bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical layer authentication for 5G/6G millimeter wave communications by using channel sparsity
Authors: Tang Jie , Wen Hong , Song Huanhuan
Published: January 2022

This paper proposes a comprehensive study for the physical layer channel based authentication (PLA) designs in mmWave communications, which reveals the principles that how does the sparse properties of mmWave channel can benefit the PLA designs and performance. First, by fully investigating the channel perturbations of mmWave channel caused by the environmental changes within the channel coherence time, the generalized detection designs are investigated for mmWave channels. In general, it shows that the mmWave channel perturbations will seriously degrade the detection performance. To solve this problem, a lightweight but effective PLA scheme is proposed by fully utilizing the sparsity of mmWave channel. The key physical factors that impact the detection performance are fully investigated by conducting thoroughly theoretical analysis and simulations, and the detection spoofing probability of the scheme is show to be higher than 95%, while keeping the probability of false rate below 1%. The study indicates that channel sparsity is with great potential to design lightweight but effective PLA mechanisms for the future mmWave communication systems.
A high‐performance insulators location scheme based on YOLOv4 deep learning network with GDIoU loss function
Authors: Ma Bin , Fu Yongkang , Wang Chunpeng , Li Jian , Wang Yuli
Published: January 2022

This paper proposes a Gaussian Distance Intersection over Union (GDIoU) loss function‐based YOLOv4 deep learning network to solve the problem of slow speed and low accuracy insulator location in power facilities health inspection. In the scheme, A GDIoU loss function is designed to accelerate the convergence speed of the YOLOv4 deep learning network; at the same time, the GDIoU loss is added as one part of the network propagation loss, and the insulator's location accuracy is accordingly improved. Moreover, a re‐location scheme for tilt insulators correction is proposed to enhance the location accuracy of the insulators in different spatial angle states. Large amounts of field insulator images were gathered as training and testing samples to evaluate the performance of the proposed scheme. The experimental results have demonstrated that the GDIoU‐based YOLOv4 deep learning network combined with the tilt correction scheme can improve the insulator location speed by three times compared with the peer schemes, and the average precision is increased by 7.37% compared with the naive YOLOv4 network. The performance of the proposed scheme meets the requirement of online insulator location adequately.
Experimental and numerical simulation of the performance of SnS based solar cells
Authors: Garmim Taoufik , Benaissa Nouhaila , Rmili Ahmed , Soussi Lahcen , Anoua Rania , El Jouad Zouhair , Louardi Ahmed , Erguig Hassane , Hartiti Bouchaib , Monkade Mohamed
Published: January 2022

In the present study, the SnS thin films have been grown using the sol gel spin coating technical deposed on a glass substrate. The structural analysis of SnS thin films was examined using X-ray diﬀraction (DRX). The optical properties of SnS thin films have been investigated using the spectrophotometer UV-V, and we calculated the sum of the optical parameters such as the absorption coefficient, refractive index, the extinction coefficient, the real and imaginary part of the dielectric constant, and the optical conductivity. The electrical resistivity has been calculated using the four-point probe method. The performance of the SnS based proposed solar cells studied from the numerical simulation using SCAPS-1D software. The SnS-thickness, CdS-thickness, and ZnO-thickness are optimized. The SnS-band gap optimization showed that the optimal value is 1.55 eV this is similar to the value found experimentally (∼1.58 eV). The influence of the operating temperature, series and shut resistor, and SnS/CdS charge interface defect on the parameters on the performance solar cells are investigated.
Surface topography and enhanced photo detecting properties of multilayer MoSe2 crystal
Authors: Dixit Vijay , Nair Salil , Joy Jolly , Vyas C. U. , Narayan Som , Jha P. K. , Solanki G. K. , Pathak V. M.
Published: January 2022

The high photo responsive property and flexibility of tailoring the optical properties of the semiconducting layered transition metal dichalcogenides are appealing and makes them potentially suitable for the optoelectronic and photo detecting applications. In the present study molybdenum, diselenide (MoSe2) crystals were grown by direct vapor transport (DVT) technique in a dual zone horizontal furnace. To affirm the elemental composition and stoichiometric proportion of the as grown crystals, energy dispersive analysis of the x-ray was adopted. The surface morphological features of the grown crystals were investigated using light microscopy and scanning electron microscopy that attested the multilayer growth of crystals. The presence of single-crystalline phase and hexagonal structure was ascertained by employing transmission electron microscopy. The direct optical energy band gap of 1.42 eV was determined by UV-Visible spectroscopy. The Raman spectroscopy analysis carried out on the grown crystals revealed the presence of an A1g mode of vibration. Photo-detecting properties of the multilayer MoSe2 crystals were studied by exposing the basal plane of the photo-detecting sample by the polychromatic source of 70 mW/cm2 intensity at different biasing voltages from 1 V to 5 V respectively. The eminent sensing properties of the grown multilayered crystals are unveiled by the high photo responsivity 58.2 mA/Wm2 and specific detectivity 2.12 × 107 Jones. The effect of biasing voltage was prominently seen in the rise of photocurrent and detecting properties MoSe2 crystals.
Stage-Oriented CT Classification and Intermodal Evolution Model in Hepatic Alveolar Echinococcosis
Authors: Graeter Tilmann , Schmidberger Julian
Published: January 2022

Alveolar echinococcosis (AE) is one of the most dangerous human parasitoses. The main site of disease manifestation is the liver (about 98 %). The Echinococcus Multilocularis Ulm Classification for Computed Tomography (EMUC-CT), presented in 2016, was the first compilation of CT morphological criteria of hepatic AE. Studies based on EMUC-CT made it possible to draw conclusions about the development of the lesions in the course of disease beyond purely diagnostic typing. Among the most important findings of these precursor studies was that EMUC-CT type IV presented as an initial lesion, whereas EMUC-CT type III lesions were mostly associated with an advanced disease constellation. An intermodal view of image morphological criteria provides further multi-layered indications for lesion evolution.

With the “Alveolar Echinococcosis Ulm Classification” (AEUC), a revision of the previous EMUC-CT was carried out with stage-oriented reorganization of the primary morphologies. Furthermore, an intermodal classification scheme for the evolution of hepatic AE lesions based on AEUC, MRI Kodama classification, and aspects of ultrasound could be outlined.

The first stage-oriented CT classification of hepatic AE “AEUC” is based with respect to its lesion characterization on the separate consideration of two classification pillars, the five “primary morphologies”, AEUC I–V (AEUC II–IV with subcriteria) and the five “patterns of calcification”. In addition, an intermodal classification scheme presents five stages of lesion evolution: “initial stage”, “progressive stage”, “advanced stage”, “transitional stage” and “regressive stage”.

The imaging modalities differ with respect to their visualization of lesion criteria. This underlines the need for unimodal classification systems. Staging of an AE lesion can be done more accurately by evaluating different modalities.
Classic Psychedelic Drugs: Update on Biological
Mechanisms
Authors: Vollenweider Franz X. , Smallridge John W.
Published: January 2022

Renewed interest in the effects of psychedelics in the treatment of psychiatric
disorders warrants a better understanding of the neurobiological mechanisms
underlying the effects of these substances. During the past two decades,
state-of-the-art studies of animals and humans have yielded new important
insights into the molecular, cellular, and systems-level actions of psychedelic
drugs. These efforts have revealed that psychedelics affect primarily
serotonergic receptor subtypes located in cortico-thalamic and cortico-cortical
feedback circuits of information processing. Psychedelic drugs modulate
excitatory-inhibitory balance in these circuits and can participate in
neuroplasticity within brain structures critical for the integration of
information relevant to sensation, cognition, emotions, and the narrative of
self. Neuroimaging studies showed that characteristic dimensions of the
psychedelic experience obtained through subjective questionnaires as well as
alterations in self-referential processing and emotion regulation obtained
through neuropsychological tasks are associated with distinct changes in brain
activity and connectivity patterns at multiple-system levels. These recent
results suggest that changes in self-experience, emotional processing, and
social cognition may contribute to the potential therapeutic effects of
psychedelics.
Synthesis of Novel Pyrazine-Substituted 1H-Pyrrole-2-carboxamides and Related Tethered Heterocycles
Authors: Howells Rachel L. , Lamont Scott G. , McGuire Thomas M. , Hughes Samantha , Borrows Rachel , Fairley Gary , Feron Lyman J. L. , Greenwood Ryan D. R. , Lenz Eva , Grant Emma , Simpson Iain
Published: January 2022

As part of a drug discovery program, 4-pyrazin-2-yl-1H-pyrrole-2-carboxamides were accessed along with a number of bicyclic analogues. Routes to these compounds were largely absent from the scientific literature. The synthesis of a 4-(pyrazin-2-yl)-1H-pyrrole-2-carboxamide and several fused bicyclic analogues all using standard procedures (SNAr, borylation, C–C cross couplings, hydrolysis, amide bond formation, cyclisation, halogenation, and alkylation) from readily available starting materials is reported. The synthetic sequences range from 4–12 steps per final compound, with yields of isolated intermediates ranging from 20 to ∼100%.
The Ototoxicity of Chloroquine and Hydroxychloroquine: A Systematic Review
Authors: Fernandes Carolina Pereira , Vernier Luíza Silva , Dallegrave Eliane , Machado Márcia Salgado
Published: January 2022

Introduction Chloroquine and hydroxychloroquine are antimalarial drugs widely used in the treatment of rheumatic diseases. With the global pandemic caused by the new coronavirus, there was an increase in the prescription of these drugs, which led to a major concern regarding their ototoxic effects.

Objectives The objective of the present study was to assess existing scientific evidence about the toxic effects of chloroquine and hydroxychloroquine on the peripheral and/or central auditory system.

Data Synthesis A systematic literature review was performed by searching the PubMed (Medline), Scopus, Web of Science, LILACS, and SciELO electronic databases, in a search of articles that fullfiled the predefined inclusion and exclusion criteria. The review was conducted in three phases and, in all of them, analyses were performed by two independent researchers. Disagreements were discussed with a third researcher until a consensus was reached. A total of 437 articles were found and 8 were included in this review. Seven of the included studies reported hearing loss in their samples and presented a diagnostic hypothesis of ototoxicity induced by chloroquine or hydroxychloroquine. The most common type of hearing loss was sensorineural, with varying laterality and degrees of severity. The most frequently used audiological test was pure tone audiometry, and only two studies assessed brainstem evoked responses.

Conclusion The scientific evidence compiled in this research showed that chloroquine and hydroxychloroquine have an ototoxic effect in the peripheral auditory system. These drugs can cause cochlear damage, including changes in the stria vascularis and lesions in sensory hair cells.
Safety for the Rhinologist in the Age of COVID-19: Mask Use, Nasal Corticosteroids, Saline Irrigation, and Endoscopic Procedures – Literature Review
Authors: Kosugi Eduardo Macoto , Villa Jonatas Figueiredo , Ramos Henrique Faria , Luz-Matsumoto Gabriela Ricci , Serrano Thiago Luis Infanger , Campos Carlos Augusto Correia de , Barreto Carolina Cincurá , Lima Clara Mônica , Fornazieri Marco Aurélio , Piltcher Otavio , Lessa Marcus Miranda , Romano Fabrizio Ricci
Published: January 2022

Introduction Coronavirus disease 2019 (COVID-19) has claimed millions of lives. Adequate protection of the professionals involved in patient care is essential in the battle against this disease. However, there is much uncertainty involving safety-relarted topics that are of particular interest to the rhinologist in the context of COVID-19.

Objective To evaluate the current evidence regarding three safety-related topics: mask and respirator use, performance of nasal endoscopic procedures, and use of topical nasal and intranasal medications (saline irrigation and nasal corticosteroids).

Methods A literature review was performed on the PubMed, Scopus, and Cochrane databases, with standardized search queries for each of the three topics of interest.

Results In total, 13 articles on mask use, 6 articles on the safety of nasal corticosteroids, 6 articles on the safety of nasal endoscopic procedures, and 1 article on nasal irrigation with saline solution were included in the final analysis.

Conclusion N95 respirators are essential for the adequate protection of otolaryngologists. If reuse is necessary, physical methods of sterilization must be employed. No evidence was found to contraindicate the use of nasal corticosteroids, whether acute (in the management of sinonasal inflammatory conditions) or continued (in patients who use them chronically). Nasal irrigation with saline solution apparently does not increase the risk in the context of COVID-19. Nasal endoscopic procedures should only be performed after testing the patient for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the surgical team must wear full personal protective equipment to prevent aerosol exposure.
Creating value through autonomous shipping: an ecosystem perspective
Authors: Tsvetkova Anastasia , Hellström Magnus
Published: January 2022

The expected benefits of Maritime Autonomous Surface Ships (MASS) include increased safety, reduced costs and increased earning potential due to operational efficiencies and reduction in vessel manning. However, autonomous shipping enabled by such ships bears a greater potential than just replacing humans with machines. Rather, MASS can play a role in transforming supply and logistics chains. The value creation potential of these ships depends on the degree to which they disrupt logistics. Our aim here is to clarify how MASS create value and for whom, as well as how different actors in the maritime logistics ecosystem are able to monetize or otherwise benefit from the innovation. Based on interviews with experts in maritime logistics and autonomous technology, and a desktop study of the opinions of the leaders in maritime innovation, we analyse the different facets of value creation by MASS. We distinguish between the two key sources of value – onboard crew reduction and increased ship intelligence and their effects (cost reductions, earning potential, increased safety and system value) – and explicate for which actors in the ecosystem the value is created. We identify the key changes in the maritime logistics ecosystem, which concern the changing roles of technology providers, shipowners and operators, and we highlight the need for developing complementary infrastructure and activities in the ecosystem.
Analysis of experiments on the study of electrical activity in helium
Authors: Maidanov V. A. , Syvokon V. E. , Sokolov S. S.
Published: January 2022

From the experimental point of view, the works on the study of the so-called electrical activity in superfluid helium are analyzed. Based on the analysis of published data on the results of experiments on the appearance of such electrical activity under the propagation of second sound waves, during oscillations of a torsion oscillator filled with helium and microwave electromagnetic pumping of helium, one concludes that the experimental results published before 2016 do not give sufficient reasons to assume the presence of any special electrical activity of helium, and the appearance of an electric signal in a cell with superfluid helium at the propagation of acoustic waves in it can only be said after 2016. The nature of this signal needs further investigation.
Optimizing topological switching in confined 2D-Xene nanoribbons via finite-size effects
Authors: Nadeem Muhammad , Zhang Chao , Culcer Dimitrie , Hamilton Alex R. , Fuhrer Michael S. , Wang Xiaolin
Published: January 2022

In a blueprint for topological electronics, edge state transport in a topological insulator material can be controlled by employing a gate-induced topological quantum phase transition. Here, by studying the width dependence of electronic properties, it is inferred that zigzag-Xene nanoribbons are promising materials for topological electronics with a display of unique physical characteristics associated with the intrinsic band topology and the finite-size effects on gate-induced topological switching. First, due to intertwining with intrinsic band topology-driven energy-zero modes in the pristine case, spin-filtered chiral edge states in zigzag-Xene nanoribbons remain gapless and protected against backward scattering even with finite inter-edge overlapping in ultra-narrow ribbons, i.e., a 2D quantum spin Hall material turns into a 1D topological metal. Second, mainly due to width- and momentum-dependent tunability of the gate-induced inter-edge coupling, the threshold-voltage required for switching between gapless and gapped edge states reduces as the width decreases, without any fundamental lower bound. Third, when the width of zigzag-Xene nanoribbons is smaller than a critical limit, topological switching between edge states can be attained without bulk bandgap closing and reopening. This is primarily due to the quantum confinement effect on the bulk band spectrum, which increases the nontrivial bulk bandgap with decrease in width. The existence of such protected gapless edge states and reduction in threshold-voltage accompanied by enhancement in the bulk bandgap overturns the general wisdom of utilizing narrow-gap and wide channel materials for reducing the threshold-voltage in a standard field effect transistor analysis and paves the way toward low-voltage topological devices.
Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ
Authors: Belsare Ketaki D. , Wu Haifan , Mondal Dibyendu , Bond Annalise , Castillo Erika , Jin Jia , Jo Hyunil , Roush Addison E. , Pilla Kala Bharath , Sali Andrej , Condello Carlo , DeGrado William F.
Published: January 2022

Significance

Mutations in a microglial protein, TREM2, represents a risk for Alzheimer’s disease (AD). We show that the soluble form of TREM2, sTREM2, can bind and inhibit fibrillization of Aβ peptides. sTREM2 increases uptake of Aβ fibrils into microglial and neuroglioma cell lines. Contrastingly, mutation R47H was found to have little effect on fibril nucleation and binding, but decreased uptake and functional responses. Our findings using integrative molecular modeling based on cross-linking mass spectrometry data for WT sTREM2–Aβ fibril complex demonstrate that TREM2 has at least two ligand-binding surfaces: one binding Aβ fibrils and the other anionic polyvalent ligands. R47H mutation lies on the latter surface. These findings inform mechanisms by which TREM2 modulates key processes in AD progression.
Sailing toIthaka
Authors: Serafis Dimitris , Kitis E. Dimitris , Assimakopoulos Stavros
Published: January 2022

This paper examines the reasoning lines in PM Alexis Tsipras’ political discourse in critical moments of SYRIZA’s tenure as the ruling party in Greece. Adopting a CDS perspective, we zoom in on the patterns that underlie the (de)legitimization of the crisis-ridden EU in three seminal speeches by PM Tsipras during the Greek/EU financial crisis. To this end, we integrate systemic-functional and cognitive linguistic tools with a view to scrutinizing representational meaning, before turning to employ the notions ofendoxonandtopos/locusas a means of studying the particularargumentative inferences, triggered by the respective discursive representations. Through this lens, we show how the overall argumentation can be seen as supporting the (de-)legitimation of dominant EU austerity perspectives while transforming SYRIZA into a pro-austerity voice.
De/legitimising EUrope through the performance of crises
Authors: Forchtner Bernhard , Özvatan Özgür
Published: January 2022

This article illuminates the far-right populist Alternative for Germany's (AfD) performances of delegitmisation vis-à-vis EUrope and
legitmisation of itself/the nation by articulating two paradigmatic, transnational crises: climate change and COVID-19. It asks: ‘how
does the far-right AfD perform these two crises to legitimise itself and delegitimize others?’ and ‘what similarities/differences
exist between the performance of these two crises in terms of topics, narrative (genres) and their linguistic realisations?’. To
explore AfD’s de/legitimisation efforts, written texts and videos by AfD representatives through which they intervene in
discourses about climate change in 2019 and COVID-19 in 2020 are analysed. The analysis identifies a two-dimensional process of
narrative delegitimization, vilifying national and backgrounding EUropean ‘others’, and illustrates that a
comic-romantic emplotment of ethno-national rebirth pre-configures the largely same topics and topoi. In so
doing, the article, furthermore, takes another step towards the conceptual integration of narrative (genre) into the
Discourse-Historical Approach in Critical Discourse Studies.
The delegitimisation of Europe in a pro-European country
Authors: Maccaferri Marzia , Newth George
Published: January 2022

The European project has always played a pivotal role in Italy’s politics and Italian political discourse. The European Union (EU) represented the primary vehicle through which to regain international legitimacy. From this perspective, the intensification in the last few years of the Eurosceptic and populist discourse of Matteo Salvini’s Lega has marked a critical turning point. This article contributes to an understanding of such process from critical discursive and historical perspectives. Building on the concept of recontextualization as elaborated in CDS but also more generally appealing to conceptual history and Discourse-Historical Approach (DHA) frameworks, this study deconstructs the Lega’s Euroscepticism diachronically, interpreting populism as a key discursive element of the Lega’s Far Right ideology. We thus highlight how the Lega’s Eurosceptic discourse and the recontextualisation of the European legitimisation process present a dramatic change and seem highly indicative of a new ideological and extra-party cleavage of ‘sovereignism’.
Geometrical effects on luminescent dosimeter energy response
Authors: Benali A. , Medkour Ishak-Boushaki G. , Riffaud J. , Nourreddine A.-M.
Published: January 2022

Luminescent dosimeters are widely used in medical
applications. For an optimal use of these dosimeters, comparative
studies of their characteristics, under clinical radiations, are
very useful.

The purpose of this study is to establish the effect of dosimeter
geometry on the luminescent dosimeter energy response for different
clinical radiation beams.

Monte Carlo simulations were used to calculate the energy response
of three kinds of non-commercialized luminescent dosimeters. The
dosimeters are: a) radiophotoluminescent glass dosimeter (RPLGD,
typeFD-7 glass), b) thermoluminescent dosimeter (TLD, type
LiF:Mg,Ti) and c) optically stimulated dosimeter (OSLD, type
Al2O3:C).The studied dosimeters have cylindrical geometry
with a thickness of 2mm and diameters ranging from 1 to 13 mm. The
radiation beams were 70 kV X-ray beam, clinical photon beam of
15 MV and clinical electron beam of 9 MeV.

This study confirms a non-negligible effect on the dosimeter
geometry on its energy response for these beams.
Northward expansion of fire-adaptative vegetation in future warming
Authors: Liu Meng , Yang Linqing
Published: January 2022

Fire frequency and intensity are increasing due to higher temperatures and more droughts. The distributions of fuels (vegetation in natural conditions) are also changing in response to climate change. The vegetation in cold environments such as high latitudes and high altitudes is found to move upward or northward due to global warming. However, few studies have investigated the distribution changes of fire adaptive species in warm environments. This study estimated and compared the distributions of a typical fuelwood, the Eucalyptus globulus, under different climate scenarios. The species distribution modeling techniques were adopted to estimate the current distributions of the Eucalyptus globulus and the future distributions under scenarios of both SSP245 and SSP585 in 2060. Results show that the probability of the existence of the Eucalyptus globulus in the Northern Hemisphere increases significantly (p < 0.001) under both SSP245 and SSP585, especially in North America and Europe. However, the probability in the Southern Hemisphere decreases. The distribution of the Eucalyptus globulus expands in the mid-latitude (40 N–60 N) of the Northern Hemisphere. High carbon emissions contribute to the boost of the establishment of the Eucalyptus globulus in the Northern Hemisphere. These findings demonstrate that the fire adaptive species shows the tendency of shifting northward in response to climate change, highlighting the challenge of northward expansion of fires in future warming.
Rapid restratification of the ocean surface boundary layer during the suppressed phase of the MJO in austral spring
Authors: Hsu Je-Yuan , Feng Ming , Wijffels Susan
Published: January 2022

Rapid restratification of the ocean surface boundary layer in the Indonesian-Australian Basin was captured in austral spring 2018, under the conditions of low wind speed and clear sky during the suppressed phase of Madden–Julian Oscillations (MJOs). Despite sunny days, strong diurnal variations of sea surface temperature (SST) were not observed until the wind speed became extremely low, because the decreasing wind speed modulated the latent heat flux. Combined with the horizontal advection of ocean current, the reduced upward heat loss inhibited the nighttime convective mixing and facilitated the restratification of the subsurface ocean layers. The surface mixed layer was thus shoaled up to 40 m in two days. The restratified upper ocean then sustained high SSTs by trapping heat near the sea surface until the onset of the MJO convection. This restratification process might be initialized under the atmospheric downwelling conditions during the suppressed phase of MJOs. The resulted high SSTs may affect the development and trajectories of MJOs, by enhancing air-sea heat and moisture fluxes as the winds pick up. Simulating this detailed interaction between the near-surface ocean and atmospheric features of MJOs remains a challenge, but with sufficient vertical resolution and realistic initial conditions, several features of the observations can be well captured.
Numerical analysis on the effect of process parameters on deposition geometry in wire arc additive manufacturing
Authors: FAN Shilong , YANG Fei , ZHU Xiaonan , DIAO Zhaowei , CHEN Lin , RONG Mingzhe
Published: January 2022

Here we develop a two-dimensional numerical model of wire and arc additive manufacturing (WAAM) to determine the relationship between process parameters and deposition geometry, and to reveal the influence mechanism of process parameters on deposition geometry. From the predictive results, a higher wire feed rate matched with a higher current could generate a larger and hotter droplet, and thus transfer more thermal and kinetic energy into melt pool, which results in a wider and lower deposited layer with deeper penetration. Moreover, a higher preheat temperature could enlarge melt pool volume and thus enhance heat and mass convection along both axial and radial directions, which gives rise to a wider and higher deposited layer with deeper penetration. These findings offer theoretical guidelines for the acquirement of acceptable deposition shape and optimal deposition quality through adjusting process parameters in fabricating WAAM components.
Non-covalent interactions between molecular dimers (S66) in electric fields
Authors: Schwilk Max , Mezei Pál D , Tahchieva Diana N , von Lilienfeld O Anatole
Published: January 2022

Fine tuning and microscopic control of van der Waals interactions through oriented external electric fields (OEEFs) mandates an accurate and systematic understanding of intermolecular response properties. Having taken exploratory steps into this direction, we present a systematic study of interaction induced dipole electric properties of all molecular dimers in the S66 set, relying on CCSD(T)-F12b/aug-cc-pVDZ-F12 as reference level of theory. For field strengths up to ≈5 GV m−1 the interaction induced electric response beyond second order is found to be insignificant. Large interaction dipole moments (i.e. dipole moment changes due to van der Waals binding) are observed in the case of hydrogen bonding oriented along the intermolecular axis, and mostly small interaction dipole moments are found in dimers bonded by π-stacking or London dispersion. The interaction polarizabilities (i.e. polarizability changes due to van der Waals binding) were generally found to be small but always with a positive-valued principal component approximately aligned with the intermolecular axis, and two other negative-valued components. Energy decompositions according to symmetry adapted perturbation theory (SAPT0/jun-cc-pVDZ) suggest that electrostatics dominates the interaction dipole moment, with exchange and induction contributing on a smaller scale, and with dispersion having the smallest effect. First-order SAPT0 decomposition into monomer-resolved contributions enables us to establish a quantitative link between electric properties of monomers and dimers, which is found to be in qualitative agreement with the coupled cluster reference method. Using the aug-cc-pVQZ basis and non-empirical Perdew–Burke–Ernzerhof (PBE) semilocal exchange–correlation kernels, we also assess how density functional approximations in the nonlocal exchange and correlation parts affect the predictive accuracy: while dRPA@PBE0 based predictions are in excellent overall agreement with coupled cluster results, the computationally more affordable LC-ωPBE0-D3 level of theory also yields reliable results with relative errors below 5%. PBE alone, even when dispersion corrected, produces larger errors in interaction dipole moments (≈10%) and polarizabilities (≈20%). We also resolve the mutual impact of the three dimensions of the OEEF, and we present a discussion of the intermolecular distance dependence of the perturbations.
Persistent calyces increase floral longevity and female fitness inSalvia miltiorrhiza(Lamiaceae)
Authors: Li Deng-Fei , Yu Yan , Yang Hao-Jin , Yan Xian-Chun
Published: January 2022

The evolution of persistent calyces may be an adaptation to ensure reproductive success of certain flowering plants. However, experimental evidence of the functions of persistent calyces during flowering and seed development remains scarce. We explored the possible functions of persistent calyces in Salvia miltiorrhiza, a perennial herb with campanulate calyx. We conducted calyx manipulation experiments to examine whether persistent calyces affect visitation rates of nectar robbers and pollinators, individual flower longevity, fruit set, seed set and seed mass. Our findings suggested that shortening of the calyx significantly decreased individual flower longevity, fruit set and seed mass, but did not affect visitation of pollinators and nectar robbers. In addition, the seed set of control flowers and the flowers with calyx shortened at the beginning of fruiting stage (CSF flowers) did not significantly differ, but both were higher than that of the flowers with calyx shortened at the beginning of blooming stage (CSB flowers). The seed set and fruit set of CSB flowers were limited by pollination due to the reduction in floral longevity. We conclude that persistent calyces of S. miltiorrhiza may represent adaptive strategies to maintain floral longevity and increase plant fitness. Persistent calyces may provide protection for the growth of flowers and contribute resources to the development of fruits and seeds.
De-epithelialized Dermal Flap to Reduce Sacral Wound Healing Complications After Lower Body Lift Procedure
Authors: Zaussinger Maximilian , Wenny Raphael , Schwartz Bernhard , Ehebruster Gudrun , Huemer Georg M , Schmidt Manfred
Published: January 2022

Background

Lower or circumferential body lift procedures in the massive-weight-loss population have been associated with significant complication rates. Particularly, the sacral area is at risk of wound-healing problems due to high wound tension or shear forces.

Objectives

The authors introduced a de-epithelialized dermal flap to reinforce the sacral area.

Methods

Within this retrospective study, outcomes of 40 consecutive patients who underwent lower body lift between 2017 and 2021 were analyzed. The patient population was divided into 2 study groups (sacral flap vs no flap) including 20 patients each. Demographic and surgical data as well as complications were evaluated and compared. Appropriate statistical analysis was performed.

Results

Thirty-seven female and 3 male patients with a median age of 36.5 years (range, 23-54 years) and a mean weight loss of 46.3 ± 12 kg participated in the study. The most common complication was sacral wound dehiscence (n = 7, 17.5%), and its occurrence was statistically significantly lower in the sacral flap group (P = 0.037). The odd ratios for complications when executing the sacral flap procedure were reduced to 0.306 (95% confidence interval = 0.075 to 1.246) and 0.261 (95% confidence interval = 0.055 to 1.250) for the uncorrected and corrected logistic regressions, respectively. In addition, findings showed a significantly shorter hospital stay as well as statistical trends towards a lower occurrence of overall complications in the sacral flap group. Concerning the remaining data, no statistically significant differences between study groups were detected.

Conclusions

The presented de-epithelialized dermal flap leads to a significant reduction of sacral wound-healing complications and a shorter hospital stay for patients. This surgical technique is easily reproduceable, rapid, and effective; therefore, we would recommend it for each circumferential or lower body lift procedure.

Level of Evidence: 4
Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures
Authors: Wang Xiangwen , Lu Yonggang , Lin Xianghong
Published: January 2022

Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream technologies in the field of structural biology to determine the three-dimensional (3D) structures of biological macromolecules. Heterogeneous cryo-EM projection image classification is an effective way to discover conformational heterogeneity of biological macromolecules in different functional states. However, due to the low signal-to-noise ratio of the projection images, the classification of heterogeneous cryo-EM projection images is a very challenging task. In this paper, two novel distance measures between projection images integrating the reliability of common lines, pixel intensity and class averages are designed, and then a two-stage spectral clustering algorithm based on the two distance measures is proposed for heterogeneous cryo-EM projection image classification. In the first stage, the novel distance measure integrating common lines and pixel intensities of projection images is used to obtain preliminary classification results through spectral clustering. In the second stage, another novel distance measure integrating the first novel distance measure and class averages generated from each group of projection images is used to obtain the final classification results through spectral clustering. The proposed two-stage spectral clustering algorithm is applied on a simulated and a real cryo-EM dataset for heterogeneous reconstruction. Results show that the two novel distance measures can be used to improve the classification performance of spectral clustering, and using the proposed two-stage spectral clustering algorithm can achieve higher classification and reconstruction accuracy than using RELION and XMIPP.
Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants
Authors: Li Jing , Wu Ya-Nan , Zhang Sen , Kang Xiao-Ping , Jiang Tao
Published: January 2022

Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype–genotype relationships. We introduced a framework involving dinucleotide (DNT) composition representation (DCR) to parse the general human adaptation of RNA viruses and applied a three-dimensional convolutional neural network (3D CNN) analysis to learn the human adaptation of other existing coronaviruses (CoVs) and predict the adaptation of SARS-CoV-2 variants of concern (VOCs). A markedly separable, linear DCR distribution was observed in two major genes—receptor-binding glycoprotein and RNA-dependent RNA polymerase (RdRp)—of six families of single-stranded (ssRNA) viruses. Additionally, there was a general host-specific distribution of both the spike proteins and RdRps of CoVs. The 3D CNN based on spike DCR predicted a dominant type II adaptation of most Beta, Delta and Omicron VOCs, with high transmissibility and low pathogenicity. Type I adaptation with opposite transmissibility and pathogenicity was predicted for SARS-CoV-2 Alpha VOCs (77%) and Kappa variants of interest (58%). The identified adaptive determinants included D1118H and A570D mutations and local DNTs. Thus, the 3D CNN model based on DCR features predicts SARS-CoV-2, a major type II human adaptation and is qualified to predict variant adaptation in real time, facilitating the risk-assessment of emerging SARS-CoV-2 variants and COVID-19 control.
PERCC1, a new member of theYap/TAZ/FAM181transcriptional co-regulator family
Authors: Sanchez-Pulido Luis , Jia Siyang , Hansen Carsten Gram , Ponting Chris P
Published: January 2022

Motivation

Disrupted PERCC1 gene expression causes an intractable congenital diarrhoea in infants. However, this gene’s molecular mechanism is unknown and no homologous proteins have been reported.

Results

Our detailed evolutionary analysis of PERCC1 sequence reveals it to be a previously unappreciated member of the YAP/TAZ/FAM181 family of homologous transcriptional regulators. Like YAP and TAZ, PERCC1 likely interacts with DNA via binding to TEA/ATTS domain transcription factors (TEADs) using its conserved interface-2 and -3 sequences. We compare the expression patterns of PERCC1 with those of YAP, TAZ, TEADs. Our report provides the identification and first in-depth bioinformatic analysis of a YAP/TAZ homologue, and a likely new regulator of the YAP/TAZ-TEAD transcriptional complex.

Availability and implementation

The data underlying this article are available in UniProt Database.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
SangeR: the high-throughput Sanger sequencing analysis pipeline
Authors: Schmid Kai , Dohmen Hildegard , Ritschel Nadja , Selignow Carmen , Zohner Jochen , Sehring Jannik , Acker Till , Amsel Daniel
Published: January 2022

In the era of next generation sequencing and beyond, the Sanger technique is still widely used for variant verification of inconclusive or ambiguous high-throughput sequencing results or as a low-cost molecular genetical analysis tool for single targets in many fields of study. Many analysis steps need time-consuming manual intervention. Therefore, we present here a pipeline-capable high-throughput solution with an optional Shiny web interface, that provides a binary mutation decision of hotspots together with plotted chromatograms including annotations via flat files.

Availability and implementation

SangeR is freely available at https://github.com/Neuropathology-Giessen/SangeR and https://hub.docker.com/repository/docker/kaischmid/sange_r

Contact

Kai.Schmid@patho.med.uni-giessen.de or Daniel.Amsel@patho.med.uni-giessen.de

Supplementary information

Supplementary data are available at Bioinformatics online.
A mixture model for determining SARS-Cov-2 variant composition in pooled samples
Authors: Valieris Renan , Drummond Rodrigo D , Defelicibus Alexandre , Dias-Neto Emmanuel , Rosales Rafael A , Tojal da Silva Israel
Published: January 2022

Motivation

Despite of the fast development of highly effective vaccines to control the current COVID–19 pandemics, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) variants of concern. Therefore, it is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary to follow the spread of the disease and the evolution of the virus. In this context, new genomic variants of SARS-CoV-2, including variants refractory to current vaccines, makes genomic surveillance programs tools of utmost importance. Nevertheless, the lack of appropriate analytical tools to quickly and effectively access the viral composition in meta-transcriptomic sequencing data, including environmental surveillance, represent possible challenges that may impact the fast adoption of this approach to mitigate the spread and transmission of viruses.

Results

We propose a statistical model for the estimation of the relative frequencies of SARS-CoV-2 variants in pooled samples. This model is built by considering a previously defined selection of genomic polymorphisms that characterize SARS-CoV-2 variants. The methods described here support both raw sequencing reads for polymorphisms-based markers calling and predefined markers in the variant call format. Results obtained using simulated data show that our method is quite effective in recovering the correct variant proportions. Further, results obtained by considering longitudinal data from wastewater samples of two locations in Switzerland agree well with those describing the epidemiological evolution of COVID-19 variants in clinical samples of these locations. Our results show that the described method can be a valuable tool for tracking the proportions of SARS-CoV-2 variants in complex mixtures such as waste water and environmental samples.

Availability and implementation

http://github.com/rvalieris/LCS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Optimizing nodal and staging classification in low rectal cancers with lateral node metastasis: multicentre retrospective cohort study
Authors: Shinto Eiji , Ike Hideyuki , Ito Masaaki , Takahashi Keiichi , Ohue Masayuki , Kanemitsu Yukihide , Suto Takeshi , Kinugasa Tetsushi , Watanabe Jun , Hida Jin-ichi , Itabashi Michio , Ozawa Heita , Nozawa Hiroaki , Kobayashi Hirotoshi , Hashiguchi Yojiro , Hase Kazuo , Sugihara Kenichi
Published: January 2022

Background

Patients with lateral node metastasis in low rectal cancers have a poor prognosis. However, variability in patient survival in terms of lateral metastatic status has not been thoroughly investigated. This study was conducted to assess the prognostic value of lateral node involvement and to review nodal classification.

Methods

Patients with stage III low rectal cancers who underwent lateral node dissection were retrospectively reviewed. Two cohorts were set: the first one (1995–2006) was selected using a Japanese multi-institutional database and was used for development of a new nodal system, and the second (2007–2013) was collected from referral institutions for validation of findings. Variables correlated with poor prognosis were investigated. Next, a modified classification of lateral-positive nodal cancers was created. Finally, this new classification was compared with TNM and Japanese classification-based systems according to the Akaike information criterion (AIC) and concordance index (c-index).

Results

Overall, 742 and 508 patients were selected for cohorts 1 and 2, respectively. Based on the analyses on cohort 1, patients with two or more lateral metastatic nodes partially spreading into regions outside of internal iliac area exhibited poor prognosis; accordingly, a modified N classification was created, where TNM-N1 and N2a cancers with this feature were upgraded, respectively, to N2a and N2b. The modified N classification yielded the most favourable indices (AIC = 2661.08; c-index = 0.6477) compared with the TNM (AIC = 2662.36; c-index = 0.6457) and Japanese classification-based systems (AIC = 2684.06; c-index = 0.6302). All findings were confirmed by analysing cohort 2.

Conclusion

A modified nodal system is proposed to account for the significance of lateral node metastasis.
Association between visit-to-visit blood pressure variability and risks of dementia in CKD patients: a nationwide observational cohort study
Authors: Park Sehoon , Cho Semin , Lee Soojin , Kim Yaerim , Park Sanghyun , Huh Hyeok , Kim Yong Chul , Han Seung Seok , Lee Hajeong , Lee Jung Pyo , Joo Kwon Wook , Lim Chun Soo , Kim Yon Su , Han Kyungdo , Kim Dong Ki
Published: January 2022

Background

The association between visit-to-visit blood pressure (BP) variability and dementia risk in chronic kidney disease (CKD) patients has rarely been studied.

Methods

In this retrospective observational study, individuals who received three or more general health screenings were identified in the nationwide database of Korea. Those with persistent non-dialysis-dependent CKD [estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 or dipstick albuminuria ≥1+] were included. The study exposure was systolic or diastolic BP variability, calculated as the variation independent of the mean and categorized into quartiles (Q4: the highest quartile; Q1: the lowest quartile). The risks of all-cause dementia, including Alzheimer's disease and vascular dementia, were analyzed by Cox regression adjusted for various clinical characteristics, including baseline BP and eGFR values.

Results

We included 103 139 CKD patients and identified 7574 (7%) dementia events, including 5911 (6%) Alzheimer's disease cases, 886 (1%) vascular dementia events and 777 (1%) cases categorized as other types of dementia. Higher systolic BP variability was significantly associated with higher risks of all-cause dementia {[Q4 versus Q1], hazard ratio [HR] 1.173 [95% confidence interval (CI) 1.102–1.249], P for trend < .001}. The results were also significant for the risk of Alzheimer's disease [HR 1.162 (95% CI 1.083–1.248), P < .001] and vascular dementia [HR 1.282 (95% CI 1.064–1.545), P = .039]. The results were similar when diastolic BP variability was the exposure, as high diastolic BP variability was significantly associated with higher risks of all-cause dementia [HR 1.191 (95% CI 1.117,1.270), P < .001].

Conclusions

Higher visit-to-visit BP variability is significantly associated with a higher risk of dementia in CKD patients.