bluuebunny/crossref_metadata_2025 huggingface dataset:
Coefficient roughness of the riverbeds in conditions of regulated water flow
Authors: Ibragimov Ilhom A. , Inomov Dilmurod I. , Xaydarova Fotimabonu T.
Published: November 2022

In article results change of coefficients of roughness riverbeds for conditions of regulated water streams for the river Amudarya are resulted. In the bottom of Amudarya current abounding in water years during the period from the beginning of operation Tahiatash and Tuyamuyun hydrounits to present time have been chosen and for each chosen year on the basis of correlation connections the analysis change of factor of a roughness is carried out.
Analysis of the SC8-0071-014 and sc47-18 loci co-segregated with Ren1 gene in the genotypes of seedless grape varieties
Authors: Ilnitskaya Elena , Makarkina Marina , Kozhevnikov Evgeny
Published: November 2022

Powdery mildew (Erysiphe necator) is one of the most common and economically significant diseases of grapes. The main method of controlling the disease is pesticide treatment. To reduce chemical treatments, it is necessary to select and introduce resistant varieties into production. DNA markers are currently actively used in the study of grape genetic resources. Seedless grape varieties are highly demanded by consumers. Ren1 is one of the known and mapped vine resistance genes to powdery mildew, inherited from V. vinifera; linked DNA markers for this resistance locus are known. A study of 34 seedless grape genotypes was carried out using DNA markers SC8-0071-014 and sc47-18 co-segregated with Ren1. In the studied sample of varieties, 12 types of alleles were identified in the sc47-18 locus and 9 types of alleles in the SC8-0071-014 locus. Target fragments, according to linked marker loci, indicating the presence of the Ren1 resistance gene, were identified in grape variety Lotus (Kriulyanskiy x Yangi Er).
Features of somatic embryogenesis in the culture in vitro in hybrid grape form E-342
Authors: Zlenko V.A. , Kosyuk M.I. , Pavlova I.A. , Luschay E.A. , Abdurashitova A.S.
Published: November 2022

Correlation analysis of the influence of media variants with introducing various biologically active substances on the development of somatic embryoids and germinating seedlings in the hybrid form E-342 was carried out during two repeated subculturings on the same variant of media, and during the third subculturing - on different variants of media. The repeated subculturing in media with the same growth regulator BAP or IAA caused the development of abnormal large somatic embryoids without the expressed hypocotyls and cotyledons. Only the use of medium variant with DLPA in two subculturings (the third subculturing into the medium with BAP or IAA) and the third repeated subculturing with DLPA, but to a smaller extent, have led to the development of torpedo-shaped embryoids, to be growing into germinating seedlings. Strong positive correlation dependence of influence was established for: BAP on the development of heart-shaped embryoids; IAA on the increase in the size of globular embryoids and transformation of heart-shaped embryoids into torpedo-shaped ones; DLPA on the development of a great number of normal torpedo-shaped embryoids. After longstanding culturing of suspensions of cells and embryoids, it was not possible to get rid of chlorophyll deficiency in the resulting germinating seedlings due to somaclonal variability.
The interrelation of holstein black pied cattle’s productive qualities by lactation
Authors: Gorelik O.V. , Lihodeevskaya О.Е. , Zezin N.N. , Sevostyanov M.Yu. , Leshonok О.I.
Published: November 2022

Holsteinized Russian black pied cattle of the Ural type are bred in the Sverdlovsk region, which is represented by large highly productive animals with a high genetic potential of productivity. The purpose of the work was to study the productive qualities of Holsteinized black pied cattle with a high proportion of thorough-bredness in the Holstein breed and their interrelation. Milk yield per lactation increases reaching the maximum for the third lactation. The increase amounted to o 1409 kg or 14.9% relative to the first one. The study has found changes in milk quality indicators; the indicators fluctuated depending on lactation, yet a tendency to increase MFF in milk from the first to the third lactation was revealed. The highest indicators were shown in the second lactation. During this lactation, the highest milk protein content was observed – 3.26%. Due to the increase in milk yield and milk quality indicators, an increase in the amount of milk fat and milk protein per lactation is observed from 679 kg (1 lactation) to 782 kg (2 lactation). The correlation between milk yield and milk quality indicators being MFF and MFP varies depending on lactation. Mainly, with the exception of the first lactation and the interrelation of milk yield per lactation - MFP in milk was negative and amounted to 0.11. That is, with an increase in milk yield, there is a decrease in MFF and MFP in milk.
Safety evaluation of the use of one- and two-component fungicides to protect grapes
Authors: Chermenskaya Taisiya , Petrova Mariya
Published: November 2022

Viticulture and winemaking are traditional industry of agriculture in the southern regions of the Russian Federation, which playing an important role in their economy. A rich and undamaged crop is almost impossible to grow without plant protection measures. Preparations used to spray plants are by no means harmless, and do not always completely disintegrate before harvesting. The objective of the work was to study the dynamics of degradation of fungicides of systemic action, belonging to different classes, in grapes. The two-component preparation was a combination of 120 g/l difenoconazole + 60 g/l tetraconazole (MEC). The one-component preparation contained 250 g/l of cyprodinil (EC). The work was done in the Krasnodar region for 2 years. The half-lives of difenoconazole and tetraconazole were about 5 days, cyprodinil 2.7 and 4 days, 1 and 2 years, respectively. The concentration of difenoconazole and tetraconazole went down to below the MRL in the first year of the study, two weeks after the last spraying, and in the second – after three weeks, which was most likely caused by the prevailing weather conditions – “dangerous phenomenon – intense heat”. At the time of harvest, no residual amounts of difenoconazole, tetraconazole and cyprodinil were found, which indicates the safety of the products obtained for consumers.
Improving the criteria of assessing grapes and base wines in the production of sparkling wines
Authors: Makarov Aleksandr , Shmigelskaya Natalia , Lutkov Igor , Maksimovskaya Viktoria , Sivochoub Galina
Published: November 2022

The production of high-quality sparkling wines consists in an integrated approach at all stages of production, taking into account the potential of grapes, soil and climatic conditions of its cultivation, etc. As a research result of 2016-2021, a comprehensive assessment in the system “grapes - base wine - sparkling wine” made it possible to establish additional indicators of grapes and base wines that allow obtaining high-quality sparkling wines. Based on the established criteria, significantly correlated with the quality of the finished product, promising grape varieties for the production of sparkling wines were identified. The results obtained will allow improving the quality of local sparkling wines, creating a great variety of products.
Asymptotic behavior for a time-inhomogeneous Kolmogorov type diffusion
Authors: Gradinaru Mihai , Luirard Emeline
Published: November 2022

We study a kinetic stochastic model with a non-linear time-inhomogeneous friction force and a Brownian-type random force. More precisely, a Kolmogorov type diffusion (V, X) is considered: here, X is the position of the particle, and V is its velocity. The process V is solution to a stochastic differential equation driven by a one-dimensional Brownian motion, with a drift of the form t−βF(v). The function F satisfies some homogeneity condition, and β is a real number. The behavior in large time of the process (V, X) is proved by using stochastic analysis tools.
Gute Blutdruckeinstellung hemmt Progression der chronischen Niereninsuffizienz (CKD)
Authors: Obermüller Nicholas
Published: November 2022

Die chronische Niereninsuffizienz (CKD) ist eine häufig erst in späteren Stadien erkannte Erkrankung, deren weltweite Inzidenz tendenziell ansteigt. Einerseits bedingen kardiovaskuläre Erkrankungen eine CKD, andererseits häufen sich durch einen fortschreitenden Nierenfunktionsverlust diverse kardiovaskuläre Ereignisse. Die Primärursache einer Niereninsuffizienz sollte möglichst immer kausal behandelt werden. Dies ist jedoch häufig nur partiell möglich, wenn glomerulär-tubuläre Schäden bereits vorhanden sind und der meistens schon früh bestehende (renale) Bluthochdruck die Nierenfunktion auch unabhängig von der Primärursache verschlechtert. Daher sollte der (renale) Blutdruck gut eingestellt werden, da allein dadurch die CKD-Progression verlangsamt werden kann. Hemmer des Renin-Angiotensin-Aldosteron-Systems haben sich als vorteilhafte Substanzen etabliert, da sie Systemdruck und intrarenalen Druck, aber auch die Proteinurie günstig beeinflussen. Das bedeutet, „gute“ Blutdrucksenkung“ verringert auch den glomerulären „Blutdruck“ bzw. den Druck im Gefäßsystem der Niere. Was der optimale Zielblutdruck ist, hängt stets vom Risikoprofil ab.
Sinnvolle Diagnose und Therapie von hormonabhängigen Hypertonusformen
Authors: Schmidt Sebastian , Kloos Christof , Busch Martin , Wolf Gunter
Published: November 2022

Sekundäre Hypertonieformen entstehen überwiegend durch renovaskuläre, renoparenchymatöse und endokrine Ursachen. Ein unzureichend eingestellter Blutdruck unter mindestens 3 Antihypertensiva unter Einschluss eines Diuretikums sollte auf sekundäre Ursachen abgeklärt werden. Die Diagnostik umfasst Anamnese, klinische Untersuchung, Laborscreening, Bestätigungstests, Bildgebung und ggf. selektiven Venenkatheter. Therapieoptionen sind primär die Operation und/oder medikamentöse Ansätze. Antihypertensiva können postoperativ oft reduziert werden. Nach bilateraler Adrenalektomie ist die lebenslange Hormonsubstitution erforderlich. Die endokrinologische Verlaufskontrolle und Nachsorge postoperativ sollte mindestens jährlich erfolgen. Die Zusammenarbeit zwischen Hausärzten und Ärzten der Inneren Medizin und Chirurgie mit endokriner Expertise ist notwendig. Die wichtigsten endokrinen Erkrankungen primärer Hyperaldosteronismus, Cushing-Syndrom und Paragangliom/Phäochromozytom (PGL/PCC) werden in dieser Übersicht detailliert dargestellt.
Evaluation of the Optic Nerve Head Using Optical Coherence Tomography Angiography in Systemic Sclerosis Patients
Authors: Zirtiloglu Sibel , Alikma Mustafa Suat , Acar Ozge Pinar Akarsu , Güven Fatih , Icacan Ozan Cemal , Yigit Fadime Ulviye
Published: November 2022

Purpose To quantify microvascular vessel density in the optic disc using optical coherence tomography angiography (OCTA) in patients with systemic sclerosis (SS); to determine
whether there is a difference in values between patients and controls; and to correlate the OCTA measurements with disease activity, damage risk, and drug usage.

Methods Patients aged 20 – 76 years who were followed up after a diagnosis of SS and age- and gender-matched controls. The patients underwent RTVue-XR AngioVue OCTA imaging in this
cross-sectional observational study.

Results A total of 61 eyes of 61 consecutive SS patients and 60 eyes of 60 controls were investigated. There was no statistically significant difference between the patients and
control groups regarding the average RNFL (retinal fiber layer) and radial peripapillary capillary (RPC) vessel density (VD) measurements (p = 0.35, p = 0.25, respectively). As the
antinuclear antibody (ANA) titer increased, RNFLsuperior (p = 0.01, r = − 0.327), RPCwhole (p = 0.029, r = 0.279), RPCperipapillary (p = 0.037, r = − 0.267), RPCsuperior (p = 0.003,
r = − 0.371), and RPCinferior (p = 0.02, r = 0.297) values decreased with statistical significance. The RPCinside values were lower in anti-Scl-70-positive patients compared to patients
negative for anti-Scl-70 (topoisomerase I) (p = 0.021). The RNFLnasal (p = 0.03, r = − 0.278) value decreased as the years of disease increased. The RPCinside value was higher in patients
using hydroxychloroquine and calcium channel blockers than those who did not use them (p = 0.021 and p = 0.027, respectively). The RPCwhole, RPCperipapillary, and RPCnasal values were
higher, with statistical significance in corticosteroid users than in those patients who did not use corticosteroids (p = 0.043, 0.030, and 0.033, respectively).

Conclusion There was no significant difference between the patients and control groups regarding the average RPC VD measurements. However, since this is the first study to analyze
optic disc vessel density in SS patients, optic nerve blood flow changes in scleroderma with OCTA could be studied.
Endoscopic ultrasound-guided gastroenterostomy for the management of gastric outlet obstruction: A large comparative study with long-term follow-up
Authors: Jaruvongvanich Veeravich , Mahmoud Tala , Abu Dayyeh Barham K. , Chandrasekhara Vinay , Law Ryan , Storm Andrew C. , Levy Michael J. , Vargas Eric J. , Marya Neil B. , Abboud Donna M. , Ghazi Rabih , Matar Reem , Rapaka Babusai , Buttar Navtej , Truty Mark J. , Aerts Maridi , Messaoudi Nouredin , Kunda Rastislav
Published: November 2022

Background and study aims Gastric outlet obstruction (GOO) is traditionally managed with surgical gastroenterostomy (surgical-GE) and enteral stenting (ES). Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) is now a third option. Large studies assessing their relative risks and benefits with adequate follow-up are lacking. We conducted a comparative analysis of patients who underwent EUS-GE, ES, or surgical-GE for GOO.

Patients and methods In this retrospective comparative cohort study, consecutive patients presenting with GOO who underwent EUS-GE, ES, or surgical-GE at two academic institutions were reviewed and independently cross-edited to ensure accurate reporting. The primary outcome was need for reintervention. Secondary outcomes were technical and clinical success, length of hospital stay (LOS), and adverse events (AEs).

Results A total of 436 patients (232 EUS-GE, 131 ES, 73 surgical-GE) were included. The median duration of follow-up of the entire cohort was 185.5 days (interquartile range 55.25–454.25 days). The rate of reintervention in the EUS-GE group was lower than in the ES and surgical-GE groups (0.9 %, 12.2 %, and 13.7 %, P < 0.0001). Technical success was achieved in 98.3 %, 99.2 %, and 100 % (P = 0.58), and clinical success was achieved in 98.3 %, 91.6 %, and 90.4 % (P < 0.0001) in the EUS-GE, ES, and surgical-GE groups, respectively. The EUS-GE group had a shorter LOS (2 days vs. 3 days vs. 5 days, P < 0.0001) and a lower AE rate than the ES and surgical-GE groups (8.6 % vs. 38.9 % vs. 27.4 %, P < 0.0001).

Conclusion This large cohort study demonstrates the safety and palliation durability of EUS-GE as an alternative strategy for GOO palliation in select patients.
XantPhos Pd-G3 as an Efficient Catalyst: Microwave-Assisted C–S Cross-Coupling Reaction in DMF
Authors: Katla Rakhi , Katla Ramesh , Domingues Nelson L. C.
Published: November 2022

Buchwald precatalyst (XantPhos Pd-G3) was employed for the first time in a C–S cross-coupling reaction involving 2-(4-bromophenyl)benzothiazole or 5-bromo-2,1,3-benzothiadiazole with various benzenethiols in DMF, K2CO3 as a base, under microwave irradiation at 80 °C, 200 W. Good to excellent yields of the desired products were obtained under microwave conditions. Other significant benefits of this synthetic approach are low catalyst loading, short reaction times, and eco-friendly conditions. Additionally, 29 compounds were successfully synthesized, some of which are new in this protocol.
Extracellular Vesicles: A New Promise for the Prevention of Bronchopulmonary Dysplasia
Authors: Bonadies Luca , De Vos Beatrice , Muraca Maurizio , Baraldi Eugenio
Published: November 2022

Bronchopulmonary dysplasia (BPD) despite numerous efforts of neonatologists remains one of the most frequent and long-lasting chronic respiratory diseases consequent to extreme preterm birth. New clinical trials are exploring the possible use of mesenchymal stem cells (MSCs) and especially their products, extracellular vesicles (EVs), that overcome some of the possible issues related to the use of live cells. MSCs already reached clinical implementation; MSC-EVs, on the contrary, showed extremely promising results in the preclinical setting but are still waiting their first in human results that are likely to happen soon.

Key Points
Subacute Aortic Rupture Due to Mechanical Chest Compression with Indwelling Impella
Authors: Penov Kiril , Radakovic Dejan , Madrahimov Nodir , Aleksic Ivan
Published: November 2022

Mechanical cardiopulmonary resuscitation (CPR) devices like Lund University Cardiopulmonary Assist System (LUCAS) cause more skeletal and visceral injuries than standard CPR. A 62-year-old woman with ST-elevation myocardial infarction was resuscitated with LUCAS and Impella CP for refractory cardiogenic shock during percutaneous coronary intervention. She suffered delayed ascending aortic rupture necessitating supracommissural ascending aortic replacement plus triple bypass grafting. Prolonged mechanical CPR with concomitant Impella may lead to aortic rupture. The combined use of LUCAS and Impella may have disastrous consequences.
100 years of Brillouin scattering: Historical and future perspectives
Authors: Merklein Moritz , Kabakova Irina V. , Zarifi Atiyeh , Eggleton Benjamin J.
Published: November 2022

The Year 2022 marks 100 years since Leon Brillouin predicted and theoretically described the interaction of optical waves with acoustic waves in a medium. Accordingly, this resonant multi-wave interaction is referred to as Brillouin scattering. Today, Brillouin scattering has found a multitude of applications, ranging from microscopy of biological tissue, remote sensing over many kilometers, and signal processing in compact photonic integrated circuits smaller than the size of a thumbnail. What allows Brillouin scattering to be harnessed over such different length scales and research domains are its unique underlying properties, namely, its narrow linewidth in the MHz range, a frequency shift in the GHz range, large frequency selective gain or loss, frequency tunability, and optical reconfigurability. Brillouin scattering is also a ubiquitous effect that can be observed in many different media, such as freely propagating in gases and liquids, as well as over long lengths of low-loss optical glass fibers or short semiconductor waveguides. A recent trend of Brillouin research focuses on micro-structured waveguides and integrated photonic platforms. The reduction in the size of waveguides allows tailoring the overlap between the optical and acoustic waves and promises many novel applications in a compact footprint. In this review article, we give an overview of the evolution and development of the field of Brillouin scattering over the last one hundred years toward current lines of active research. We provide the reader with a perspective of recent trends and challenges that demand further research efforts and give an outlook toward the future of this exciting and diverse research field.
On the flow dynamics of wall-mounted low-aspect-ratio rotating cylinders
Authors: Shehata Hisham M. , Medina Albert
Published: November 2022

The flow physics and vortical features attributed to a low-aspect-ratio circular cylinder cantilevered on a laminar boundary layer plate and rotated about its respective axial coordinate were investigated experimentally using Stereo Particle Image Velocimetry. The investigation documents the three-dimensional spatial evolution of on-body dynamics to deep-wake phenomena. In disseminating the more salient global characteristics of the resultant flowfield, the analysis focuses on the particular case of an aspect ratio of 1 driven in continuous rotary motion at a speed ratio of 3. The two key findings are (i) vortex source: a wall-normal swirl develops and reorients into a streamwise vortex at the cylinder's mid-diameter location due to the heavy influence of the incoming boundary layer, local fluid entrainment, and proximity to the wall. (ii) Enhanced downwash: in return, the streamwise vortex primarily drives the production of additional downwash in the wake, which appends to the downwash generated by the cylinder's free end. A two-dimensional planar particle image velocimetry campaign in service of a parametric survey reveals the sensitivity of streamwise vortex production and downwash to rotational rate and cylinder height relative to boundary layer thickness. The streamwise vortex production tends to deteriorate when the cylinder is immersed in the boundary layer due to reduced downwash.
Plasma emission induced by ring-distributed energetic electrons in overdense plasmas
Authors: Chen Yao , Zhang Zilong , Ni Sulan , Ning Hao , Li Chuanyang , Li Yaokun
Published: November 2022

According to the standard scenario of plasma emission, escaping radiations are generated by the nonlinear development of the kinetic bump-on-tail instability driven by a single beam of energetic electrons interacting with plasmas. Here, we conduct fully-kinetic electromagnetic particle-in-cell simulations to investigate plasma emission induced by the ring-distributed energetic electrons interacting with overdense plasmas. Efficient excitations of the fundamental (F) and harmonic (H) emissions are revealed with radiation mechanism(s) different from the standard scenario: (1) The primary modes accounting for the radiations are generated through the electron cyclotron maser instability [for the upper-hybrid (UH) and Z modes] and the thermal anisotropic instability [for the whistler (W) mode]; the F emission is generated by the nonlinear coupling of the Z and W modes and the H emission by the nonlinear coupling of the UH modes. This presents an alternative mechanism of coherent radiation in overdense plasmas.
Key role of neuronal diversity in structured reservoir computing
Authors: Thivierge Jean-Philippe , Giraud Eloïse , Lynn Michael , Théberge Charbonneau Annie
Published: November 2022

Chaotic time series have been captured by reservoir computing models composed of a recurrent neural network whose output weights are trained in a supervised manner. These models, however, are typically limited to randomly connected networks of homogeneous units. Here, we propose a new class of structured reservoir models that incorporates a diversity of cell types and their known connections. In a first version of the model, the reservoir was composed of mean-rate units separated into pyramidal, parvalbumin, and somatostatin cells. Stability analysis of this model revealed two distinct dynamical regimes, namely, (i) an inhibition-stabilized network (ISN) where strong recurrent excitation is balanced by strong inhibition and (ii) a non-ISN network with weak excitation. These results were extended to a leaky integrate-and-fire model that captured different cell types along with their network architecture. ISN and non-ISN reservoir networks were trained to relay and generate a chaotic Lorenz attractor. Despite their increased performance, ISN networks operate in a regime of activity near the limits of stability where external perturbations yield a rapid divergence in output. The proposed framework of structured reservoir computing opens avenues for exploring how neural microcircuits can balance performance and stability when representing time series through distinct dynamical regimes.
Second harmonic generation from grating-coupled hybrid plasmon–phonon polaritons
Authors: Kohlmann Marcel , Denker Christian , Passler Nikolai C. , Kredl Jana , Wolf Martin , Münzenberg Markus , Paarmann Alexander
Published: November 2022

Polaritons can provide strong optical field enhancement allowing them to boost light–matter interaction. Here, we experimentally observe enhancement in mid-infrared second-harmonic generation (SHG) using grating-coupled surface phonon polaritons of the 6H-SiC surface. In our experiment, we measure the SHG along the polariton dispersion by changing the incidence angle of the excitation beam. We observe hybridization between the propagating surface phonon polaritons and localized plasmon resonances in the gold grating, evidenced by the modification of the polariton dispersion as we change the area ratio of grating and substrate. Design options for engineering the plasmon–phonon polariton hybridization are discussed. Overall, we find a rather low yield of polariton-enhanced SHG in this geometry compared to prism-coupling and nanostructures and discuss possible origins.
Thermoacoustic instabilities with varying geometries of the main-stage exit in a centrally staged burner
Authors: Han Meng , Han Xiao , Wang Xinyao , Li Lei
Published: November 2022

The present study investigates the effect of the exit geometry of the main stage on thermoacoustic instabilities in a model combustor with a dual-swirl layout. In practical combustors, the main stage has a much larger airflow than the pilot stage, therefore dominating the aerodynamics of the global flame. In this paper, six different geometries of the main-stage exit are designed to cover the common styles in engineering applications. Their effects on thermoacoustic instability and flame shape are examined experimentally. Sudden transitions from the attached flame to the blurred flame are found in most of the exit geometries, excluding the outer-rough case. This transition of flame shape triggers the onset of strong thermoacoustic oscillation, leading to a jump in the pressure fluctuation amplitude. Frequency drop and the acoustic mode shift are also found at the transition point. Flame dynamics are further analyzed using the dynamic mode decomposition method. It is concluded that the outer-rough case has the best thermoacoustic stability within the tested range. The mechanisms of the observed phenomena are analyzed by measuring the reacting flow fields. It is found that the increased roughness of the outer wall can prevent the flame shape transition and the onset of thermoacoustic instability, possibly due to the weakened vortex structures and strain rate in the outer shear layer.
Emission spectral non-Markovianity in qubit–cavity systems in the ultrastrong coupling regime
Authors: Zhang Chenyi , Yu Minghong , Yan Yiying , Chen Lipeng , Lü Zhiguo , Zhao Yang
Published: November 2022

We study the emission spectra of the dissipative Rabi and Jaynes–Cummings models in the non-Markovian and ultrastrong coupling regimes. We have derived a polaron-transformed Nakajima–Zwanzig master equation (PTNZE) to calculate the emission spectra, which eliminates the well-known limitations of the Markovian approximation and the standard second-order perturbation. Using the time-dependent variational approach with the multiple Davydov ansatz as a benchmark, the PTNZE is found to yield accurate emission spectra in certain ultrastrong coupling regimes where the standard second-order Nakajima–Zwanzig master equation breaks down. It is shown that the emission spectra of the dissipative Rabi and Jaynes–Cummings models are, in general, asymmetric under various initial conditions. Direct comparisons of spectra for the two models illustrate the essential role of the qubit–cavity counter-rotating term and the spectral features under different qubit–cavity coupling strengths and system initial conditions.
A unified framework of mixed quantum–classical dynamics with trajectory branching
Authors: Li Guijie , Shao Cancan , Xu Jiabo , Wang Linjun
Published: November 2022

As popular mixed quantum–classical dynamics methods, trajectory surface hopping and Ehrenfest mean field have been widely utilized to simulate nonadiabatic dynamics. Recently, we have proposed the branching-corrected surface hopping and the branching-corrected mean field methods, both of which closely reproduce the exact quantum dynamics in a series of standard scattering models. Here, the mixed surface hopping and mean field with branching correction (BCSHMF) is presented as a unified framework of mixed quantum–classical dynamics. As benchmarked in thousands of diverse three-level and four-level scattering models, BCSHMF achieves high reliability and flexibility, implying that surface hopping and mean field are compatible with each other in nature, and trajectory branching is essential for the mixed quantum–classical description of nonadiabatic dynamics.
Transport of ions in hydrophobic nanotubes
Authors: Vinogradova Olga I. , Silkina Elena F. , Asmolov Evgeny S.
Published: November 2022

The theory of electrokinetic ion transport in cylindrical channels of a fixed surface charge density is revisited. Attention is focused on the impact of the hydrophobic slippage and mobility of adsorbed surface charges. We formulate generalized Onsager relations for a cylinder of an arbitrary radius and then derive exact expressions for the mean electro-osmotic mobility and conductivity. To employ these expressions, we perform additional electrostatic calculations with a special focus on the non-linear electrostatic effects. Our theory provides a simple explanation of a giant enhancement of the electrokinetic mobility and conductivity of hydrophobic nanotubes by highlighting the role of appropriate electrostatic and hydrodynamic length scales and their ratios. We also propose a novel interpretation of zeta potentials of cylindrical channels.
Translocating captive female white-tailed deer
Authors: Elliott Jace R. , Newbolt Chad H. , Gulsby William D. , Ditchkoff Stephen S.
Published: November 2022

Context Thousands of captive white-tailed deer (Odocoileus virginianus) breeding facilities exist across North America for the purpose of producing trophy-class deer (i.e. exceptionally large-antlered). Many of these deer get marketed to private landowners, with the expectation that introduced deer will enhance genetics in the population, resulting in larger-antlered male deer. Previous research suggests that survival and reproductive success of translocated wild white-tailed deer are highly variable; however, little is known about the fate of white-tailed deer translocated from captive-breeding operations. Aims To assess the efficacy of translocating captive female white-tailed deer for the purpose of increasing average antler size within a high-fence property. Methods We translocated 24 adult female deer into a private, 300-ha high-fence shooting preserve in east-central Alabama over a 3-year period. We monitored survival, reproductive success, and fawn recruitment for the translocated deer by using VHF radio collars and vaginal-implant transmitters (VITs). Key results We found a 12-month survival rate of 0.54 for translocated deer. We captured nine fawns throughout our study, leading to a rate of 0.9 fawns per VIT, after accounting for doe mortality and premature VIT expulsion. We found 60-day and 6-month fawn survival rates of 0.33 and 0.22 respectively. Conclusions Survival of translocated captive deer was comparable to rates reported in previous studies that translocated wild deer, although lower than what is found in wild populations that undergo no translocation. Translocated does produced a low number of fawns relative to the national average, although fawn recruitment was within the range of survival rates reported in studies of wild deer. Implications We believe our findings provide a baseline of expectations for captive-deer translocations. Given our results, we believe it is infeasible to expect increased average antler size within this study site by translocating adult female white-tailed deer.
The effect of scent lures on detection is not equitable among sympatric species
Authors: Dart Marlin M. , Perkins Lora B. , Jenks Jonathan A. , Hatfield Gary , Lonsinger Robert C.
Published: November 2022

Context Camera trapping is an effective tool for cost-efficient monitoring of species over large temporal and spatial scales and it is becoming an increasingly popular method for investigating wildlife communities and trophic interactions. However, camera trapping targeting rare and elusive species can be hampered by low detection rates, which can decrease the accuracy and precision of results from common analytical approaches (e.g., occupancy modeling, capture-recapture). Consequently, researchers often employ attractants to increase detection without accounting for how attractants influence detection of species among trophic levels. Aims We aimed to evaluate the influences of a commonly used non-species-specific olfactory lure (i.e. sardines) and sampling design on detection of four species (i.e. bobcat [Lynx rufus], coyote [Canis latrans], raccoon [Procyon lotor], and eastern cottontail [Sylvilagus floridanus]) that represented a range of foraging guilds in an agricultural landscape. Methods We set 180 camera stations, each for ∼28 days, during the summer of 2019. We set cameras with one of three lure treatments: (1) olfactory lure, (2) no olfactory lure, or (3) olfactory lure only during the latter half of the survey. We evaluated the influence of the lure at three temporal scales of detection (i.e. daily probability of detection, independent sequences per daily detection, and triggers per independent sequence). Key results The lure tended to positively influence detection of coyotes and raccoons but negatively influenced detection of bobcats and eastern cottontails. The influence of the lure varied among temporal scales of detection. Conclusions Scent lures can differentially influence detection of species within or among tropic levels, and the influence of a scent lure may vary among temporal scales. Implications Our results demonstrate the importance of evaluating the influence of an attractant for each focal species when using camera data to conduct multi-species or community analyses, accounting for variation in sampling strategies across cameras, and identifying the appropriate species-specific temporal resolution for assessing variation in detection data. Furthermore, we highlight that care should be taken when using camera data as an index of relative abundance (e.g. as is commonly done with prey species) when there is variation in the use of lures across cameras.
L’intelligence interculturelle en traduction
Authors: Le Poder Marie-Évelyne
Published: November 2022

Cet article aborde le concept de l’intelligence interculturelle en traduction à partir d’une étude de cas, concrètement la traduction de l’espagnol vers le français de la pièce de théâtre Bodas de sangre (« Noces de sang ») de Federico García Lorca. L’objectif principal consiste à analyser les références culturelles présentes dans le texte source et la façon dont elles ont été traduites dans le texte cible. Pour ce qui est des objectifs spécifiques, il s’agit de proposer une définition du concept de l’intelligence interculturelle au sens large d’abord, puis en rapport avec la traduction ; délimiter le concept de référence culturelle ; catégoriser les références culturelles du texte source ; examiner les procédés de traduction utilisés par les traducteurs pour recréer les références culturelles du texte source dans le texte cible.
The Cdc42 GAP Rga6 promotes monopolar outgrowth of spores
Authors: Wei Wenfan , Zheng Biyu , Zheng Shengnan , Wu Daqiang , Chu Yongkang , Zhang Shenghao , Wang Dongmei , Ma Xiaopeng , Liu Xing , Yao Xuebiao , Fu Chuanhai
Published: November 2022

The molecular mechanisms underlying the establishment of the monopolar growth of fission yeast spores have been less characterized. Here, we report that the Cdc42 GTPase-activating protein (GAP) Rga6 is required for promoting monopolar growth during spore germination. The absence of Rga6 increases the number of spores that grow in a bipolar fashion. Rga6 decorates the non-growing cortical region, binds phosphatidylinositol 4,5-bisphosphate, and colocalizes with the phosphatidylinositol 4,5-bisphosphate-binding protein Opy1. Overexpression of Opy1 diminishes the cortical localization of Rga6. The characteristic localization of Rga6 on the cell cortex depends on the C-terminal PBR region of Rga6. Moreover, engineered chimera composed of the Rga6 C-terminal PBR region fused to the GAP domain of Rga3 or Rga4 are sufficient to rescue the spore growth phenotype caused by the absence of Rga6. Hence, our work establishes a paradigm in which the lipid composition of the plasma membrane directs polarized cell growth by specifying the cortical localization of a GAP protein.
CNN-GRU-Based intelligent online prediction of screw machine rotation speed for Earth pressure balance shield machine
Authors: Liu Xuan-Yu , Gan Xin-Yang , Shao Cheng , Wang Yu-Dong , Cong Qiu-Mei
Published: November 2022

During shield machine construction, the precise determination of control parameters is particularly important for construction safety. By effectively using construction big data and mining the information in it, accurate construction control parameters with geological adaptability can be obtained in real time. To this end, this study proposes an intelligent online prediction method for screw machine rotation speed of Earth pressure balanced (EPB) shield based on convolutional neural network gated recursive unit (CNN-GRU). Firstly, the construction data is processed with Pearson correlation coefficient, the 10-dimensional data of the current moment is selected as the input variable, and screw machine rotation speed at the next moment is chosen as the output. Next, CNN is used to extract features from the input variables to find a nonlinear relationship between the input and output. Then, in order to construct a complete screw machine rotation speed prediction model, the GRU is used to filter the features to establish a more accurate nonlinear relationship. Finally, the control effect of the method was verified by simulation experiments. The simulation results show that the proposed method can accurately predict the rotation speed of the screw machine online. The traditional control mode in shield tunnel construction can lead to unstable excavation surface due to time lag and inaccuracy. Meanwhile, once the excavation surface is unstable, soil collapse or uplift can lead to construction safety problems, while the the required construction data to the control room at the next moment can be quickly and accurately fed by the online prediction method proposed in this study, thereby effectively avoiding the above construction safety problems and having certain practical application value.
Atomic structure generation from reconstructing structural fingerprints
Authors: Fung Victor , Jia Shuyi , Zhang Jiaxin , Bi Sirui , Yin Junqi , Ganesh P
Published: November 2022

Data-driven machine learning methods have the potential to dramatically accelerate the rate of materials design over conventional human-guided approaches. These methods would help identify or, in the case of generative models, even create novel crystal structures of materials with a set of specified functional properties to then be synthesized or isolated in the laboratory. For crystal structure generation, a key bottleneck lies in developing suitable atomic structure fingerprints or representations for the machine learning model, analogous to the graph-based or SMILES representations used in molecular generation. However, finding data-efficient representations that are invariant to translations, rotations, and permutations, while remaining invertible to the Cartesian atomic coordinates remains an ongoing challenge. Here, we propose an alternative approach to this problem by taking existing non-invertible representations with the desired invariances and developing an algorithm to reconstruct the atomic coordinates through gradient-based optimization using automatic differentiation. This can then be coupled to a generative machine learning model which generates new materials within the representation space, rather than in the data-inefficient Cartesian space. In this work, we implement this end-to-end structure generation approach using atom-centered symmetry functions as the representation and conditional variational autoencoders as the generative model. We are able to successfully generate novel and valid atomic structures of sub-nanometer Pt nanoparticles as a proof of concept. Furthermore, this method can be readily extended to any suitable structural representation, thereby providing a powerful, generalizable framework towards structure-based generation.
Improving protein structure prediction using templates and sequence embedding
Authors: Wu Fandi , Jing Xiaoyang , Luo Xiao , Xu Jinbo
Published: November 2022

Motivation

Protein structure prediction has been greatly improved by deep learning, but the contribution of different information is yet to be fully understood. This article studies the impacts of two kinds of information for structure prediction: template and multiple sequence alignment (MSA) embedding. Templates have been used by some methods before, such as AlphaFold2, RoseTTAFold and RaptorX. AlphaFold2 and RosetTTAFold only used templates detected by HHsearch, which may not perform very well on some targets. In addition, sequence embedding generated by pre-trained protein language models has not been fully explored for structure prediction. In this article, we study the impact of templates (including the number of templates, the template quality and how the templates are generated) on protein structure prediction accuracy, especially when the templates are detected by methods other than HHsearch. We also study the impact of sequence embedding (generated by MSATransformer and ESM-1b) on structure prediction.

Results

We have implemented a deep learning method for protein structure prediction that may take templates and MSA embedding as extra inputs. We study the contribution of templates and MSA embedding to structure prediction accuracy. Our experimental results show that templates can improve structure prediction on 71 of 110 CASP13 (13th Critical Assessment of Structure Prediction) targets and 47 of 91 CASP14 targets, and templates are particularly useful for targets with similar templates. MSA embedding can improve structure prediction on 63 of 91 CASP14 (14th Critical Assessment of Structure Prediction) targets and 87 of 183 CAMEO targets and is particularly useful for proteins with shallow MSAs. When both templates and MSA embedding are used, our method can predict correct folds (TMscore > 0.5) for 16 of 23 CASP14 FM targets and 14 of 18 Continuous Automated Model Evaluation (CAMEO) targets, outperforming RoseTTAFold by 5% and 7%, respectively.

Availability and implementation

Available at https://github.com/xluo233/RaptorXFold.

Supplementary information

Supplementary data are available at Bioinformatics online.
End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
Authors: Petti Samantha , Bhattacharya Nicholas , Rao Roshan , Dauparas Justas , Thomas Neil , Zhou Juannan , Rush Alexander M , Koo Peter , Ovchinnikov Sergey
Published: November 2022

Motivation

Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for.

Results

Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood.

Availability and implementation

Our code and examples are available at: https://github.com/spetti/SMURF.

Supplementary information

Supplementary data are available at Bioinformatics online.
Role of genetic testing in young patients with idiopathic atrioventricular conduction disease
Authors: Auricchio Angelo , Demarchi Andrea , Özkartal Tardu , Campanale Daniela , Caputo Maria Luce , di Valentino Marcello , Menafoglio Andrea , Regoli Francois , Facchini Marco , Del Bufalo Alessandro , Foglia Pietro , Ferrari Nicola , Bomio Fulvio , Medeiros-Domingo Argelia , Moccetti Tiziano , Pedrazzini Giovanni B , Klersy Catherine , Conte Giulio
Published: November 2022

Aims

To investigate the role of genetic testing in patients with idiopathic atrioventricular conduction disease requiring pacemaker (PM) implantation before the age of 50 years.

Methods and results

All consecutive PM implantations in Southern Switzerland between 2010 and 2019 were evaluated. Inclusion criteria were: (i) age at the time of PM implantation: < 50 years; (ii) atrioventricular block (AVB) of unknown aetiology. Study population was investigated by ajmaline challenge and echocardiographic assessment over time. Genetic testing was performed using next-generation sequencing panel, containing 174 genes associated to inherited cardiac diseases, and Sanger sequencing confirmation of suspected variants with clinical implication. Of 2510 patients who underwent PM implantation, 15 (0.6%) were young adults (median age: 44 years, male predominance) presenting with advanced AVB of unknown origin. The average incidence of idiopathic AVB computed over the 2010–2019 time window was 0.7 per 100 000 persons per year (95% CI 0.4–1.2). Most of patients (67%) presented with specific genetic findings (pathogenic variant) or variants of uncertain significance (VUS). A pathogenic variant of PKP2 gene was found in one patient (6.7%) with no overt structural cardiac abnormalities. A VUS of TRPM4, MYBPC3, SCN5A, KCNE1, LMNA, GJA5 genes was found in other nine cases (60%). Of these, three unrelated patients (20%) presented the same heterozygous missense variant c.2531G > A p.(Gly844Asp) in TRPM4 gene. Diagnostic re-assessment over time led to a diagnosis of Brugada syndrome and long-QT syndrome in two patients (13%). No cardiac events occurred during a median follow-up of 72 months.

Conclusion

Idiopathic AVB in adults younger than 50 years is a very rare condition with an incidence of 0.7 per 100 000 persons/year. Systematic investigations, including genetic testing and ajmaline challenge, can lead to the achievement of a specific diagnosis in up to 20% of patients. Heterozygous missense variant c.2531G > A p.(Gly844Asp) in TRPM4 gene was found in an additional 20% of unrelated patients, suggesting possible association of the variant with the disease.