Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor

Abstract Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG data set to date. Comprising 376 sequences, our data set allows for phylogenetic reconstructions of RG with unprecedented size and detail. These RG phylogenies are strikingly different from those of universal proteins inferred to be present in the LUCA, even when using the same set of species. Unlike such proteins, RG does not form monophyletic archaeal and bacterial clades, suggesting RG emergence after the formation of these domains, and/or significant horizontal gene transfer. Additionally, the branch lengths separating archaeal and bacterial groups are very short, inconsistent with the tempo of evolution from the time of the LUCA. Despite this, phylogenies limited to archaeal RG resolve most archaeal phyla, suggesting predominantly vertical evolution since the time of the last archaeal ancestor. In contrast, bacterial RG indicates emergence after the last bacterial ancestor followed by significant horizontal transfer. Taken together, these results suggest a nonhyperthermophilic LUCA and bacterial ancestor, with hyperthermophily emerging early in the evolution of the archaeal and bacterial domains.
Electromyography in Clinical Practice: Electrodiagnostic Aspects of Neuromuscular Disease

Electromyography in Clinical Practice-Michael Jeffrey Aminoff 1998 A concise and practical guide to the electrodiagnostic procedures in current use for the investigation of patients with neuromuscular disease. Covers basic and clinical aspects of these diseases and related electrodiagnostic techniques, with special sections focusing on nerves in the upper limbs, cranial nerves, and the central nervous system. Covers scope and limitations of EMG procedures Explains apparatus used for electrodiagnostic study Emphasizes both clinical applications of current techniques and their physiologic basis Discusses all the latest advances in this fast-growing field Offers precise guidelines for practical application of techniques in a clinical setting I have no hesitation in recommending the book to clinical neurophysiologists and to their clinical colleagues striving to assess the relevance of test results. Journal of Neurology, Neurosurgery and Psychiatry Tables and illustrations are very good and the general presentation is notably clear. This book is eminently suitable as an introduction to electromyography for neurologists and clinical neurophysiologists. Brain
Mediator function in plant metabolism revealed by large-scale biology.

Mediator is a multi-subunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent process include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8) and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
Growth factor and receptor malfunctions associated with human genetic deafness

A variety of different signaling pathways are necessary for development and maintenance of the human auditory system. Normal hearing allows for the detection of soft sounds within the frequency range of 20 to 20 000 Hz, but more importantly to perceive the human voice frequency band of 250 to 6000 Hz. Loss of hearing is common, and is a clinically heterogeneous disorder that can be caused by environmental factors such as exposure to loud noise, infections and ototoxic drugs. In addition, variants of hundreds of genes have been reported to disrupt processes required for hearing. Noncoding regulatory variants and variants of additional genes necessary for hearing remain to be discovered as many individuals with inherited deafness are without a genetic diagnosis, despite the advent of whole exome sequencing. Here, we discuss in detail some of these deafness‐causing variants of genes encoding a ligand or its receptor. Spotlighted in this review are three growth factor‐receptor‐pairs EDN3/EDNRB, HGF/MET and JAG/NOTCH, which individually are necessary for normal hearing. We also offer our perspective on unanswered questions, future challenges and potential opportunities for treatments emerging from molecular genetic and mechanistic studies of deafness due to these causes.
Rheumatoid Factors in Hepatitis B and C Infections: Connecting Viruses, Autoimmunity, and Cancer.

BACKGROUND Serum rheumatoid factors are autoantibodies of different isotypes directed against the Fc fraction of immunoglobulin G (IgG) and represent paradigmatic autoantibodies that have been largely used in clinical practice for decades. Traditionally IgG has been associated with rheumatoid arthritis and more recently included also in the classification criteria for Sjӧgren's syndrome. Researchers have established that rheumatoid factors are positive in a variety of infectious, autoimmune, and neoplastic disorders, thus requiring a comprehensive evaluation of seropositive patients. Of note, hepatitis B and C viruses represent a crossroad that includes the high rheumatoid factor seroprevalence and chronic inflammatory disease, as well as progression to non-Hodgkin's lymphomas. Chronic antigen stimulation is the likely common ground of these processes and rheumatoid factors may represent mere bystanders or drivers of pathology. Mixed cryoglobulinemia and lymphoproliferative disease are prime examples of the deleterious effects of rheumatoid factor-B cell activity, possibly associated with hepatitis B and C. More importantly, they show a clear association in a physiological host response to infection, chronic inflammation, and the slide toward autoimmunity and malignancy. The association between hepatitis B and C infections and the appearance of serum rheumatoid factors is further supported by prevalence data, which support a coexistence of these markers in a significant proportion of cases, with viral infections being frequent causes of rheumatoid factors in patients without a rheumatic condition. We provide a comprehensive overview of the known connections between hepatitis B and C infections and rheumatoid factors.
The characteristics and mechanism of co-administration of lovastatin solid dispersion with kaempferol to increase oral bioavailability

Abstract Lovastatin shows low bioavailability (lower than 5%) after oral administration because of the poor aqueous solubility and widely metabolized by CYP3A4. Lovastatin solid dispersion was designed to enhance the dissolution. The in vitro intestinal absorption study indicated an increase in the apparent permeability of different intestinal segments compared with crude lovastatin. In the range of 12.5–50 μg/ml, the absorption of both lovastatin and lovastatin solid dispersion were found to be a passive process in rat’s jejunum and ileum, but not endocytosis process. CYP3A4 inhibitor (ketoconazole) significantly increased the intestinal absorption of lovastatin and lovastatin solid dispersion. However, P-glycoprotein efflux inhibitor (verapamil) had little effect on them. The absolute bioavailability of lovastatin and lovastatin acid after oral administration of lovastatin solid dispersion were increased by about 2.01-fold and 1.40-fold than that of lovastatin suspension. The oral bioavailability of lovastatin and lovastatin acid after oral administration of lovastatin solid dispersion with 10 mg/kg kaempferol (CYP3A4 inhibitor) were increased about 3.79-fold and 2.51-fold than that of lovastatin suspension, and the absolute bioavailability of lovastatin was up to 33.0%. As a result, co-administration of lovastatin solid dispersion with kaempferol could be a promising delivery system to improve the oral bioavailability of lovastatin.
Fabrication of OSA starch/chitosan polysaccharide-based high internal phase emulsion via altering interfacial behaviors.

This paper attempted to construct high internal phase emulsion (HIPE) through altering interfacial behaviors using the electrostatic interaction between positive chitosan and negative octenyl succinic anhydride (OSA) starch. Partial polysaccharide complex of OSA starch/chitosan was used to stabilize HIPE, which was able to adsorb at oil droplets interface and prevent the coalescence of oil droplets. The wettability of OSA starch was enhanced with the addition of positively charged chitosan, leading to the formation of partial complexes. The impact of pH and concentration of chitosan on the droplet size, surface charge and interface behavior were investigated, and the formation of polysaccharide complex was further confirmed by the AFM. The presence of OSA starch/chitosan complex facilitated the formation of stable HIPE with gel-like structure, satisfactory centrifugal and oxidative stability. These results are useful to provide information for fabricating polysaccharide-based HIPE delivery systems, which may help to expand their application in food industry.
Auxin promotion of seedling growth via ARF5 is dependent on the brassinosteroid‐regulated transcription factors BES1 and BEH4

Seedlings must continually calibrate their growth in response to the environment. Auxin and brassinosteroids (BRs) are plant hormones that work together to control growth responses during photomorphogenesis. We used our previous analysis of promoter architecture in an auxin and BR target gene to guide our investigation into the broader molecular bases and biological relevance of transcriptional co-regulation by these hormones. We found that the auxin-regulated transcription factor AUXIN RESPONSIVE FACTOR 5 (ARF5) and the brassinosteroid-regulated transcription factor BRI1-EMS-SUPPRESOR 1/BRASSINOZOLERESISTANT 2 (BES1) co-regulated a subset of growth promoting genes via conserved bipartite cis-regulatory elements. Moreover, ARF5 binding to DNA could be enriched by increasing BES1 levels. The evolutionary loss of bipartite elements in promoters results in loss of hormone responsiveness. We also identified another member of the BES1/BZR1 family called BEH4 that acts partially redundantly with BES1 to regulate seedling growth. Double mutant analysis showed that BEH4 and not BZR1 were required alongside BES1 for normal auxin response during early seedling development. We propose that an ARF5-BES1/BEH4 transcriptional module acts to promote growth via modulation of a diverse set of growth-associated genes.
Fireworks and Seafood Boils: The Epidemiology of Burns in Louisiana.

Epidemiologic trends provide a means for targeting efforts in burn prevention. There have been but few regional-specific studies concerning burns in the southern United States. This study describes burn injury trends experienced by a single burn center in Louisiana. We also investigate the temporal relationships of several activities informally known for having a high risk for burn injury among local providers. Data were retrospectively extracted from the records of all patients treated for burn injuries at the regional burn center from 2012 to 2018 in both inpatient and outpatient settings. Demographical data and burn injury characteristics were noted. A total of 6,498 patients were included (1,593 inpatient, 4,905 outpatient). The most common burn etiologies were scald and flame, with flame being associated with more severe injuries. Overall incidence was disproportionally high in males and children less than 4 years of age. Total incidence was highest in Caucasians, though African Americans held the highest annual incidence rate specific to this population. The most common situation at the time of burn injury involved the consumption or preparation of food or beverages. Significant variation was observed in the rates of different injury situations throughout the year. Notably, burns related to seafood, heating, and firework activity occurred more often during crawfish season, colder months, and the months of January and July, respectively. In addition to establishing preliminary trends, these data may be useful in guiding the development of future evidence-based prevention efforts to target the most detrimental burn injuries in this population.
Transcriptome Analysis of Female and Male Conopomorpha sinensis (Lepidoptera: Gracilariidae) Adults With a Focus on Hormone and Reproduction

Abstract Conopomorpha sinensis Bradley is the dominant borer pest of litchi and longan in the Asian-pacific area. Reduction or interference of reproduction and mating of adult moths is one of the most used strategies to control C. sinensis. Insect reproduction is a critical biological process closely related to endocrine control. Conopomorpha sinensis genome and transcriptome information is limited, hampering both our understanding of the molecular mechanisms underlying hormone activity and reproduction and the development of control strategies for this borer pest. To explore the sex differences in gene expression profiles influencing these biological processes, de novo transcriptomes were assembled from female and male adult C. sinensis specimens. This analysis yielded 184,422 unigenes with an average length of 903 bp and 405,961 transcripts after sequencing and assembly. About 45.06, 22.41, 19.53, 34.05, 35.82, 36.42, and 19.85% of the unigenes had significant matches in seven public databases. Subsequently, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis revealed comprehensive information about the function of each gene and identified enriched categories and pathways that were associated with the 2,890 female-biased genes and 2,964 male-biased genes. In addition, we identified some important unigenes related to hormone activity and reproduction among the sex-differentially expressed genes (DEGs), including unigenes coding for ecdysone-induced protein 78C, juvenile hormone (JH)-regulated gene fatty acyl-CoA reductase, vitellogenin, etc. Our findings provide a more comprehensive portrait of the sex differences involved in the relationship of two important physiological features—hormone activity and reproduction in C. sinensis and members of the family Gracillariidae.
Characterization of the microbiome and bioluminescent symbionts across life stages of Ceratioid Anglerfishes of the Gulf of Mexico

ABSTRACT The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission electron microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas. 16S rDNA sequencing results from adult fishes corroborate the previously published identity of ceratioid bioluminescent symbionts and support the findings that these symbionts do not consistently exhibit host specificity at the host family level. Bioluminescent symbiont amplicon sequence variants were absent from larval ceratioid samples, but were found at all depths in the seawater, with a highest abundance found at mesopelagic depths. As adults spend the majority of their lives in the meso- and bathypelagic zones, the trend in symbiont abundance is consistent with their life history. These findings support the hypothesis that bioluminescent symbionts are not present throughout host development, and that ceratioids acquire their bioluminescent symbionts from the environment.
How do cancer-sniffing dogs sort biological samples? Exploring case-control samples with non-targeted LC-Orbitrap, GC-MS, and immunochemistry methods

Early identification of disease onset is regarded as an important factor for successful medical intervention. However, cancer and other long-term latency diseases are rare and may take years to manifest clinically. As such, there are no gold standards with which to immediately validate proposed preclinical screening methodologies. There is evidence that dogs can sort samples reproducibly into yes/no categories based on case-control training, but the basis of their decisions is unknown. Because dogs are sniffing air, the distinguishing chemicals must be either in the gas-phase or attached to aerosols and/or airborne particles. Recent biomonitoring research has shown how to extract and analyze semi- and non-volatile compounds from human breath in exhaled condensates and aerosols. Further research has shown that exhaled aerosols can be directly collected on standard hospital-style olefin polypropylene masks and that these masks can be used as a simple sampling scheme for canine screening. In this article, detailed liquid chromatography-high resolution mass spectrometry (LC-HR-MS) with Orbitrap instrumentation and gas chromatography-mass spectrometry (GC-MS) analyses were performed on two sets of masks sorted by consensus of a four-dog cohort as either cancer or control. Specifically, after sorting by the dogs, sample masks were cut into multiple sections and extracted for LC-MS and GC-MS non-targeted analyses. Extracts were also analyzed for human cytokines, confirming the presence of human aerosol content above levels in blank masks. In preliminary evaluations, 345 and 44 high quality chemical features were detected by LC-MS and GC-MS analyses, respectively. These features were used to develop provisional orthogonal projection to latent structures-discriminant analysis (OPLS-DA) models to determine if the samples classified as cancer (case) or non-cancer (control) by the dogs could be separated into the same groups using analytical instrumentation. While the OPLS-DA model for the LC-HR-MS data was able to separate the two groups with statistical significance, although weak explanatory power, the GC-MS model was not found to be significant. These results suggest that the dogs may rely on the less volatile compounds from breath aerosol that were analyzed by LC-HR-MS than the more volatile compounds observed by GC-MS to sort mask samples into groups. These results provide justification for more expansive studies in the future that aim to characterize specific chemical features, and the role(s) of these features in maintaining homeostatic biological processes.
Can acute suicidality be predicted by Instagram data? Results from qualitative and quantitative language analyses

Background Social media has become increasingly important for communication among young people. It is also often used to communicate suicidal ideation. Aims To investigate the link between acute suicidality and language use as well as activity on Instagram. Method A total of 52 participants, aged on average around 16 years, who had posted pictures of non-suicidal self-injury on Instagram, and reported a lifetime history of suicidal ideation, were interviewed using Instagram messenger. Of those participants, 45.5% reported suicidal ideation on the day of the interview (acute suicidal ideation). Qualitative text analysis (software ATLAS.ti 7) was used to investigate experiences with expressions of active suicidal thoughts on Instagram. Quantitative text analysis of language use in the interviews and directly on Instagram (in picture captions) was performed using the Linguistic Inquiry and Word Count software. Language markers in the interviews and in picture captions, as well as activity on Instagram were added to regression analyses, in order to investigate predictors for current suicidal ideation. Results Most participants (80%) had come across expressions of active suicidal thoughts on Instagram and 25% had expressed active suicidal thoughts themselves. Participants with acute suicidal ideation used significantly more negative emotion words (Cohen’s d = 0.66, 95% CI: 0.088–1.232) and words expressing overall affect (Cohen’s d = 0.57, 95% CI: 0.001–1.138) in interviews. However, activity and language use on Instagram did not predict acute suicidality. Conclusions While participants differed with regard to their use of language in interviews, differences in activity and language use on Instagram were not associated with acute suicidality. Other mechanisms of machine learning, like identifying picture content, might be more valuable.
Testing Mediators of Youth Intervention Outcomes Using Single‐Case Experimental Designs

Abstract The major aim of this manuscript is to bring together two important topics that have recently received much attention in child and adolescent research, albeit separately from each other: single‐case experimental designs and statistical mediation analysis. Single‐case experimental designs (SCEDs) are increasingly recognized as a valuable alternative for Randomized Controlled Trials (RCTs) to test intervention effects in youth populations. Statistical mediation analysis helps provide understanding about the most potent mechanisms of change underlying youth intervention outcomes. In this manuscript we: (i) describe the conceptual framework and outline desiderata for methods for mediation analysis in SCEDs; (ii) describe the main aspects of several data‐analytic techniques potentially useful to test mediation in SCEDs; (iii) apply these methods to a single‐case treatment data set from one clinically anxious client; and (iv) discuss pros and cons of these methods for testing mediation in SCEDs, and provide future directions.
Research Note: Role of the hippocampus in spatial memory in Japanese quail

The Japanese quail is a powerful model to characterize behavioral, physiological, and neurobiological processes in Galliformes. Behavioral tests have already been adapted for quail to assess memory systems, but despite the pivotal role of the hippocampus in this cognitive process, its involvement in spatial memory has not been demonstrated in this species. In this study, lesions were created in the hippocampus of Japanese quail, and both lesioned and control quail were tested for spatial and cue-based learning performances. These hippocampal lesions specifically impacted spatial learning performance, but spared learning performance when birds could solve the task using their cue-based memory. These findings, thus, highlight that the hippocampus plays a crucial role and is essential for spatial declarative memory. Future studies could aim to elucidate the cellular or molecular mechanisms involved in this form of memory.
Practice of Epidemiology Estimating the Intracluster Correlation Coefficient for the Clinical Sign “Trachomatous Inflammation—Follicular” in Population-Based Trachoma Prevalence Surveys: Results From a Meta-Regression Analysis of 261 Standardized Preintervention Surveys Carried Out in Ethiopia, Moza

Colin K. Macleod∗, Robin L. Bailey, Michael Dejene, Oumer Shafi, Biruck Kebede, Nebiyu Negussu, Caleb Mpyet, Nicholas Olobio, Joel Alada, Mariamo Abdala, Rebecca Willis, Richard Hayes, and Anthony W. Solomon ∗ Correspondence to Dr. Colin Macleod, Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, United Kingdom (e-mail: colin.macleod@lshtm.ac.uk).