Miracle-dz/UniFAR-FTUs huggingface dataset:
The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.
Myeloid-Specific Deletion of the AMPKα2 Subunit Alters Monocyte Protein Expression and Atherogenesis

The AMP-activated protein kinase (AMPK) is an energy sensing kinase that is activated by a drop in cellular ATP levels. Although several studies have addressed the role of the AMPKα1 subunit in monocytes and macrophages, little is known about the α2 subunit. The aim of this study was to assess the consequences of AMPKα2 deletion on protein expression in monocytes/macrophages, as well as on atherogenesis. A proteomics approach was applied to bone marrow derived monocytes from wild-type mice versus mice specifically lacking AMPKα2 in myeloid cells (AMPKα2∆MC mice). This revealed differentially expressed proteins, including methyltransferases. Indeed, AMPKα2 deletion in macrophages increased the ratio of S-adenosyl methionine to S-adenosyl homocysteine and increased global DNA cytosine methylation. Also, methylation of the vascular endothelial growth factor and matrix metalloproteinase-9 (MMP9) genes was increased in macrophages from AMPKα2∆MC mice, and correlated with their decreased expression. To link these findings with an in vivo phenotype, AMPKα2∆MC mice were crossed onto the ApoE-/- background and fed a western diet. ApoExAMPKα2∆MC mice developed smaller atherosclerotic plaques than their ApoExα2fl/fl littermates, that contained fewer macrophages and less MMP9 than plaques from ApoExα2fl/fl littermates. These results indicate that the AMPKα2 subunit in myeloid cells influences DNA methylation and thus protein expression and contributes to the development of atherosclerotic plaques.
Same Queries, Different Data: Can we Predict Query Performance?

We consider MapReduce workloads that are produced by analytics applications. In contrast to ad hoc query workloads, analytics applications are comprised of fixed data flows that are run over newly arriving data sets or on different portions of an existing data set. Examples of such workloads include document analysis/indexing, social media analytics, and ETL (Extract Transform Load). Motivated by these workloads, we propose a technique that predicts the runtime performance for a fixed set of queries running over varying input data sets. Our prediction technique splits each query into several segments where each segment’s performance is estimated using machine learning models. These per-segment estimates are plugged into a global analytical model to predict the overall query runtime. Our approach uses minimal statistics about the input data sets (e.g., tuple size, cardinality), which are complemented with historical information about prior query executions (e.g., execution time). We analyze the accuracy of predictions for several segment granularities on both standard analytical benchmarks such as TPC-DS [17], and on several real workloads. We obtain less than 25% prediction errors for 90% of predictions.
Cohort profile: the Hortega Study for the evaluation of non-traditional risk factors of cardiometabolic and other chronic diseases in a general population from Spain

Purpose The Hortega Study is a prospective study, which investigates novel determinants of selected chronic conditions with an emphasis on cardiovascular health in a representative sample of a general population from Spain. Participants In 1997, a mailed survey was sent to a random selection of public health system beneficiaries assigned to the University Hospital Rio Hortega’s catchment area in Valladolid (Spain) (n=11 423, phase I), followed by a pilot examination in 1999–2000 of 495 phase I participants (phase II). In 2001–2003, the examination of 1502 individuals constituted the Hortega Study baseline examination visit (phase III, mean age 48.7 years, 49% men, 17% with obesity, 27% current smokers). Follow-up of phase III participants (also termed Hortega Follow-up Study) was obtained as of 30 November 2015 through review of health records (9.5% of participants without follow-up information). Findings to date The Hortega Study integrates baseline information of traditional and non-traditional factors (metabolomic including lipidomic and oxidative stress metabolites, genetic variants and environmental factors, such as metals), with 14 years of follow-up for the assessment of mortality and incidence of chronic diseases. Preliminary analysis of time to event data shows that well-known cardiovascular risk factors are associated with cardiovascular incidence rates, which add robustness to our cohort. Future plans In 2020, we will review updated health and mortality records of this ongoing cohort for a 5-year follow-up extension. We will also re-examine elder survivors to evaluate specific aspects of ageing and conduct geolocation to study additional environmental exposures. Stored biological specimens are available for analysis of new biomarkers. The Hortega Study will, thus, enable the identification of novel factors based on time to event data, potentially contributing to the prevention and control of chronic diseases in ageing populations.
Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea

The emerging pollutants antibiotic resistance genes (ARGs) are prevalent in aquatic environments such as estuary. Coastal mangrove ecosystems always serve as natural wetlands for receiving sewage which always carry ARGs. Currently, the research considering ARG distribution in mangrove ecosystems gains more interest. In this work, we investigated the diversity of ARGs in an urban estuary containing mangrove and nonmangrove areas of the South China Sea. A total of 163 ARGs that classified into 22 resistance types and six resistance mechanisms were found. ARG abundance of the samples in the estuary is between 0.144 and 0.203. This is within the general range of Chinese estuaries. The difference analysis showed that abundances of total ARGs, six most abundant ARGs (mtrA, rpoB, rpoC, rpsL, ef‐Tu, and parY), the most abundant resistance types (elfamycin, multidrug, and peptide), and the most abundant resistance mechanism (target alteration) were significantly lower in mangrove sediment than that in nonmangrove sediment (p < 0.05). Network and partial redundancy analysis showed that sediment properties and mobile genetic elements were the most influential factors impacting ARG distribution rather than microbial community. The two factors collectively explain 51.22% of the differences of ARG distribution. Our study indicated that mangrove sediments have the capacity to remove ARGs. This work provides a research paradigm for analysis of ARG prevalence and proliferation in the subtropical marine coastal mangrove ecosystem.
Mapping the Affective Dimension of Embodiment with the Sensation Manikin: Validation Among Chronic Pain Patients and Modification by Mindfulness-Oriented Recovery Enhancement.

OBJECTIVE Mindfulness-based interventions (MBIs) target novel pain relief mechanisms not captured by legacy pain scales, including 1) cultivating awareness of pleasant and neutral sensations proximal to unpleasant sensations and 2) interoceptively mapping sensation locations and spatial distributions. METHODS We created a digital sensation manikin (SM), by overlaying a human figure silhouette with a grid of 469 "sensation" pixels. A series of five research questions examined the SM's discriminant validity, construct validity, incremental validity, convergence with an objective measure of pain attentional bias, and sensitivity to a mindfulness-based psychological treatment. A sample of opioid treated chronic pain patients (n=108, Age=53.79±12.94, Female=65%) was recruited to answer research questions 1-5, and a sample of healthy controls (n=91, Age=36.47±13.50, Female=55%) was recruited as the comparison group for research question 1. RESULTS Chronic pain patients reported significantly more unpleasant sensation than healthy controls (p<.001, d=1.23) and significantly fewer pleasant sensations (p=.001, d=0.50). The SM also evidenced expected relationships with multiple measures of pain (r=.26-.29) and well-being (r=-.21-.28), uniquely predicted pain interference (β=-.18), and exhibited a significant association with pain attentional bias (r=.25). Finally, MBI involvement significantly increased the ratio of pleasant to unpleasant sensations reported by chronic pain patients relative to an active control condition (p=.036, d=.51). CONCLUSIONS This study supports the SM's validity and indicates that assessing both pleasant and unpleasant sensations broadens the scope of pain measurement. Although the SM would benefit from further optimization, its continued use is likely to contribute to improved assessment and treatment options for chronic pain patients.
Air Pollution Predicts Harsh Moral Judgment

The present research recruited participants from China, which is suffering from serious air pollution, and examined whether air pollution would be associated with moral judgment and immoral behavioral intention. Study 1 (n = 145) used the objective Air Quality Index to indicate the level of air pollution and found that it predicted harsh judgment on others’ moral violations but did not predict judgment on others’ non-moral negative behaviors or their own immoral behavioral intentions. Study 2 (n = 90) asked participants either to recall a past experience of being exposed to air pollution or to recall a neutral experience and consistently found that air pollution only influenced judgment on moral violations. The findings also ruled out the feeling of threat or the trust of government as possible mediators in the relationship between air pollution and harsh moral judgment.
Interaction, cytotoxicity and sustained release assessment of a novel anti-tumor agent using bovine serum albumin nanocarrier

Abstract The interaction ability of bovine serum albumin (BSA) with 2,6-divanillylidenecyclohexanone (DVH) as a stable curcumin derivative was investigated using fluorescence and circular dichroism (CD) spectroscopy techniques under simulative physiological conditions (pH = 7.2). Following the obtained results of binding studies, bovine serum albumin nanoparticles (BSANPs) were synthesized and characterized using Fourier transform infrared spectroscopy (FT-IR), filed emission scanning electron microscopy (FE-SEM), atomic force microscope (AFM) and dynamic light scattering (DLS). The stable BSANPs showed a spherical shape with a diameter of 149.14 ± 46.69 nm and the formulation of BSA had no change during the fabrication process. DVH was loaded on BSANPs (DVH@BSANPs) and the release studies showed sustained release of DVH from BSANPs. The validation of DVH@BSANPs system confirmed that the Fickian release mechanism of DVH followed on Korsmeyer–Pepas model. The in vitro studies on HFFF2 and MDA-MB-231 were investigated using MTT assay, DAPI and annexinV/PI staining that showed biocompatible BSANPs reduced the cytotoxicity of DVH in normal cell lines significantly, and antitumor activity of DVH was increased when it was loaded onto BSANPs without necrosis. These results suggest that DVH@BSANPs are a novel biocompatible sustained release system for effective therapeutic approach. Communicated by Ramaswamy H. Sarma
Quality of life outcomes in multiple myeloma patients: a summary of recent clinical trials

ABSTRACT Introduction: Management of multiple myeloma (MM) has improved over recent years. Health-related quality of life (HRQoL) data is becoming increasingly important, owing to improved survival outcomes. Areas covered: The authors performed an expert review of the literature to identify evidence-based data available on HRQoL in frontline and relapsed/refractory MM (RRMM) patients. Expert opinion: De-novo patients should be informed that the HRQoL is expected to improve during first-line treatment with different degrees of possible deterioration during the first cycles. Achievement of a maximal response should be strongly considered, particularly in the frontline setting, but must also be balanced with tolerability, HRQoL, and patient preferences. The same degree of improvement in HRQoL cannot be expected during conventional relapse treatments, where patients should be prepared only for stabilization of HRQoL. However, focusing attention only on measures such as toxicity may provide just a partial view of overall treatment effectiveness. Nonetheless, the authors believe the added value of taking into consideration the patient’s perspectives and the importance of patient-reported outcomes in the evaluation of treatment effects should be considered mandatory. The incorporation of quality of life assessment into clinical and research practice has the potential of improving treatment outcomes.
A Problematic Tyrannosaurid (Dinosauria: Theropoda) Skeleton and Its Implications for Tyrannosaurid Diversity in the Horseshoe Canyon Formation (Upper Cretaceous) of Alberta

Several published censuses have noted the presence of two tyrannosaurids, Daspletosaurus sp. and Albertosaurus sarcophagus, within the Upper Cretaceous Horseshoe Canyon Formation of Alberta. Although A. sarcophagus is known from more than a dozen major discoveries in these strata, Daspletosaurus sp. is known from just a single problematic skeleton (lacking most of the skull) of a young individual. Here we describe and figure this skeleton, and marshal a variety of osteohistologic, morphometric, and phylogenetic methods to accurately determine its taxonomic status. Although none of these methods individually provides convincing evidence regarding the affinities of the specimen, together (and including other historical and biostratigraphic considerations) they strongly imply that the skeleton instead pertains to a young A. sarcophagus. In this way, we show that only a single species of tyrannosaurid is definitively present in the Horseshoe Canyon Formation, greatly simplifying interpretations of tyrannosaurid evolution and ecology in this setting. Anat Rec, 303:673–690, 2020. © 2019 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
Effect of preventive or therapeutic treatment with angiotensin 1–7 in a model of bleomycin‐induced lung fibrosis in mice

Idiopathic pulmonary fibrosis is characterized by aberrant fibroblast activation and excessive collagen deposition that may eventually lead to organ dysfunction. Lung fibrosis is frequently observed in cancer patients undergoing bleomycin (BLM) treatment. Therefore, BLM instillation in mice is the most frequent model used to investigate pulmonary fibrosis. Angiotensin 1–7 [Ang‐(1‐7)] is a heptapeptide with anti‐inflammatory and proresolving activity. Here, we studied the effects of preventive and therapeutic oral administration of Ang‐(1‐7) in a model of BLM‐induced lung fibrosis in mice. Male C57Bl/6j mice were instilled with BLM and followed for weight loss and survival or euthanized to examine pulmonary inflammation, fibrosis, and lung function. For preventive treatment, mice were treated with Ang‐(1‐7) 1 h before instillation and then twice daily. We observed that preventive treatment with Ang‐(1‐7) decreased weight loss, inflammation and collagen deposition, increased survival, and ameliorated lung function. Therapeutic treatment with Ang‐(1‐7), starting 3 days after BLM instillation resulted in decreased inflammation, decreased collagen deposition, and ameliorated lung function, although the effects were of lower magnitude than the preventive treatment. Therapeutic treatment with Ang‐(1‐7) starting 7 or 14 days after BLM instillation failed to alter any of the changes observed. Therefore, although oral preventive treatment with Ang‐(1‐7) is effective to decrease pulmonary inflammation, fibrosis, and functional changes induced by BLM, therapeutic effects are much less significant, arguing against its use in patients with chronic fibrosis. It remains to be determined whether other proresolving molecules will have better therapeutic effects in the context of chronic pulmonary fibrosis.
Chapter 3. Training for Language Documentation: Experiences at the School of Oriental and African Studies

Since 2003 the Endangered Languages Project at SOAS has been involved in various types of training for documentation of endangered languages, ranging from one-day workshops through to MA and PhD post-graduate degree programs. The training events have been attended by specialists, research grantees, students, and members of the general public, and have covered a wide range of topics and involved delivery in a range of contexts and delivery modes, including hands-on practical sessions and e-learning in the Blackboard framework. We have covered both theory and practice of language documentation and endangered language support, including the development of multimedia and curriculum materials for language teaching, some of it experimental and, we think, quite innovative. In this paper I discuss some of our experiences in developing and running these training workshops and courses, reporting on the models, and successes (and failures) over the past three and a half years. My goal is to share our accumulated knowledge and experience with others with similar interests, and in doing so to advance our understanding of the possibilities for language documentation training.
Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae

Disease resistance genes encoding proteins with nucleotide binding sites and Leucine-Rich Repeat (NB-LRR) domains include many members involved in the effector-triggered immunity pathway in plants. The transcript levels of these defense genes are negatively regulated by diverse microRNAs (miRNAs) in angiosperms and gymnosperms. In wheat, using small RNA expression datasets and degradome datasets, we identified five miRNA families targeting NB-LRR defense genes in monocots, some of which arose in the Triticeae species era. These miRNAs regulate different types of NB-LRR genes, most of them with coil-coiled domains, and trigger the generation of secondary small interfering RNAs (siRNA) as a phased pattern in the target site regions. In addition to acting in response to biotic stresses, they are also responsive to abiotic stresses such as heat, drought, salt, and light stress. Their copy number and expression variation in Triticeae suggest a rapid birth and death frequency. Altogether, non-conserved miRNAs as conserved transcriptional regulators in gymnosperms and angiosperms regulating the disease resistance genes displayed quick plasticity including the variations of sequences, gene copy number, functions, and expression level, which accompanied with NB-LRR genes may be tune-regulated to plants in natural environments with various biotic and abiotic stresses.
Examination of Recreational and Spiritual Peyote Use Among American Indian Youth.

OBJECTIVE Some American Indians legally use hallucinogenic substances as part of religious and spiritual ceremonies. Research to date has either failed to differentiate spiritual versus recreational use or has categorized hallucinogen use in an "other drug" or "illegal drug" category. This approach could contribute to ineffectual models of prevention and treatment intervention and limit understanding of hallucinogen use in American Indian cultures. METHOD This study is a secondary data analysis of an ongoing epidemiologic and etiologic investigation of substance use among American Indian youth (N = 3,861). Two Firth logistic regression models were run with (a) spiritual peyote use and (b) recreational peyote use as the dependent variables, and grade, sex, 30-day alcohol use, 30-day marijuana use, religiosity, religious affiliation, and cultural identity as predictors, as well as a grade by sex interaction term. RESULTS Grade, sex, religious affiliation, and the interaction term did not predict either recreational or spiritual peyote use. Thirty-day alcohol and marijuana use predicted both spiritual and recreational peyote use, but the effects were stronger for predicting recreational use. Religiosity and cultural identity predicted spiritual but not recreational use, such that American Indian youth who identified as more religious and identified more strongly with their culture were more likely to report using peyote for spiritual purposes. CONCLUSIONS Our results suggest that current self-reported use of alcohol and/or marijuana by American Indian youth indicates an increased likelihood of using peyote. In addition, use of Firth logistic regression models proved feasible for analyzing rare events like peyote use.
Biochemical characterization of digestive membrane-associated alkaline phosphatase from the velvet bean caterpillar Anticarsia gemmatalis.

In Brazil, the use of transgenic plants expressing the insect-toxic Bacillus thuringiensis endotoxin has been successfully used as pest control management since 2013 in transgenic soybean lineages against pest caterpillars such as Helicoverpa armigera. These toxins, endogenously expressed by the plants or sprayed over the crops, are ingested by the insect and bind to receptors in the midgut of these animals, resulting in disruption of digestion and lower insect survival rates. Here, we identified and characterized a membrane-associated alkaline phosphatase (ALP) in the midgut of Anticarsia gemmatalis, the main soybean defoliator pest in Brazil, and data suggested that it binds to Cry1Ac toxin in vitro. Our data showed a peak of ALP activity in homogenate samples of the midgut dissected from the 4th and 5th instars larvae. The brush border membrane vesicles obtained from the midgut of these larvae were used to purify a 60 kDa ALP, as detected by in-gel activity and in vitro biochemical characterization using pharmacological inhibitors and mass spectrometry. When Cry1Ac toxin was supplied to the diet, it was efficient in decreasing larval weight gain and survival. Indeed, in vitro incubation of Cry1Ac toxin with the purified ALP resulted in a 43% decrease in ALP specific activity and enzyme-linked immunosorbent assay showed that ALP interacts with Cry1Ac toxin in vitro, thus suggesting that ALP could function as a Cry toxin ligand. This is a first report characterizing an ALP in A. gemmatalis.