Miracle-dz/UniFAR-FTUs huggingface dataset:
Elimination of Foreign DNA during Somatic Differentiation in Tetrahymena thermophila Shows Position Effect and Is Dosage Dependent

ABSTRACT In the ciliate Tetrahymena thermophila, approximately 15% of the germ line micronuclear DNA sequences are eliminated during formation of the somatic macronucleus. The vast majority of the internal eliminated sequences (IESs) are repeated in the micronuclear genome, and several of them resemble transposable elements. Thus, it has been suggested that DNA elimination evolved as a means for removing invading DNAs. In the present study, bacterial neo genes introduced into the germ line micronuclei were eliminated from the somatic genome. The efficiency of elimination from two different loci increased dramatically with the copy number of the neo genes in the micronuclei. The timing of neo elimination is similar to that of endogenous IESs, and they both produce bidirectional transcripts of the eliminated element, suggesting that the deletion of neo occurred by the same mechanism as elimination of endogenous IESs. These results indicate that repetition of an element in the micronucleus enhances the efficiency of its elimination from the newly formed somatic genome of Tetrahymena thermophila. The implications of these data in relation to the function and mechanism of IES elimination are discussed.
Implications of Cardiovascular Disease Risk Assessment Using the WHO/ISH Risk Prediction Charts in Rural India

Cardiovascular disease (CVD) risk in India is currently assessed using the World Health Organization/International Society for Hypertension (WHO/ISH) risk prediction charts since no population-specific models exist. The WHO/ISH risk prediction charts have two versions—one with total cholesterol as a predictor (the high information (HI) model) and the other without (the low information (LI) model). However, information on the WHO/ISH risk prediction charts including guidance on which version to use and when, as well as relative performance of the LI and HI models, is limited. This article aims to, firstly, quantify the relative performance of the LI and HI WHO/ISH risk prediction (for WHO-South East Asian Region D) using data from rural India. Secondly, we propose a pre-screening (simplified) point-of-care (POC) test to identify patients who are likely to benefit from a total cholesterol (TC) test, and subsequently when the LI model is preferential to HI model. Analysis was performed using cross-sectional data from rural Andhra Pradesh collected in 2005 with recorded blood cholesterol measurements (N = 1066). CVD risk was computed using both LI and HI models, and high risk individuals who needed treatment(T HR) were subsequently identified based on clinical guidelines. Model development for the POC assessment of a TC test was performed through three machine learning techniques: Support Vector Machine (SVM), Regularised Logistic Regression (RLR), and Random Forests (RF) along with a feature selection process. Disagreement in CVD risk predicted by LI and HI WHO/ISH models was 14.5% (n = 155; p<0.01) overall and comprised 36 clinically relevant T HR patients (31% of patients identified as T HR by using either model). Using two patient-specific parameters (age, systolic blood pressure), our POC assessment can pre-determine the benefit of TC testing and choose the appropriate risk model (out-of-sample AUCs:RF-0.85,SVM-0.84,RLR:0.82 and maximum sensitivity-98%). The identification of patients benefitting from a TC test for CVD risk stratification can aid planning for resource-allocation and save costs for large-scale screening programmes.
A Three-Component Gene Expression System and Its Application for Inducible Flavonoid Overproduction in Transgenic Arabidopsis thaliana

Inducible gene expression is a powerful tool to study and engineer genes whose overexpression could be detrimental for the host organisms. However, only limited systems have been adopted in plant biotechnology. We have developed an osmotically inducible system using three components of plant origin, RD29a (Responsive to Dehydration 29A) promoter, CBF3 (C-repeat Binding Factor 3) transcription factor and cpl1-2 (CTD phosphatase-like 1) mutation. The osmotic stress responsible RD29a promoter contains the CBF3 binding sites and thus RD29A-CBF3 feedforward cassette enhances induction of RD29a promoter under stress. The cpl1-2 mutation in a host repressor CPL1 promotes stress responsible RD29a promoter expression. The efficacy of this system was tested using PAP1 (Production of Anthocyanin Pigment 1) transgene, a model transcription factor that regulates the anthocyanin pathway in Arabidopsis. While transgenic plants with only one or two of three components did not reproducibly accumulate anthocyanin pigments above the control level, transgenic cpl1 plants containing homozygous RD29a-PAP1 and RD29a-CBF3 transgenes produced 30-fold higher level of total anthocyanins than control plants upon cold treatment. Growth retardation and phytochemical production of transgenic plants were minimum under normal conditions. The flavonoid profile in cold-induced transgenic plants was determined by LC/MS/MS, which resembled that of previously reported pap1-D plants but enriched for kaempferol derivatives. These results establish the functionality of the inducible three-component gene expression system in plant metabolic engineering. Furthermore, we show that PAP1 and environmental signals synergistically regulate the flavonoid pathway to produce a unique flavonoid blend that has not been produced by PAP1 overexpression or cold treatment alone.
Atmospheres Modeling East Asian Dust and Its Radiative Feedbacks in CAM 4-BAM

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments reveals that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10 m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution, and size distribution.
A low ankle brachial index is associated with an increased risk of cardiovascular disease: the Hisayama study.

AIM Peripheral artery disease (PAD), defined as a decreased ankle brachial index (ABI), is a risk factor for cardiovascular disease; however, few studies have assessed the relationship between a low ABI and cardiovascular risks in Asian populations. We herein examined the relationship between the ABI and the development of cardiovascular disease in a Japanese community. METHODS A total of 2,954community-dwelling Japanese individuals without prior cardiovascular disease ≥ 40years of age were followed up for an average of 7.1years. The subjects' ABIs were categorized into the three groups: low (≤0.90), borderline (0.91-0.99) and normal (1.00-1.40). We estimated the relationship between the ABI and cardiovascular risk using a Cox proportional hazards model. RESULTS During the follow-up period, 134subjects experienced cardiovascular events. The incidence of cardiovascular disease across the ABI values was significantly different (p＜0.001). After adjusting for confounding factors, namely age, sex, systolic blood pressure, use of anti-hypertensive drugs, diabetes, total cholesterol, high-density lipoprotein cholesterol, obesity, smoking, alcohol intake and regular exercise, individuals with a low ABI were at 2.40-fold (95% confidence interval [CI] 1.14-5.06) greater risk of cardiovascular disease and 4.13-fold (95% CI 1.62-10.55) greater risk of coronary heart disease. CONCLUSIONS Our findings suggest that individuals with an ABI of ≤ 0.90 have an increased risk of cardiovascular events, independent from traditional risk factors, in the general Japanese population.
Prenatal exposure to antipsychotic medication and use of primary health care system in childhood: a population-based cohort study in Denmark

Background Antipsychotic (AP) medication is increasingly used for many health conditions. Prenatal exposure to AP medication has been associated with several adverse outcomes, but the findings remain inconsistent. Purpose We aimed to investigate prenatal exposure to AP medication and the use of primary health care system in childhood. Subjects and methods All live-born singletons in Denmark during 1997–2012 were identified in the nationwide Danish National Patient Register and followed until December 31, 2013 (n = 963,010). Information on prenatal exposure to AP medication was obtained from the Danish Register of Medicinal Product Statistics. Contacts to the general practitioner (GP) were used as a proxy for the overall health of the children. Negative binomial regression was used to calculate incidence rate ratios (IRRs) and 95% confidence intervals (CIs) for the association between prenatal exposure to AP medication and number and type of GP contacts, excluding routine well-child visits and vaccinations. The models were adjusted for sex and birth date of the child, maternal age, parity, cohabitation status, income, education, smoking status, diagnosis of substance abuse, severe psychiatric disorder, depression and epilepsy as well as the use of antiepileptic drugs, antidepressants, benzodiazepines and insulin. Results The prenatally AP-exposed children had 7% more GP contacts than unexposed children, IRR: 1.07 (95% CI: 1.03, 1.11). The association was slightly stronger among children of mothers with no diagnosis of severe psychiatric disorder (IRR: 1.08, 95% CI: 1.04–1.13) than among children of mothers with severe psychiatric disorder (IRR: 1.03, 95% CI: 0.96–1.11), but the difference was not statistically significant. We found no difference between prenatally AP-exposed children and their unexposed siblings, IRR: 1.00 (95% CI: 0.97–1.04) for total contacts. Conclusion Children of women using AP medication in pregnancy had more GP contacts in childhood than children of mothers not using AP medication. However, this might be explained by confounding from maternal behavior and mental illness.
Steel Corrosion Induced by Chloride or Carbonation in Mortar with Bending Cracks or Joints

Steel in concrete may corrode due to chloride or carbonation especially at cracks and joints. The objective of this study is to experimentally investigate comprehensively the pattern of corrosion cell formation (macrocell and microcell) as well as the corrosion rate using mortar specimens with defects simulating cracks and/or joints. The three important factors are listed as follows: 1) supply position of chloride ions or carbon dioxide, 2) environmental conditions, and 3) water-cement ratio of mortar. The results indicate that, in the case of chloride induced corrosion, decreasing the water-cement ratio (0.3) increased the activity of macrocell prominent corrosion. On the other hand, increasing the water-cement ratio (0.7) increased the activity of microcell prominent corrosion. Therefore, in the presence of defects, a high corrosion rate might be promoted even at a low water-cement ratio. The study also reveals that, in the case of carbonation induced corrosion, macrocell prominent corrosion occurred regardless of the water-cement ratio, and the lower the water-cement ratio, the lower the corrosion rate. Finally, the study proves that the corrosion rate induced by chloride was higher than that induced by carbonation.
Cognitive enhancement therapy for adult autism spectrum disorder: Results of an 18‐month randomized clinical trial

Cognitive remediation is a promising approach to treating core cognitive deficits in adults with autism, but rigorously controlled trials of comprehensive interventions that target both social and non‐social cognition over a sufficient period of time to impact functioning are lacking. This study examined the efficacy of cognitive enhancement therapy (CET) for improving core cognitive and employment outcomes in adult autism. Verbal adult outpatients with autism spectrum disorder (N = 54) were randomized to an 18‐month, single‐blind trial of CET, a cognitive remediation approach that integrates computer‐based neurocognitive training with group‐based training in social cognition, or an active enriched supportive therapy (EST) comparison focused on psychoeducation and condition management. Primary outcomes were composite indexes of neurocognitive and social‐cognitive change. Competitive employment was a secondary outcome. Intent‐to‐treat analyses indicated that CET produced significant differential increases in neurocognitive function relative to EST (d = .46, P = .013). Both CET and EST were associated with large social‐cognitive improvements, with CET demonstrating an advantage at 9 (d = .58, P = 0.020), but not 18 months (d = .27, P = 0.298). Effects on employment indicated that participants treated with CET were significantly more likely to gain competitive employment than those in EST, OR = 6.21, P = 0.023, which was mediated by cognitive improvement. CET is a feasible and potentially effective treatment for core cognitive deficits in adult autism spectrum disorder. The treatment of cognitive impairments in this population can contribute to meaningful improvements in adult outcomes. Autism Res 2018, 11: 519–530. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Isolation of endophytic bacteria from arboreal species of the Amazon and identification by sequencing of the 16S rRNA encoding gene

Endophytic bacteria from three arboreal species native to the Amazon (Carapa guianenses, Ceiba pentandra, and Swietenia macrophylla), were isolated and identified, through partial sequencing of the 16S rRNA encoding gene. From these, 16 isolates were obtained, although, when compared to sequences deposited in GenBank, only seven had produced identifiable fragments. Bacillus, Pantoea and two non-culturable samples were identified. Results obtained through sequence analysis revealed low genetic diversity across the isolates, even when analyzing different species and plant structures. This is the first report concerning the isolation and identification of endophytic bacteria in these plant species.
Determinants of platelet conjugate formation with polymorphonuclear leukocytes or monocytes in whole blood

Summary Following preliminary in-vitro experiments, platelet-leukocyte conjugates and their determinants were evaluated in citrated whole blood from 349 subjects (209 women, age 16–92 years) randomly recruited from the general population. Platelet activation by ADP/collagen but not leukocyte stimulation by fMLP or LTB4 resulted in formation of platelet conjugates with PMN or monocytes. In the population study, mixed cell conjugates, platelet P-selectin and leukocyte CD11b were measured by flow cytometry both at baseline and after in-vitro stimulation with ADP/collagen. The latter significantly increased platelet conjugates with either PMN or monocytes, platelet P-selectin and leukocyte CD11b expression. Platelet count significantly correlated with platelet-PMN, platelet-monocyte conjugates and P-selectin both at baseline and upon stimulation. In all conditions, both conjugate levels correlated with each other, when adjusted for gender, age and platelet count. Age correlated with platelet-PMN conjugate numbers in basal and stimulated conditions and with basal P-selectin. ADP/collagen stimulation resulted in higher P-selectin and conjugates values in women. Among risk factors, a significant correlation was found between conjugate and glucose levels. In conclusion, the presence and formation in whole blood from a large population of plateletleukocyte conjugates reflects primary platelet – but not leukocyte – activation and varies with gender, age, platelet count and blood glucose.
ExtraV: Boosting Graph Processing Near Storage with a Coherent Accelerator

In this paper, we propose ExtraV, a framework for near-storage graph processing. It is based on the novel concept of graph virtualization, which efficiently utilizes a cache-coherent hardware accelerator at the storage side to achieve performance and flexibility at the same time. ExtraV consists of four main components: 1) host processor, 2) main memory, 3) AFU (Accelerator Function Unit) and 4) storage. The AFU, a hardware accelerator, sits between the host processor and storage. Using a coherent interface that allows main memory accesses, it performs graph traversal functions that are common to various algorithms while the program running on the host processor (called the host program) manages the overall execution along with more application-specific tasks. Graph virtualization is a high-level programming model of graph processing that allows designers to focus on algorithm-specific functions. Realized by the accelerator, graph virtualization gives the host programs an illusion that the graph data reside on the main memory in a layout that fits with the memory access behavior of host programs even though the graph data are actually stored in a multi-level, compressed form in storage. We prototyped ExtraV on a Power8 machine with a CAPI-enabled FPGA. Our experiments on a real system prototype offer significant speedup compared to state-of-the-art software only implementations.
Vulnerability of the Great Barrier Reef to climate change and local pressures

Australia's Great Barrier Reef (GBR) is under pressure from a suite of stressors including cyclones, crown‐of‐thorns starfish (COTS), nutrients from river run‐off and warming events that drive mass coral bleaching. Two key questions are: how vulnerable will the GBR be to future environmental scenarios, and to what extent can local management actions lower vulnerability in the face of climate change? To address these questions, we use a simple empirical and mechanistic coral model to explore six scenarios that represent plausible combinations of climate change projections (from four Representative Concentration Pathways, RCPs), cyclones and local stressors. Projections (2017–2050) indicate significant potential for coral recovery in the near‐term, relative to current state, followed by climate‐driven decline. Under a scenario of unmitigated emissions (RCP8.5) and business‐as‐usual management of local stressors, mean coral cover on the GBR is predicted to recover over the next decade and then rapidly decline to only 3% by year 2050. In contrast, a scenario of strong carbon mitigation (RCP2.6) and improved water quality, predicts significant coral recovery over the next two decades, followed by a relatively modest climate‐driven decline that sustained coral cover above 26% by 2050. In an analysis of the impacts of cumulative stressors on coral cover relative to potential coral cover in the absence of such impacts, we found that GBR‐wide reef performance will decline 27%–74% depending on the scenario. Up to 66% of performance loss is attributable to local stressors. The potential for management to reduce vulnerability, measured here as the mean number of years coral cover can be kept above 30%, is spatially variable. Management strategies that alleviate cumulative impacts have the potential to reduce the vulnerability of some midshelf reefs in the central GBR by 83%, but only if combined with strong mitigation of carbon emissions.
The effects of four days of intensive mindfulness meditation training (Templestay program) on resilience to stress: a randomized controlled trial

Abstract The interest in mindfulness meditation interventions has surged due to their beneficial effects in fostering resilience and reducing stress in both clinical and non-clinical populations. However, the relaxation benefits that may occur while practicing mindfulness meditation and long-term benefits of these interventions remain unclear. Fifty-one participants were recruited and randomized into the experimental and control groups, which underwent 4 days of Intensive Meditation (Templestay program, n = 33) and Relaxation (Control, n = 18), respectively. The self-report measures of Cognitive and Affective Mindfulness Scale-Revised (CAMS) and the modified Korean version of the Resilience Quotient Test (RQT) were administered pre-, post- and 3 months after the intervention to measure participants’ levels of mindfulness and resilience. Participants in both the Templestay program and Control groups showed significant increases in their scores on CAMS and RQT after completing the program. During the 3-month follow-up, a significant interaction effect of the intervention method and time was revealed for the individuals’ CAMS and RQT scores. Our findings support the hypothesis that while relaxation practices may have certain stress reduction effects, the effects are predominantly mediated by the mindfulness meditation practice. Furthermore, the long-term benefits of increased resilience observed in the Templestay program group suggest that the practice may be a possible treatment strategy in clinical populations, such as patients with depression and anxiety.
H-CNN: Spatial Hashing Based CNN for 3D Shape Analysis

We present a novel spatial hashing based data structure to facilitate 3D shape analysis using convolutional neural networks (CNNs). Our method builds hierarchical hash tables for an input model under different resolutions that leverage the sparse occupancy of 3D shape boundary. Based on this data structure, we design two efficient GPU algorithms namely <bold/><monospace><bold>hash2col</bold></monospace><bold/> and <bold/><monospace><bold>col2hash</bold></monospace><bold/> so that the CNN operations like convolution and pooling can be efficiently parallelized. The perfect spatial hashing is employed as our spatial hashing scheme, which is not only free of hash collision but also nearly minimal so that our data structure is almost of the same size as the raw input. Compared with existing 3D CNN methods, our data structure significantly reduces the memory footprint during the CNN training. As the input geometry features are more compactly packed, CNN operations also run faster with our data structure. The experiment shows that, under the same network structure, our method yields comparable or better benchmark results compared with the state-of-the-art while it has only one-third memory consumption when under high resolutions (i.e., <inline-formula><tex-math notation="LaTeX">$256^3$</tex-math><alternatives><mml:math><mml:msup><mml:mn>256</mml:mn><mml:mn>3</mml:mn></mml:msup></mml:math><inline-graphic xlink:href="shao-ieq1-2887262.gif"/></alternatives></inline-formula>).