Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

Abstract Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
Interleukin-10 rs1800896 polymorphism is associated with increased head and neck cancer risk but not associated with its clinical stages

Background The association of interleukin-10 rs1800896 polymorphism with head and neck cancer risk and its clinical stages has been investigated by many published studies, but the results remain inconsistent. Therefore, we conducted this meta-analysis for further investigation. Results Six case-control studies involving 1,781 head and neck cancer patients and 1,978 controls were yielded. The results indicated an association between rs1800896 polymorphism and increased head and neck risk [odds ratio (95%confidence interval) for G vs. A, GA vs. AA, GG vs. AA, GA+GG vs. AA, and GG vs. AA + GA were 1.63 (1.30–2.04), 3.17 (2.11–4.76), 1.63 (1.17–2.26), 1.73 (1.25–2.39), and 2.73 (1.82–4.09), respectively]. The subgroup analyses all obtained similar results with overall populations. The results of clinical stages yielded a non-significant association. No publication bias was detected. Materials and Methods The PubMed and Chinese National Knowledge Infrastructure databases were searched up to December 27, 2016. Two authors independently selected studies, extracted and analyzed the data using the RevMan 5 software. Either a fixed effect or a random effect model was used to estimate pooled odds ratio and its 95% confidence intervals. Conclusions We concluded that interleukin-10 rs1800896 polymorphism was significantly associated with head and neck cancer risk but not with the clinical stages thereof.
Robot learning from demonstration of force-based tasks with multiple solution trajectories

A learning framework with a bidirectional communication channel is proposed, where a human performs several demonstrations of a task using a haptic device (providing him/her with force-torque feedback) while a robot captures these executions using only its force-based perceptive system. Our work departs from the usual approaches to learning by demonstration in that the robot has to execute the task blindly, relying only on force-torque perceptions, and, more essential, we address goal-driven manipulation tasks with multiple solution trajectories, whereas most works tackle tasks that can be learned by just finding a generalization at the trajectory level. To cope with these multiple-solution tasks, in our framework demonstrations are represented by means of a Hidden Markov Model (HMM) and the robot reproduction of the task is performed using a modified version of Gaussian Mixture Regression that incorporates temporal information (GMRa) through the forward variable of the HMM. Also, we exploit the haptic device as a teaching and communication tool in a human-robot interaction context, as an alternative to kinesthetic-based teaching systems. Results show that the robot is able to learn a container-emptying task relying only on force-based perceptions and to achieve the goal from several non-trained initial conditions.
Development of Accelerated Evaluation Method for Microbially Influenced Corrosion Resistance of Stainless Steels

The accelerated evaluation method for microbially influenced corrosion (MIC) resistance of stainless steels was investigated on the basis of the mechanism for MIC . Corrosion potential of stainless steels was determined in natural seawater and in synthetic seawater containing glucose oxidase (GOD) to simulate the bacterial metabolism because the corrosion potential of stainless steels in natural seawater becomes noble by hydrogen peroxide as an intermediate of the metabolism. The corrosion potential ennoblement was re-
Drop test for evaluating effect of cushioning material and servo gain on parachute landing impact using a small one-legged robot

To drop a humanoid robot with a parachute from an airplane is one of the promising ways of delivering robots to a disaster site, and this research has focused on how to absorb parachute landing shock. Two large impacts were observed in one drop test using a small one-legged robot in our previous experiment. The second peak could be reduced by the shock absorbing motion, but the first peak did not change dramatically even if the landing posture was changed. Therefore, this paper forces on how to reduce the first impact acceleration and discusses on effect of cushioning material and servo gain on the impact. It was found that the difference in the hardness of the cushioning material greatly influences the impact acceleration. There was a difference in impact acceleration more than twice between a soft cushion and a hard cushion. On the other hand, impact absorption effect by change of servo gain of robot's actuators was minor. Therefore, it is concluded that flexibility with hardware is also necessary for joints.
Effects of ketamine on brain function during smooth pursuit eye movements

The uncompetitive NMDA receptor antagonist ketamine has been proposed to model symptoms of psychosis. Smooth pursuit eye movements (SPEM) are an established biomarker of schizophrenia. SPEM performance has been shown to be impaired in the schizophrenia spectrum and during ketamine administration in healthy volunteers. However, the neural mechanisms mediating SPEM impairments during ketamine administration are unknown. In a counter‐balanced, placebo‐controlled, double‐blind, within‐subjects design, 27 healthy participants received intravenous racemic ketamine (100 ng/mL target plasma concentration) on one of two assessment days and placebo (intravenous saline) on the other. Participants performed a block‐design SPEM task during functional magnetic resonance imaging (fMRI) at 3 Tesla field strength. Self‐ratings of psychosis‐like experiences were obtained using the Psychotomimetic States Inventory (PSI). Ketamine administration induced psychosis‐like symptoms, during ketamine infusion, participants showed increased ratings on the PSI dimensions cognitive disorganization, delusional thinking, perceptual distortion and mania. Ketamine led to robust deficits in SPEM performance, which were accompanied by reduced blood oxygen level dependent (BOLD) signal in the SPEM network including primary visual cortex, area V5 and the right frontal eye field (FEF), compared to placebo. A measure of connectivity with V5 and FEF as seed regions, however, was not significantly affected by ketamine. These results are similar to the deviations found in schizophrenia patients. Our findings support the role of glutamate dysfunction in impaired smooth pursuit performance and the use of ketamine as a pharmacological model of psychosis, especially when combined with oculomotor biomarkers. Hum Brain Mapp 37:4047–4060, 2016. © 2016 Wiley Periodicals, Inc.
Contribution by the methanogenic endosymbionts of anaerobic ciliates to methane production in Dutch freshwater sediments

Summary. Biogenic methane contributes substantially to the atmospheric methane concentration and thus to global warming. This trace gas is predominantly produced by strictly anaerobic methanogenic archaea, which thrive in the most divergent ecological niches, e. g. paddy fields, sediments, landfills, and the digestive tract of various animals. Methanogenic archaea also live as endosymbionts in th e cytoplasm of anaerobic protozoa. In marine sediments these endosymbionts can contribute up to 90% to the overall rate of methanogenesis, whereas their role of in freshwater sediments is largely unknown. Here we describe the results of a one year’s survey of the methanogen esis by endosymbiotic methanogens in four different Dutch freshwater sediments. The abundance of anaerobic protozoa, in particular cili ates, the methane production rates by the ecosystem and by the protists, and a number of abiotic parameters were measured. A novel method (heatshock for 5 min) for estimating the contribution by endosymbiotic methanogens was established. Our results reveal large fluctua tions of ciliate abundance throughout the year, but on average, only minor contributions by methanogenic endosymbionts to the total meth anogenesis in these environments.
NUMERICAL METHODS

The challenge to solve complex problems implies to develop the proper numerical methods, which guarantees the correct solution of our problem. Many issues have to be considered due to the different aspects involved in the resolution of computational mechanical problems: discretization, solvers, numerical instabilities and multiphysics problems. The numerical methods developed in CASE and implemented in Alyta code are suitably adapted to different architectures in order to be able to run in moderns supercomputers.
LML1, Encoding a Conserved Eukaryotic Release Factor 1 Protein, Regulates Cell Death and Pathogen Resistance by Forming a Conserved Complex with SPL33 in Rice

Lesion mimic mutants are powerful tools for unveiling the molecular connections between cell death and pathogen resistance. Various proteins responsible for lesion mimics have been identified; however, the mechanisms underlying lesion formation and pathogen resistance are still unknown. Here, we identify a lesion mimic mutant in rice, lesion mimic leaf 1 (lml1). The lml1 mutant exhibited abnormal cell death and resistance to both bacterial blight and rice blast. LML1 is expressed in all types of leaf cells, and encodes a novel eukaryotic release factor 1 (eRF1) protein located in the endoplasmic reticulum. Protein sequences of LML1 orthologs are conserved in yeast, animals and plants. LML1 can partially rescue the growth delay phenotype of the LML1 yeast ortholog mutant, dom34. Both lml1 and mutants of AtLML1 (the LML1 Arabidopsis ortholog) exhibited a growth delay phenotype like dom34. This indicates that LML1 and its orthologs are functionally conserved. LML1 forms a functional complex with a eukaryotic elongation factor 1A (eEF1A)-like protein, SPL33/LMM5.1, whose mutant phenotype was similar to the lml1 phenotype. This complex was conserved between rice and yeast. Our work provides new insight into understanding the mechanism of cell death and pathogen resistance, and also lays a good foundation for studying the fundamental molecular function of Pelota/DOM34 and its orthologs in plants.
Piezoelectric immunosensor for detection of bacteria by immobilizing antibodies on TiO_2 porous films

Nanocrystalline TiO_2 porous films were coated on the surface of silver-plated piezoelectric crystal, and used for the immobilization of antibodies (anti-Salmonella enteritidis antibodies) after activation by (3-aminopropyl)trimethoxysilane and glutaraldehyde. The piezoelectric immunosensor developed by the present modification method was used to detect Salmonella enteritidis. A detection limit of 4×10~4 cell/mL and an assay time of 30 min were achieved. Considering its simplicity, reproducibility and cost, it is feasible to develop disposable piezoelectric crystal detectors for immunological test.
Live Imaging of Type I Collagen Assembly Dynamics in Osteoblasts Stably Expressing GFP and mCherry‐Tagged Collagen Constructs

Type I collagen is the most abundant extracellular matrix protein in bone and other connective tissues and plays key roles in normal and pathological bone formation as well as in connective tissue disorders and fibrosis. Although much is known about the collagen biosynthetic pathway and its regulatory steps, the mechanisms by which it is assembled extracellularly are less clear. We have generated GFPtpz and mCherry‐tagged collagen fusion constructs for live imaging of type I collagen assembly by replacing the α2(I)‐procollagen N‐terminal propeptide with GFPtpz or mCherry. These novel imaging probes were stably transfected into MLO‐A5 osteoblast‐like cells and fibronectin‐null mouse embryonic fibroblasts (FN‐null‐MEFs) and used for imaging type I collagen assembly dynamics and its dependence on fibronectin. Both fusion proteins co‐precipitated with α1(I)‐collagen and remained intracellular without ascorbate but were assembled into α1(I) collagen‐containing extracellular fibrils in the presence of ascorbate. Immunogold‐EM confirmed their ultrastuctural localization in banded collagen fibrils. Live cell imaging in stably transfected MLO‐A5 cells revealed the highly dynamic nature of collagen assembly and showed that during assembly the fibril networks are continually stretched and contracted due to the underlying cell motion. We also observed that cell‐generated forces can physically reshape the collagen fibrils. Using co‐cultures of mCherry‐ and GFPtpz‐collagen expressing cells, we show that multiple cells contribute collagen to form collagen fiber bundles. Immuno‐EM further showed that individual collagen fibrils can receive contributions of collagen from more than one cell. Live cell imaging in FN‐null‐MEFs expressing GFPtpz‐collagen showed that collagen assembly was both dependent upon and dynamically integrated with fibronectin assembly. These GFP‐collagen fusion constructs provide a powerful tool for imaging collagen in living cells and have revealed novel and fundamental insights into the dynamic mechanisms for the extracellular assembly of collagen. © 2018 American Society for Bone and Mineral Research.
Static Fatigue Limit of Crack-Healed Mullite/ SiC Multi-Composite

Static fatigue behavior of mullite/ 15 vol% SiC whiskers/ 10 vol% SiC particles multi-composite crack-healed was investigated at room temperature and high temperatures from 1000°C to 1200°C. The multi-composite is the most candidate material as ceramic spring, because it has low Young's modulus as well as its reliability is guaranteed by excellent crack-healing ability. For estimating the usefulness of the composite as ceramic spring at high temperature, we must know the static fatigue limit at high temperature. The multi-composite having pre-crack was crack-healed at 1300°C for 2 h in air. The times to failure were investigated when the crack-healed specimens were applied the elevated tensile stress in air at room temperature and high temperatures from 1000°C to 1200°C. From the obtained results, the static fatigue limit was determined. Below 1000°C, the static fatigue limit of the composite crack-healed was found to be almost equal to the corresponding bending strength. Alternatively the static fatigue limit of the composite crack-healed was found to have lower value than the corresponding bending strength above 1100°C. Thus, the heat-resistance limit temperature for static fatigue of the multi-composite was determined to be 1000°C.
Zinc-oxide nanocoating for improvement of the antibacterial and frictional behavior of nickel-titanium alloy.

AIM To fabricate a friction-reducing and antibacterial coating with zinc oxide (ZnO) nanoparticles on nickel-titanium (NiTi) wire. MATERIALS & METHODS NiTi orthodontic wires were coated with ZnO nanoparticles using the chemical deposition method. Characteristics of the coating as well as the physical, mechanical and antibacterial properties of the wires were investigated. RESULTS A stable and well-adhered ZnO coating on the NiTi wires was obtained. The hardness and elastic modulus of the ZnO nanocoating were 2.3 ± 0.2 and 61.0 ± 3.6 GPa, respectively. The coated wires presented up to 21% reduction in the frictional forces and antibacterial activity against Streptococcus mutans. ZnO nanocoating significantly improved the surface quality of NiTi wires. The modulus of elasticity, unloading forces and austenite finish temperature were not significantly different after coating. CONCLUSION This unique coating could be implemented into practice for safer and faster treatment to the benefit of both patient and clinician.
Study of magnetic resonance imaging at 1.5 Tesla based on pH-sensitive magnetization transfer technology

Objective:To investigate the feasibility of magnetization transfer(MT) technology in application of magnetic resonance pH imaging on 1.5 T clinical MR scanner.Materials and Methods:Two groups of agarose-creatine pH phantoms were prepared and imaged by improved spin-echo-magnetization transfer pulse sequence.Results:At radiofrequency offset of 224 Hz,the signal intensity magnetization transfer image of same pH phantoms showed no difference.The signal intensity of different pH phantoms depended on pH values.The higher pH was,the stronger signal intensity was.Conclusions:pH-sensitive magnetization transfer image can be acquired by improving the parameters and choosing appropriate radiofrequency offset of spin-echo-magnetization transfer pulse sequence on clinical 1.5 T MR scanner.This experimental study laid a solid foundation for further clinical applications.
Novel Method to Predict In Vivo Liver-to-Plasma Kpuu for OATP Substrates Using Suspension Hepatocytes

The ability to predict human liver-to-plasma unbound partition coefficient (Kpuu) is of great importance to estimate unbound liver concentration, develop PK/PD relationships, predict efficacy and toxicity in the liver, and model the drug-drug interaction potential for drugs that are asymmetrically distributed into the liver. A novel in vitro method has been developed to predict in vivo Kpuu with good accuracy using cryopreserved suspension hepatocytes in InVitroGRO HI media with 4% BSA. Validation was performed using six OATP substrates with rat in vivo Kpuu data from i.v. infusion studies where a steady state was achieved. Good in vitro-in vivo correlation (IVIVE) was observed as the in vitro Kpuu values were mostly within 2-fold of in vivo Kpuu. Good Kpuu IVIVE in human was also observed with in vivo Kpuu data of dehydropravastatin from positron emission tomography and in vivo Kpuu data from PK/PD modeling for pravastatin and rosuvastatin. Under the specific Kpuu assay conditions, the drug-metabolizing enzymes and influx/efflux transporters appear to function at physiologic levels. No scaling factors are necessary to predict in vivo Kpuu from in vitro data. The novel in vitro Kpuu method provides a useful tool in drug discovery to project in vivo Kpuu.
Lansoprazole Exacerbates Pemetrexed-Mediated Hematologic Toxicity by Competitive Inhibition of Renal Basolateral Human Organic Anion Transporter 3

Pemetrexed, a multitargeted antifolate, is eliminated by tubular secretion via human organic anion transporter 3 (hOAT3). Although proton pump inhibitors (PPIs) are frequently used in cancer patients, the drug interaction between PPIs and pemetrexed remains to be clarified. In this study, we examined the drug interaction between pemetrexed and PPIs in hOAT3-expressing cultured cells, and retrospectively analyzed the impact of PPIs on the development of hematologic toxicity in 108 patients who received pemetrexed and carboplatin treatment of nonsquamous non–small cell lung cancer for the first time between January 2011 and June 2015. We established that pemetrexed was transported via hOAT3 (Km = 68.3 ± 11.1 µM). Lansoprazole, rabeprazole, pantoprazole, esomeprazole, omeprazole, and vonoprazan inhibited hOAT3-mediated uptake of pemetrexed in a concentration-dependent manner. The inhibitory effect of lansoprazole was much greater than those of other PPIs and the apparent IC50 value of lansoprazole against pemetrexed transport via hOAT3 was 0.57 ± 0.17 µM. The inhibitory type of lansoprazole was competitive. In a retrospective study, multivariate analysis revealed that coadministration of lansoprazole, but not other PPIs, with pemetrexed and carboplatin was an independent risk factor significantly contributing to the development of hematologic toxicity (odds ratio: 10.004, P = 0.005). These findings demonstrated that coadministration of lansoprazole could exacerbate the hematologic toxicity associated with pemetrexed, at least in part, by competitive inhibition of hOAT3. Our results would aid clinicians to make decisions of coadministration drugs to avoid drug interaction-induced side effects for achievement of safe and appropriate chemotherapy with pemetrexed.
The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species

Rosa chinensis var. spontanea, an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp) genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC) region of 85,910 bp and one small single copy (SSC) region of 18,762 bp, separated by two inverted repeat (IR) regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. spontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses. This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa, and it might also facilitate the genetics and breeding of modern roses.