Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloroviruses

Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
Optimal Dosing of Acetylsalicylic Acid

CARDIOVASCULAR DISEASE IS THE LEADING CAUSE OF DEATH IN Canada, and it costs the Canadian economy over $18 billion annually. The use of acetylsalicylic acid (ASA) for the secondary prevention of cardiovascular events (e.g., myocardial infarction and stroke) is widely accepted based on the results of randomized controlled trials, and its role in primary prevention is becoming more firmly established. However, despite the numerous studies available, there is still controversy about the appropriate dose of ASA to optimize benefits and minimize risks.
Thrombocytopenia in Cirrhosis: A Review of Pathophysiology and Management Options

Thrombocytopenia is one of the most common hematological abnormalities and is often the first abnormality seen in patients with chronic liver disease. Thrombocytopenia affects approximately 6% of patients without cirrhosis and 70% of patients with cirrhosis. It is defined as a platelet count of less than 150,000/μL, with 100,000 to 150,000/μL considered as mild thrombocytopenia, 50,000 to 100,000/μL labeled as moderate thrombocytopenia, and less than 50,000/μL defined as severe thrombocytopenia. Thrombocytopenia can often be used as a marker of advanced liver disease, and some studies have shown moderate-to-severe thrombocytopenia to be a strong independent predictor of mortality. Mild-to-moderate thrombocytopenia rarely has any clinical significance because spontaneous bleeding is unlikely to occur at these levels. However, moderate-to-severe thrombocytopenia can prevent patients from receiving vital interventions such as medications and invasive procedures. Delayed procedures and correction of platelet abnormalities for these procedures can increase hospitalization time and increase overall health care costs.
Bioengineering advancements, innovations and challenges on green synthesis of 2, 5-furan dicarboxylic acid

ABSTRACT The major drawback of chemical transformations for the production of 2, 5-furan dicarboxylic acid (FDCA) implies the usage of hazardous chemicals, high temperature and high pressure from nonrenewable resources. Alternate to chemical methods, biological methods are promising. Microbial FDCA production is improved through engineering approaches of media conditions, homologous and heterologous expression of genes, genetic and metabolic engineering, etc. The highest FDCA production of 41.29 g/L is observed by an engineered Raultella ornitholytica BF 60 from 35 g/L HMF in sodium phosphate buffer with a 95.14% yield in 72 h. Also, an enzyme cascade system of recombinant and wild enzymes like periplasmic aldehyde oxidase ABC, galactose oxidase M3-5, HRP and catalase have transformed 6.3 g/L HMF to 7.81 g/L FDCA in phosphate buffer with 100% yield in 6 h. Still, these processes are emerging for fulfilling the industrial needs due to the challenges in ‘green FDCA production’. Graphical abstract
Polysaccharides in Ocular Drug Delivery

Polysaccharides, such as cellulose, hyaluronic acid, alginic acid, and chitosan, as well as polysaccharide derivatives, have been successfully used to augment drug delivery in the treatment of ocular pathologies. The properties of polysaccharides can be extensively modified to optimize ocular drug formulations and to obtain biocompatible and biodegradable drugs with improved bioavailability and tailored pharmacological effects. This review discusses the available polysaccharide choices for overcoming the difficulties associated with ocular drug delivery, and it explores the reasons for the dependence between the physicochemical properties of polysaccharide-based drug carriers and their efficiency in different formulations and applications. Polysaccharides will continue to be of great interest to researchers endeavoring to develop ophthalmic drugs with improved effectiveness and safety.
Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development

Abstract Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previously reported granulocytes. During B-cell differentiation, we found an increase in IR from the bone marrow precursors to cells residing in secondary lymphoid organs. B-cells that undergo affinity maturation to become antibody producing plasma cells steadily decrease retention. In general, we found an inverse relationship between global IR levels and both the proliferative state of cells, and the global levels of expression of splicing factors. IR dynamics during B-cell differentiation appear to be conserved between human and mouse, suggesting that IR plays an important biological role, evolutionary conserved, during blood cell differentiation. By correlating the expression of non-core splicing factors with global IR levels, and analyzing RNA binding protein knockdown and eCLIP data, we identify a few splicing factors likely playing an evolutionary conserved role in IR regulation. Our work provides new insights into the role of IR during hematopoiesis, and on the main factors involved in regulating IR.
Preparation of Ionic Liquid-Coated Graphene Nanosheets/PTFE Nanocomposite for Stretchable, Flexible Conductor via a Pre-Stretch Processing

The various volume concentrations of ionic liquid-modified graphene nanosheets filled polytetrafluoroethylene nanocomposites (IL-GNs/PTFE) for flexible conductors were fabricated via a pre-stretch processing method after cold-press sintering. The results indicated that pre-stretching has no significant weakening in the electrical conductivity of the nanocomposites, while the Young’s modulus greatly reduced by 62.5%, which is more suitable for flexible conductors. This may be because the reduced conductivity by the destructive conductive pathway cancels out the enhanced conductivity by the increased interlamellar spacing of IL-GNs via a pre-stretch processing, and the nanocomposite exhibits a phase transition from two to three-phase (with the introduction of an air phase) during pre-stretching. It was also found that the tensile strength of the nanocomposites was enhanced by 42.9% and the elongation at break and thermal conductivity decreased slightly with the same filler content after pre-stretching. The electrical conductivity of the pre-stretched nanocomposites tended to stabilize at 5.5 × 10−2 s·m−1, when the volume content of the packings achieved a percolation threshold (1.49 vol%). Meanwhile, the electrical resistivity of the pre-stretched 3.0 vol% IL-GNs/PTFE nanocomposite was slightly reduced by 0.30%, 0.38%, and 0.87% respectively after 180° twisting, 180° bending, and 10% stretching strain for 1000 cycles.
Environmental Toxicology and Chemistry

Since the early 2000s, biotic ligand models and related constructs have been a dominant paradigm for risk assessment of aqueous metals in the environment. We critically review 1) the evidence for the mechanistic approach underlying metal bioavailability models; 2) considerations for the use and refinement of bioavailability‐based toxicity models; 3) considerations for the incorporation of metal bioavailability models into environmental quality standards; and 4) some consensus recommendations for developing or applying metal bioavailability models. We note that models developed to date have been particularly challenged to accurately incorporate pH effects because they are unique with multiple possible mechanisms. As such, we doubt it is ever appropriate to lump algae/plant and animal bioavailability models; however, it is often reasonable to lump bioavailability models for animals, although aquatic insects may be an exception. Other recommendations include that data generated for model development should consider equilibrium conditions in exposure designs, including food items in combined waterborne–dietary matched chronic exposures. Some potentially important toxicity‐modifying factors are currently not represented in bioavailability models and have received insufficient attention in toxicity testing. Temperature is probably of foremost importance; phosphate is likely important in plant and algae models. Acclimation may result in predictions that err on the side of protection. Striking a balance between comprehensive, mechanistically sound models and simplified approaches is a challenge. If empirical bioavailability tools such as multiple‐linear regression models and look‐up tables are employed in criteria, they should always be informed qualitatively and quantitatively by mechanistic models. If bioavailability models are to be used in environmental regulation, ongoing support and availability for use of the models in the public domain are essential. Environ Toxicol Chem 2020;39:60–84. © 2019 SETAC
A Perspective and Framework for Developing Sample Type Specific Databases for LC/MS-Based Clinical Metabolomics

Metabolomics has the potential to greatly impact biomedical research in areas such as biomarker discovery and understanding molecular mechanisms of disease. However, compound identification (ID) remains a major challenge in liquid chromatography mass spectrometry-based metabolomics. This is partly due to a lack of specificity in metabolomics databases. Though impressive in depth and breadth, the sheer magnitude of currently available databases is in part what makes them ineffective for many metabolomics studies. While still in pilot phases, our experience suggests that custom-built databases, developed using empirical data from specific sample types, can significantly improve confidence in IDs. While the concept of sample type specific databases (STSDBs) and spectral libraries is not entirely new, inclusion of unique descriptors such as detection frequency and quality scores, can be used to increase confidence in results. These features can be used alone to judge the quality of a database entry, or together to provide filtering capabilities. STSDBs rely on and build upon several available tools for compound ID and are therefore compatible with current compound ID strategies. Overall, STSDBs can potentially result in a new paradigm for translational metabolomics, whereby investigators confidently know the identity of compounds following a simple, single STSDB search.
How best to reduce unhealthy risk-taking behaviours? A meta-review of evidence syntheses of interventions using self-regulation principles

ABSTRACT Self-regulation is a key antecedent of health and behaviour-change interventions have utilised self-regulation approaches to promote health. The present study used a novel methodology, a nested meta-review, to: (a) integrate and summarise information from evidence syntheses of diverse self-regulation interventions to reduce risk-taking, in the behavioural domains of smoking, alcohol and drug use, unhealthy eating, externalising problem behaviours, and sexual risk-taking; (b) identify intervention features implicated in risk-taking prevention or reduction; and (c) provide recommendations for future research and practice. Searches of eight databases yielded 21 eligible evidence syntheses, 15 taking a primarily social-cognitive strategy (k = 1,103 total studies), and 6 taking a primary trait/developmental strategy (k = 119); total N > 650,000. Intervention features most frequently associated with reduced risk-taking included: delivery of multiple components through (either, or a mix of) group, individual, computer, and one-one-one delivery; screening and pharmacotherapy, where relevant; targeting only one behavioural outcome; provision of counselling, stress-management, skills-training, self-monitoring, self-control and impulsivity training, and personalised feedback; identification of barriers and ‘resolution’ of barriers; tailoring to age and ethnicity; and, also, incorporating social support by peers. Some of these patterns were more visible in meta-analyses with higher methodological quality. Recommendations for research and practice are offered.
Molecular Mechanism Underlying Hypoxic Preconditioning-Promoted Mitochondrial Translocation of DJ-1 in Hypoxia/Reoxygenation H9c2 Cells

DJ-1 was recently reported to be involved in the cardioprotection of hypoxic preconditioning (HPC) against hypoxia/reoxygenation (H/R)-induced oxidative stress damage, by preserving mitochondrial complex I activity and, subsequently, inhibiting mitochondrial reactive oxygen species (ROS) generation. However, the molecular mechanism by which HPC enables mitochondrial translocation of DJ-1, which has no mitochondria-targeting sequence, to preserve mitochondrial complex I, is largely unknown. In this study, co-immunoprecipitation data showed that DJ-1 was associated with glucose-regulated protein 75 (Grp75), and this association was significantly enhanced after HPC. Immunofluorescence imaging and Western blot analysis showed that HPC substantially enhanced the translocation of DJ-1 from cytosol to mitochondria in H9c2 cells subjected to H/R, which was mimicked by DJ-1 overexpression induced by pFlag-DJ-1 transfection. Importantly, knockdown of Grp75 markedly reduced the mitochondrial translocation of DJ-1 induced by HPC and pFlag-DJ-1 transfection. Moreover, HPC promoted the association of DJ-1 with mitochondrial complex I subunits ND1 and NDUFA4, improved complex I activity, and inhibited mitochondria-derived ROS production and subsequent oxidative stress damage after H/R, which was also mimicked by pFlag-DJ-1 transfection. Intriguingly, these effects of HPC and pFlag-DJ-1 transfection were also prevented by Grp75 knockdown. In conclusion, these results indicated that HPC promotes the translocation of DJ-1 from cytosol to mitochondria in a Grp75-dependent manner and Grp75 is required for DJ-1-mediated protection of HPC on H/R-induced mitochondrial complex I defect and subsequent oxidative stress damage.
Assessment of Influenza D Virus in Domestic Pigs and Wild Boars in France: Apparent Limited Spread within Swine Populations Despite Serological Evidence of Breeding Sow Exposure

In order to assess influenza D virus (IDV) infections in swine in France, reference reagents were produced in specific pathogen free pigs to ensure serological and virological analyses. Hemagglutination inhibition (HI) assays were carried out on 2090 domestic pig sera collected in 2012–2018 in 102 farms. Only 31 sera from breeding sows sampled in 2014–2015 in six farrow-to-finish herds with respiratory disorders contained IDV-specific antibodies. In two of them, within-herd percentage of positive samples (73.3% and 13.3%, respectively) and HI titers (20–160) suggested IDV infections, but virus persistence was not confirmed following new sampling in 2017. All growing pigs tested seronegative, whatever their age and the sampling year. Moreover, PB1-gene RT-qPCR performed on 452 nasal swabs taken in 2015–2018 on pigs with acute respiratory syndrome (137 farms) gave negative results. In Corse, a Mediterranean island where pigs are mainly bred free-range, 2.3% of sera (n = 177) sampled on adult pigs in 2013–2014 obtained low HI titers. Finally, 0.5% of sera from wild boars hunted in 2009–2016 (n = 644) tested positive with low HI titers. These results provide the first serological evidence that sows were exposed to IDV in France but with a limited spread within the swine population.
Acupuncture for the Relief of Chronic Pain: A Synthesis of Systematic Reviews

Background and Objectives: It is estimated that 28 million people in the UK live with chronic pain. A biopsychosocial approach to chronic pain is recommended which combines pharmacological interventions with behavioural and non-pharmacological treatments. Acupuncture represents one of a number of non-pharmacological interventions for pain. In the current climate of difficult commissioning decisions and constantly changing national guidance, the quest for strong supporting evidence has never been more important. Although hundreds of systematic reviews (SRs) and meta-analyses have been conducted, most have been inconclusive, and this has created uncertainty in clinical policy and practice. There is a need to bring all the evidence together for different pain conditions. The aim of this review is to synthesise SRs of RCTs evaluating the clinical efficacy of acupuncture to alleviate chronic pain and to consider the quality and adequacy of the evidence, including RCT design. Materials and Methods: Electronic databases were searched for English language SRs and meta-analyses on acupuncture for chronic pain. The SRs were scrutinised for methodology, risk of bias and judgement of efficacy. Results: A total of 177 reviews of acupuncture from 1989 to 2019 met our eligibility criteria. The majority of SRs found that RCTs of acupuncture had methodological shortcomings, including inadequate statistical power with a high risk of bias. Heterogeneity between RCTs was such that meta-analysis was often inappropriate. Conclusions: The large quantity of RCTs on acupuncture for chronic pain contained within systematic reviews provide evidence that is conflicting and inconclusive, due in part to recurring methodological shortcomings of RCTs. We suggest that an enriched enrolment with randomised withdrawal design may overcome some of these methodological shortcomings. It is essential that the quality of evidence is improved so that healthcare providers and commissioners can make informed choices on the interventions which can legitimately be provided to patients living with chronic pain.
A calcium‐mediated actin redistribution at egg activation in Drosophila

Egg activation is the essential process in which mature oocytes gain the competency to proceed into embryonic development. Many events of egg activation are conserved, including an initial rise of intracellular calcium. In some species, such as echinoderms and mammals, changes in the actin cytoskeleton occur around the time of fertilization and egg activation. However, the interplay between calcium and actin during egg activation remains unclear. Here, we use imaging, genetics, pharmacological treatment, and physical manipulation to elucidate the relationship between calcium and actin in living Drosophila eggs. We show that, before egg activation, actin is smoothly distributed between ridges in the cortex of the dehydrated mature oocytes. At the onset of egg activation, we observe actin spreading out as the egg swells though the intake of fluid. We show that a relaxed actin cytoskeleton is required for the intracellular rise of calcium to initiate and propagate. Once the swelling is complete and the calcium wave is traversing the egg, it leads to a reorganization of actin in a wavelike manner. After the calcium wave, the actin cytoskeleton has an even distribution of foci at the cortex. Together, our data show that calcium resets the actin cytoskeleton at egg activation, a model that we propose to be likely conserved in other species.
Decentralization Policies of the Park Geun-Hye Administration-Korea: Characteristics and Future Policy Directions -1)

본 연구는 박근혜 정부의 지방분권 정책의 특징을 일정한 분석틀에 의거하여 분석해 보고 향후 바람직스러운 분권정책의 방향을 제시해 보고자 하는데 목적이 있다. 이를 위 해서 지방분권 정책의 성공적 추진을 담보하는 요소를 살펴보고, 이러한 요소들을 역대 정부의 지방분권 정책에 적용하여 일반적인 한계들을 도출한 이후 박근혜정부의 지방분 권 정책을 성공적으로 추진하기 위한 대안들을 제시하고자 하였다. 본 연구의 결과를 간 추리면 다음과 같다. 박근혜정부의 지방분권도 기본적으로는 이전정부와 연속성을 갖는 것이다. 현재까지 발굴된 지방분권 국정과제의 전반적인 내용도 이전정부에서 핵심적으 로 추진하던 다수의 과제들이 포함되어 있다. 물론 이전정부에서 제시하지 않았던 새로 운 과제들도 추가적으로 발굴 및 포함됨으로써 신규수요의 대응성도 구비하고 있다. 이 와 같은 지방분권 국정과제의 성공적 추진이야말로 지방분권의 수준을 한 단계 높이는 결과를 가져 올 것이다. 그러기 두 가지의 전략에 대한 충분한 고려가 필요하다. 하나는 이전정부와 달리 박근혜정부에서 제시한 지방주도 및 국가지원의 접근방법에 대한 구체적이고 체계적인 내용이 사전에 제시되어야 한다. 이전정부의 지방분권 정책이 성공적이지 못했다는 경험에 따르면, 박근혜정부의 새로운 접근방식은 과거의 오류를 개 선할 수 있는 효과를 기대할 수도 있으나, 중요한 것은 구체적 내용여부에 달려 있다는 점이다. 다른 하나는 이전정부의 시행착오가 반복되어서는 아니 된다는 것이다.
Personalising margins for bladder radiotherapy

Abstract This patient case study represents the introduction of adaptive radiotherapy (ART) at the Andrew Love Cancer Centre (ALCC) with non-uniform margins for invasive bladder cancer treatment. Invasive bladder cancer has historically had poor local control with radiotherapy treatment; however, with the introduction of cone-beam computer tomography (CBCT) and adaptive treatment, there is potential for improvements in disease control and reduced toxicities.
The Onset of Evolutionary Stalling and the Limit on the Power of Natural Selection to Improve a Cellular Module

11 Cells consist of molecular modules which perform vital biological functions. Modules are key 12 units of adaptive evolution because organismal fitness depends on their performance. Yet, our 13 understanding of adaptive evolution at the level of modules is limited. Theory predicts that in 14 rapidly evolving populations, such as those of many microbes, natural selection focuses on 15 improving one or a few modules at a time and its focus shifts to other modules as adaptation 16 continues. Such shifts have never been directly observed, their timescale is unknown and the 17 extent to which they limit the power of natural selection to improve any particular module is 18 unclear. Here, we empirically characterize how natural selection improves the translation 19 machinery (TM), one of the most essential cellular modules. To this end, we experimentally 20 evolved populations of Escherichia coli with genetically perturbed TMs for 1,000 generations. 21 Populations with different TMs embarked on statistically distinct adaptive trajectories. Yet, in all 22 genetic backgrounds, the focus of natural selection shifted away from the TM before its 23 performance was fully restored. Our results show that shifts in the focus of selection can occur 24 on time scales comparable to those of environmental fluctuations. Variability in selection 25 pressures can delay the resumption of adaptation in stalled modules, which would make it 26 difficult for evolution to fully optimize even essential modules. 27 . CC-BY-NC 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . http://dx.doi. org/10.1101/850644 doi: bioRxiv preprint first posted online Nov. 24, 2019;