Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcript-Level Analysis in Combination with Real-Time PCR Elucidates Heat Adaptation Mechanism of Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) Larvae

Abstract Tribolium castaneum (Herbst) ranks as one of the most prevalent insects in food processing and storage facilities worldwide. Heat treatment has been revisited to disinfest food processing and storage facilities due to increasingly strict regulation on chemicals. The effect of acclimation of T. castaneum larvae to sublethal high temperatures of 36 and 42°C for 10 h on their heat adaptation was investigated, and transcript-level analysis combinating with real-time PCR (RT–qPCR) was applied for elucidating the heat adaptation mechanism of T. castaneum larvae. Short-term sublethal high temperature acclimation could greatly enhance the thermal adaptability in T. castaneum larvae. In total, 575, 875, and 1017 differentially expressed genes (DEGs) were, respectively, determined in comparisons between the 28 and 36°C treatments, the 28 and 42°C treatments, and the 36 and 42°C treatments. Fifty-three and 96 genes were commonly up- and down-regulated in both the 36 and 42°C treatments relative to 28°C, respectively. The results of RT-qPCR analysis further confirmed the RNA-seq analysis. The current results are in favor of enhancing the insecticidal effectiveness of extreme high temperature treatment and elucidating the heat adaptation mechanism in T. castaneum larvae.
Reporting gaps between news media and scientific papers on outdoor air pollution-related health outcomes: A content analysis.

OBJECTIVES In China, news media are useful for educating the public about the health threats of air pollution. To explore the potential gaps between scientific findings and the public's understanding of them, the characteristics of news media articles and their corresponding scientific papers were analysed. METHODS We used 22 articles relating to the health outcomes of exposure to outdoor air pollution published on Baidu News over the past year. An assessment tool developed by Robinson et al was used to evaluate the quality scores of news articles. Pearson correlation coefficients were used to measure the relationship between news media reporting and the characteristics of scientific papers. Misleading reporting, interpretation, or extrapolation in headlines and text bodies of news articles were examined. RESULTS The quality scores of the news articles ranged from -4 to 8, with an overall median score of 3. Correlation results showed that the scientific papers citation in Twitter (r = .88, P < .001) and Facebook (r = .64, P < .01) were significantly and positively associated with their citations in news stories. Media misunderstanding of scientific findings was common: 15 news headlines were identified with at least one spin (misrepresentation of scientific results), and 12 news articles had seven types of spin in the body texts. CONCLUSION Little media attention has been paid to scientific findings by Chinese researchers. Therefore, researchers and science journalists in China should make a better effort to engage in accurate and informative public discourse on domestic research.
Health-related quality of life in systemic sclerosis before and after autologous haematopoietic stem cell transplant-a systematic review.

OBJECTIVES In severe rapidly progressive SSc, autologous haematopoietic stem cell transplantation (AHSCT) allows significant improvements in overall and event-free survival. We undertook this study to identify, appraise and synthesize the evidence on health-related quality of life (HRQoL) before and after AHSCT for SSc. METHODS We performed a systematic review of the literature, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, in PubMed and ScienceDirect from database inception to 1 February 2019. All articles with original HRQoL data were selected. RESULTS The search identified 1080 articles, of which 8 were selected: 3 unblinded randomized controlled trials [American Scleroderma Stem Cell versus Immune Suppression Trial (ASSIST), Autologous Stem Cell Transplantation International Scleroderma, Scleroderma: Cyclophosphamide or Transplantation), 3 uncontrolled phase I or II trials and 2 cohort studies. HRQoL data from 289 SSc patients treated with AHSCT and 125 treated with intravenous CYC as a comparator with median 1.25-4.5 years follow-up were included. HRQoL was evaluated with the HAQ Disability Index (HAQ-DI; 275 patients), the 36-item Short Form Health Survey (SF-36; 249 patients) and the European Quality of Life 5-Dimensions questionnaire (EQ-5D; 138 patients). The quality of the studies was moderate to low. AHSCT was associated with significant improvement in the HAQ-DI (P = 0.02-<0.001), SF-36 Physical Component Summary score (P = 0.02-<0.0001) and EQ-5D index-based utility score (P < 0.001). The SF-36 Mental Component Summary score improved in the ASSIST (n = 19) and one small retrospective cohort (n = 30 patients, P = 0.005) but did not improve significantly in 2 randomized controlled trials (n = 200 patients, P = 0.1-0.91). CONCLUSION AHSCT in severe SSc patients is associated with significant and durable improvement in physical HRQoL.
Development and Characterization of the Solvent-Assisted Active Loading Technology (SALT) for Liposomal Loading of Poorly Water-Soluble Compounds

A large proportion of pharmaceutical compounds exhibit poor water solubility, impacting their delivery. These compounds can be passively encapsulated in the lipid bilayer of liposomes to improve their water solubility, but the loading capacity and stability are poor, leading to burst drug leakage. The solvent-assisted active loading technology (SALT) was developed to promote active loading of poorly soluble drugs in the liposomal core to improve the encapsulation efficiency and formulation stability. By adding a small volume (~5 vol%) of a water miscible solvent to the liposomal loading mixture, we achieved complete, rapid loading of a range of poorly soluble compounds and attained a high drug-to-lipid ratio with stable drug retention. This led to improvements in the circulation half-life, tolerability, and efficacy profiles. In this mini-review, we summarize our results from three studies demonstrating that SALT is a robust and versatile platform to improve active loading of poorly water-soluble compounds. We have validated SALT as a tool for improving drug solubility, liposomal loading efficiency and retention, stability, palatability, and pharmacokinetics (PK), while retaining the ability of the compounds to exert pharmacological effects.
Environmental Toxicology and Chemistry

Environmental contaminants frequently occur as part of a chemical mixture, potentially resulting in competitive inhibition among multiple substrates metabolized by the same enzyme. Trout liver S9 fractions were used to evaluate the biotransformation of 3 polycyclic aromatic hydrocarbons (PAHs): phenanthrene, pyrene, and benzo[a]pyrene, tested as binary mixtures. Initial rates of biotransformation were determined using a substrate‐depletion approach. The resulting data were then fitted by simultaneous nonlinear regression to a competitive inhibition model. In each case, the PAH possessing the lower Michaelis‐Menten affinity constant (KM) competitively inhibited biotransformation of the other compound. Inhibition constants determined for the lower‐KM compound were generally close to previously determined KM values, consistent with the suggestion that phase I biotransformation of PAHs is largely catalyzed by one or a small number of cytochrome P450 enzymes. The use of a substrate‐depletion approach to perform enzyme‐inhibition studies imposes practical limitations on experimental design and complicates the interpretation of derived kinetic constants. Nevertheless, the resulting information may have utility for chemical hazard assessments as well as the design and interpretation of controlled laboratory studies. Depletion experiments informed by measured chemical concentrations in tissues may also provide a means of determining whether enzyme inhibition occurs under relevant environmental conditions. Environ Toxicol Chem 2019;38:2729–2739. Published 2019 Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work, and as such, is in the public domain in the United States of America.
Chronic hexavalent chromium exposure induces cancer stem cell-like property and tumorigenesis by increasing c-Myc expression.

Hexavalent chromium [Cr(VI)] is one of the most common environmental carcinogen causing lung cancer in humans; however, the mechanism of Cr(VI) carcinogenesis remains elusive. Cancer stem cells (CSCs) are considered as cancer initiating and maintaining cells. Ours and other recent studies showed that chronic Cr(VI) exposure induces CSC-like property representing an important mechanism of Cr(VI) carcinogenesis. However, how Cr(VI) exposure induces CSC-like property remains largely unknown. In this study, we found that stably knocking down the expression of c-Myc, a proto-oncogene and one of key stemness factors playing critical roles in cancer initiation and progression, in Cr(VI)-transformed human bronchial epithelial cells [BEAS-2B-Cr(VI)] significantly decreased their CSC-like property and tumorigenicity in mice. Moreover, stably knocking down c-Myc expression in parental non-transformed BEAS-2B cells significantly impaired the capability of chronic Cr(VI) exposure to induce CSC-like property and cell transformation. It was also found that stably overexpressing c-Myc alone in parental non-transformed BEAS-2B cells is capable of causing CSC-like property and cell transformation. Mechanistic studies showed that chronic Cr(VI) exposure increases c-Myc expression by down-regulating the level of microRNA-494 (miR-494). It was further determined that overexpressing miR-494 significantly reduces Cr(VI)-induced CSC-like property, cell transformation and tumorigenesis mainly through down-regulating c-Myc expression. Together, these findings indicate that chronic low dose Cr(VI) exposure induces CSC-like property and tumorigenesis by increasing c-Myc expression through down-regulating the level of miR-494, revealing an important role of the proto-oncogene c-Myc in Cr(VI) carcinogenesis.
Use of the aqueous biphasic system as an alternative for concentration of Ascaris lumbricoides eggs, with non‐toxic separation of faecal residues and fats

Human enteroparasites are considered a serious public health problem in underdeveloped countries located in world regions with tropical, subtropical and equatorial climates. These parasites are commonly diagnosed by the Parasitological Examination of Faeces (PEF), performed by conventional techniques and/or commercial kits that result in tests with low‐to‐moderate sensitivity, due to the use of destructive chemical solvents to parasite structures, and to present excess adipose substance and digestive residues in their microscopic slides. In order to improve the efficacy of these tests/examinations, this study aimed to investigate a new alternative for the PEF, with the use of Aqueous Biphasic System (ABS).
Nurses' Role in Implementing and Sustaining Acute Telemedicine: A Mixed-Methods, Pre-Post Design Using an Extended Technology Acceptance Model.

PURPOSE Technology-based systems like telemedicine are frequently being implemented into healthcare settings, impacting clinician practices. Little is known about factors influencing acute telemedicine uptake, if factors differ across time, or between nurses and non-nurses. DESIGN A mixed-methods, pre-post design with implementation of a new acute stroke telemedicine service. METHODS A survey based on an extended Technology Acceptance Model (TAM) was administered to clinicians involved in acute stroke care at 16 regional hospitals (2014-2017). Open-ended questions postimplementation (at 6 months) included strengths of the program and areas to improve. Subsequently, a secondary analysis of nurses' semistructured interviews at the first telemedicine site (2010-2011) was completed to provide greater explanatory detail. FINDINGS Surveys were completed by nurses (preimplementation n = 77, postimplementation n = 92) and non-nurses (pre n = 90, post n = 44). Preimplementation, perceived usefulness was the only significant predictor of intending to use telemedicine for nurses, while perceived ease of use and social influence were significant for non-nurses. Postimplementation, perceived usefulness was significant for both groups, as was facilitating conditions for nurses. Specific examples aligned to TAM categories from our detailed interviews (n = 11 nurses) included perceived usefulness (improved clinical support and patient care), perceived ease of use (technical, clinical aspects), facilitating conditions (setting, education, confidence), and social influence (working relationships). CONCLUSIONS Important factors for acute stroke telemedicine varied between nurses and non-nurses, and changed after implementation. The benefits of telemedicine should be emphasized to nurses. Preimplementation, more non-nurses wanted systems to be easy. Support in clinical, technical, and relationship aspects of telemedicine consultations is required. CLINICAL RELEVANCE Nurses are influential in implementing acute telemedicine, which is complex, with clinical and technical aspects entwined. Evidence-based implementation strategies must be tailored over time, and between nurses and non-nurses, to ensure initial uptake and ongoing use.
Proposed Lyme Disease Guidelines and Psychiatric Illnesses

The Infectious Disease Society of America, American Academy of Neurology, and American Academy of Rheumatology jointly proposed Lyme disease guidelines. Four areas most relevant to psychiatry were reviewed—the disclaimer, laboratory testing, and adult and pediatric psychiatric sections. The disclaimer and the manner in which these guidelines are implemented are insufficient to remove the authors and sponsoring organizations from liability for harm caused by these guidelines. The guidelines and supporting citations place improper credibility upon surveillance case definition rather than clinical diagnosis criteria. The guidelines fail to address the clear causal association between Lyme disease and psychiatric illnesses, suicide, violence, developmental disabilities and substance abuse despite significant supporting evidence. If these guidelines are published without very major revisions, and if the sponsoring medical societies attempt to enforce these guidelines as a standard of care, it will directly contribute to increasing a national and global epidemic of psychiatric illnesses, suicide, violence, substance abuse and developmental disabilities and the associated economic and non-economic societal burdens. The guideline flaws could be improved with a more appropriate disclaimer, an evidence-based rather than an evidence-biased approach, more accurate diagnostic criteria, and recognition of the direct and serious causal association between Lyme disease and psychiatric illnesses.
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice

Microglia have been implicated in amyloid beta-induced neuropathology, but their role in tau-induced neurodegeneration remains unclear. Mancuso et al. report that blockade of microglial proliferation by CSF1R inhibitor JNJ-40346527 modifies brain inflammation and ameliorates disease progression in P301S tauopathy mice. CSF1R inhibition may have therapeutic potential in tau-mediated neurodegenerative diseases.
The Forearm Musculature of the Gray Mouse Lemur (Microcebus murinus): An Ontogenetic Study

Although studies have sought to characterize variation in forearm muscular anatomy across the primate order, none have attempted to quantify ontogenetic changes in forearm myology within a single taxon. Herein, we present muscle architecture data for the forearm musculature (flexors and extensors of the wrist and digits) of Microcebus murinus, a small Lemuroid that has been the focus of several developmental studies. A quadratic curvilinear model described ontogenetic changes in muscle mass and fascicle length; however, fascicle lengths reached peak levels at an earlier age and showed a stronger decline during senescence. Conversely, physiological cross‐sectional area followed a more linear trend, increasing steadily throughout life. As previous studies into the functional role of the primate forelimb emphasize the importance of long muscle fascicles within arboreal taxa in order to maximize mobility and flexibility, the early attainment of peak fascicle lengths may consequently reflect the importance of agility within this mobile and highly arboreal species. Similarly, observed myological trends in forearm strength are supported by previous in vivo data on grip strength within M. murinus in which senescent individuals showed no decline in forearm force relative to prime age individuals. This trend is interpreted to reflect compensation for the previously reported decline in hind limb grip strength in the hind limb with age, such that older individuals are able to maintain arboreal stability. Interestingly, the ontogenetic trajectory of each architectural variable mirrored previous observations of the masticatory musculature in M. murinus, suggesting that ontogenetic trends are relatively conserved between anatomical regions. Anat Rec, 303:1354–1363, 2020. © 2019 American Association for Anatomy
Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution

The widely accepted view that evolution proceeds in small steps is based on two premises: i) negative selection acts strongly against large differences (Kimura 1983); and ii) positive selection favors small-step changes (Fisher 1930). The two premises are not biologically connected and should be evaluated separately. We now extend the approach of Tang et al. (2004) to codon evolution for the entire genome. Codon substitution rate is a function of the physico-chemical distance between amino acids (AAs), equated with the step size of evolution. This step size depends on a large number of physico-chemical properties as 46 of the 48 properties examined affect the rate. Between 9 pairs of closely-related species of plants, invertebrates and vertebrates, the evolutionary rate is indeed strongly and negatively correlated with the AA distance (ΔU, scaled to [0, 1]). While the analyses corroborate the published results that relied on partial genomes, there is an important difference: ΔU is strongly correlated with the evolutionary rate (R2 > 0.8) only when the genes are under predominant negative selection. Nevertheless, since most genes in most taxa are strongly constrained by negative selection, ΔU would appear to be a nearly-universal measure of codon evolution. In conclusion, the driving force of the small-step evolution at the codon level is negative selection. The unanswered question of whether positive selection may, or may not, follow the small-step rule will be addressed in a companion study (Chen, et al. 2019).
Unique Features of Sub-Cortical Circuits in A Macaque Model of Congenital Blindness

There is extensive modification of the functional organization of the brain in the congenital blind human, although there is little understanding of the structural underpinnings of these changes. The visual system of macaque has been extensively characterized both anatomically and functionally. We have taken advantage of this to examine the influence of the congenital blindness in macaque resulting from the removal of the retina during in utero development. Developmental anophthalmia in macaque effectively removes the normal influence of the thalamus on cortical development leading to an induced hybrid cortex (HC) combining features of primary visual and extrastriate cortex. Here we show that retrograde tracers injected in early visual areas including hybrid cortex reveals a drastic reduction of cortical projections of the reduced lateral geniculate nucleus. In addition, there is an important expansion of projections from the pulvinar complex to the hybrid cortex, compared to the controls. These findings show that the functional consequences of congenital blindness need to be considered in terms of both modifications of the inter-areal cortical network and the ascending visual pathways.
Molecular evolution of auxin-mediated root initiation in plants.

The root originated independently in euphyllophytes (ferns and seed plants) and lycophytes; however, the molecular evolutionary route of root initiation remains elusive. By analyses of the fern Ceratopteris richardii and seed plants, here we show that the molecular pathway involving auxin, intermediate-clade WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes, and WUSCHEL-clade WOX (WC-WOX) genes could be conserved in root initiation. We propose that the "auxin>IC-WOX>WC-WOX" module in root initiation might have arisen in the common ancestor of euphyllophytes during the second origin of roots, and that this module has further developed during the evolution of different root types in ferns and seed plants.
Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus

Heat stress (HS) is an important factor for the survival of the marine organism Apostichopus japonicus. Lysine acetylation is a pivotal post-translational modification that modulates diverse physiological processes including heat shock response (HSR). In this study, 4028 lysine acetylation sites in 1439 proteins were identified in A. japonicus by acetylproteome sequencing. A total of 13 motifs were characterized around the acetylated lysine sites. Gene Ontology analysis showed that major acetylated protein groups were involved in “oxidation–reduction process”, “ribosome”, and “protein binding” terms. Compared to the control group, the acetylation quantitation of 25 and 41 lysine sites changed after 6 and 48 h HS. Notably, lysine acetyltransferase CREB-binding protein (CBP) was identified to have differential acetylation quantitation at multiple lysine sites under HS. Various chaperones, such as caseinolytic peptidase B protein homolog (CLBP), T-complex protein 1 (TCP1), and cyclophilin A (CYP1), showed differential acetylation quantitation after 48 h HS. Additionally, many translation-associated proteins, such as ribosomal proteins, translation initiation factor (IF), and elongation factors (EFs), had differential acetylation quantitation under HS. These proteins represented specific interaction networks. Collectively, our results offer novel insight into the complex HSR in A. japonicus and provide a resource for further mechanistic studies examining the regulation of protein function by lysine acetylation.