Miracle-dz/UniFAR-FTUs huggingface dataset:
Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias

Abstract Gene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
The Curious Case of the Missing Strokes During the COVID-19 Pandemic

Despite worldwide efforts, the incidence of coronavirus disease 2019 (COVID-19) continues to increase. To address this ongoing public health emergency, most countries implemented strict social containment measures and reorganized health care systems. Although these were necessary changes to contain the spread of disease and to deal with a rapidly rising number of severe cases that overwhelmed medical systems, the care of patients with other time-sensitive emergencies, such as stroke, has been impacted. Globally, physicians have noted reduced admissions for stroke.1,2 However, high-quality clinical registry data confirming this trend and exploring possible reasons has been lacking.
Fc receptor beta chain deficiency exacerbates murine arthritis in the anti-type II collagen antibody-induced experimental model

Abstract Objective Fc receptor β chain (FcRβ) acts as a signaling component of FcγRIII in immune cells such as mast cells (MCs) or basophils. Recent studies reported that FcγRIII contributes to the development of arthritic inflammation. These findings suggest that FcRβ may play a pivotal role in the pathogenesis of arthritic inflammation. To address this possibility, we examined the function of FcRβ in arthritic inflammation employing a mouse model. Methods For the induction of arthritis, we injected 2 mg of a cocktail of anti-type II collagen (CII) monoclonal antibodies (mAbs) into C57BL/6J mice (FcRβ+/+) and FcRβ−/− mice intravenously. Three days later, 100 μg lipopolysaccharide (LPS; Escherichia coli 055:B5) was intraperitoneally injected. Joint swelling was evaluated by inspection. Histopathology of joint tissues was examined by hematoxylin and eosin (H&E) or tartrate-resistant acid phosphatase staining. Results Here, we demonstrate in a well-established experimental arthritis model induced by LPS and anti-CII mAbs that FcRβ−/− mice exhibit exacerbated arthritic inflammation manifested in paw swelling, leukocyte infiltration into the knee joint, and bone erosion and tissue cytokine expression. Conclusion Our findings clearly indicate that FcRβ negatively regulates arthritic inflammation in an experimental arthritis model.
An Investigation into the Accuracy of Herbivore Diet Analysis

A commonly used technique of herbivore diet analysis consists of grinding ingested material to homogenise the size of particles, extracting a sub-set of these by sieving, and then reconstructing the diet by counting the particles referable to various plant species. A set of experiments revealed that this technique is inaccurate because of variation between species in the number of particles produced per unit dry weight, in the proportion of these retained by the sieve, and in the proportion that could be identified. Thus the technique is badly flawed even without the added complication of differential digestibility, which in itself is shown to be considerable. Certain correction factors derived to cope with these effects are shown to be only partly successful.
Multivariate Statistical Network Monitoring–Sensor: An effective tool for real-time monitoring and anomaly detection in complex networks and systems

Technology evolves quickly. Low-cost and ready-to-connect devices are designed to provide new services and applications. Smart grids or smart health care systems are some examples of these applications. In this totally connected scenario, some security issues arise due to the large number of devices and communications. In this way, new solutions for monitoring and detecting security events are needed to address new challenges brought about by this scenario, among others, the real-time requirement allowing quick security event detection and, consequently, quick response to attacks. In this sense, Intrusion Detection Systems are widely used though their evaluation often relies on the use of predefined network datasets that limit their application in real environments. In this work, a real-time and ready-to-use tool for monitoring and detecting security events is introduced. The Multivariate Statistical Network Monitoring–Sensor is based on the Multivariate Statistical Network Monitoring methodology and provides an alternative way for evaluating Multivariate Statistical Network Monitoring–based Intrusion Detection System solutions. Experimental results based on the detection of well-known attacks in hierarchical network systems prove the suitability of this tool for complex scenarios, such as those found in smart cities or Internet of Things ecosystems.
Fungos micorrízicos arbusculares em solos de área de mineração de bauxita em reabilitação

Despite the fact that bauxite mining activity promotes changes in soil characteristics, with negative effects on arbuscular mycorrhizas (AM), the effects of rehabilitation on AM fungi and their symbiosis are unknown. The purpose of this study was to evaluate the occurrence, diversity and efficiency of AM fungi, in bauxite mining areas, with different vegetation types and rehabilitation ages. Rhizosphere soil samples were collected for evaluations of extraradical mycelium, spore density, richness and diversity of AM fungi and to evaluate root colonization and symbiotic efficiency of fungal populations. Mining activity had negative effects on AM fungi and the AM recovering was more related to vegetation types than to areas rehabilitation age. Six species were found: Gigaspora margarita, Gigaspora sp. , Paraglomus occultum, Glomus sp. , Entrophospora colombiana and Acaulospora scrobiculata. AM fungi occurrence was favored by both grasses and Mimosa scabrella. Although Eucalyptus saligna was not a good host for these fungi, its presence associated with a well developed and diverse understore contributed for the recovering of AM fungi. The fungal populations isolated from areas with Brachiaria decumbens and Cajanus cajan and from Mimosa scabrella and Melinis minutiflora were highly efficient for bean plants growth, showing that it is possible to recover the function of AM fungi using different vegetation types. These AM fungi present a high potential of utilization for the rehabilitation of mining disturbed areas.
Tracing Mycobacterium ulcerans along an alimentary chain in Côte d’Ivoire: A one health perspective

Background Mycobacterium ulcerans is an environmental mycobacterium responsible for an opportunistic, noncontagious tropical infection named Buruli ulcer that necrotizes the skin and the subcutaneous tissues. M. ulcerans is thought to penetrate through breached skin after contact with contaminated wetland environments, yet the exact biotopes where M. ulcerans occurs remain elusive, hence obscuring the epidemiological chain of transmission of this opportunistic pathogen. Methodology/Principal findings Polymerase chain reaction investigations detected M. ulcerans in 39/46 (84.7%) rhizosphere specimens collected in 13 Buruli ulcer-endemic areas in Côte d’Ivoire and 3/20 (15%) specimens collected in a nonendemic area (P = 5.73.E-7); only 3/63 (4.7%) sediment specimens from sediment surrounding the rhizospheres were positive in endemic area (P = 6.51.E-12). High-throughput sequencing further detected three PCR-positive plants, Croton hirtus, Corton kongensis and Oriza sativa var. japonica (rice), in the rectal content of two M. ulcerans-positive wild Thryonomys swinderianus grasscutters that were hunted in Buruli ulcer-endemic areas, while no PCR-positive plants were detected in the rectal content of two negative control animals that were farmed in a nonendemic area. Conclusions/Significance Our data suggest an alimentary chain of transmission of M. ulcerans from plants to T. swinderianus grasscutters and people that utilize T. swinderianus as bush meat in Buruli ulcer-endemic areas in Côte d’Ivoire. Guidance to adopt protective measures and avoid any direct contact with potentially contaminated rhizospheres and with grasscutter intestinal content when preparing the animals for cooking should be established for at-risk populations.
The Effects of Different Crude Protein Levels in the Concentrates on Carcass and Meat Quality Characteristics of Hanwoo Steers

Moksan Hanwoo Research Institute, Gyeongsan 712-821, KoreaABSTRACTThe purpose of this study was to determine the effects of different crude protein levels in the concentrates on carcass and meat quality of Hanwoo steers. A total of thirty 5.3-month-old castrated Hanwoo calves(135.6±10.52kg) were randomly allocated into either control or treatment group. The animals were separately housed to 5 heads per group. Crude protein levels in concentrates for growing, fattening, and finishing phases were 14, 13, and 11% for control group and 16, 15, and 14% for treatment group respectively. Comparative analysis of carcass characteristics, physico-chemical characteristics, and fatty acid composition in M. longissimus dorsi of Hanwoo steers were carried out. There was no statistical difference in average cold carcass weight between control(411.9kg) and treatment(419.9kg) group. Also, dietary crude protein level in concentrates did not affect M. longissimus dorsi area, backfat thickness, and meat yield index. In contrast, the marbling score in treatment group was higher(p<0.05) than the control group. Also, treatment group showed significantly higher(p<0.05) values than control group for CIE L-value, Mono-unsaturated fatty acids and oleic acid composition. Therefore increasing crude protein levels of concentrates in Hanwoo steers during growing and fattening phases might be beneficial for the improvement of meat quality. (Key words :Crude protein level, Carcass characteristics, Meat quality, Hanwoo steer)
Effects of Olive Oil on Blood Pressure: Epidemiological, Clinical, and Mechanistic Evidence

The increasing access to antihypertensive medications has improved longevity and quality of life in hypertensive patients. Nevertheless, hypertension still remains a major risk factor for stroke and myocardial infarction, suggesting the need to implement management of pre- and hypertensive patients. In addition to antihypertensive medications, lifestyle changes, including healthier dietary patterns, such as the Dietary Approaches to Stop Hypertension (DASH) and the Mediterranean diet, have been shown to favorably affect blood pressure and are now recommended as integrative tools in hypertension management. An analysis of the effects of nutritional components of the Mediterranean diet(s) on blood pressure has therefore become mandatory. After a literature review of the impact of Mediterranean diet(s) on cardiovascular risk factors, we here analyze the effects of olive oil and its major components on blood pressure in healthy and cardiovascular disease individuals and examine underlying mechanisms of action. Both experimental and human studies agree in showing anti-hypertensive effects of olive oil. We conclude that due to its high oleic acid and antioxidant polyphenol content, the consumption of olive oil may be advised as the optimal fat choice in the management protocols for hypertension in both healthy and cardiovascular disease patients.
DIET OF WEDDELL SEALS LEPTONYCHOTES WEDDELLII AT VESTKAPP, EASTERN WEDDELL SEA (ANTARCTICA), IN RELATION TO LOCAL FOOD SUPPLY

Thirteen Weddell seals (Leptonychotes weddellii) were collected at Vestkapp, eastern Weddell Sea coast, in austral spring 1986. All stomachs contained partially digested food. The mean wet weight of stomach contents was 7.5 kg, 3.3% of the. mean body weight of the collected seals. Twelve fish species and three cephalopod species were identified from 372 left otoliths and 25 lower beaks, representing 58.4% of 679 total prey items obtained. Composition by number of total prey was: Chionodraco myersi (15.8%), Trematomus eulepidotus (10.0%), Pagetopsis maculatus (9.7%), Racovitzia glacialis (9.6%) and Cryodraco antarcticus (4.1%). Otoliths of the seven other fish species and beaks of the three cephalopod species together represented 9.1% of total prey numbers. The pooled wet weights calculated from 13 prey species (regressions for two octopod species were not available) amounted to 43.5 kg food mass and represented 44.7% of the combined food mass in all stomachs. Composition by mass was: C. myersi (44.5%), T. eulepidotus (19.8%), squid Psychroteuthis glacialis (8.5%), P. maculates (7.9%), C. antarcticus (7.1%) and R. glacialis (6.2%). The remaining 7 fish species together represented 5.8% by mass. Temporal variation in food availability was apparent. Midwater fish Pleuragramma antarcticum was the staple food of Weddell seals from the same area during the 1985 summer, whereas it was absent in the samples taken in spring 1986. Estimates of fish biomass from net hauls demonstrate a highly variable availability of pelagic food resources for top predators in the Vestkapp area.
High contribution of Synechococcus to phytoplankton biomass in the aphotic hypolimnion in a deep freshwater lake (Lake Biwa, Japan)

The effective transportation of picophytoplankton to the mesopelagic layer in the ocean by cell aggregation and attachment to large particles has been reported. Those findings suggest that picophytoplankton play important roles in ecological processes in the deep ocean. However, there is no information about vertical transportation of picophytoplankton cells from the epilimnion in lakes, though the presence of picophytoplankton cells in the hypolimnion has been reported. The present study demonstrated the possible importance of Synechococcus (Cyanobacteria) in ecological processes of the hypolimnion in the deep mesotrophic Lake Biwa, Japan. The chlorophyll a concentration in the 0.2−2.0-μm fraction, which is mainly derived from Synechococcus, accounted for a large portion (up to 28.8%) of the total chlorophyll a concentration in the hypolimnion during the thermal stratification period. We found a significant positive correlation between Synechococcus abundances in the epilimnion and hypolimnion during the stratification period. In addition, our incubation experiment revealed that Synechococcus did not show significant growth during the first 2 d in dark conditions. These results suggest the recent delivery of a significant fraction of Synechococcus cells from the epilimnion to the hypolimnion. Our results indicate that the abundance of Synechococcus makes a greater contribution to ecological processes in the hypolimnion of Lake Biwa than previously hypothesized, and this may also be the case for other deep lakes.
Phytochemical Study on Prunus davidiana

From the stem of Prunus davidiana, naringenin and its glucoside, kaempferol and its glucoside, dihydrokaempferol, kaempferide glucoside, hesperetin glucoside, quer- cetin glucoside, d-catechin and 13-sitosterol glucoside were isolated.
Allele-Frequency Change in a Class-Structured Population

Suppose that in a population with a class structure, we wish to calculate the change in frequency of an allele under the action of selection. If the allele affects the behavior of individuals in different classes differently and if parents of different classes have different class distributions of offspring, then the allele frequencies in different classes may be different, and any overall calculation of allele-frequency change must decide how to weight the different class frequencies. I show that the correct weights to use are the class reproductive values, and, using these, I formulate a covariance equation for allele-frequency change. This equation also provides the classical inclusive-fitness formulation if benefits (increased numbers of offspring) are calculated by weighting each offspring by the individual reproductive value that pertains to his class.
Pharmacogenetics in Model-Based Optimization of Bevacizumab Therapy for Metastatic Colorectal Cancer

Vascular endothelial growth factor A (VEGF-A) and intercellular adhesion molecule 1 (ICAM-1) are significant regulators of angiogenesis, an important biological process involved in carcinogenesis. Bevacizumab, an anti-VEGF monoclonal antibody (MAB), is approved for the treatment of metastatic Colorectal cancer (mCRC), however clinical outcomes are highly variable. In the present study, we developed a pharmacokinetic (PK), a simplified quasi-steady state (QSS) and a pharmacokinetic/pharmacodynamic (PK/PD) model to identify potential sources of variability. A total of 46 mCRC patients, who received bevacizumab in combination with chemotherapy were studied. VEGF-A (rs2010963, rs1570360, rs699947) and ICAM-1 (rs5498, rs1799969) genes’ polymorphisms, age, gender, weight, and dosing scheme were investigated as possible co-variates of the model’s parameters. Polymorphisms, trough, and peak levels of bevacizumab, and free VEGF-A were determined in whole blood and serum. Data were analyzed using nonlinear mixed-effects modeling. The two-compartment PK model showed that clearance (CL) was significantly lower in patients with mutant ICAM-1 rs1799969 (p < 0.0001), inter-compartmental clearance (Q) was significantly higher with mutant VEGF-A rs1570360 (p < 0.0001), and lower in patients with mutant VEGF-A rs699947 (p < 0.0001). The binding QSS model also showed that mutant ICAM-1 rs1799969 was associated with a lower CL (p = 0.0177). Mutant VEGF-A rs699947 was associated with a lower free VEGF-A levels, prior to the next dose (p = 0.000445). The above results were confirmed by the PK/PD model. Findings of the present study indicated that variants of the genes regulating angiogenesis might affect PK and PD characteristics of bevacizumab, possibly influencing the clinical outcomes.
Resistance to Puccinia recondita f. sp. tritici in 50 Mexican bread wheat cultivars

Bread wheat (Triticum aestivum L.) cultivars derived from CIM-MYT germplasm are currently grown on a large area worldwide. Since limited information is available on genes for resistance to leaf rust in these wheats, the two main objectives of the study were to postulate the known Lr genes conferring low seeding reactions to 18 pathotypes of Puccinia recondita Roberge ex Desmaz. f. sp. tritici in 50 Mexican cultivars released between 1960 and 1988; and to evaluate the presence of additional adult-plant resistance
Robot-Assisted versus Laparoscopic Donor Nephrectomy: A Comparison of 250 Cases

Living kidney donation is the best treatment for end-stage renal disease, however, the best surgical approach for minimally-invasive donor nephrectomy (DN) is still a matter of debate. This bi-centric study aimed to retrospectively compare perioperative outcomes and postoperative kidney function after 257 transperitoneal DNs including 52 robot-assisted (RDN) and 205 laparoscopic DNs (LDN). As primary outcomes, the intraoperative (operating time, warm ischemia time (WIT), major complications) and postoperative (length of stay, complications) results were compared. As secondary outcomes, postoperative kidney and graft function were analyzed including delayed graft function (DGF) rates, and the impact of the surgical approach was assessed. Overall, the type of minimally-invasive donor nephrectomy (RDN vs. LDN) did not affect primary outcomes, especially not operating time and WIT; and major complication and DGF rates were low in both groups. A history of smoking and preoperative kidney function, but not the surgical approach, were predictive for postoperative serum creatinine of the donor and recipient. To conclude, RDN and LDN have equivalent perioperative results in experienced centers. For this reason, not the surgical approach, but rather the graft- (preoperative kidney function) and patient-specific (history of smoking) aspects impacted postoperative kidney function.
Ataxia as the Major Manifestation of Fragile X-Associated Tremor/Ataxia Syndrome (FXTAS): Case Series

Fragile X-associated tremor and ataxia syndrome (FXTAS) is a neurodegenerative disease developed by carriers of a premutation in the fragile X mental retardation 1 (FMR1) gene. The core clinical symptoms usually manifest in the early 60s, typically beginning with intention tremor followed by cerebellar ataxia. Ataxia can be the only symptom in approximately 20% of the patients. FXTAS has a slow progression, and patients usually experience advanced deterioration 15 to 25 years after the initial diagnosis. Common findings in brain imaging include substantial brain atrophy and white matter disease (WMD). We report three cases with an atypical clinical presentation, all presenting with gait problems as their initial manifestation and with ataxia as the dominant symptom without significant tremor, as well as a faster than usual clinical progression. Magnetic resonance imaging (MRI) was remarkable for severe brain atrophy, ventriculomegaly, thinning of the corpus callosum, and periventricular WMD. Two cases were diagnosed with definite FXTAS on the basis of clinical and radiological findings, with one individual also developing moderate dementia. Factors such as environmental exposure and general anesthesia could have contributed to their clinical deterioration. FXTAS should be considered in the differential diagnosis of patients presenting with ataxia, even in the absence of tremor, and FMR1 DNA testing should be sought in those with a family history of fragile X syndrome or premutation disorders.