Miracle-dz/UniFAR-FTUs huggingface dataset:
Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retroviruses

Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. We surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice: Mus caroli, M. cervicolor, and M. cookii. The presence of flanking repeats suggested it arose by LINE-mediated retroduplication within their most recent common ancestor. A high degree of natural variation was observed in both Fv1 and Fv7 and, on top of positive selection at certain residues, insertions and deletions were present that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes, with activities directed against gamma-, spuma-, and lentiviruses. It seems likely, at least in the case of M. caroli, that the observed gene duplication may expand the breadth of restriction beyond the capacity of Fv1 alone and that one or more such viruses have recently driven or continue to drive the evolution of the Fv1 and Fv7 genes.
Life and Death in Moving Fluids: Hydrodynamic Effects on Chemosensory‐Mediated Predation

Previous studies in taxonomically diverse marine animals have established the general existence, and importance, of the olfactory sense in a wide variety of behavioral processes. Evidence suggests that the sense of smell mediates predatory search in many marine animals. Past investigations have not, however, been designed to link either the degree of successful olfactory-mediated search or guidance mechanisms with the hydraulic environment in which predatory activities naturally take place. In an effort to examine the interaction between hydrodynamics and chemoreception, we investigated predatory success and search strategies of blue crabs foraging in controlled hydrodynamic environments generated in a flume. Hydrodynamics were characterized by quantifying boundary layer shear velocity (u*) and roughness Reynolds number (Re.), two measures that describe the structure of boundary layer flows. Flow properties affected the ability of crabs to orient to odor plumes emanating from actively pumping infaunal bivalves (Mercenaria mercenaria). High flow speed or large sediment particle size increased boundary layer turbulence, thereby decreasing the success of crab chemo-orientation ability. In addition, high flow speed also lessened the probability that crabs contacted odor plumes. Thus, habitats with high flows can provide hydrodynamic refuges from olfactory-mediated predation. Because search ability is contingent on the magnitude of boundary layer turbulence, olfactory-mediated predation may also be ineffective in slow flows, if bottom roughness elements can generate sufficient turbulence. Further, search ability in blue crabs is extremely sensitive to small changes in benthic boundary layer structure. The presence of a thick viscous sublayer, dominated by quasilaminar flow, seems especially critical for successful location of an odor source by crabs. Benthic estuarine crustaceans inhabit an environment where flows are transitional between smooth- and rough-turbulent conditions. Accordingly, chemosensory systems appear geared primarily to extracting information from hydraulically smooth flows. These results indicate that mechanisms governing the physical transport of odor signals can have profound influences, not only on the development of sensory and behavioral mechanisms, but also on biotic interactions such as predation, which, in turn, can mediate community structure.
Recent insights into myeloma bone disease

Multiple myeloma, a clonal neoplasm of plasma cells, is the second most common adult hematological malignancy and the most common cancer with the skeleton as its primary site. It has a worldwide prevalence of about 145,000 cases, affects 70,000 people in the United States, accrues 15,000 new cases yearly, and accounts for 1% to 2% of cancer-related deaths (1). The average life span after diagnosis is less than three years, and this has not changed significantly over the past three decades. The beneficial effects of conventional therapeutic regimens on myeloma tumor burden are modest, and relapse is invariable. Although newer treatment modalities, like stem cell transplantation, have the potential to increase life span modestly, they do not in general avert relapse or cure the disease. Myeloma thus remains a uniformly fatal cancer, and novel and effective therapies are badly needed.
The cost of sexual reproduction in ragwort (Senecio jacobaea L.).

Probability of overwinter survival is inversely related to the allocation of resources to sexual reproduction in thepreceding summer. There is a marked similarity between the 2 study sites in the relationship between numbers of flowerheads and rootstock volume. The effect of herbivory on overwinter survival of plants varies with site and timing of feeding. Different herbivores may either exacerbate the effect of sexual reproduction on survival (eg through root feeding), reduce the effect (eg through early consumption of flowers) or have no influence on the effect of sexual reproduction on survival (eg by consumption of flowers later in the season). -from Authors
Adverse Drug Reactions in the Emergency Department: Is There a Role for Pharmacogenomic Profiles at Risk?—Results from the ADRED Study

Individual differences in required drug dosages exist based on the pharmacogenomic (PGx) profiles. This study aimed to assess associations between PGx profiles and adverse drug reactions (ADR) that lead to admissions to the emergency department (ED). ADR cases of the prospective multi-center observational trial in EDs (ADRED study) were analyzed (n = 776) together with the relevant PGx phenotypes of the enzymes CYP2D6, CYP2C19, CYP2C9, and VKORC1. Overall, the allele frequency distribution in this cohort did not differ from the population frequencies. We compared the frequencies of phenotypes in the subgroups with the drugs suspected of certain ADR, in the remaining cases. The frequency distribution of CYP2C19 differed for the ADR bleeding cases suspected of clopidogrel (p = 0.020). In a logistic regression analysis, higher CYP2C19 activity (OR (95% CI): 4.97 (1.73−14.27)), together with age (1.05 (1.02−1.08)), showed an impact on the clopidogrel-suspecting ADRs, when adjusting for the clinical parameters. There was a trend for an association of phenprocoumon-risk profiles (low VKORC1 or CYP2C9 activity) with phenprocoumon-suspecting ADRs (p = 0.052). The PGx impact on serious ADRs might be highest in drugs that cannot be easily monitored or those that do not provoke mild ADR symptoms very quickly. Therefore, patients that require the intake of those drugs with PGx variability such as clopidogrel, might benefit from PGx testing.
Mechanisms and evidence of vertical transmission of infections in pregnancy including SARS‐CoV‐2s

There remain unanswered questions concerning mother‐to‐child‐transmission of SARS‐CoV‐2. Despite reports of neonatal COVID‐19, SARS‐CoV‐2 has not been consistently isolated in perinatal samples, thus definitive proof of transplacental infection is still lacking. To address these questions, we assessed investigative tools used to confirm maternal‐fetal infection and known protective mechanisms of the placental barrier that prevent transplacental pathogen migration. Forty studies of COVID‐19 pregnancies reviewed suggest a lack of consensus on diagnostic strategy for congenital infection. Although real‐time polymerase chain reaction of neonatal swabs was universally performed, a wide range of clinical samples was screened including vaginal secretions (22.5%), amniotic fluid (35%), breast milk (22.5%) and umbilical cord blood. Neonatal COVID‐19 was reported in eight studies, two of which were based on the detection of SARS‐CoV‐2 IgM in neonatal blood. Histological examination demonstrated sparse viral particles, vascular malperfusion and inflammation in the placenta from pregnant women with COVID‐19. The paucity of placental co‐expression of ACE‐2 and TMPRSS2, two receptors involved in cytoplasmic entry of SARS‐CoV‐2, may explain its relative insensitivity to transplacental infection. Viral interactions may utilise membrane receptors other than ACE‐2 thus, tissue susceptibility may be broader than currently known. Further spatial‐temporal studies are needed to determine the true potential for transplacental migration.
Modeling thinning effects on ring width distribution in loblolly pine (Pinus taeda)

Measurements were made on loblolly pine (Pinus taeda L.) from permanent sample plots to study the effects of thinning on ring width distribution and to develop a ring width prediction model. Thinning significantly increased ring width over most of the tree bole, and its effects tended to persist over the 12 years since thinning. Significant regional variation in average ring width was evident, with average ring width tending to decrease from the Highlands, to the Coastal Plain, to the Piedmont. A ring width prediction model that accounts for position in tree, tree size, stand, and site factors as well as thinning effects was developed. While ring width showed considerable variation within trees and among trees, the model predicted a substantial portion of the variation in ring width. The model can be used to obtain reasonably good volume estimates in individual growth rings, thus enabling the direct evaluation of the effects of silvicultural treatments on volume production. The data used in this study consisted of correlated observations; hence, direct covariance modeling was used to address biases in the standard error of estimates and hypothesis tests.
Interprofessional rounding design features and associations with collaboration and team effectiveness

ABSTRACT Multiple models of interprofessional rounding (IPR) exist. However, researchers find mixed effects for the impact of IPR, pointing to the possibility that variations in design may influence the effectiveness of the practice. We explored whether IPR design variations (location, use of script, and role of the leader) are associated with team collaboration (partnership and cooperation) and team effectiveness as perceived by practitioners and patients (i.e., patient inclusion). A cross-sectional, survey-based method design was used targeting practitioners on 15 different hospital units at two academic health centers. Routinely collected Hospital Consumer Assessment of Healthcare Practitioners and Systems scores were used to capture patients’ perceptions. Statistical methods included multilevel modeling with moderation analysis. There were several significant relationships among design, team collaboration, and team effectiveness. For the design, role of the leader and use of a script had a significant positive association with cooperation. Practitioners’ perceptions of team effectiveness were associated with use of script, and cooperation moderated the relationships between practitioners’ perceptions of team effectiveness and location, as well as the role of the leader. There was a significant inverse relationship between cooperation and patient inclusion. Results can inform organizations that are exploring, implementing, or improving IPR as well as considering alternative ways to evaluate their practices.
Evaluation of usefulness in surfactant protein D as a predictor of mortality in myositis-associated interstitial lung disease

Objective Surfactant protein D (SP-D) is considered a serum biomarker of various forms of interstitial lung disease (ILD). In this study, we examined the utility of SP-D as a predictive biomarker for mortality in patients with ILD associated with polymyositis/dermatomyositis (PM/DM) using large-scale multicentre cohort data. Methods We enrolled 381 patients with incident PM/DM-associated ILD in a multicentre retrospective cohort based on the availability of serum SP-D at the baseline. Demographic and clinical characteristics as well as the presence of autoantibodies to melanoma differentiation-associated gene 5 (MDA5) and aminoacyl tRNA synthetase were measured at the time of diagnosis, and follow-up survival data were collected prospectively. Results Seventy-eight patients died during the median observation period of 18 months, and the majority of patients died of ILD. The SP-D levels at baseline were significantly lower (P = 0.02) in a non-survivor subset than in a survivor subset among the entire enrolled patients. However, the SP-D levels were higher in the non-survivor subset than in the survivor subset based on the stratification by anti-MDA5-positive, anti-ARS-positive and, double-negativity, although there was an only statistically significant difference (P = 0.01) in the double-negative group. Surprisingly, the SP-D levels were within the upper limit of normal, 110 ng/mL, in 54 (87%) of 62 anti-MDA5-positive patients who died. In the double-negative group, the mortality rates were significantly higher (P = 0.002) in a subset with SP-D ≥127.6 ng/mL, the cut-off value for mortality calculated by the receiver operating characteristic curve, than the other subset. All of patients with SP-D <127.6 ng/mL survived. Conclusion Serum SP-D levels behave differently among patients with stratified by anti-MDA5 antibody, anti-ARS antibody and both negativity in PM/DM-associated ILD. Its use in clinical practice should be applied with caution on the basis of the presence or absence of anti-MDA5 antibody or anti-ARS antibody.
Estimating the Mean Leaf Inclination Angle of Wheat Canopies Using Reflected Polarized Light

Abstract In this study, we extended previous work linking the polarization of reflected light from crop canopies with characteristics of the canopy structure, such as the leaf inclination angle. We obtained reflectance and polarized reflectance in 8 spectral bands from the canopies of two varieties of wheat, planted in plots fertilized with a basal dressing and topdressed at the jointing and booting stages. The optical measurements were carried out on 3 clear-sky days when the plants were at the stem-elongation, heading and ripening stages, respectively. On each measurement date, we assessed the leaf orientation geometry of the plants using a Plant Canopy Analyzer (LAI-2000), measured the leaf greenness (an indicator of leaf chlorophyll content) using a handheld SPAD-502 (SPAD) optical sensor, and also measured plant height. Both polarization and leaf greenness observations at the heading stage were able to distinguish the canopies that had received topdressing from those without topdressing. However, no significant correlation was observed between the polarization in the blue, green and red bands and the SPAD (r = 0.425ᵻ0.456, n = 12 observations, p < 0.05). On the other hand, the mean leaf inclination angle (= mean tip angle: MTA) measured by the LAI-2000 was inversely correlated with the polarization in the 3 visible bands (r = −0.85ᵻ−0.88, n = 12, p < 0.001). Adjusting the view zenith angle according to the solar position at the time of measurement improved the accuracy. We tested a linear regression model to predict the MTA of the two wheat varieties based on polarized reflectance in the red band centered at 660 nm (r 2 = 0.73, n = 12, p < 0.001). Validation of this model obtained in the subsequent cropping season confirmed that polarization measurements were potentially useful for estimating the MTA of wheat stands in which the panicles were located below the topmost leaf layer of the canopy.
Many-body effects and optical properties of single and double layer α-T3 lattices

An extensive analytical and numerical investigation has been carried out to examine the role played by many-body effects on various α-T3 materials under an off-resonance optical dressing field. Additionally, we explore its dependence on the hopping parameter α as well as the electron–light coupling strength λ0. The obtained dressed states due to mutual interaction between Dirac electrons and incident light are shown to demonstrate rather different electronic and optical properties in comparison with those in the absence of incident light. Specifically, various collective transport and optical properties of these electron dressed states are discussed in detail and compared for both single- and double layer α-T3 lattices. All of these novel properties are due to the presence of a middle flat band and the interband transitions between it and an upper conduction band. Also, coupled plasmon dispersions for interacting double layer α-T3 lattices are calculated, revealing a lower acoustic-like plasmon branch with tunable group velocity determined by both the layer separation and Fermi energy of each layer. Finally, a many-body theory is presented within the random-phase approximation for calculating the optical absorbance of doped multi-layered α-T3 lattices in a linearly-polarized light field. We anticipate that the discoveries reported here could impact the design of the next-generation nano-optical and nano-plasmonic devices.
Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor

Abstract Fungal mycelia can eliminate almost all cocultured cyanobacterial cells within a short time. However, molecular mechanisms of algicidal fungi are poorly understood. In this study, a time‐course transcriptomic analysis of algicidal fungus Bjerkandera adusta T1 was applied to investigate gene expression and regulation. A total of 132, 300, 422, and 823 differentially expressed genes (DEGs) were identified at 6, 12, 24, and 48 hr, respectively. Most DEGs exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Many decomposition genes encoding endopeptidases were induced a little later in B. adusta T1 when compared with previously investigated algicidal fungus Trametes versicolor F21a. Besides, the accumulated expression of Polysaccharide lyases8 (PL8) gene with peptidoglycan and alginate decomposition abilities was greatly delayed in B. adusta T1 relative to T. versicolor F21a. It was implied that endopeptidases and enzymes of PL8 might be responsible for the strong algicidal ability of B. adusta T1 as well as T. versicolor F21a.
Outcomes in oncogenic-addicted advanced NSCLC patients with actionable mutations identified by liquid biopsy genomic profiling using a tagged amplicon-based NGS assay

Circulating tumor DNA (ctDNA)-based molecular profiling is rapidly gaining traction in clinical practice of advanced cancer patients with multi-gene next-generation sequencing (NGS) panels. However, clinical outcomes remain poorly described and deserve further validation with personalized treatment of patients with genomic alterations detected in plasma ctDNA. Here, we describe the outcomes, disease control rate (DCR) at 3 months and progression-free survival (PFS) in oncogenic-addicted advanced NSCLC patients with actionable alterations identified in plasma by ctDNA liquid biopsy assay, InVisionFirst®-Lung. A pooled retrospective analysis was completed of 81 advanced NSCLC patients with all classes of alterations predicting response to current FDA approved drugs: sensitizing common EGFR mutations (78%, n = 63) with T790M (73%, 46/63), ALK / ROS1 gene fusions (17%, n = 14) and BRAF V600E mutations (5%, n = 4). Actionable driver alterations detected in liquid biopsy were confirmed by prior tissue genomic profiling in all patients, and all patients received personalized treatment. Of 82 patients treated with matched targeted therapies, 10% were at first-line, 41% at second-line, and 49% beyond second-line. Acquired T790M at TKI relapse was detected in 73% (46/63) of patients, and all prospective patients (34/46) initiated osimertinib treatment based on ctDNA results. The 3-month DCR was 86% in 81 evaluable patients. The median PFS was of 14.8 months (12.1–22.9m). Baseline ctDNA allelic fraction of genomic driver did not correlate with the response rate of personalized treatment (p = 0.29). ctDNA molecular profiling is an accurate and reliable tool for the detection of clinically relevant molecular alterations in advanced NSCLC patients. Clinical outcomes with targeted therapies endorse the use of liquid biopsy by amplicon-based NGS ctDNA analysis in first line and relapse testing for advanced NSCLC patients.
Functioning Free Muscle Transfer for Brachial Plexus Injury: A Systematic Review and Pooled Analysis Comparing Functional Outcomes of Intercostal Nerve and Spinal Accessory Nerve Grafts

Abstract Background The aim of this study was to compare postoperative elbow flexion outcomes in patients receiving functioning free muscle transplantation (FFMT) innervated by either intercostal nerve (ICN) or spinal accessory nerve (SAN) grafts. Methods A comprehensive systematic review on FFMT for brachial plexus reconstruction was conducted utilizing Medline/PubMed database. Analysis was designed to compare functional outcomes between (1) nerve graft type (ICN vs. SAN) and (2) different free muscle graft types to biceps tendon (gracilis vs. rectus femoris vs. latissimus dorsi). Results A total of 312 FFMTs innervated by ICNs (169) or the SAN (143) are featured in 10 case series. The mean patient age was 28 years. Patients had a mean injury to surgery time of 31.5 months and an average follow-up time of 39.1 months with 18 patients lost to follow-up. Muscles utilized included the gracilis (275), rectus femoris (28), and latissimus dorsi (8). After excluding those lost to follow-up or failures due to vascular compromise, the mean success rates of FFMTs innervated by ICNs and SAN were 64.1 and 65.4%, respectively. Conclusion This analysis did not identify any difference in outcomes between FFMTs via ICN grafts and those innervated by SAN grafts in restoring elbow flexion in traumatic brachial plexus injury patients.
Biogeographic origin and phylogenetic relationships of Mepraia (Hemiptera, Reduviidae) on islands of northern Chile

Chagas disease is one of the main zoonoses mediated by vectors in America. The etiological agent is the protozoan Trypanosoma cruzi, transmitted mainly by hematophagous insects of the subfamily Triatominae. Mepraia species are triatomines endemic to Chile that play an important role in T. cruzi transmission in the wild cycle and are potential vectors for humans. In addition to the continental distribution, populations of Mepraia genus have been reported inhabiting islands of northern Chile. The presence of individuals of Mepraia in insular areas might be explained through passive dispersion by marine birds or by vicariance of an ancestral widespread population. To clarify the biogeographic origin and phylogenetic relationships of island individuals of Mepraia, mitochondrial COI and cyt b genes were sequenced in individuals from island and continental areas. Gene sequences were used to estimate phylogenetic relationships, divergence dates and migration rates between insular and continental populations. The dates of divergence estimates are congruent with sea level and tectonic changes that originated the islands during Pleistocene. Migration rates suggest symmetric historical island-continent gene flow. We suggest that the origin of island triatomines can be explained by both vicariance and dispersion. Phylogenetic relationships show that individuals from Santa María Island and the continent clustered in a clade different from those previously reported, indicating a new lineage of Mepraia genus. This study will contribute to understand the origin of the T. cruzi infection in coastal islands of northern Chile.