Miracle-dz/UniFAR-FTUs huggingface dataset:
Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.
Vertebrate scavenger guild composition and utilization of carrion in an East Asian temperate forest

Abstract Scavenging is a common feeding behavior by many species that plays an important role in ecosystem stability and function while also providing ecosystem services. Despite its importance, facultative scavenging on large animal carcasses has generally been overlooked in Asian temperate forest ecosystems. The aim of this study was to determine the composition and feeding behavior of the facultative scavenger guild as it relates to sika deer (Cervus nippon) carcasses in Japanese forests. There are no obligate scavengers or large predators that kill adult ungulates, but humans fill the role of large predators by culling deer for population management. We documented nine vertebrate species scavenging on deer carcasses and found that mammals were more frequent scavengers than birds and also fed for longer durations. This result suggests that there is a facultative scavenger guild composed mainly of mammals in our forest ecosystem and that carcass utilization by birds was restricted to only forest species. Raccoon dogs (Nyctereutes procyonoides) and Asian black bears (Ursus thibetanus) were the most frequent scavenger species and also fed for longer durations than other scavengers. There were significant seasonal differences in scavenging by Asian black bear, Japanese marten (Martes melampus), and mountain hawk‐eagle (Nisaetus nipalensis), suggesting the availability of other food resources may alter facultative scavenging by each species. Our results support that scavenging is widespread in this system and likely has important functions including building links in the food web.
Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata

Abstract Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, Littorina obtusata and L. fabalis (Gastropoda), are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north‐western Iberia to assess the extent of current and past hybridization between L. obtusata and L. fabalis under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation.
Central and Mixed Venous O2 Saturation

Mixed and central venous oxygen saturations are commonly used to ascertain the degree of systemic oxygenation in critically ill patients. This review examines the physiological basis for the use of these variables to determine systemic extraction ration, oxygen consumption and tissue oxygenation, and also understand the role they may play in the early treatment of septic individuals.
Improvements in clinical pain and experimental pain sensitivity after cognitive functional therapy in patients with severe persistent low back pain

Abstract Introduction: Multidisciplinary care is recommended for disabling persistent low back pain (pLBP) nonresponsive to primary care. Cognitive functional therapy (CFT) is a physiotherapy-led individualised intervention targeting psychological, physical, and lifestyle barriers to recovery, to self-manage pLBP. Objectives: This pilot study investigated clinical outcomes and pain thresholds after a 12-week CFT pathway in patients with severe pLBP referred to a University Pain Center. Exploratory analyses compared changes in clinical outcomes, opioid consumption, and costs after CFT with changes after a multidisciplinary pain management (MPM) pathway. Methods: In total, 47 consecutively referred pLBP patients consented to the CFT pathway. At baseline, 3 and 6 months, clinical outcomes and PPTs were assessed. Control patients (n = 99) who had completed an MPM pathway in the last 3 years were matched from the clinical pain registry used in the Pain Center in a 3:1 ratio based on propensity scores derived from relevant baseline variables of the CFT cases. Results: Most clinical outcomes and low back pressure pain threshold were improved at 3 and 6 months after the CFT pathway. Compared with MPM, CFT patients had significantly larger reductions in disability and improved quality of life after the interventions at a lower cost (−3688€ [confidence interval: −3063 to −4314€]). Reduction in pain intensity and proportion of patients withdrawing from opioids (18.2% vs 27.8%) were similar between CFT and MPM groups. Conclusion: Improvements in clinical and experimental pain were found after the CFT pathway. Fully powered randomized controlled trials comparing CFT with an MPM program in patients with disabling pLBP are warranted to control for the current limitations.
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases

Many bacterial-related databases are developed to meet the researchers' needs of analysis and search for a number of bacterial information. However, these databases have different data resources, construction methods, data formats, and analysis tools. It's difficult for researchers to select appropriate databases and analysis tools to promote their researches. In the paper, we compared the contents, construction methods, data sources, update frequency, scope and scale of data, analysis tools, and features of nine famous bacterial databases: CARD, EffectiveDB, MBGD, MPD, PATRCI, PHI-base, VFDB, gcMeta and SILVA, and help researchers to better make better use of these databases. In addition, we also hope this review can help researchers develop a more comprehensive database and better tools to meet the needs of researchers.
Glycolysis and Oxidative Phosphorylation Play Critical Roles in Natural Killer Cell Receptor-Mediated Natural Killer Cell Functions

Natural killer (NK) cells are innate lymphocytes that directly kill tumor and pathogen-infected cells upon activation by cytokines and NK cell receptors (NKRs) without previous sensitization. It is known that cell metabolism affects the differentiation and effector functions of immune cells. For instance, interleukin−2 and interleukin−15 treatment increases glycolysis and oxidative phosphorylation (OXPHOS) in NK cells to support their effector functions. However, little is known about the metabolic reprogramming of human NK cells upon their activation by NKRs. In this study, we investigated the metabolism of NK cells stimulated via NKRs. We found that NK cells upregulated glycolysis and OXPHOS in response to anti-CD16 antibody or NKG2D ligand engagement. Inhibition of either glycolysis or OXPHOS impaired NK cell production of interferon-γ. Interestingly, inhibition of glycolysis but not OXPHOS decreased NK cell killing and dampened NK cell degranulation and Fas ligand expression, suggesting that glycolysis is more critical for NKR-activated cell cytotoxicity. Thus, our study provides insight into understanding the metabolic requirements underlying different effector functions of human NK cells.
Randomised comparison of provisional side branch stenting versus a two-stent strategy for treatment of true coronary bifurcation lesions involving a large side branch: the Nordic-Baltic Bifurcation Study IV

Background It is still uncertain whether coronary bifurcations with lesions involving a large side branch (SB) should be treated by stenting the main vessel and provisional stenting of the SB (simple) or by routine two-stent techniques (complex). We aimed to compare clinical outcome after treatment of lesions in large bifurcations by simple or complex stent implantation. Methods The study was a randomised, superiority trial. Enrolment required a SB≥2.75 mm, ≥50% diameter stenosis in both vessels, and allowed SB lesion length up to 15 mm. The primary endpoint was a composite of cardiac death, non-procedural myocardial infarction and target lesion revascularisation at 6 months. Two-year clinical follow-up was included in this primary reporting due to lower than expected event rates. Results A total of 450 patients were assigned to simple stenting (n=221) or complex stenting (n=229) in 14 Nordic and Baltic centres. Two-year follow-up was available in 218 (98.6%) and 228 (99.5%) patients, respectively. The primary endpoint of major adverse cardiac events (MACE) at 6 months was 5.5% vs 2.2% (risk differences 3.2%, 95% CI −0.2 to 6.8, p=0.07) and at 2 years 12.9% vs 8.4% (HR 0.63, 95% CI 0.35 to 1.13, p=0.12) after simple versus complex treatment. In the subgroup treated by newer generation drug-eluting stents, MACE was 12.0% vs 5.6% (HR 0.45, 95% CI 0.17 to 1.17, p=0.10) after simple versus complex treatment. Conclusion In the treatment of bifurcation lesions involving a large SB with ostial stenosis, routine two-stent techniques did not improve outcome significantly compared with treatment by the simpler main vessel stenting technique after 2 years. Trial registration number NCT01496638.
MiR-10a-5p-Mediated Syndecan 1 Suppression Restricts Porcine Hemagglutinating Encephalomyelitis Virus Replication

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a single-stranded RNA coronavirus that causes nervous dysfunction in the infected hosts and leads to widespread alterations in the host transcriptome by modulating specific microRNA (miRNA) levels. MiRNAs contribute to RNA virus pathogenesis by promoting antiviral immune response, enhancing viral replication, or altering miRNA-mediated host gene regulation. Thus, exploration of the virus–miRNA interactions occurring in PHEV-infected host may lead to the identification of novel mechanisms combating the virus life cycle or pathogenesis. Here, we discovered that the expression of miR-10a-5p was constitutively up-regulated by PHEV in both the N2a cells in vitro and mice brain in vivo. Treatment with miR-10a-5p mimics allowed miR-10a-5p enrichment and resulted in a significant restriction in PHEV replication, suggesting widespread negative regulation of the RNA virus infection by miR-10a-5p. The outcomes were also evidenced by miR-10a-5p inhibitor over-expression. Luciferase reporter, quantitative real-time PCR (qRT-PCR), and western blotting analysis further showed that Syndecan 1 (SDC1), a cell surface proteoglycan associated with host defense mechanisms, acts as a target gene of miR-10a-5p during PHEV infection. Naturally, siRNA-mediated knockdown of SDC1 leads to a reduction in viral replication, implying that SDC1 expression is likely a favorable condition for viral replication. Together, the findings demonstrated that the abundant miR-10a-5p leads to downstream suppression of SDC1, and it functions as an antiviral mechanism in the PHEV-induced disease, providing a potential strategy for the prevention and treatment of PHEV infection in the future work.
Dual pH-sensitive nanodrug blocks PD-1 immune checkpoint and uses T cells to deliver NF-κB inhibitor for antitumor immunotherapy

A potent drug delivery strategy promotes tumor infiltration of T cells and unleashes antitumor immunity. The response to programmed cell death protein-1 (PD-1)/programmed death ligand-1 (PD-L1) blockade in cancer immunotherapy is limited because of multiple immune evasion mechanisms. Here, a previously unknown strategy is proposed to synergize the nuclear factor κB (NF-κB) inhibition and PD-1 blockade for antitumor immunotherapy. A dual pH-sensitive nanocarrier loading curcumin (CUR) and anti–PD-1 monoclonal antibody (aPD-1) may bind to circulating PD-1+ T cells and then follow their infiltration into the tumor. Furthermore, the nanodrug bound to PD-1+ T cells may be released in the tumor microenvironment, leaving aPD-1 to block PD-1 on T cells and generating a CUR-encapsulated cationic nanodrug that can be easily taken up by tumor cells/tumor associated macrophages (TAMs). Thus, not only the antitumor T cells mediate efficient CUR delivery to tumor but also the efficient CUR delivery promotes the tumor infiltration of antitumor T cells, thereby resulting in effective activation of antitumor immunity.
Boreal predator co‐occurrences reveal shared use of seismic lines in a working landscape

Abstract Interspecific interactions are an integral aspect of ecosystem functioning that may be disrupted in an increasingly anthropocentric world. Industrial landscape change creates a novel playing field on which these interactions take place, and a key question for wildlife managers is whether and how species are able to coexist in such working landscapes. Using camera traps deployed in northern Alberta, we surveyed boreal predators to determine whether interspecific interactions affected occurrences of black bears (Ursus americanus), coyotes (Canis latrans), and lynx (Lynx canadensis) within a landscape disturbed by networks of seismic lines (corridors cut for seismic exploration of oil and gas reserves). We tested hypotheses of species interactions across one spatial‐only and two spatiotemporal (daily and weekly) scales. Specifically, we hypothesized that (1) predators avoid competition with the apex predator, gray wolf (Canis lupus), (2) they avoid competition with each other as intraguild competitors, and (3) they overlap with their prey. All three predators overlapped with wolves on at least one scale, although models at the daily and weekly scale had substantial unexplained variance. None of the predators showed avoidance of intraguild competitors or overlap with prey. These results show patterns in predator space use that are consistent with both facilitative interactions or shared responses to unmeasured ecological cues. Our study provides insight into how predator species use the working boreal landscape in relation to each other, and highlights that predator management may indirectly influence multiple species through their interactions.
New View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota

Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. ABSTRACT Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. The use of such fibers as prebiotics targeted to specific microbes would result in predictable shifts independent of the background microbial composition.
Environmental Toxicology and Chemistry

Performing toxicity testing on multiple species with differing degrees of evolutionary relatedness can provide important information on how chemical sensitivity varies among species and can help pinpoint the biological drivers of species sensitivity. Such knowledge could ultimately be used to design better multispecies predictive ecological risk assessment models and identify particularly sensitive species. However, laboratory toxicity tests involving multiple species can also be resource intensive, especially when each species has unique husbandry conditions. We performed lethality tests with 2 metals, copper chloride and zinc chloride, on 5 different nematode species, which are nested in their degree of evolutionary relatedness: Caenorhabditis briggsae, Caenorhabditis elegans, Oscheius myriophila, Oscheius tipulae, and Pristionchus pacificus. All species were successfully cultured and tested concurrently with limited resources, demonstrating that inexpensive, multispecies nematode toxicity testing systems are achievable. The results indicate that P. pacificus is the most sensitive to both metals. Conversely, C. elegans is the least sensitive species to copper, but the second most sensitive to zinc, indicating that species relationships do not necessarily predict species sensitivity. Toxicity testing with additional nematode species and types of chemicals is feasible and will help form more generalizable conclusions about relative species sensitivity. Environ Toxicol Chem 2020;39:1006–1016. © 2020 SETAC
Korean Consumers’ Recognition of Risks Depending on the Provision of Safety Information for Chemical Products

After the 2011 “Oxy accident” involving deaths from humidifier disinfectants, Korean consumers’ anxiety about chemical products has risen. To provide timely, appropriate information to consumers, we must understand their risk recognition and explore methods of safety information provision. We investigated Korean consumers’ level of risk perception for chemical products depending on the provision of safety information and other factors. We conducted an online survey for 10 days with 600 adult Korean consumer participants and analyzed seven factors: catastrophic potential, controllability, familiarity, fear, scientific knowledge, and risk for future generations. Our results showed that married women over 30 perceived chemical products as higher risk, but when information was provided on how to use products safely, catastrophic potential, controllability, fear, scientific knowledge, as well as risk perception, increased significantly. When only risk diagnosis information was provided, catastrophic potential, fear, and risk for future generations remained static, but familiarity had a negative effect (R^2 = 0.586). Age and scientific knowledge affected the recognition of risk when safe risk management methods were provided (R^2 = 0.587). Risk controllability did not have any effect on risk perception. These results suggest that providing information about avoiding or dealing with risks has a positive effect on consumers’ risk perception.
Leptin-Responsive MiR-4443 Is a Small Regulatory RNA Independent of the Canonic MicroRNA Biogenesis Pathway

The human small RNA miR-4443 is functionally involved in several types of cancer and in the biology of the immune system, downstream of insulin and leptin signaling. Next generation sequencing evidence and structural prediction suggest that miR-4443 is not produced via the canonical Drosha–Exportin 5–Dicer pathway of microRNA biogenesis. We tested this hypothesis by using qRT-PCR to measure miR-4443 and other microRNA levels in HCT-116 cells with Drosha, Exportin 5, and Dicer knockouts, as well as in the parental cell line. Neither of the knockouts decreased miR-4443 levels, while the levels of canonical microRNAs (miR-21 and let-7f-5p) were dramatically reduced. Previously published Ago2-RIP-Seq data suggest a limited incorporation of miR-4443 into RISC, in agreement with the functional studies. The miR-4443 locus shows conservation in primates but not in other mammals, while its seed region appears in additional microRNAs. Our results suggest that miR-4443 is a Drosha, Exportin 5, and Dicer-independent, non-canonical small RNA produced by a yet unknown biogenesis pathway.