Miracle-dz/UniFAR-FTUs huggingface dataset:
Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum

It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form of Structural Variants (SVs). To better understand how SVs arise and their significance to the California NA1 population, we studied the evolutionary histories of SVs and the forest conditions associated with their emergence. Ancestral state reconstruction suggests that SVs arose by somatic mutations among multiple independent lineages, rather than by recombination. We asked if this unusual phenomenon of parallel evolution between isolated populations is transmitted to extant lineages and found that SVs persist longer in a population if their genetic background had a lower mutation load. Genetic parallelism was also found in geographically distant demes where forest conditions such as host density, solar radiation, and temperature, were similar. Parallel SVs overlap with genes involved in pathogenicity such as RXLRs and have the potential to change the course of an epidemic. By combining genomics and environmental data, we identified an unexpected pattern of repeated evolution in an asexual population and identified environmental factors potentially driving this phenomenon.
Coronary Access and Percutaneous Coronary Intervention Up to 3 Years After Transcatheter Aortic Valve Implantation With a Balloon-Expandable Valve

Background: Coronary artery disease and aortic stenosis often coexist. Transcatheter aortic valve implantation (TAVI) has emerged as a valid therapeutic option for younger, lower-risk patients who may eventually require coronary artery disease treatment. Thus, post-TAVI coronary access (CA) and percutaneous coronary intervention are expected to increase. The purpose of this study was to retrospectively evaluate patients who were enrolled in the SOURCE 3 (SAPIEN 3 Aortic Bioprosthesis European Outcome) European registry for treatment with the balloon-expandable SAPIEN 3 transcatheter heart valve and underwent CA with or without percutaneous coronary intervention after TAVI. Methods: Baseline characteristics and clinical outcomes of patients with or without CA up to 3 years after TAVI were compared. A Kaplan-Meier estimate with a univariate model determined the impact of CA on cardiac mortality. Results: Of 1936 TAVI patients (mean age 81.6 years, 52% male), 68 (3.5%) had CA within 3 years (mean 441±332 days) after TAVI. At baseline, the logistic EuroSCORE was similar (20.2% versus 18.3%, P=0.2, CA and non-CA groups, respectively). Higher rates of coronary artery disease (76.5% versus 50.6%, P<0.001), myocardial infarction (20.6% versus 11.5%, P=0.03) and previous coronary artery bypass graft (22.1% versus 11.0%, P=0.01) were present in the CA group. In 100% of patients, CA was successfully achieved. The clinical success of percutaneous coronary intervention was 97.9%. Cardiovascular mortality was numerically higher in patients with CA than in those without CA. Conclusions: In the large SOURCE 3 European registry, CA was needed at 3-year follow-up after TAVI with a balloon-expandable valve in 3.5% of patients and was successful in all patients. The clinical success of percutaneous coronary intervention was 97.9%. Registration: URL: https://www.clinicaltrials. gov. Unique identifier: NCT02698956.
Guidelines for the Capture, Handling, and Care of Mammals as Approved by the American Society of Mammalogists

INTRODUCTION _ . _ 1416 Background and history. 1416 Field work in mammalogy . 1417 Why mammalogists collect specimens . 1418 What is an adequate sample? 1418 Sampling in threatened habitats . 1418
Development of arginine-synthesizing enzymes in mouse intestine

The urea biosynthetic pathway functions in mammalian liver to convert excess ammonia to urea and to maintain the concentration of ammonia in blood at nontoxic levels. This action is accomplished by enzymatic adaptation to quantitative changes in dietary protein. The first two enzymes of the pathway are found in the intestine of the adult mouse, but they do not adapt to dietary change. The enzymes in the intestine produce citrulline, which is carried by the bloodstream to the kidney, where it is converted by the next two enzymes of the pathway to arginine. This mechanism serves as the major source of circulating arginine. We have demonstrated that, at birth, the arginine-synthesizing enzymes in the kidney of the C57Bl/6 mouse are minimally developed, whereas in the intestine activity of carbamoyl-phosphate synthase is elevated and argininosuccinate synthase and lyase, usually present only in trace quantities in the adult intestine, are markedly increased in the newborn. The arginine formed cannot be converted to urea, since arginase does not appear in intestinal cells of the mouse until the age of 15 days. Except for liver, intestine has the most rapid protein turnover of any normal tissue. Our study indicates that, at a time when no other endogenous source of arginine for protein synthesis is available, the intestine of the newborn C57Bl mouse is capable of synthesizing arginine from either citrulline or NH3 and CO2.
Attenuated Visual Function in Patients with Major Depressive Disorder

Background: We sought to investigate visual function, primarily, and structural changes in retinal ganglion cells, secondarily, in patients with major depressive disorder. Methods: A total of 50 normal participants and 49 patients with major depressive disorder were included in this cross-sectional study. The participants underwent 24–2 standard automated perimetry and spectral-domain optical coherence tomography. Results: The pattern standard deviation (PSD) in the visual field test was higher in the major depressive disorder patients than in the normal control subjects (p = 0.017). The patients with major depressive disorder showed reduced minimum ganglion cell–inner plexiform layer (GCIPL) thickness relative to the normal control participants (p = 0.015). The average score on the Hamilton Depression Rating scale showed a significant correlation with the PSD, minimum GCIPL thickness, and inferior GCIPL thickness (r = 0.265, p = 0.009; r = −0.239, p = 0.017; and r = −0.204, p = 0.043, respectively). The multivariate analysis of factors associated with PSD showed old age and a high Hamilton Depression Rating score to be relevant (p = 0.002 and 0.028, respectively). Conclusions: Visual function was decreased and the GCIPL thickness was reduced in major depressive disorder patients. The retinal neurodegenerative process in depression might be considered in patients with depression.
HEPATIC UREA SYNTHESIS AND SITE AND RATE OF UREA REMOVAL FROM BLOOD OF BEEF STEERS FED ALFALFA HAY OR A HIGH CONCENTRATE DIET

Five Hereford × Angus steers, 240 ± 6 kg liveweight with chronic indwelling catheters in various sites in the splanchnic bed were used to evaluate effects of dietary energy source and nitrogen (N) level on urea synthesis and site and rate of urea removal from blood. Alfalfa hay (162 g N d−1) or a high concentrate diet (95 g N d−1) were fed at similar metabolizable energy intake (54.8 MJ d−1). Compared with the alfalfa, the high concentrate, low N diet decreased (P 0.10) by diet. A greater (.
Investigation of Termite Attack on Cultural Heritage Buildings: A Case Study in Aceh Province, Indonesia

Surveys of the conditions of termite attack were conducted in two regencies, Pidie and Greater Aceh, Aceh Province, Indonesia (40 houses in each location). Interviews were also conducted with home owners to collect data on the building history; culture, such as daily life in the house; the frequency and intensity of termite attacks; and traditional knowledge for avoiding and/or suppressing termite attacks. We found that 51% of traditional houses were infested by two termite species: Coptotermes gestroi and Nasutitermes matangensis. The lower parts of traditional houses were frequently attacked and severely damaged by termites. Previous land use and the ages of the traditional houses affected the intensity of the termite attacks. Several measures for avoiding and/or suppressing termite attacks on cultural heritage buildings are also proposed.
EPIBIONT PRESERVATIONAL AND OBSERVATIONAL BIAS IN FOSSIL MARINE DECAPODS

Abstract Epibionts on both living and fossil decapod crustaceans may serve as valuable proxies for paleoecological factors such as behavior and environment. Prevalence of epibionts, as observed primarily on the carapaces of fossil brachyurous decapod crustaceans, appears to be less than observed on living crabs, based upon observations in the literature, and from the study of a limited preserved biological and fossil collection. Among these factors, the three most important are that many extant epibionts do not possess skeletal structures and, therefore, are unlikely to be preserved; the epicuticle upon which epibionts attach to living brachyurans is lightly calcified and tends to be lost readily as a result of taphonomic processes; and the most common mode of preservation of fossil brachyurans is in concretions which tend to break open and leave a layer of cuticle on the counterpart, thus obscuring the potential surface of attachment of epibionts. Other factors such as the life habits of the crab, whether burrowing, burying, or remaining above the substrate; lifestyle, whether benthic or pelagic; and duration of the intermolt phase of the organism also play important roles in potential prevalence of epibionts. Careful preparation of part and counterpart remains of brachyurans as well as reference to the occurrence of epibionts in systematic studies will enhance knowledge of the host and epibiont.
Effects of a new recombinant phytase on performance and mineral utilization of laying ducks fed phosphorus-deficient diets

SUMMARY An experiment was conducted to evaluate the effects of a new phytase supplementation in Jinding laying ducks fed different concentrations of non-phytate P (NPP) on production performance, mineral retention, and bone and plasma minerals. A 14-wk experiment was conducted using 200-d-old female laying ducks. A total of 1,000 laying ducks were randomly allocated to 5 treatments and fed 5 diets: a control diet that contained an adequate concentration of NPP (0.45%) and 4 diets that were deficient in NPP (0.38, 0.32, 0.25, and 0.18%, respectively) but supplemented with phytase at 500 U/kg. Decreasing the NPP content from 0.45 to 0.18% in the diets with phytase supplementation had no detrimental effects on performance. However, Cu and Zn retention was significantly lower (P < 0.05) for laying ducks consuming the 0.18% NPP diet with phytase supplementation. Likewise, laying ducks fed the 0.18% NPP diet had a significant reduction in bone ash, Ca, P, and Cu contents, and in serum P and Cu (P < 0.05). Furthermore, the decrease in NPP content in the diet with phytase supplementation significantly increased (P < 0.05) P retention. Therefore, with the supplementation of this novel phytase at 500 U, it is possible to reduce dietary concentrations of NPP to 0.25% and maintain the normal performance of laying ducks.
Lipid content and fatty acid composition of target tissues in wild Perca fluviatilis females in relation to hepatic status and gonad maturation

Variation in liver ultra-structure and composition in relation to energy mobilization was investigated in female perch Perca fluviatilis from the Meuse River between August 2001 and June 2002. In April, just before spawning, the lipo-somatic index (I F ) was 0.3%, the gonado-somatic index (I G ) was 28% and the total lipid content of the liver was 2.53%. The average areas of lipid droplets and mitochondria were 0.05 and 0.06 μm 2 , respectively. Glycogen supply reached 7.9% of the total area of the hepatocyte. During the sexual resting period, females accumulated energy in perivisceral fat and in the liver to reach 1.6% IF and 4.85% of liver lipid content in August with lipid droplets average size of 0.09 μm 2 and glycogen average area of 15%. Liver cells contained a weakly developed rough endoplasmic reticulum (RER) and a great number of small mitochondria (average size 0.02 μm 2 ). The I G was 0.6% at this time. During the whole annual cycle, the average lipid content of female liver never exceeded 3.9±1.9%. The concentration of docosahexaenoic (DHA), linolenic and linoleic acids increased in mature gonads while linolenic and linoleic acids decreased in the liver during the same period. Fatty acid composition of muscles of perch was characterized by a high content of DHA.
Potential use of triticale in diets for rainbow trout: effects of dietary levels and incidence of cooking

It is recognized that an increase in digestible energy (DE) can improve the growth performance and protein retention efficiency in rainbow trout. Growth and digestibility trials were conducted to evaluate possible incorporation of triticale (Clercal, a soft wheat x rye hybrid, hexaploid variety) as a potential source of DE for rainbow trout. Four diets were formulated with graded levels of native triticale (0-30% of dry matter) and 2 others with pre-cooked triticale at 20 and 30% of DM. All diets were isoproteic (crude protein: 43% DM) and isoenergetic (gross energy: 20 kJ/g DM). Digestibility of dry matter, starch and energy was affected by both level and nature of triticale. Cooking (15 5 min, 110 °C) improved nutrient digestibilities of diets containing triticale. Growth performance and nutrient retention efficiencies were higher in fish fed diets containing precooked triticale than in those receiving equivalent amounts of native triticale. Triticale appears to hold potential value as an ingredient in trout diets provided some pretreatment of the cereal is made to improve starch digestibility.
Reliable Nickel-Free Surface Finish Solution for High-Frequency, HDI PCB Applications

The evolution of internet-enabled mobile devices has driven innovation in the manufacturing and design of technology capable of high-frequency electronic signal transfer. Among the primary factors affecting the integrity of high-frequency signals is the surface finish applied on PCB copper pads – a need commonly met through the electroless nickel immersion gold process, ENIG. However, there are well-documented limitations of ENIG due to the presence of nickel, the properties of which result in an overall reduced performance in high-frequency data transfer rate for ENIG-applied electronics, compared to bare copper. An innovation over traditional ENIG is a nickel-less approach involving a special nano-engineered barrier designed to coat copper contacts, finished with an outermost gold layer. In this paper, assemblies involving this nickel-less novel surface finish have been subjected to extended thermal exposure, then intermetallics analyses, contact/sheet resistance comparison after every reflow cycle (up to 6 reflow cycles) to assess the prevention of copper atom diffusion into the gold layer, solder ball pull and shear tests to evaluate the aging and long-term reliability of solder joints, and insertion loss testing to gauge whether this surface finish can be used for high-frequency, high density interconnect (HDI) applications.
cGAS-STING–mediated DNA sensing maintains CD8+ T cell stemness and promotes antitumor T cell therapy

Cell-intrinsic cGAS-STING–mediated DNA sensing promotes the formation of stem cell–like CD8+ T cells for effective cancer T cell therapy. Intuitive CD8+ T cells sense DNA Stimulator of interferon genes (STING) agonism is an area of active exploration for cancer immunotherapy. Li et al. examined the cGAS-STING DNA sensing cascade in antitumor CD8+ T cells. They observed dampened STING activity in CD8+ T cells from patients with cancer or mice implanted with tumors. STING signaling supported a stem-like memory phenotype in the T cells, which is known to be beneficial for responses to immunotherapy. Cytosolic DNA was enriched in activated T cells, and STING agonism improved efficacy of adoptive cell therapy in multiple mouse models. These results highlight that CD8+ T cell DNA sensing could be exploited for therapeutic benefit in immunotherapy. Although cGAS-STING–mediated DNA sensing in tumor cells or phagocytes is central for launching antitumor immunity, the role of intrinsic cGAS-STING activation in T cells remains unknown. Here, we observed that peripheral blood CD8+ T cells from patients with cancer showed remarkably compromised expression of the cGAS-STING cascade. We demonstrated that the cGAS-STING cascade in adoptively transferred CD8+ T cells was essential for antitumor immune responses in the context of T cell therapy in mice. Mechanistically, cell-autonomous cGAS and STING promoted the maintenance of stem cell–like CD8+ T cells, in part, by regulating the transcription factor TCF1 expression. Moreover, autocrine cGAS-STING–mediated type I interferon signaling augmented stem cell–like CD8+ T cell differentiation program mainly by restraining Akt activity. In addition, genomic DNA was selectively enriched in the cytosol of mouse CD8+ T cells upon in vitro and in vivo stimulation. STING agonism enhanced the formation of stem-like central memory CD8+ T cells from patients with cancer and potentiated antitumor responses of CAR-T cell therapy in a xenograft model. These findings advance our understanding of inherent cGAS-STING activation in T cells and provide insight into the development of improved T cell therapy by harnessing the cGAS-STING pathway for cancer immunotherapy.
Truncated tests for combining evidence of summary statistics

To date, thousands of genetic variants to be associated with numerous human traits and diseases have been identified by genome‐wide association studies (GWASs). The GWASs focus on testing the association between single trait and genetic variants. However, the analysis of multiple traits and single nucleotide polymorphisms (SNPs) might reflect physiological process of complex diseases and the corresponding study is called pleiotropy association analysis. Modern day GWASs report only summary statistics instead of individual‐level phenotype and genotype data to avoid logistical and privacy issues. Existing methods for combining multiple phenotypes GWAS summary statistics mainly focus on low‐dimensional phenotypes while lose power in high‐dimensional cases. To overcome this defect, we propose two kinds of truncated tests to combine multiple phenotypes summary statistics. Extensive simulations show that the proposed methods are robust and powerful when the dimension of the phenotypes is high and only part of the phenotypes are associated with the SNPs. We apply the proposed methods to blood cytokines data collected from Finnish population. Results show that the proposed tests can identify additional genetic markers that are missed by single trait analysis.
Brain networks processing temporal information in dynamic facial expressions

Perception of emotional expressions in faces relies on the integration of distinct facial features. We used fMRI to examine the role of local and global motion information in facial movements during exposure to novel dynamic face stimuli. We found that synchronous expressions distinctively engaged medial prefrontal areas in the ventral anterior cingulate cortex (vACC), supplementary premotor areas, and bilateral superior frontal gyrus (global temporal-spatial processing). Asynchronous expressions in which one part of the face (e.g., eyes) unfolded before the other (e.g., mouth) activated more the right superior temporal sulcus (STS) and inferior frontal gyrus (local temporal-spatial processing). DCM analysis further showed that processing of asynchronous expression features was associated with a differential information flow, centered on STS, which received direct input from occipital cortex and projected to the amygdala. Moreover, STS and amygdala displayed selective interactions with vACC where the integration of both local and global motion cues (present in synchronous expressions) could take place. These results provide new evidence for a role of both local and global temporal dynamics in emotional expressions, extracted in partly separate brain pathways. Importantly, we show that dynamic expressions with synchronous movement cues may distinctively engage brain areas responsible for motor execution of expressions.
Nephroprotective effects of Datura metel extract in gentamicin induced mice model: biochemical and histological evidences.

Datura metel is traditionally used as a remedy for renal toxicity. However, the nephroprotection has not been scientifically validated yet. To evaluate the nephroprotective like effect of methanolic extract of D. metel in gentamicin induced mice model, mice of either sex were divided into groups. One group received normal saline as negative control. The 2nd group received gentamicin 100mg/kg for 8 days as positive control, 3rd group received 50mg/kg silymarin as standard, while the reaming groups received 100, 200 and 300 mg/kg of MEDM and gentamicin 100mg/kg, for 8 days. The blood and urine samples were collected on 9th day, animals were then dissected and whole kidneys were removed and preserved in formalin for later histological examinations. The level of serum creatinine, blood urea nitrogen, urine creatinine and urine urea were significantly (P<0.05) elevated and the renal MDA level was also elevated significantly (P<0.05) by gentamicin in mice. After the treatment of test animals with MEDM, the elevated level of serum and urine biomarkers by gentamicin were reversed by MEDM. The nephroprotective effect was found in dose dependent manner. As the MEDM significantly protected the nephrotoxicity via its antioxidant effect. The findings of our study thus proved the scientific background for the nephroprotective effect of MEDM.
Stable and Biocompatible Carbon Nanotube Ink Mediated by Silk Protein for Printed Electronics

Ink‐based processes, which enable scalable fabrication of flexible devices based on nanomaterials, are one of the practical approaches for the production of wearable electronics. However, carbon nanotubes (CNTs), which possess great potential for flexible electronics, are facing challenges for use in inks due to their low dispersity in most solvents and suspicious cytotoxicity. Here, a stable and biocompatible CNT ink, which is stabilized by sustainable silk sericin and free from any artificial chemicals, is reported. The ink shows stability up to months, which can be attributed to the formation of sericin–CNT (SSCNT) hybrid through non‐covalent interactions. It is demonstrated that the SSCNT ink can be used for fabricating versatile circuits on textile, paper, and plastic films through various techniques. As proofs of concept, electrocardiogram electrodes, breath sensors, and electrochemical sensors for monitoring human health and activity are fabricated, demonstrating the great potential of the SSCNT ink for smart wearables.
Effect of emigration on cannibalism and intraguild predation in aphidophagous ladybirds

Abstract. 1. The incidence and timing of emigration, cannibalism, and intraguild predation of larvae of three aphidophagous ladybirds (Coleoptera: Coccinellidae), Harmonia axyridis Pallas, Coccinella septempunctata brucki Mulsant, and Propylea japonica Mulsant, relative to the presence of prey was determined in the laboratory in single‐ and mixed‐species populations.