bluuebunny/crossref_metadata_2025 huggingface dataset:
Disentangling elevation, annual flooding regime and salinity as hydrochemical determinants of halophyte distribution in non-tidal saltmarsh
Authors: Vélez-Martín Alberto , Davy Anthony J , Luque Carlos J , Castellanos Eloy M
Published: April 2020

Background and Aims

Hydrological disconnection, especially in a Mediterranean climate, creates coastal saltmarshes with an annual cycle of flooding that are unlike tidally inundated systems. Winter rainfall produces long, continuous hydroperiods, alternating with continuous exposure caused by evaporation in warm, rain-free summers. We aimed to distinguish the effects of elevation, hydroperiod and salinity on annual and perennial halophytes in such a system.

Methods

We recorded vegetation and sediment salinity in permanent quadrats on a marsh in the Doñana National Park, Spain, over seven consecutive years with widely differing rainfall. Elevation was determined from LIDAR data and the duration of the annual hydroperiod from satellite imagery. The independent effects of collaterally varying elevation, hydroperiod and salinity on species distribution were examined using generalized linear models and hierarchical partitioning.

Key Results

Both hydroperiod and salinity were inversely related to elevation but interannual fluctuations in rainfall facilitated discrimination of independent effects of the three collaterally varying factors on halophyte distribution. Perennial distribution was strongly structured by elevation, whereas many annual species were more sensitive to hydroperiod. The independent effects of salinity varied according to individual species’ salt tolerance from positive to negative. Thus life-history and, in the case of annuals, phenology were important in determining the relative impact of elevation and hydroperiod.

Conclusions

The consequences of elevation for halophyte distribution in seasonally flooded saltmarshes are fundamentally different from those in tidal marshes, because protracted and frequent flooding regimes require different adaptations, and because of the unpredictability of flooding from year to year. These differences could explain greater species diversity in non-tidal marshes and the absence of key saltmarsh species prominent in tidal marshes. The vegetation of non-tidal marshes will be particularly susceptible to the more extreme annual cycles of temperature and rainfall predicted for Mediterranean climates.
Queen succession conflict in the paper wasp Polistes dominula is mitigated by age-based convention
Authors: Taylor Benjamin A , Cini Alessandro , Cervo Rita , Reuter Max , Sumner Seirian
Published: April 2020

Reproduction in cooperative animal groups is often dominated by one or a few individuals, with the remaining group members relegated to nonreproductive helping roles. This reproductive skew can evolve if helpers receive fitness benefits such as potential future inheritance of the breeding position, but the mechanisms by which inheritance is determined are not well resolved. Polistes paper wasps form highly reproductively skewed groups and inheritance of the breeding position is likely to play a key role in the maintenance of this social structure, making them excellent models for the processes by which simple societies are maintained. Reproductive succession is thought to be determined via an age-based convention in some Polistes species, but there is also evidence for contest-based succession systems in which the replacement queen uses physical aggression to overpower and thereby subordinate her nestmates. Here, we provide evidence that queen succession in colonies of the European paper wasp Polistes dominula is determined via convention rather than contest, with little disruption to the colony’s social functioning. We use queen removal experiments and fine-scale behavioral analyses to confirm that age is a strong predictor of succession, and that behavioral responses to queen removal are restricted to the oldest individuals rather than being experienced equally across the group. We provide the most comprehensive and detailed experimental analysis on the dynamics of breeder succession in a cooperatively breeding invertebrate to date, thereby shedding light on the mechanisms by which animal societies are able to maintain cohesion in the face of within-group conflict.
Molecular phylogeny and biogeography ofTriplophysastone loaches in the Central Chinese Mountains
Authors: Wu Huihui , Gu Qianhong , Zhou Chuanjiang , Tang Yongtao , Husemann Martin , Meng Xiaolin , Zhang Jianxin , Nie Guoxing , Li Xuejun
Published: April 2020

The geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.
Morphometrics and genetics highlight the complex history of Eastern Mediterranean spiny mice
Authors: Renaud Sabrina , Hardouin Emilie A , Chevret Pascale , Papayiannis Katerina , Lymberakis Petros , Matur Ferhat , Garcia-Rodriguez Oxala , Andreou Demetra , Çetintaş Ortaç , Sözen Mustafa , Hadjisterkotis Eleftherios , Mitsainas George P
Published: April 2020

Spiny mice of the Acomys cahirinus group display a complex geographical structure in the Eastern Mediterranean area, as shown by previous genetic and chromosomal studies. To better elucidate the evolutionary relationships between insular populations from Crete and Cyprus and continental populations from North Africa and Cilicia in Turkey, genetic and morphometric variations were investigated, based on mitochondrial D-loop sequences, and the size and shape of the first upper molar. The Cypriot and the Cilician populations show idiosyncratic divergence in molar size and shape, while Cretan populations present a geographical structure with at least three differentiated subpopulations, as shown by congruent distributions of haplogroups, Robertsonian fusions and morphometric variation. A complex history of multiple introductions is probably responsible for this structure, and insular isolation coupled with habitat shift should have further promoted a pronounced and rapid morphological evolution in molar size and shape on Crete and Cyprus.
Phylogeography and genetic structure of an iconic tree of the Sonoran Desert, the Cirio (Fouquieria columnaris), based on chloroplast DNA
Authors: Martínez-Noguez Josué J , León de la Luz José Luis , Delgadillo Rodríguez José , García-De León Francisco J
Published: April 2020

We have examined the phylogeographical distribution of chloroplast DNA (cpDNA) lineages of Fouquieria columnaris (Kellogg) Kellogg ex Curran (Fouquieriaceae) in the Sonoran Desert, to understand how historical climatic and/or geological changes have influenced genetic patterns in the species. Using two chloroplast intergenic DNA spacers (psbJ-petA and ndhF-rpl32), we found low levels of nucleotide diversity (π = 0.0025) but high levels of haplotype diversity (h = 0.9339). Analysis of 28 haplotypes revealed four lineages, one belonging to the continental massif and three to the peninsula of Baja California. This structure may be explained and dated by three events: (1) formation of the Gulf of California during the late Miocene (7.24 Mya), (2) activity of the Tres Vírgenes volcanic field (1.20 Mya) and (3) opening of the mid-peninsula seaway during the late Pleistocene (1.53 Mya). Furthermore, the cpDNA lineages show evidence for population contraction during the Last Glacial Maximum, with a subsequent population expansion in the Holocene.
Impact of Community-Based Mass Testing and Treatment on Malaria Infection Prevalence in a High-Transmission Area of Western Kenya: A Cluster Randomized Controlled Trial
Authors: Samuels Aaron M , Odero Nobert Awino , Odongo Wycliffe , Otieno Kephas , Were Vincent , Shi Ya Ping , Sang Tony , Williamson John , Wiegand Ryan , Hamel Mary J , Kachur S Patrick , Slutsker Laurence , Lindblade Kim A , Kariuki Simon K , Desai Meghna R
Published: April 2020

Background

Global gains toward malaria elimination have been heterogeneous and have recently stalled. Interventions targeting afebrile malaria infections may be needed to address residual transmission. We studied the efficacy of repeated rounds of community-based mass testing and treatment (MTaT) on malaria infection prevalence in western Kenya.

Methods

Twenty clusters were randomly assigned to 3 rounds of MTaT per year for 2 years or control (standard of care for testing and treatment at public health facilities along with government-sponsored mass long-lasting insecticidal net [LLIN] distributions). During rounds, community health volunteers visited all households in intervention clusters and tested all consenting individuals with a rapid diagnostic test. Those positive were treated with dihydroartemisinin-piperaquine. Cross-sectional community infection prevalence surveys were performed in both study arms at baseline and each year after 3 rounds of MTaT. The primary outcome was the effect size of MTaT on parasite prevalence by microscopy between arms by year, adjusted for age, reported LLIN use, enhanced vegetative index, and socioeconomic status.

Results

Demographic and behavioral characteristics, including LLIN usage, were similar between arms at each survey. MTaT coverage across the 3 annual rounds ranged between 75.0% and 77.5% in year 1, and between 81.9% and 94.3% in year 2. The adjusted effect size of MTaT on the prevalence of parasitemia between arms was 0.93 (95% confidence interval [CI], .79–1.08) and 0.92 (95% CI, .76–1.10) after year 1 and year 2, respectively.

Conclusions

MTaT performed 3 times per year over 2 years did not reduce malaria parasite prevalence in this high-transmission area.

Clinical Trials Registration

NCT02987270.
Genetic basis and molecular biology of cardiac arrhythmias in cardiomyopathies
Authors: Marian Ali J , Asatryan Babken , Wehrens Xander H T
Published: April 2020

Cardiac arrhythmias are common, often the first, and sometimes the life-threatening manifestations of hereditary cardiomyopathies. Pathogenic variants in several genes known to cause hereditary cardiac arrhythmias have also been identified in the sporadic cases and small families with cardiomyopathies. These findings suggest a shared genetic aetiology of a subset of hereditary cardiomyopathies and cardiac arrhythmias. The concept of a shared genetic aetiology is in accord with the complex and exquisite interplays that exist between the ion currents and cardiac mechanical function. However, neither the causal role of cardiac arrhythmias genes in cardiomyopathies is well established nor the causal role of cardiomyopathy genes in arrhythmias. On the contrary, secondary changes in ion currents, such as post-translational modifications, are common and contributors to the pathogenesis of arrhythmias in cardiomyopathies through altering biophysical and functional properties of the ion channels. Moreover, structural changes, such as cardiac hypertrophy, dilatation, and fibrosis provide a pro-arrhythmic substrate in hereditary cardiomyopathies. Genetic basis and molecular biology of cardiac arrhythmias in hereditary cardiomyopathies are discussed.
Feeding exogenous dsRNA interferes with endogenous sRNA accumulation inParamecium
Authors: Karunanithi Sivarajan , Oruganti Vidya , de Wijn Raphael , Drews Franziska , Cheaib Miriam , Nordström Karl , Simon Martin , Schulz Marcel H
Published: April 2020

Supply of exogenous dsRNA (exo-dsRNA), either by injection or by feeding, is a fast and powerful alternative to classical knockout studies. The biotechnical potential of feeding techniques is evident from the numerous studies focusing on oral administration of dsRNA to control pests and viral infection in crops/animal farming. We aimed to dissect the direct and indirect effects of exo-dsRNA feeding on the endogenous short interfering RNA (endo-siRNA) populations of the free-living ciliate Paramecium. We introduced dsRNA fragments against Dicer1 (DCR1), involved in RNA interference (RNAi) against exo- and few endo-siRNAs, and an RNAi unrelated gene, ND169. Any feeding, even the control dsRNA, diminishes genome wide the accumulation of endo-siRNAs and mRNAs. This cannot be explained by direct off-target effects and suggests mechanistic overlaps of the exo- and endo-RNAi mechanisms. Nevertheless, we observe a stronger down-regulation of mRNAs in DCR1 feeding compared with ND169 knockdown. This is likely due to the direct involvement of DCR1 in endo-siRNA accumulation. We further observed a cis-regulatory effect on mRNAs that overlap with phased endo-siRNAs. This interference of exo-dsRNA with endo-siRNAs warrants further investigations into secondary effects in target species/consumers, risk assessment of dsRNA feeding applications, and environmental pollution with dsRNA.
M∖L is Not Closed
Authors: Lima Davi , Matheus Carlos , Gustavo Moreira Carlos , Vieira Sandoel
Published: April 2020

We show that $1+3/\sqrt{2}$ is a point of the Lagrange spectrum $L$ that is accumulated by a sequence of elements of the complement $M\!\setminus\! L$ of the Lagrange spectrum in the Markov spectrum $M$. In particular, $M\!\setminus\! L$ is not a closed subset of $\mathbb{R}$, so that a question by T. Bousch has a negative answer.
Neglected Variables in the Interpretation of Serum Procalcitonin Levels in Patients With Septic Shock
Authors: Gilbert David N
Published: April 2020

The interpretation of serum procalcitonin (PCT) levels in septic patients is facilitated by reviewing the known stimuli that activate the PCT family of genes. Herein we describe 7 pathways that, alone or in combination, can increase serum PCT levels. As a marker of activation of innate immunity, high PCT levels affect clinical diagnosis, can be trended as a measure of “source” control, and can guide duration of antibacterial therapy in septic patients. Low PCT levels reflect little to no activation of an innate immune response, influence the differential diagnosis, and support the discontinuation of empiric antibiotic therapy. Understanding the pathways that result in elevated serum PCT levels is necessary for interpretation and subsequent clinical management.
Free market versus state or something else?: civic sector and competition law’s roles during the COVID-19 pandemic in Japan
Authors: Wakui Masako
Published: April 2020

COVID-19 is a highly transmittable disease. Until a vaccine is found, social distancing is the only way to prevent the virus from killing millions. Lockdown may also be necessary. Such measures inevitably cause an economic recession, so supplementing individuals’ incomes prove vital. Without income support, employees must go to work and risk contracting and spreading the virus. Instituting protective measures is the role of the government; however, a dysfunctional government causes citizens to seek alternative solutions from either the civic sector or charitable organizations.
Impact of increasing the levels of insoluble fiber and on the method of diet formulation measures of energy and nutrient digestibility in growing pigs
Authors: Acosta Jesus A , Stein Hans H , Patience John F
Published: April 2020

The objective of this study was to determine the differences in response to distillers dried grains with solubles (DDGS) level under constant nutrient or floating nutrient concentrations. A total of 21 ileal-cannulated gilts (33.1 ± 0.4 kg body weight) were randomly allotted to one of seven dietary treatments in a 3-period incomplete Latin square design (n = 9). Treatments consisted of a 0% DDGS basal diet, plus diets containing 15%, 30%, or 45% DDGS. Diets were formulated using one of two different formulation methods: 1) constant nutrient (CNU) where nutrients were held equal to the basal diet or 2) constant ingredients (CIN) where DDGS were added at the expense of corn and all other ingredients remained constant, so nutrient levels were allowed to “float.” Chromic oxide was added to the diets at 0.5% as an indigestible marker. Increasing the level of DDGS decreased the apparent ileal digestibility (AID) of dry matter (DM), gross energy (GE), starch, dispensable amino acids (AA), and fiber components (P < 0.050). The decrease in the AID of Lys, Met, Thr, and Trp was more pronounced under CNU compared with the CIN formulation method (P < 0.050). The decrease in the AID of hemicellulose was less pronounced under CNU compared with the CIN formulation method (P = 0.045). There was a DDGS level × formulation method interaction for the AID of acid hydrolyzed ether extract (AEE; P = 0.015); for the CNU formulation method, increasing level of DDGS decreased the AID of AEE from 0% to 30% and remained similar from 30% to 45% DDGS, whereas the CIN had no effect on the AID of AEE. Increasing the level of DDGS decreased the apparent total tract digestibility (ATTD) of DM, GE, and fiber components (P < 0.050), except for acid detergent fiber, which was not affected. The decrease in the ATTD of insoluble dietary fiber and total dietary fiber was less pronounced under CNU compared with CIN (P < 0.050). The ATTD of AEE decreased for CNU compared with CIN (P < 0.010). In conclusion, increasing the insoluble fiber level in the form of DDGS decreased the digestibility of most dietary components, including DM, GE, starch, insoluble fiber, and AA. The CNU and CIN formulation methods are equivalent when evaluating the digestibilities of DM, GE, starch, crude protein, and AA (when they were not added in purified synthetic forms). Differences between CNU and CIN formulation methods were detected for the digestibility of insoluble fiber, fat, and essential AA (when added as crystalline AA).
First arrivalQtomography based on an adjoint-state method
Authors: Huang Xinwei , Guo Zhenbo , Zhou Huawei , Yue Yubo
Published: April 2020

Under the assumption of invariant ray path in a weakly dissipative (high quality factor Q) subsurface medium, a tomographic inversion approach composed of two cascading applications of first arrival traveltime and Q tomography is proposed for compensating amplitude loss caused by near-surface anomalies, such as unconsolidated soils or the overburden gas cloud. To improve the computational efficiency, these two related tomography methods were adopted with an adjoint-state technique. First, arrival traveltime tomography will be performed to provide an inverted velocity model as one of the inputs for the following first arrival Q tomography. Then, the synthetic first break generated by the inverted velocity model will be used as a stable guidance of accessing the scopes of first arrival waveforms in the time domain where the potential attenuated time information is contained. The attenuated time will be estimated through a logarithmic spectral ratio linear regression corresponding to frequency-dependent propagation responses of different wave types. All these estimated attenuated times will be applied with reference signals to generate synthetic attenuated seismic data in the time domain, and their discrepancies with real data will be evaluated using similarity coefficients. The ones with larger values will be selected as optimal attenuated time inputs for the following Q tomographic inversion. Examples of both synthetic and field data reveal the feasibility and potential of this method.
Fundamentals of Anorectal Technical Skills: A Concise Surgical Skills Course
Authors: Kucera Walter B , Nealeigh Matthew D , Dyke Christopher , Ritter E Matthew , Artino Anthony R , Durning Steven J , Sweeney W Brian
Published: April 2020

Introduction

Anorectal diseases, among the most common surgical conditions, are underrepresented in medical training. The Fundamentals of Anorectal Technical Skills course was developed to provide cost-effective formal training in diagnosis of common anorectal conditions and in commonly performed anorectal procedures using the theories of deliberative practice and perceptual and adaptive learning.

Materials and Methods

First- through third-year general surgery and internal medicine residents and third- and fourth-year medical students participated in a course consisting of didactic instruction and hands on skills stations. The course covered common anorectal conditions, including internal and external hemorrhoids, fissures, condylomata, abscesses, fistula-in-ano, rectal prolapse, pilonidal disease, pruritis ani, and anal and rectal cancer, as well as common procedures such as anoscopy, excision of thrombosed external hemorrhoids, banding of internal hemorrhoids, rigid proctoscopy, incision and drainage of an abscess, administration of local anesthesia, and reduction of rectal prolapse. Before the course, participants completed a questionnaire consisting of demographics; previous anorectal experience, as measured by procedural case volume; confidence diagnosing and treating anorectal conditions; and a clinical knowledge multiple-choice quiz. Immediately following the course, participants took an additional survey reassessing their confidence and testing their clinical knowledge. This study was granted an educational exception by the Institutional Review Board at Walter Reed National Military Medical Center.

Results

Forty-three learners participated in this course. Forty-six percent of participants had not participated in any anorectal cases, 26% had participated in 1 to 5 cases, 17% had participated in 6 to 10 cases, 6% had been involved with 11 to15 cases, and 6% had been involved with more than 15 cases. For learners who had no prior experience, 1 to 5 prior cases, or 6 to 10 cases, there were statistically and educationally significant increases in confidence for all diagnoses and procedures. Additionally, there were statistically and educationally significant increases between pre-course and post-course quiz scores for learners who had no prior experience (7.8 ± 2.0 vs. 11.8 ± 2.5, P < 0.01, Cohen’s d = 1.8) and for those who had only participated in 1 to 5 cases (11.0 ± 3.7 vs. 14.2 ± 2.0, P = 0.04, Cohen’s d = 1.1). The changes in quiz scores for learners who previously had been involved with six or more cases were not statistically significant.

Conclusion

This course provides a cost-effective training that significantly boosts learners’ confidence in diagnosis of common anorectal procedures and confidence in performance of common anorectal procedures, in addition to improving objectively measured anorectal clinical knowledge.
An Attempt to Utilize the Body Composition Analyzer and the Functional Movement Screen (FMS) Test to Determine Injury Risk in Soldiers
Authors: Bertrandt Jerzy , Szarska Ewa , Łakomy Roman , Lepionka Tomasz , Anyżewska Anna , Lorenz Katarzyna , Maculewicz Ewelina
Published: April 2020

Introduction

Injuries are the most significant health problem of military services. Military medical surveillance data are useful for determining the magnitude and causes of the injury problem, identifying possible prevention targets and monitoring trends among military personnel. Soldiers serving in the Polish Armed Forces took part in the research. The aim of the study was to identify the most common injuries of the musculoskeletal system and to analyze causes of injuries. An additional goal was to examine whether there is a relationship between selected values of body composition indexes, the result of the functional movement screen (FMS) test and occurrence of an injury.

Material and Methods

The Polish Armed Forces soldiers serving in the land forces, military police, air forces took part in the research. The first stage was to complete the questionnaire regarding injuries in the last 5 years, their reasons, and the circumstances of their occurrence. After completing the survey, subjects were measured and weighed on the body composition analyzer. The next step was to perform a FMS to evaluate the locomotor system.

Results

In the groups of examined Polish soldiers, the most frequent injuries concerned lower limbs and, above all, a knee joint. The leading causes of injuries were activities resulting from the service as well as playing football and volleyball.

Conclusions

Parameters from the body composition analyzer such as body mass index, muscle mass distribution on lower limbs as well as evaluation in the FMS test may be helpful for the initial assessment of predisposition to injury.
Kinematic analysis of eagle simulations: evolution of λRe and its connection with mergers and gas accretion
Authors: Walo-Martín D , Falcón-Barroso J , Dalla Vecchia C , Pérez I , Negri A
Published: April 2020

We have developed a new tool to analyse galaxies in the eagle simulations as close as possible to observations. We investigated the evolution of their kinematic properties by means of the angular momentum proxy parameter, λRe, for galaxies with M⋆ ≥ 5 × 109 M⊙ in the RefL0100N1504 simulation up to redshift two (z = 2). Galaxies in the simulation show a wide variety of kinematic features, similiar to those found in integral-field spectroscopic studies. At z = 0 the distribution of galaxies in the λRe–ε plane is also in good agreement with results from observations. Scaling relations at z = 0 indicate that there is a critical mass, Mcrit /M⊙ = 1010.3, that divides two different regimes when we include the λRe parameter. The simulation shows that the distribution of galaxies in the λRe–ε plane evolves with time until z = 2 when galaxies are equally distributed in both λRe and ε. We studied the evolution of λRe with time and found that there is no connection between the angular momentum at z = 2 and z = 0. All systems reach their maximum λRe at z = 1 and then steadily lose angular momentum regardless of their merger history, except for the high star-forming systems that sustain that maximum value over time. The evolution of λRe in galaxies that have not experienced any merger in the last 10 Gyr can be explained by their level of gas accretion.
Centrifugally driven mass-loss and outbursts of massive stars
Authors: Zhao Xihui , Fuller Jim
Published: April 2020

Rotation and mass-loss are crucially interlinked properties of massive stars, strongly affecting their evolution and ultimate fate. Massive stars rotating near their break-up limit shed mass centrifugally, creating Be stars with circumstellar discs and possibly driving outbursts. Using the mesa stellar evolution code, we examine the effects of efficient angular momentum transport on the main-sequence and post-main-sequence rotational evolution of massive stars. In rapid rotators, angular momentum transported from the contracting core to the expanding envelope can spin-up the surface layers past the break-up rate, particularly for stars near (or beyond) the end of the main-sequence and in low-metallicity environments. We also demonstrate that centrifugal instabilities could arise in rapidly rotating massive stars, potentially triggering the S Doradus outbursts observed in luminous blue variable stars. Prior mass accretion from a binary companion increases both the likelihood and the intensity of centrifugal mass-loss. We discuss implications for massive stellar evolution, Be stars, and luminous blue variables.
Tidal evolution of exoplanetary systems hosting potentially habitable exoplanets. The cases of LHS-1140 b-c and K2-18 b-c
Authors: Gomes G O , Ferraz-Mello S
Published: April 2020

We present a model to study secularly and tidally evolving three-body systems composed by two low-mass planets orbiting a star, in the case where the bodies rotation axes are always perpendicular to the orbital plane. The tidal theory allows us to study the spin and orbit evolution of both stiff Earth-like planets and predominantly gaseous Neptune-like planets. The model is applied to study two recently discovered exoplanetary systems containing potentially habitable exoplanets (PHE): LHS-1140 b-c and K2-18 b-c. For the former system, we show that both LHS-1140 b and c must be in nearly circular orbits. For K2-18 b-c, the combined analysis of orbital evolution time-scales with the current eccentricity estimation of K2-18 b allows us to conclude that the inner planet (K2-18 c) must be a Neptune-like gaseous body. Only this would allow for the eccentricity of K2-18 b to be in the range of values estimated in recent works (e = 0.20 ± 0.08), provided that the uniform viscosity coefficient of K2-18 b is greater than 2.4 × 1019 Pa s (which is a value characteristic of stiff bodies) and supposing that such system has an age of some Gyr.
On Spin dependence of the Fundamental Plane of black hole activity
Authors: Ünal Caner , Loeb Abraham
Published: April 2020

The Fundamental Plane (FP) of black hole (BH) activity in galactic nuclei relates X-ray and radio luminosities to BH mass and accretion rate. However, there is a large scatter exhibited by the data, which motivated us for a new variable. We add BH spin as a new variable and estimate the spin dependence of the jet power and disc luminosity in terms of radio and X-ray luminosities. We assume the Blandford–Znajek process as the main source of the outflow, and find that the jet power depends on BH spin stronger than quadratically at moderate and large spin values. We perform a statistical analysis for 10 active galactic nuclei (AGNs) which have sub-Eddington accretion rates and whose spin values are measured independently via the reflection or continuum-fitting methods, and find that the spin-dependent relation describes the data significantly better. This analysis, if supported with more data, could imply not only the spin dependence of the FP relation, but also the Blandford–Znajek process in AGN jets.
Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins
Authors: Lindenburg Laurens , Huovinen Tuomas , van de Wiel Kayleigh , Herger Michael , Snaith Michael R , Hollfelder Florian
Published: April 2020

Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method—termed SpliMLiB for Split-and-Mix Library on Beads—was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.
Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2
Authors: Schellenberg Matthew J , Appel C Denise , Riccio Amanda A , Butler Logan R , Krahn Juno M , Liebermann Jenna A , Cortés-Ledesma Felipe , Williams R Scott
Published: April 2020

Tyrosyl-DNA phosphodiesterase 2 (TDP2) reverses Topoisomerase 2 DNA–protein crosslinks (TOP2-DPCs) in a direct-reversal pathway licensed by ZATTZNF451 SUMO2 E3 ligase and SUMOylation of TOP2. TDP2 also binds ubiquitin (Ub), but how Ub regulates TDP2 functions is unknown. Here, we show that TDP2 co-purifies with K63 and K27 poly-Ubiquitinated cellular proteins independently of, and separately from SUMOylated TOP2 complexes. Poly-ubiquitin chains of ≥ Ub3 stimulate TDP2 catalytic activity in nuclear extracts and enhance TDP2 binding of DNA–protein crosslinks in vitro. X-ray crystal structures and small-angle X-ray scattering analysis of TDP2-Ub complexes reveal that the TDP2 UBA domain binds K63-Ub3 in a 1:1 stoichiometric complex that relieves a UBA-regulated autoinhibitory state of TDP2. Our data indicates that that poly-Ub regulates TDP2-catalyzed TOP2-DPC removal, and TDP2 single nucleotide polymorphisms can disrupt the TDP2-Ubiquitin interface.
The omics discovery REST interface
Authors: Dass Gaurhari , Vu Manh-Tu , Xu Pan , Audain Enrique , Hitz Marc-Phillip , Grüning Björn A , Hermjakob Henning , Perez-Riverol Yasset
Published: April 2020

The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.
The Multifunctional Dioxygenases of Gibberellin Synthesis
Authors: Lange Theo , Pimenta Lange Maria Jo�o
Published: April 2020

Gibberellin (GA) hormones regulate the development of plants and their responses to environmental signals. The final part of GA biosynthesis is catalyzed by multifunctional 2-oxoglutarate-dependent dioxygenases, which are encoded by multigene families. According to their enzymatic properties and physiological functions, GA-oxidases are classified as anabolic or catabolic enzymes. Together they allow complex regulation of the GA biosynthetic pathway, which adapts the specific hormonal needs of a plant during development and interaction with its environment. In this review, we combine recent advances in enzymatic characterization of the multifunctional GA-oxidases, in particular, from cucumber and Arabidopsis that have been most comprehensively investigated.
Interrelationships Between BDNF, Superoxide Dismutase, and Cognitive Impairment in Drug-Naive First-Episode Patients With Schizophrenia
Authors: Xiu Mei Hong , Li Zezhi , Chen Da Chun , Chen Song , Curbo Maile E , Wu Hanjing Emily , Tong Yong Sheng , Tan Shu Ping , Zhang Xiang Yang
Published: April 2020

The pathogenesis and etiology of schizophrenia (SCZ) remains unclear. Accumulating studies showed that complex interrelationships between brain-derived neurotrophic factor (BDNF) and an imbalanced redox system has a crucial role in the psychopathology of SCZ. However, the influence of the interrelationships of BDNF and superoxide dismutase (SOD) on cognitive impairment and clinical symptomatology in drug-naive first-episode (DNFE) SCZ patients has not been studied thoroughly. Serum BDNF levels, plasma total SOD, manganese-SOD (Mn-SOD), copper/zinc-containing SOD (CuZn-SOD) activities, and malondialdehyde (MDA) levels were measured in 327 DNFE patients with SCZ and 391 healthy controls. Cognitive functions were measured using the Repeatable Battery for the Assessment of Neuropsychological status (RBANS) and clinical symptoms were evaluated by the Positive and Negative Syndrome Scale (PANSS). Compared with the controls, the DNFE patients had increased activities of total SOD and CuZn-SOD, and reduced levels of BDNF and MDA. BDNF levels were positively correlated with CuZn-SOD activity in patients. In addition, we found that elevated Mn-SOD and CuZn-SOD activities were related to PANSS depression factor. Moreover, an interactive effect of BDNF levels and Mn-SOD activity was associated with attentional index score in the patients. Therefore, our findings suggested that interrelationships between BDNF and antioxidant mechanisms might underlie the pathological mechanisms of cognitive impairments and symptomatology in the DNFE patients with SCZ.
Antipsychotic Dose in Acute Schizophrenia: A Meta-analysis
Authors: Takeuchi Hiroyoshi , MacKenzie Nicole E , Samaroo Dominic , Agid Ofer , Remington Gary , Leucht Stefan
Published: April 2020

Little is known regarding optimal antipsychotic doses in the acute phase of schizophrenia. The aim of the present study was to employ the concept of minimum effective dose (MED) in examining efficacy and tolerability within this population. MED was identified for each antipsychotic through a previous systematic review. We then identified double-blind placebo-controlled randomized trials that involved fixed-dose antipsychotic monotherapy in acute schizophrenia and compared the identified MED vs higher doses of the same oral antipsychotic. Studies were selected from a recent meta-analysis examining dose–response relationship of second-generation antipsychotics and haloperidol. We extracted the data on study discontinuation, psychopathology, extrapyramidal symptoms, and treatment-emergent adverse events. For each antipsychotic, we conducted a meta-analysis to compare outcomes between MED and 2-fold MED, and MED and 3-fold MED. A total of 26 studies involving 5618 patients were included in the meta-analysis. In terms of study discontinuation, significant differences were found in study discontinuation due to lack of efficacy between MED and higher doses, in favor of 2-fold and 3-fold MEDs. Regarding psychopathology, both 2-fold and 3-fold MEDs were superior to MED for total and positive symptom scores. As for side effects, 2-fold MED proved inferior to MED for parkinsonism scores and diarrhea, whereas 3-fold MED was inferior for akathisia, somnolence, and vomiting. Findings suggest that clinicians can dose an antipsychotic at 2-fold or 3-fold MED for patients with acute schizophrenia but should closely monitor side effects.
A new stem-neopterygian fish from the Middle Triassic (Anisian) of Yunnan, China, with a reassessment of the relationships of early neopterygian clades
Authors: Xu Guang-Hui
Published: April 2020

Neopterygii is a taxonomically diverse group of ray-finned fishes, including Teleostei, Holostei and their closely related fossil taxa. Here, a new small-sized stem-neopterygian with extraordinarily long teeth, Louwoichthys pusillus gen. et sp. nov., is described based on 14 well-preserved specimens from the Middle Triassic (Anisian) marine deposits of Yunnan, China. Louwoichthys is closely related to Luopingichthys from the same fossil beds and Ctenognathichthys from the Middle Triassic of the Monte San Giorgio area in Europe; the three genera are grouped into the family Louwoichthyidae fam. nov., which is recovered as sister to the ‘perleidiform’ Pseudobeaconiidae. Given that ‘Perleidiformes’ is notoriously paraphyletic, a new order, Louwoichthyiformes ord. nov., is introduced to group both families. The louwoichthyiform monophyly is strongly supported by a series of derived features, such as a relatively short maxilla, an anteriorly inclined preopercle, a subopercle with a prominent anteroventral extension, and two or three pairs of branchiostegal rays. Louwoichthys is one of the smallest louwoichthyiforms, having a largest standard length of 39 mm. It is deduced to be a scavenger that might use its long and sharp teeth to grasp and tear the prey from the substrate or to bite a piece from a larger prey item.
Genomic Variability ofPhytophthora palmivoraIsolates from Different Oil Palm Cultivation Regions in Colombia
Authors: Gil Juanita , Herrera Mariana , Duitama Jorge , Sarria Greicy , Restrepo Silvia , Romero Hernán Mauricio
Published: April 2020

Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control.
Kindlin‐3 organizes a ring of clustered high affinity β2 integrins during human neutrophil spreading under flow
Authors: Fan Zhichao , Wen Lai , Yeh Yi-Ting , Kiosses William B. , Gutierrez Edgar , Groisman Alex , Francois Joshua , Lasheras Juan C. , del Alamo Juan C. , Chien Shu , Ginsberg Mark H. , Petrich Brian G. , Ley Klaus
Published: April 2020

Neutrophils are vital for inflammation and immune defense. Dependent on β2 integrins, spherical neutrophils spread on vascular endothelium after arrest, which is critical for their recruitment from circulation to resist high shear flow and to initiate intravascular crawling. Here, we use high‐resolution quantitative dynamic footprinting microscopy to monitor neutrophil spreading on a substrate of recombinant ICAM‐1 and P‐selectin under flow. A homogenous binding assay using the conformation‐reporter antibodies mAb24 (reporting high‐affinity β2, H+) and KIM127 (reporting extended β2, E+) showed three conformations of activated β2 integrins. E−H+ β2 integrins increased before E+H− and E+H+ conformations at the beginning of neutrophil spreading. Integrin extension depended on Syk‐mediated integrin outside‐in signaling. The ring of E−H+ and E+H+, but not E+H− β2 integrins was fully formed during late neutrophil spreading just before migration. Using kindlin‐3‐GFP fusion proteins, a ring of kindlin‐3 was observed before the ring of H+ integrins appeared. These findings show spatially coordinated integrin activation during spreading. The previously unrecognized E−H+ conformation is the pioneer integrin for neutrophil spreading and appears to be organized by kindlin‐3.

Support or Funding Information

This research was supported by funding from the National Institutes of Health, USA (NIH, HL078784 and R01HL145454), WSA postdoctoral fellowships and a Career Development Award from the American Heart Association, USA (AHA, 16POST31160014, 19POST34450228, and 18CDA34110426).

Integrin activation on a spread neutrophil footprint. Red is the mAb KIM127, which reports integrin extension; Green is the mAb24, which reports integrin high‐affinity; Blue is conformational non‐specific aLb2 integrins.

Figure 1

Kindlin‐3‐GFP molecules formed a ring after the spreading of a neutrophil‐like HL60 cell.

Figure 2
Inhibitory effect of fructo‐oligosaccharides on inflammation‐associated apoptosis in GLP‐1 secreting L cells via inhibition of iNOS and cleaved caspase‐3 expression
Authors: Wongkrasant Preedajit , Muanprasat Chatchai
Published: April 2020

Glucagon‐like peptide 1 (GLP‐1) released from enteroendocrine L‐cells regulate insulin secretion. Intestinal inflammation and GLP‐1 secretion impairment are the dominant phenotype in type 2 diabetes mellitus (T2DM) patients. Fructo‐oligosaccharides (FOS) is a prebiotic known to be associated with GLP‐1 release and glucose homeostasis. This study aimed to investigate effect of FOS on inflammation‐associated GLP‐1 unresponsiveness. Herein, using cell death assays, immunofluorescence staining, real time PCR and western blot analyses, we demonstrated that FOS suppressed the effect of tumor necrosis factor‐α (TNF‐α), a key pathogenic cytokine in T2DM, on L‐cells apoptosis. Interestingly, FOS did not suppress TNF‐α‐induced NF‐κB nuclear translocation, but inhibited expression of IL‐6, IL‐1β and TNF‐α mRNA levels and iNOS and cleaved caspase‐3. Of particular importance, GLP‐1 secretion assay revealed that FOS rescued TNF‐α‐mediated GLP‐1 unresponsiveness in L cells. In conclusion, our study demonstrated the beneficial effects of FOS in maintaining GLP‐1 level and its mechanistic insights. Therefore, FOS exerts a novel class of drug candidate for the treatment of T2DM, at least in part, by targeting GLP‐1 signaling.

Support or Funding Information

This work is supported by the Thailand Research Fund (DBG6180029), Faculty of Science Mahidol University and Faculty of Medicine Ramathibodi Hospital Mahidol University. Financial support from the Thailand Research Fund and Mahidol University through the Royal Golden Jubilee Ph.D. Program (Grant No. PHD/0045/2558) to P.W. and C.M.

Figure 1