have low nicotine dependence. However, the association of HND with high SES in this study suggests that although cessation treatment based on an integrated lifestyle behavioural intervention package may suffice for most smokers, a more intense cessation treatment package is needed for smokers of higher SES.
Factors predicting rehabilitation outcomes after severe acquired brain injury in trauma, stroke and anoxia populations: A cohort study

ABSTRACT Severe acquired brain injury has long-term physical and cognitive effects. Identifying patient variables predictive of recovery in different brain injury populations would generate improved prognostic information and help rehabilitation teams set appropriate therapeutic goals. This cohort study of 447 NHS neurorehabilitation inpatients aimed to identify functional and cognitive predictors of recovery following severe acquired brain injury caused by trauma, stroke and anoxia. Motor and cognitive impairment ratings were collected at admission and discharge using the Functional Independence Measure and Functional Assessment Measure (FIM+FAM), and injury-related and demographic data were collated from medical records. Predictors of physical, cognitive and overall recovery were identified via hierarchical regression analyses. Several key findings emerged. Firstly, on-admission motor skills predicted functional and overall outcomes across groups. Secondly, on-admission social interaction skills predicted cognitive discharge outcomes in stroke and trauma, and overall outcomes for stroke, but did not predict anoxia outcomes. Thirdly, age predicted all forms of recovery for stroke only. Further group-specific factors were also identified as predicting motor and cognitive recovery, indicating that factors key to the rehabilitation trajectory may differ between populations. These variables should be considered in rehabilitation goal planning, although further research is required to explore their contributions to recovery.
Time to Next Treatment, Health Care Resource Utilization, and Costs Associated with Ibrutinib Use Among U.S. Veterans with Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma: A Real-World Retrospective Analysis

BACKGROUND: Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) is the most common adult leukemia, accounting for ≈ 37% of all leukemias in the United States. Limited real-word evidence is available on the outcomes of ibrutinib use among previously untreated patients in the U.S. Veterans Health Administration (VHA) population diagnosed with CLL/SLL. OBJECTIVES: To (a) evaluate time to next treatment (TTNT) among U.S. veterans with CLL/SLL who initiated ibrutinib versus chemoimmunotherapy (CIT) in first line (1L) and 1L ibrutinib versus ibrutinib in later lines (2L+) and (b) compare health care resource utilization (HRU) and costs between the 1L ibrutinib and CIT cohorts. METHODS: Adults with CLL/SLL and claims for 1L single-agent ibrutinib or CIT (index date = first prescription claim date) were included from Veterans Health Administration Data (April 1, 2013-March 31, 2018). A subset of the CIT 1L cohort with evidence of ibrutinib in 2L/3L was defined as the ibrutinib 2L+ cohort. Kaplan-Meier curves and Cox proportional hazard models were used to evaluate TTNT, and generalized linear models were used to determine all-cause per patient per month (PPPM) HRU and costs during 1L among propensity score-matched (PSM) cohorts. RESULTS: After PSM, 614 patients were included in each of the 1L ibrutinib and 1L CIT cohorts, and 149 were included in each of the 1L ibrutinib and 2L+ ibrutinib cohorts. The 1L ibrutinib cohort had significantly longer TTNT compared with each of the 1L CIT and 2L+ ibrutinib cohorts (P <0.0001 and P =0.0001, respectively) and was less likely to have a next line of treatment than the CIT 1L cohort (HR = 0.52; 95% CI = 0.42-0.65; P < 0.0001) and the 2L+ ibrutinib cohort (HR = 0.39; 95% CI = 0.22-0.69; P = 0.0012). The 1L ibrutinib cohort had significantly fewer inpatient visits (rate ratio [RR] = 0.38; 95% CI = 0.28-0.52; P ≤ 0.05) and outpatient visits PPPM (RR =0.72; 95% CI = 0.68-0.77; P ≤ 0.5) compared with the CIT 1L cohort. Additionally, the 1L ibrutinib cohort had $7,308 significantly lower monthly medical costs (95% CI = −$9,892 to −$4,895; P ≤ 0.05) versus the 1L CIT cohort, resulting in comparable monthly total health care cost (medical and pharmacy) between real-world 1L patients treated by ibrutinib and CIT (−$2,160; 95% CI = −$4,840-$347; P > 0.05). CONCLUSIONS: These findings demonstrate that among U.S. veterans with CLL/SLL, 1L ibrutinib use was associated with significantly longer TTNT versus that of 1L CIT. Similarly, early treatment with ibrutinib was associated with longer TTNT as compared to ibrutinib use in later lines of therapy. Moreover, 1L ibrutinib was associated with lower HRU and medical costs compared with 1L CIT, completely offsetting the higher pharmacy costs related to 1L ibrutinib treatment.
An Efficient and Robust Method for Selective Conversion of Aniline to Azobenzene Using nano‐TiO2‐P25‐SO3H, under Visible Light Irradiation

Nano‐TiO2‐P25‐SO3H as our previous report has successfully been utilized to synthesize azobenzene through the selective conversion of aniline under visible light irradiation. According to PL emission spectra, the immobilizing a solid Brønsted acid of ‐SO3H groups on the pure‐TiO2‐P25 surface with a close interface is an approach to amplify the nano‐TiO2‐P25 response to visible light, which can productively hinder the recombination rate of photogenerated electrons and holes as carriers. Therefore, the photocatalytic activity of the semiconductor is highly likely to increase. Photooxidation of aniline to azobenzene was achieved by applying nano‐TiO2‐P25‐SO3H (Eg = 2.6 eV) that activated by blue photons (λmax = 460 nm), green photons (λmax = 510 nm) and red photons (λmax = 630 nm) which is introducing as a sustainable procedure. Central composite design (CCD) was employed for evaluating the effects of photocatalyst amount, oxidant concentration and irradiation time on the synthesis of azobenzene by this approach. Easily synthesizing, recyclability of the photocatalyst, mild reaction condition and short reaction time could be considered as plus points of this process.
Differences in GPS variables according to playing formations and playing positions in U19 male soccer players

ABSTRACT The aims of this study were 1) to investigate Global Positioning System (GPS)-based match physical performance according to players’ playing position in three different playing formations (4-4-2, 3-5-2, 4-3-3) and 2) to analyse the differences in match performance between 1st and 2nd half. Twenty-three U19 elite male soccer players (age: 18 ± 1 year, height: 1.80 ± 0.04 m, body mass: 70.65 ± 6.02 kg), categorized as Central Back (CB, n = 5), Full Back (FB, n = 4), Central Midfielders (CM, n = 4), Wingers (W, n = 3), Strikers (S, n = 7), were monitored using 10 Hz GPS during 31 competitive matches. The results showed that FB and W always had the highest very high-speed running distance and number of sprints in all playing formations. Significant decrease in all GPS variables was observed in the 2nd half of the match for all playing positions. Strength coaches should adopt specific training regimes in accordance with players’ playing position.
Economic evaluation of 'Men on the Move', a 'real world' community-based physical activity programme for men.

BACKGROUND Physical activity (PA) interventions capable of producing health benefits cost effectively are a public health priority across the Western world. 'Men on the Move' (MOM), a community-based PA intervention for men, demonstrated significant health benefits up to 52-weeks (W) post-baseline. This article details the economic evaluation of MOM with a view to determining its cost-effectiveness as a public health intervention to be rolled out nationally in Ireland. METHODS Cost-effectiveness was determined by comparing the costs (direct and indirect) of the programme to its benefits, which were captured as the impact on quality-adjusted life-years (QALYs). For the benefits, cost-utility analysis was conducted by retrospectively adapting various health-related measures of participants to generate health states using Brazier et al.'s (2002) short form-6D algorithm. This in turn allowed for 'utility measures' to be generated, from which QALYs were derived. RESULTS Findings show MOM to be cost-effective in supporting an 'at risk' cohort of men achieves significant improvements in aerobic fitness, weight loss and waist reduction. The total cost per participant (€125.82 for each of the 501 intervention participants), the QALYs gained (11.98 post-12-W intervention, or 5.3% health improvement per participant) and estimated QALYs ratio costs of €3723 represents a cost-effective improvement when compared to known QALY guidelines. CONCLUSIONS The analysis shows that the cost per QALY achieved by MOM is significantly less than the existing benchmarks of £20 000 and €45 000 in the UK and Ireland respectively, demonstrating MOM to be cost-effective.
Hepatic lipids promote liver metastasis

Obesity predisposes to cancer and a virtual universality of nonalcoholic fatty liver disease (NAFLD). However, the impact of hepatic steatosis on liver metastasis is enigmatic. We find that while control mice were relatively resistant to hepatic metastasis, those which were lipodystrophic or obese, with NAFLD, had a dramatic increase in breast cancer and melanoma liver metastases. NAFLD promotes liver metastasis by reciprocal activation initiated by tumor-induced triglyceride lipolysis in juxtaposed hepatocytes. The lipolytic products are transferred to cancer cells via fatty acid transporter protein 1, where they are metabolized by mitochondrial oxidation to promote tumor growth. The histology of human liver metastasis indicated the same occurs in humans. Furthermore, comparison of isolates of normal and fatty liver established that steatotic lipids had enhanced tumor-stimulating capacity. Normalization of glucose metabolism by metformin did not reduce steatosis-induced metastasis, establishing the process is not mediated by the metabolic syndrome. Alternatively, eradication of NAFLD in lipodystrophic mice by adipose tissue transplantation reduced breast cancer metastasis to that of control mice, indicating the steatosis-induced predisposition is reversible.
Molecular phylogeny of three mudskippers (Gobiidae) from the Persian Gulf and Gulf of Oman (Makran)

Presented is a phylogenetic reconstruction of mudskippers using sequences of the mitochondrial COI and cytb genes. The phylogeny combines the sequences of 12 species from GenBank with those of three species (Boleophthalmus dussumieri, Periophthalmus waltoni and Scartelaos tenuis) collected from the coastal area of the Persian Gulf and Oman (Makran) Sea and sequenced for the first time. Based on the Maximum likelihood and Bayesian methods, Periophthalmus forms a separate clade that is the sister lineage to a group formed by all remaining genera. The subfamilies Oxudercinae and Amblyopinae established on the basis of morphological characters have been shown to be paraphyletic and their use as taxonomic units is no longer recommended. The evolution of Periophthalmus waltoni, Periophthalmus barbarous and Boleophthalmus dussumieri is discussed based on molecular phylogenetic reconstruction.
Importance of wintertime anthropogenic glyoxal and methylglyoxal emissions in Beijing and implications for the secondary organic aerosol formation in megacity.

Atmospheric glyoxal (GLY) and methylglyoxal (MGLY) are key precursors of secondary organic aerosol (SOA). However, anthropogenic emissions of GLY and MGLY and their contribution to surface GLY and MGLY concentrations, as well as the secondary organic aerosol (SOA) formation, are not well quantified. By developing an emission inventory of anthropogenic GLY and MGLY and improving Community Multiscale Air Quality Model (CMAQ) with SOA formation from irreversible surface uptake of GLY and MGLY, as well as a precursor-origin resolved technique, we quantified the source contributions of GLY and MGLY and their impact on wintertime SOA formation in Beijing, China. The total emissions of GLY and MGLY in Beijing in 2017 are 1.1×104 kmol and 7.0×103 kmol, respectively. Anthropogenic primary emissions are found to be the dominant contributor to wintertime GLY and MGLY concentrations (~74% for GLY and ~63% for MGLY). Anthropogenic primary emissions of GLY and MGLY contributes to 30% of GLY/MGLY SOA daily average concentration and accounts for up to 45% of nighttime GLY/MGLY SOA in winter. The study suggests that the anthropogenic GLY and MGLY emissions, mainly from gasoline vehicles and cooking, are important for SOA formation and shall be strictly controlled in Chinese megacities.
Management of Non-Tubal Ectopic Pregnancies: A Single Center Experience

Non-tubal ectopic pregnancies (NT-EPs) are rare but potentially life-threatening conditions. The incidence ranges are between 5–8.3% of all ectopic pregnancies. For this retrospective observational study, 16 patients with NT-EP and treated from January 2014 to May 2020 were recruited. Demographic details, symptoms, Beta human chorionic gonadotrophin (β-hCG) levels, ultrasound findings, management and treatment outcomes were presented. In hemodynamically stable patients, diagnosis was made using ultrasounds and β-hCG levels. Laparoscopy was essential to identify and remove the ectopic pregnancy in clinical unstable patients. A radical laparoscopic approach was chosen in one case of cervical pregnancy diagnosed late in the first trimester. Medical treatment and minimally invasive procedure, alone or combined, resulted in effective strategies in asymptomatic women with an early diagnosis of NT-EP. We report cases of cervical pregnancies successfully treated by hysteroscopy alone or combined with medical treatment, the first case of scar pregnancy treated by mini-reseptoscope and curettage and the fifth case of interstitial pregnancy treated with Methotrexate and Mifepristone. In this manuscript we report a single center experience in the management of NT-EPs with the aim of outlining the importance of the early diagnosis for a minimally invasive treatment in order to reduce maternal morbidity and mortality and preserve future fertility.
Cardiac hypertrophy in a dish: a human stem cell based model

ABSTRACT Cardiac hypertrophy is an important and independent risk factor for the development of heart failure. To better understand the mechanisms and regulatory pathways involved in cardiac hypertrophy, there is a need for improved in vitro models. In this study, we investigated how hypertrophic stimulation affected human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CMs). The cells were stimulated with endothelin-1 (ET-1) for 8, 24, 48, 72, or 96 h. Parameters including cell size, ANP-, proBNP-, and lactate concentration were analyzed. Moreover, transcriptional profiling using RNA-sequencing was performed to identify differentially expressed genes following ET-1 stimulation. The results show that the CMs increase in size by approximately 13% when exposed to ET-1 in parallel to increases in ANP and proBNP protein and mRNA levels. Furthermore, the lactate concentration in the media was increased indicating that the CMs consume more glucose, a hallmark of cardiac hypertrophy. Using RNA-seq, a hypertrophic gene expression pattern was also observed in the stimulated CMs. Taken together, these results show that hiPSC-derived CMs stimulated with ET-1 display a hypertrophic response. The results from this study also provide new molecular insights about the underlying mechanisms of cardiac hypertrophy and may help accelerate the development of new drugs against this condition. Summary: This research describes a functional in vitro model of cardiac hypertrophy, and how the time of stimulation with endothelin-1 affects the cells.
Observation of the Sedative Effect of Dexmedetomidine Combined With Midazolam Nasal Drops Before a Pediatric Craniocerebral MRI.

OBJECTIVE This study aimed to investigate the sedative effect of dexmedetomidine combined with midazolam nasal drops before a pediatric craniocerebral magnetic resonance imaging (MRI). METHODS Eighty children who needed an MRI examination were enrolled in the present study and randomly divided into 2 groups: the observation group (dexmedetomidine combined with midazolam nasal drops) and the control group. After the children were given the medication, their heart rate, blood oxygen saturation (SpO2), and respiratory rate were continuously monitored and the adverse reactions such as nausea and vomiting, cough, restlessness, heart rate slowdown, and respiratory depression were observed. RESULTS The difference in the onset time between the 2 groups was not statistically significant (P > 0.05), but the duration was significantly longer in the observation group than in the control group (P < 0.01) and the examination success rate were significantly higher in the observation group than in the control group (P < 0.05). CONCLUSION The protocol of 3 μg/kg of a dexmedetomidine injection combined with 0.3 mg/kg of midazolam nasal drops is safe, easy to operate, and has a high success rate, which is worthy of clinical promotion.