Complete mitochondrial and chloroplast DNA sequences of the freshwater green microalga Medakamo hakoo

We report the complete organellar genome sequences of an ultrasmall green alga, Medakamo hakoo strain M-hakoo 311, which has the smallest known nuclear genome in freshwater green algae. Medakamo hakoo has 90.8-kb chloroplast and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein-coding genes, respectively. The mitochondrial genome is the smallest in the Trebouxiophyceae algae studied so far. The GC content of the nuclear genome is 73%, but those of chloroplast and mitochondrial genomes are 41% and 35%, respectively. Codon usages in the organellar genomes have a different tendency from that in the nuclear genome. The organellar genomes have unique characteristics, such as the biased encoding of mitochondrial genes on a single strand and the absence of operon structures in chloroplast ribosomal genes. Medakamo hakoo will be helpful for understanding the evolution of the organellar genome and the regulation of gene expression in chloroplasts and mitochondria.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga

Reef-building corals thrive in oligotrophic environments due to their possession of endosymbiotic algae. Confined to the low pH interior of the symbiosome within the cell, the algal symbiont provides the coral host with photosynthetically fixed carbon. However, it remains unknown how carbon is released from the algal symbiont for uptake by the host. Here we show, using cultured symbiotic dinoflagellate, Breviolum sp., that decreases in pH directly accelerates the release of monosaccharides, that is, glucose and galactose, into the ambient environment. Under low pH conditions, the cell surface structures were deformed and genes related to cellulase were significantly upregulated in Breviolum. Importantly, the release of monosaccharides was suppressed by the cellulase inhibitor, glucopyranoside, linking the release of carbon to degradation of the agal cell wall. Our results suggest that the low pH signals the cellulase-mediated release of monosaccharides from the algal cell wall as an environmental response in coral reef ecosystems.

Establishment of a New Model Sea Anemone for Comparative Studies on Cnidarian-Algal Symbiosis

Frequent coral bleaching has drawn attention to the mechanisms of coral dinoflagellate endosymbiosis. Owing to the difficulty of rearing corals in the laboratory, model symbiosis systems are desired. The sea anemone Exaiptasia diaphana, hosting clade B1 of the genus Breviolum, has long been studied as a model system; however, a single species is insufficient for comparative studies and thus provides only limited resources for symbiosis research, especially regarding the specificity of host-symbiont associations. We established a clonal strain of the sea anemone Anthopleura atodai, whose symbiont was identified as a novel subclade of Symbiodinium (clade A) using a novel feeding method. We also developed a method to efficiently bleach various sea anemone species using a quinoclamine-based herbicide. Bleached A. atodai polyps were vital and able to reproduce asexually, exhibiting no signs of harmful effects of the drug treatment. Pilot studies have suggested that host-symbiont specificity is influenced by multiple steps differently in A. atodai and E. diaphana. RNAseq analyses of A. atodai showed that multiple NPC2 genes were expressed in the symbiotic state, which have been suggested to function in the transport of sterols from symbionts to host cells. These results reveal the usefulness of A. atodai in comparative studies of cnidarian-algal symbiosis.

On the origin of appetite: GLWamide in jellyfish represents an ancestral satiety neuropeptide

Food intake is regulated by internal state. This function is mediated by hormones and neuropeptides, which are best characterized in popular model species. However, the evolutionary origins of such feeding-regulating neuropeptides are poorly understood. We used the jellyfish Cladonema to address this question. Our combined transcriptomic, behavioral, and anatomical approaches identified GLWamide as a feeding-suppressing peptide that selectively inhibits tentacle contraction in this jellyfish. In the fruit fly Drosophila, myoinhibitory peptide (MIP) is a related satiety peptide. Surprisingly, we found that GLWamide and MIP were fully interchangeable in these evolutionarily distant species for feeding suppression. Our results suggest that the satiety signaling systems of diverse animals share an ancient origin.

Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Ultrasmall algae have attracted the attention of biologists investigating the basic mechanisms underlying living systems. Their potential as effective organisms for producing useful substances is also of interest in bioindustry. Although genomic information is indispensable for elucidating metabolism and promoting molecular breeding, many ultrasmall algae remain genetically uncharacterized. Here, we present the nuclear genome sequence of an ultrasmall green alga of freshwater habitats, Medakamo hakoo. Evolutionary analyses suggest that this species belongs to a new genus within the class Trebouxiophyceae. Sequencing analyses revealed that its genome, comprising 15.8 Mbp and 7629 genes, is among the smallest known genomes in the Viridiplantae. Its genome has relatively few genes associated with genetic information processing, basal transcription factors, and RNA transport. Comparative analyses revealed that 1263 orthogroups were shared among 15 ultrasmall algae from distinct phylogenetic lineages. The shared gene sets will enable identification of genes essential for algal metabolism and cellular functions.

TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets

Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs.

For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).

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Minimizes sequence redundancy in large phylogenetic datasets

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Trims thousands of operational taxonomic units (OTUs) from a preliminary tree

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Maintains the desired minimal taxonomic diversity and retains specific OTUs for analysis

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Available coarse- and fine-tuning options depending on the phylogenetic question at hand

Gene expression alterations from reversible to irreversible stages during coral metamorphosis

For corals, metamorphosis from planktonic larvae to sedentary polyps is an important life event, as it determines the environment in which they live for a lifetime. Although previous studies on the reef-building coral Acropora have clarified a critical time point during metamorphosis when cells are committed to their fates, as defined by an inability to revert back to their previous states as swimming larvae (here referred to as the "point of no return"), the molecular mechanisms of this commitment to a fate remain unclear. To address this issue, we analyzed the transcriptomic changes before and after the point of no return by inducing metamorphosis of Acropora tenuis with Hym-248, a metamorphosis-inducing neuropeptide. Gene Ontology and pathway enrichment analysis of the 5893 differentially expressed genes revealed that G protein-coupled receptors (GPCRs) were enriched, including GABA receptor and Frizzled gene subfamilies, which showed characteristic temporal expression patterns. The GPCRs were then classified by comparison with those of Homo sapiens, Nematostella vectensis and Platynereis dumerilii. Classification of the differentially expressed genes into modules based on expression patterns showed that some modules with large fluctuations after the point of no return were biased toward functions such as protein metabolism and transport. This result suggests that in precommitted larvae, different types of GPCR genes function to ensure a proper environment, whereas in committed larvae, intracellular protein transport and proteolysis may cause a loss of the reversibility of metamorphosis as a result of cell differentiation.

Sequential variation of super periodic structures emerged in Bi-layered perovskite pillar-matrix epitaxial nanocomposite films with spinel ferrites

The phase stability of Aurivillius bismuth-layer structured Bi5Ti3FeO15 (BTFO15) has been investigated in an epitaxial pillar-matrix nanocomposite system with spinel ferrites.

Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians

Increases in seawater temperature can cause coral bleaching through loss of symbiotic algae (dinoflagellates of the family Symbiodiniaceae). Corals can recover from bleaching by recruiting algae into host cells from the residual symbiont population or from the external environment. However, the high coral mortality that often follows mass-bleaching events suggests that recovery is often limited in the wild. Here, we examine the effect of pre-exposure to heat stress on the capacity of symbiotic algae to infect cnidarian hosts using the Aiptasia (sea-anemone)-Symbiodiniaceae model system. We found that the symbiont strain Breviolum sp. CS-164 (ITS2 type B1), both free-living and in symbiosis, loses the capacity to infect the host following exposure to heat stress. This loss of infectivity is reversible, however, a longer exposure to heat stress increases the time taken for reversal. Under the same experimental conditions, the loss of infectivity was not observed in another strain Breviolum psygmophilum CCMP2459 (ITS2 type B2). Our results suggest that recovery from bleaching can be limited by the loss of symbiont infectivity following exposure to heat stress.

Complement profile in microscopic polyangiitis and granulomatosis with polyangiitis: analysis using sera from a nationwide prospective cohort study

OBJECTIVE

The complement cascade, especially the alternative pathway of complement, has been shown in basic research to be associated with anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV). We aimed to elucidate relationships between serum complement components and clinical characteristics in AAV.

METHOD

In a nationwide prospective cohort study (RemIT-JAV-RPGN), we measured the serum levels of C1q, C2, C3, C3b/iC3b, C4, C4b, C5, C5a, C9, factor B, factor D, factor H, factor I, mannose-binding lectin, and properdin in 52 patients with microscopic polyangiitis (MPA) and 39 patients with granulomatosis with polyangiitis (GPA).

RESULTS

The properdin level of MPA and GPA was significantly lower than that of healthy donors. The properdin level was negatively correlated with the Birmingham Vasculitis Activity Score (BVAS) (ρ = -0.2148, p = 0.0409). The factor D level at 6 months was significantly positively correlated with the Vasculitis Damage Index (VDI) at 6, 12, and 24 months (ρ = 0.4207, 0.4132, and 0.3115, respectively). Patients with a higher ratio of C5a to C5 had higher neutrophil percentage and serum immunoglobulin G levels, and significantly lower creatinine levels. Cluster analysis divided the MPA and GPA patients into three subgroups. A principal component (PC) analysis aggregated 15 types of complements into alternative pathway-related PC 1 and complement classical pathway and common pathway-related PC 2.

CONCLUSIONS

The serum levels of properdin and factor D were correlated with the BVAS and the VDI in MPA and GPA, respectively. Our analyses suggested the pathological heterogeneity of MPA and GPA from the aspect of complement components.

Outcome of maintenance systemic chemotherapy with drug-free interval for metastatic urothelial carcinoma

OBJECTIVE

Aiming to achieve long-term disease control, maintenance systemic chemotherapy (MSC) with a 1-3-month drug-free interval is continued in selected patients. We report our experience of MSC for metastatic urothelial carcinoma (UC).

METHODS

Of 228 metastatic UC patients treated with systemic chemotherapy, 40 (17.5%, 40/228) had continuously undergone MSC. Data on the regimen, cycle number, and reason for the discontinuation of MSC were also collected. We analyzed OS from the initiation of MSC until death or the last follow-up, using the log-rank test to assess the significance of differences.

RESULTS

The median number of cycles of chemotherapy was 6, and the responses were CR in 6, PR in 20, SD in 13, and PD in 1 before MSC. Gemcitabine plus CDDP or carboplatin was mainly performed as MSC (70%, 28/40). MSC was repeated quarterly in 30 (75%, 30/40), every two months in 8 (20%, 8/40), and with other intervals in 2 (5%, 2/40). Overall, a median of 3.5 cycles (range: 1-29) of MSC was performed. The reason for the discontinuation of MSC was PD in 24 (60%, 24/40), favorable disease control in 9 (22.5%, 9/40), and myelosuppression in 3 (7.5%, 3/40), and for other reasons in 2 (5%, 2/40). MSC was ongoing in 2 (5%, 2/40). The median OS was 27 months from the initiation of MSC. PS0 (P = 0.0169), the absence of lung metastasis (P = 0.0387), and resection of the primary site (P = 0.0495) were associated with long-term survival after MSC.

CONCLUSIONS

In selected patients, long-term systemic chemotherapy could be performed with a drug-free interval. Our maintenance strategy with cytotoxic drugs may become one of the treatment options for long-term disease control.

Environmental factors explain spawning day deviation from full moon in the scleractinian coral Acropora

Broadcast-spawning scleractinian corals annually release their gametes with high levels of synchrony, both within and among species. However, the timing of spawning can vary inter-annually. In particular, the night of spawning relative to the full moon phase can vary considerably among years at some locations. Although multiple environmental factors can affect the night of spawning, their effects have not been quantitatively assessed at the multi-regional level. In this study, we analysed environmental factors that are potentially correlated with spawning day deviation, in relation to the full moon phase, in Acropora corals inhabiting seven reefs in Australia and Japan. We accordingly found that sea surface temperature and wind speed within one to two months prior to the full moon of the spawning month were strongly correlated with spawning day deviations. In addition, solar flux had a weak effect on the night of spawning. These findings indicate that Acropora have the capacity to adjust their development and physiology in response to environmental factors for fine-tuning the timing of synchronous spawning, thereby maximizing reproductive success and post-fertilization survival.

Evolution of Photosynthetic Eukaryotes; Current Opinion, Perplexity, and a New Perspective

The evolution of eukaryotic photosynthesis marked a major transition for life on Earth, profoundly impacting the atmosphere of the Earth and evolutionary trajectory of an array of life forms. There are about ten lineages of photosynthetic eukaryotes, including Chloroplastida, Rhodophyta, and Cryptophyta. Mechanistically, eukaryotic photosynthesis arose via a symbiotic merger between a host eukaryote and either a cyanobacterial or eukaryotic photosymbiont. There are, however, many aspects of this major evolutionary transition that remain unsettled. The field, so far, has been dominated by proposals formulated following the principle of parsimony, such as the Archaeplastida hypothesis, in which a taxonomic lineage is often conceptually recognized as an individual cell (or a distinct entity). Such an assumption could lead to confusion or unrealistic interpretation of discordant genomic and phenotypic data. Here, we propose that the free-living ancestors to the plastids may have originated from a diversified lineage of cyanobacteria that were prone to symbioses, akin to some modern-day algae such as the Symbiodiniaceae dinoflagellates and Chlorella-related algae that associate with a number of unrelated host eukaryotes. This scenario, which assumes the plurality of ancestral form, better explains relatively minor but important differences that are observed in the genomes of modern-day eukaryotic algal species. Such a non-typological (or population-aware) way of thinking seems to better-model empirical data, such as discordant phylogenies between plastid and host eukaryote genes.

Laser-Beam-Patterned Topological Insulating States on Thin Semiconducting MoS_{2}

Identifying the two-dimensional (2D) topological insulating (TI) state in new materials and its control are crucial aspects towards the development of voltage-controlled spintronic devices with low-power dissipation. Members of the 2D transition metal dichalcogenides have been recently predicted and experimentally reported as a new class of 2D TI materials, but in most cases edge conduction seems fragile and limited to the monolayer phase fabricated on specified substrates. Here, we realize the controlled patterning of the 1T^{'} phase embedded into the 2H phase of thin semiconducting molybdenum-disulfide by laser beam irradiation. Integer fractions of the quantum of resistance, the dependence on laser-irradiation conditions, magnetic field, and temperature, as well as the bulk gap observation by scanning tunneling spectroscopy and theoretical calculations indicate the presence of the quantum spin Hall phase in our patterned 1T^{'} phases.

Pulsed laser deposition with rapid beam deflection by a galvanometer mirror scanner

A pulsed laser deposition system with rapid beam deflection (RBD-PLD) by a galvanometer mirror scanner has been developed for alternating ablation of multiple targets with a single laser instrument. In this system, the alternating deposition of different target materials is carried out by scanning the laser beam between the positionally fixed targets with a galvanometer mirror instead of mechanically switching the target positions on a fixed optical path of the laser beam as is done in conventional pulsed laser deposition (PLD) systems. Thus, the "wait" time required for switching target materials to be deposited, which typically takes several seconds in a conventional system, can be made as short as a few milliseconds. We demonstrate some of the advantages of this PLD system in several technologically important aspects of thin film synthesis: (1) fast fabrication of binary alloy films, (2) preparation of natural composition spread libraries, (3) effect of the target switching time on the deposition of volatile compounds, (4) control of the degree of mixing of two different materials in a film, and (5) efficient growth of compositionally graded thin films.

Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis

Stable endosymbiotic relationships between cnidarian animals and dinoflagellate algae are vital for sustaining coral reef ecosystems. Recent studies have shown that elevated seawater temperatures can cause the collapse of their endosymbiosis, known as 'bleaching', and result in mass mortality. However, the molecular interplay between temperature responses and symbiotic states still remains unclear. To identify candidate genes relevant to the symbiotic stability, we performed transcriptomic analyses under multiple conditions using the symbiotic and apo-symbiotic (symbiont free) Exaiptasia diaphana, an emerging model sea anemone. Gene expression patterns showed that large parts of differentially expressed genes in response to heat stress were specific to the symbiotic state, suggesting that the host sea anemone could react to environmental changes in a symbiotic state-dependent manner. Comparative analysis of expression profiles under multiple conditions highlighted candidate genes potentially important in the symbiotic state transition under heat-induced bleaching. Many of these genes were functionally associated with carbohydrate and protein metabolisms in lysosomes. Symbiont algal genes differentially expressed in hospite encode proteins related to heat shock response, calcium signaling, organellar protein transport, and sugar metabolism. Our data suggest that heat stress alters gene expression in both the hosts and symbionts. In particular, heat stress may affect the lysosome-mediated degradation and transportation of substrates such as carbohydrates through the symbiosome (phagosome-derived organelle harboring symbiont) membrane, which potentially might attenuate the stability of symbiosis and lead to bleaching-associated symbiotic state transition.

Acoustic emissions of Sorex unguiculatus (Mammalia: Soricidae): Assessing the echo-based orientation hypothesis

Shrew species have been proposed to utilize an echo-based orientation system to obtain additional acoustic information while surveying their environments. This system has been supported by changes in vocal emission rates when shrews encounter different habitats of varying complexity, although detailed acoustic features in this system have not been reported. In this study, behavioral experiments were conducted using the long-clawed shrew (Sorex unguiculatus) to assess this orientation system. Three experimental conditions were set, two of which contained obstacles. Short-click, noisy, and different types of tonal calls in the audible-to-ultrasonic frequency range were recorded under all experimental conditions. The results indicated that shrews emit calls more frequently when they are facing obstacles or exploring the experimental environment. Shrews emitted clicks and several different types of tonal calls while exploring, and modified the use of different types of calls for varying behavior. Furthermore, shrews modified the dominant frequency and duration of squeak calls for different types of obstacles, that is, plants and acrylic barriers. The vocalizations emitted at short inter-pulse intervals could not be observed when shrews approached these obstacles. These results are consistent with the echo-based orientation hypothesis according to which shrews use a simple echo-orientation system to obtain information from their surrounding environments, although further studies are needed to confirm this hypothesis.

Measurement of Prompt D^{0} Meson Azimuthal Anisotropy in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The prompt D^{0} meson azimuthal anisotropy coefficients, v_{2} and v_{3}, are measured at midrapidity (|y|<1.0) in Pb-Pb collisions at a center-of-mass energy sqrt[s_{NN}]=5.02  TeV per nucleon pair with data collected by the CMS experiment. The measurement is performed in the transverse momentum (p_{T}) range of 1 to 40  GeV/c, for central and midcentral collisions. The v_{2} coefficient is found to be positive throughout the p_{T} range studied. The first measurement of the prompt D^{0} meson v_{3} coefficient is performed, and values up to 0.07 are observed for p_{T} around 4  GeV/c. Compared to measurements of charged particles, a similar p_{T} dependence, but smaller magnitude for p_{T}<6  GeV/c, is found for prompt D^{0} meson v_{2} and v_{3} coefficients. The results are consistent with the presence of collective motion of charm quarks at low p_{T} and a path length dependence of charm quark energy loss at high p_{T}, thereby providing new constraints on the theoretical description of the interactions between charm quarks and the quark-gluon plasma.

Measurement of associated Z + charm production in proton-proton collisions at s = 8 TeV

A study of the associated production of a Z boson and a charm quark jet ( Z + c ), and a comparison to production with a b quark jet ( Z + b ), in p p collisions at a centre-of-mass energy of 8TeV are presented. The analysis uses a data sample corresponding to an integrated luminosity of 19.7fb - 1 , collected with the CMS detector at the CERN LHC. The Z boson candidates are identified through their decays into pairs of electrons or muons. Jets originating from heavy flavour quarks are identified using semileptonic decays of c or b flavoured hadrons and hadronic decays of charm hadrons. The measurements are performed in the kinematic region with two leptons withp T ℓ > 20 GeV ,| η ℓ | < 2.1 , 71 < m ℓ ℓ < 111 GeV , and heavy flavour jets withp T jet > 25 GeV and| η jet | < 2.5 . The Z + c production cross section is measured to be σ ( p p → Z + c + X ) B ( Z → ℓ + ℓ - ) = 8.8 ± 0.5 (stat) ± 0.6 (syst) pb . The ratio of the Z + c and Z + b production cross sections is measured to be σ ( p p → Z + c + X ) / σ ( p p → Z + b + X ) = 2.0 ± 0.2 (stat) ± 0.2 (syst) . The Z + c production cross section and the cross section ratio are also measured as a function of the transverse momentum of the Z boson and of the heavy flavour jet. The measurements are compared with theoretical predictions.

Suppression of Excited ϒ States Relative to the Ground State in Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The relative yields of ϒ mesons produced in pp and Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV and reconstructed via the dimuon decay channel are measured using data collected by the CMS experiment. Double ratios are formed by comparing the yields of the excited states, ϒ(2S) and ϒ(3S), to the ground state, ϒ(1S), in both Pb-Pb and pp collisions at the same center-of-mass energy. The double ratios, [ϒ(nS)/ϒ(1S)]_{Pb-Pb}/[ϒ(nS)/ϒ(1S)]_{pp}, are measured to be 0.308±0.055(stat)±0.019(syst) for the ϒ(2S) and less than 0.26 at 95% confidence level for the ϒ(3S). No significant ϒ(3S) signal is found in the Pb-Pb data. The double ratios are studied as a function of collision centrality, as well as ϒ transverse momentum and rapidity. No significant dependencies are observed.

Study of dijet events with a large rapidity gap between the two leading jets in pp collisions at s = 7 TeV

Events with no charged particles produced between the two leading jets are studied in proton-proton collisions ats = 7 TeV . The jets were required to have transverse momentump T jet > 40 GeV and pseudorapidity1.5 < | η jet | < 4.7 , and to have values of η jet with opposite signs. The data used for this study were collected with the CMS detector during low-luminosity running at the LHC, and correspond to an integrated luminosity of 8pb - 1 . Events with no charged particles withp T > 0.2 GeV in the interval - 1 < η < 1 between the jets are observed in excess of calculations that assume no color-singlet exchange. The fraction of events with such a rapidity gap, amounting to 0.5-1% of the selected dijet sample, is measured as a function of the p T of the second-leading jet and of the rapidity separation between the jets. The data are compared to previous measurements at the Tevatron, and to perturbative quantum chromodynamics calculations based on the Balitsky-Fadin-Kuraev-Lipatov evolution equations, including different models of the non-perturbative gap survival probability.

Observation of Correlated Azimuthal Anisotropy Fourier Harmonics in pp and p+Pb Collisions at the LHC

The azimuthal anisotropy Fourier coefficients (v_{n}) in 8.16 TeV p+Pb data are extracted via long-range two-particle correlations as a function of the event multiplicity and compared to corresponding results in pp and PbPb collisions. Using a four-particle cumulant technique, v_{n} correlations are measured for the first time in pp and p+Pb collisions. The v_{2} and v_{4} coefficients are found to be positively correlated in all collision systems. For high-multiplicity p+Pb collisions, an anticorrelation of v_{2} and v_{3} is observed, with a similar correlation strength as in PbPb data at the same multiplicity. The new correlation results strengthen the case for a common origin of the collectivity seen in p+Pb and PbPb collisions in the measured multiplicity range.

Measurements of the p p → Z Z production cross section and the Z → 4 ℓ branching fraction, and constraints on anomalous triple gauge couplings at s = 13 TeV

Four-lepton production in proton-proton collisions, p p → ( Z / γ ∗ ) ( Z / γ ∗ ) → 4 ℓ , where ℓ = e or μ , is studied at a center-of-mass energy of 13TeV with the CMS detector at the LHC. The data sample corresponds to an integrated luminosity of 35.9fb - 1 . The ZZ production cross section, σ ( p p → Z Z ) = 17.2 ± 0.5 (stat) ± 0.7 (syst) ± 0.4 (theo) ± 0.4 (lumi) pb , measured using events with two opposite-sign, same-flavor lepton pairs produced in the mass region 60 < m ℓ + ℓ - < 120 GeV , is consistent with standard model predictions. Differential cross sections are measured and are well described by the theoretical predictions. The Z boson branching fraction to four leptons is measured to be B ( Z → 4 ℓ ) = 4 . 83 - 0.22 + 0.23 ( s t a t ) - 0.29 + 0.32 ( s y s t ) ± 0.08 ( t h e o ) ± 0.12 ( l u m i ) × 10 - 6 for events with a four-lepton invariant mass in the range 80 < m 4 ℓ < 100 GeV and a dilepton massm ℓ ℓ > 4 GeV for all opposite-sign, same-flavor lepton pairs. The results agree with standard model predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous ZZZ and ZZ γ couplings at 95% confidence level: - 0.0012 < f 4 Z < 0.0010 , - 0.0010 < f 5 Z < 0.0013 , - 0.0012 < f 4 γ < 0.0013 , - 0.0012 < f 5 γ < 0.0013 .

Measurements of the p p → Z Z production cross section and the Z → 4 ℓ branching fraction, and constraints on anomalous triple gauge couplings at s = 13 TeV

Four-lepton production in proton-proton collisions, p p → ( Z / γ ∗ ) ( Z / γ ∗ ) → 4 ℓ , where ℓ = e or μ , is studied at a center-of-mass energy of 13 TeV with the CMS detector at the LHC. The data sample corresponds to an integrated luminosity of 35.9 fb - 1 . The ZZ production cross section, σ ( p p → Z Z ) = 17.2 ± 0.5 (stat) ± 0.7 (syst) ± 0.4 (theo) ± 0.4 (lumi) pb , measured using events with two opposite-sign, same-flavor lepton pairs produced in the mass region 60 < m ℓ + ℓ - < 120 GeV , is consistent with standard model predictions. Differential cross sections are measured and are well described by the theoretical predictions. The Z boson branching fraction to four leptons is measured to be B ( Z → 4 ℓ ) = 4 . 83 - 0.22 + 0.23 ( s t a t ) - 0.29 + 0.32 ( s y s t ) ± 0.08 ( t h e o ) ± 0.12 ( l u m i ) × 10 - 6 for events with a four-lepton invariant mass in the range 80 < m 4 ℓ < 100 GeV and a dilepton mass m ℓ ℓ > 4 GeV for all opposite-sign, same-flavor lepton pairs. The results agree with standard model predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous ZZZ and ZZ γ couplings at 95% confidence level: - 0.0012 < f 4 Z < 0.0010 , - 0.0010 < f 5 Z < 0.0013 , - 0.0012 < f 4 γ < 0.0013 , - 0.0012 < f 5 γ < 0.0013 .

Search for dark matter produced in association with heavy-flavor quark pairs in proton-proton collisions at s = 13 TeV

A search is presented for an excess of events with heavy-flavor quark pairs ( t t ¯ and b b ¯ ) and a large imbalance in transverse momentum in data from proton-proton collisions at a center-of-mass energy of 13TeV . The data correspond to an integrated luminosity of 2.2fb - 1 collected with the CMS detector at the CERN LHC. No deviations are observed with respect to standard model predictions. The results are used in the first interpretation of dark matter production in t t ¯ and b b ¯ final states in a simplified model. This analysis is also the first to perform a statistical combination of searches for dark matter produced with different heavy-flavor final states. The combination provides exclusions that are stronger than those achieved with individual heavy-flavor final states.

Advancement of magma fragmentation by inhomogeneous bubble distribution

Decompression times reported in previous studies suggest that thoroughly brittle fragmentation is unlikely in actual explosive volcanic eruptions. What occurs in practice is brittle-like fragmentation, which is defined as the solid-like fracture of a material whose bulk rheological properties are close to those of a fluid. Through laboratory experiments and numerical simulation, the link between the inhomogeneous structure of bubbles and the development of cracks that may lead to brittle-like fragmentation was clearly demonstrated here. A rapid decompression test was conducted to simulate the fragmentation of a specimen whose pore morphology was revealed by X-ray microtomography. The dynamic response during decompression was observed by high-speed photography. Large variation was observed in the responses of the specimens even among specimens with equal bulk rheological properties. The stress fields of the specimens under decompression computed by finite element analysis shows that the presence of satellite bubbles beneath a large bubble induced the stress concentration. On the basis of the obtained results, a new mechanism for brittle-like fragmentation is proposed. In the proposed scenario, the second nucleation of bubbles near the fragmentation surface is an essential process for the advancement of fragmentation in an upward magma flow in a volcanic conduit.

Search for Evidence of the Type-III Seesaw Mechanism in Multilepton Final States in Proton-Proton Collisions at sqrt[s]=13 TeV

A search for a signal consistent with the type-III seesaw mechanism in events with three or more electrons or muons is presented. The data sample consists of proton-proton collisions at sqrt[s]=13  TeV collected by the CMS experiment at the LHC in 2016 and corresponds to an integrated luminosity of 35.9  fb^{-1}. Selection criteria based on the number of leptons and the invariant mass of oppositely charged lepton pairs are used to distinguish the signal from the standard model background. The observations are consistent with the expectations from standard model processes. The results are used to place limits on the production of heavy fermions of the type-III seesaw model as a function of the branching ratio to each lepton flavor. In the scenario of equal branching fractions to each lepton flavor, heavy fermions with masses below 840 GeV are excluded. This is the most sensitive probe to date of the type-III seesaw mechanism.

Measurements of the associated production of a Z boson and b jets in pp collisions at s = 8 TeV

Measurements of the associated production of a Z boson with at least one jet originating from a b quark in proton-proton collisions ats = 8 TeV are presented. Differential cross sections are measured with data collected by the CMS experiment corresponding to an integrated luminosity of 19.8fb - 1 . Z bosons are reconstructed through their decays to electrons and muons. Cross sections are measured as a function of observables characterizing the kinematics of the b jet and the Z boson. Ratios of differential cross sections for the associated production with at least one b jet to the associated production with any jet are also presented. The production of a Z boson with at least two b jets is investigated, and differential cross sections are measured for the dijet system. Results are compared to theoretical predictions, testing two different flavour schemes for the choice of initial-state partons.

Measurement of the triple-differential dijet cross section in proton-proton collisions at s = 8 TeV and constraints on parton distribution functions

A measurement is presented of the triple-differential dijet cross section at a centre-of-mass energy of 8TeV using 19.7fb -1 of data collected with the CMS detector in proton-proton collisions at the LHC. The cross section is measured as a function of the average transverse momentum, half the rapidity separation, and the boost of the two leading jets in the event. The cross section is corrected for detector effects and compared to calculations in perturbative quantum chromodynamics at next-to-leading order accuracy, complemented with electroweak and nonperturbative corrections. New constraints on parton distribution functions are obtained and the inferred value of the strong coupling constant isα S ( M Z ) = 0.1199 ± 0.0015 ( exp ) - 0.0020 + 0.0031 ( theo ) , where M Z is the mass of the Z boson.