bluuebunny/crossref_metadata_2025 huggingface dataset:
Subgap spectroscopy along hybrid nanowires by nm-thick tunnel barriers
Authors: Levajac Vukan , Wang Ji-Yin , Sfiligoj Cristina , Lemang Mathilde , Wolff Jan Cornelis , Bordin Alberto , Badawy Ghada , Gazibegovic Sasa , Bakkers Erik P. A. M. , Kouwenhoven Leo P.
Published: October 2023

Tunneling spectroscopy is widely used to examine the subgap spectra in semiconductor-superconductor nanostructures when searching for Majorana zero modes (MZMs). Typically, semiconductor sections controlled by local gates at the ends of hybrids serve as tunnel barriers. Besides detecting states only at the hybrid ends, such gate-defined tunnel probes can cause the formation of non-topological subgap states that mimic MZMs. Here, we develop an alternative type of tunnel probes to overcome these limitations. After the growth of an InSb-Al hybrid nanowire, a precisely controlled in-situ oxidation of the Al shell is performed to yield a nm-thick AlOx layer. In such thin isolating layer, tunnel probes can be arbitrarily defined at any position along the hybrid nanowire by shadow-wall angle-deposition of metallic leads. In this work, we make multiple tunnel probes along single nanowire hybrids and successfully identify Andreev bound states (ABSs) of various spatial extension residing along the hybrids.
The transcription factor Zeb1 controls homeostasis and function of type 1 conventional dendritic cells
Authors: Wang Yan , Zhang Quan , He Tingting , Wang Yechen , Lu Tianqi , Wang Zengge , Wang Yiyi , Lin Shen , Yang Kang , Wang Xinming , Xie Jun , Zhou Ying , Hong Yazhen , Liu Wen-Hsien , Mao Kairui , Cheng Shih-Chin , Chen Xin , Li Qiyuan , Xiao Nengming
Published: October 2023

Type 1 conventional dendritic cells (cDC1) are the most efficient cross-presenting cells that induce protective cytotoxic T cell response. However, the regulation of their homeostasis and function is incompletely understood. Here we observe a selective reduction of splenic cDC1 accompanied by excessive cell death in mice with Zeb1 deficiency in dendritic cells, rendering the mice more resistant to Listeria infection. Additionally, cDC1 from other sources of Zeb1-deficient mice display impaired cross-presentation of exogenous antigens, compromising antitumor CD8+ T cell responses. Mechanistically, Zeb1 represses the expression of microRNA-96/182 that target Cybb mRNA of NADPH oxidase Nox2, and consequently facilitates reactive-oxygen-species-dependent rupture of phagosomal membrane to allow antigen export to the cytosol. Cybb re-expression in Zeb1-deficient cDC1 fully restores the defective cross-presentation while microRNA-96/182 overexpression in Zeb1-sufficient cDC1 inhibits cross-presentation. Therefore, our results identify a Zeb1-microRNA-96/182-Cybb pathway that controls cross-presentation in cDC1 and uncover an essential role of Zeb1 in cDC1 homeostasis.
Circular single-stranded DNA as switchable vector for gene expression in mammalian cells
Authors: Tang Linlin , Tian Zhijin , Cheng Jin , Zhang Yijing , Song Yongxiu , Liu Yan , Wang Jinghao , Zhang Pengfei , Ke Yonggang , Simmel Friedrich C. , Song Jie
Published: October 2023

Synthetic gene networks in mammalian cells are currently limited to either protein-based transcription factors or RNA-based regulators. Here, we demonstrate a regulatory approach based on circular single-stranded DNA (Css DNA), which can be used as an efficient expression vector with switchable activity, enabling gene regulation in mammalian cells. The Css DNA is transformed into its double-stranded form via DNA replication and used as vectors encoding a variety of different proteins in a wide range of cell lines as well as in mice. The rich repository of DNA nanotechnology allows to use sort single-stranded DNA effectors to fold Css DNA into DNA nanostructures of different complexity, leading the gene expression to programmable inhibition and subsequently re-activation via toehold-mediated strand displacement. The regulatory strategy from Css DNA can thus expand the molecular toolbox for the realization of synthetic regulatory networks with potential applications in genetic diagnosis and gene therapy.
Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis
Authors: Jin Shan , Chen Xingchen , Yang Jun , Ding Jianping
Published: October 2023

Mammalian lactate dehydrogenase D (LDHD) catalyzes the oxidation of D-lactate to pyruvate. LDHD mutations identified in patients with D-lactic acidosis lead to deficient LDHD activity. Here, we perform a systematic biochemical study of mouse LDHD (mLDHD) and determine the crystal structures of mLDHD in FAD-bound form and in complexes with FAD, Mn2+ and a series of substrates or products. We demonstrate that mLDHD is an Mn2+-dependent general dehydrogenase which exhibits catalytic activity for D-lactate and other D-2-hydroxyacids containing hydrophobic moieties, but no activity for their L-isomers or D-2-hydroxyacids containing hydrophilic moieties. The substrate-binding site contains a positively charged pocket to bind the common glycolate moiety and a hydrophobic pocket with some elasticity to bind the varied hydrophobic moieties of substrates. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of LDHD, and the functional roles of mutations in the pathogenesis of D-lactic acidosis.
Real higher-order Weyl photonic crystal
Authors: Pan Yuang , Cui Chaoxi , Chen Qiaolu , Chen Fujia , Zhang Li , Ren Yudong , Han Ning , Li Wenhao , Li Xinrui , Yu Zhi-Ming , Chen Hongsheng , Yang Yihao
Published: October 2023

Higher-order Weyl semimetals are a family of recently predicted topological phases simultaneously showcasing unconventional properties derived from Weyl points, such as chiral anomaly, and multidimensional topological phenomena originating from higher-order topology. The higher-order Weyl semimetal phases, with their higher-order topology arising from quantized dipole or quadrupole bulk polarizations, have been demonstrated in phononics and circuits. Here, we experimentally discover a class of higher-order Weyl semimetal phase in a three-dimensional photonic crystal (PhC), exhibiting the concurrence of the surface and hinge Fermi arcs from the nonzero Chern number and the nontrivial generalized real Chern number, respectively, coined a real higher-order Weyl PhC. Notably, the projected two-dimensional subsystem with kz = 0 is a real Chern insulator, belonging to the Stiefel-Whitney class with real Bloch wavefunctions, which is distinguished fundamentally from the Chern class with complex Bloch wavefunctions. Our work offers an ideal photonic platform for exploring potential applications and material properties associated with the higher-order Weyl points and the Stiefel-Whitney class of topological phases.
Discrete hippocampal projections are differentially regulated by parvalbumin and somatostatin interneurons
Authors: Lodge Daniel J. , Elam Hannah B. , Boley Angela M. , Donegan Jennifer J.
Published: October 2023

People with schizophrenia show hyperactivity in the ventral hippocampus (vHipp) and we have previously demonstrated distinct behavioral roles for vHipp cell populations. Here, we test the hypothesis that parvalbumin (PV) and somatostatin (SST) interneurons differentially innervate and regulate hippocampal pyramidal neurons based on their projection target. First, we use eGRASP to show that PV-positive interneurons form a similar number of synaptic connections with pyramidal cells regardless of their projection target while SST-positive interneurons preferentially target nucleus accumbens (NAc) projections. To determine if these anatomical differences result in functional changes, we used in vivo opto-electrophysiology to show that SST cells also preferentially regulate the activity of NAc-projecting cells. These results suggest vHipp interneurons differentially regulate that vHipp neurons that project to the medial prefrontal cortex (mPFC) and NAc. Characterization of these cell populations may provide potential molecular targets for the treatment schizophrenia and other psychiatric disorders associated with vHipp dysfunction.
A single-dose of intranasal vaccination with a live-attenuated SARS-CoV-2 vaccine candidate promotes protective mucosal and systemic immunity
Authors: Adam Awadalkareem , Kalveram Birte , Chen John Yun-Chung , Yeung Jason , Rodriguez Leslie , Singh Ankita , Shi Pei-Yong , Xie Xuping , Wang Tian
Published: October 2023

An attenuated SARS-CoV-2 virus with modified viral transcriptional regulatory sequences and deletion of open-reading frames 3, 6, 7 and 8 (∆3678) was previously reported to protect hamsters from SARS-CoV-2 infection and transmission. Here we report that a single-dose intranasal vaccination of ∆3678 protects K18-hACE2 mice from wild-type or variant SARS-CoV-2 challenge. Compared with wild-type virus infection, the ∆3678 vaccination induces equivalent or higher levels of lung and systemic T cell, B cell, IgA, and IgG responses. The results suggest ∆3678 as an attractive mucosal vaccine candidate to boost pulmonary immunity against SARS-CoV-2.
Restructuring and serving web-accessible streamflow data from the NOAA National Water Model historic simulations
Authors: Johnson J. Michael , Blodgett David L. , Clarke Keith C. , Pollak Jon
Published: October 2023

In 2016, the National Oceanic and Atmospheric Administration deployed the first iteration of an operational National Water Model (NWM) to forecast the water cycle in the continental United States. With many versions, an hourly, multi-decadal historic simulation is made available to the public. In all released to date, the files containing simulated streamflow contain a snapshot of model conditions across the entire domain for a single timestep which makes accessing  time series a technical and resource-intensive challenge. In the most recent release, extracting a complete streamflow time series for a single location requires managing 367,920 files (~16.2 TB). In this work we describe a reproducible process for restructuring a sequential set of NWM steamflow files for efficient time series access and provide restructured datasets for versions 1.2 (1993–2018), 2.0 (1993–2020), and 2.1 (1979–2022). These datasets have been made accessible via an OPeNDAP enabled THREDDS data server for public use and a brief analysis highlights the latest version of the model should not be assumed best for all locations. Lastly we describe an R package that expedites data retrieval with examples for multiple use-cases.
Uptake of SARS-CoV-2 vaccination among structurally-marginalized people who use drugs in Vancouver, Canada
Authors: Reddon Hudson , Barker Brittany , Bartlett Sofia , Márquez Ana Citlali , Sekirov Inna , Jassem Agatha , Morshed Muhammad , Clemens Ari , Beck McGreevy Phoenix , Hayashi Kanna , DeBeck Kora , Krajden Mel , Milloy M.-J. , Socías Maria Eugenia
Published: October 2023

We sought to evaluate the rates and predictors of SARS-CoV-2 vaccination among members of a structurally-marginalized population of people who use drugs (PWUD) during a targeted, community-wide, vaccination campaign in Vancouver, Canada. Interviewer-administered data were collected from study participants between June 2021 and March 2022. Generalized estimating equation analysis was used to identify factors associated with SARS-CoV-2 vaccine uptake, ascertained through a province-wide vaccine registry. Among 223 PWUD, 107 (48.0%) reported receipt of at least two SARS-CoV-2 vaccine doses at baseline and this increased to 151 (67.7%) by the end of the study period. Using social media as a source of vaccine information was negatively associated with SARS-CoV-2 vaccine uptake (Adjusted odds ratio [AOR] 0.27, 95% confidence interval [CI] 0.09–0.81) and HIV seropositivity (AOR 2.68, 95% CI 1.12–6.39) and older age (AOR 1.27, 95% CI 1.07–1.51) were positively associated with SARS-CoV-2 vaccine uptake. These findings suggest that the targeted vaccination campaign in Vancouver may be an effective model to promote SARS-CoV-2 vaccination in other jurisdictions. However, using social media as a source of vaccine information likely reduced SARS-CoV-2 vaccine uptake in PWUD arguing for further efforts to promote accessible and evidence-based vaccine information among marginalized populations.
A future location prediction method based on lightweight LSTM with hyperparamater optimization
Authors: Song Ha Yoon
Published: October 2023

In this study, we presented a method for future location prediction based on machine learning over geopositioning data sets. There are large amounts of geopositioning data sets collected by mobile devices mainly due to modern geopositioning systems such as GPS, GLONASS and Galileo. Based on these geopositioning data sets, it is possible to have a wide variety of location-based services. These data sets can be used for future location prediction of objects, especially humans. Additionally, they have a high possibility for further applications. The purpose of this research is to present a simple and lightweight method that can be applicable to devices with lower computing capability devices, such as AIoT (Artificial Intelligence of Things) or EdgeML (Edge Machine Learning) devices. We introduced a basic LSTM (Long Short Term Memory) model with hyperparameter optimization, especially on window size of continuous geopositioning data, using limited previous geopositioning data for location prediction purposes. We found that the results of using our method for future location prediction are considerably fast and accurate compared with existing neural network-model-based approaches. We also applied our method to non-continuous geopositioning data sets and found it to be equally effective.
Formulation and evaluation of simvastatin cubosomal nanoparticles for assessing its wound healing effect
Authors: Ahmed Lamiaa M. , Hassanein Khaled M. A. , Mohamed Fergany A. , Elfaham Tahani H.
Published: October 2023

Wound healing is one of the most challenging medical circumstances for patients. Pathogens can infect wounds, resulting in tissue damage, inflammation, and disruption of the healing process. Simvastatin was investigated recently, as a wound healing agent that may supersede the present therapies for wounds. Our goal in this paper is to focus on formulation of simvastatin cubosomes for topical delivery, as a potential approach to improve simvastatin skin permeation. By this technique its wound healing effect could be improved. Cubosomes were prepared using the top-down method and the prepared cubosomes were characterized by several techniques. The most optimal simvastatin cubosomal formulation was then included in a cubogel dosage form using different gelling agents. The results showed that the average particle size of the prepared cubosomes was 113.90 ± 0.58 nm, the entrapment efficiency was 93.95 ± 0.49% and a sustained simvastatin release was achieved. The optimized formula of simvastatin cubogel displayed pseudoplastic rheological behavior. This same formula achieved enhancement in drug permeation through excised rat skin compared to free simvastatin hydrogel with flux values of 46.18 ± 2.12 mcg cm−2 h−1 and 25.92 ± 3.45 mcg cm−2 h−1 respectively. Based on the in-vivo rat studies results, this study proved a promising potential of simvastatin cubosomes as wound healing remedy.
Centenarian lifespans of three freshwater fish species in Arizona reveal the exceptional longevity of the buffalofishes (Ictiobus)
Authors: Lackmann Alec R. , Black Stuart A. , Bielak-Lackmann Ewelina S. , Lackmann Jeffrey A.
Published: October 2023

During the 1910s three buffalofish species (Catostomidae:Ictiobus cyprinellus,I. bubalus,I. niger) were reared in ponds along the Mississippi River. Individuals of these buffalofishes were transported to locations across the United States to support or establish commercial fisheries, including Roosevelt Lake, Arizona in 1918. During the 1930s–1960s a commercial fishery existed on Roosevelt Lake, ending by 1970. Scarce information exists on Arizona buffalofishes since. From 2018 to 2023 we studied buffalofishes from nearby Apache Lake (adjacent and downstream of Roosevelt Lake) in collaboration with anglers. Here we show that > 90% of buffalofishes captured from Apache Lake are more than 80 years old and that some of the original buffalofishes from the Arizona stocking in 1918 are likely still alive. Using unique markings on old-age buffalofishes, we demonstrate how individuals are identified and inform dozens of recaptures. We now know all species of USAIctiobuscan live more than 100 years, making it the only genus of animal besides marine rockfishes (Sebastes) for which three or more species have been shown to live > 100 years. Our citizen-science collaboration has revealed remarkable longevity for freshwater fishes and has fundamentally redefined our understanding of the genusIctiobusitself.
ADAMTS-13 and HMGB1-induced oxidative stress in Taenia multiceps-infected animals
Authors: Dincel Gungor Cagdas , Yavuz Orhan , Yildirim Serkan , Al-Olayan Ebtesam M. , El-Ashram Saeed
Published: October 2023

This study investigated the cytotoxic effects of oxidative stress (OS), high mobility group box 1 (HMGB1), ADAMTS (A disintegrin and metalloproteinase with thrombospondin motifs), and neuropathology associated with coenurus cerebralis (Taenia multiceps). ADAMTS-13, HMGB1, glutathione reductase (GR), copper/zinc superoxide dismutase (Cu/Zn SOD), and 8-hydroxy-2'-deoxyguanosine (8-OHdG) expression levels were studied. The study found that ADAMTS-13 (P < 0.005), HMGB1 (P < 0.005), GR (P < 0.005), Cu/Zn SOD (P < 0.005), and 8-OHdG (P < 0.005) levels were significantly higher in T. multiceps (c. cerebralis)-infected animals compared to healthy control animals. This study's most important finding was that HMGB1 up-regulation in neurons, endothelial cells, and glial cells can directly cause brain parenchymal destruction and that HMGB1-mediated oxidative stress plays a crucial role in the neuropathogenesis of coenurosis. The results also showed that increased levels of ADAMTS-13 may play a pivotal role in regulating and protecting the blood–brain barrier integrity and neuroprotection. These findings also suggest that ADAMTS-13 and HMGB1 compete in the prevention or formation of microthrombi, which was regarded as a remarkable finding. ADAMTS-13 and HMGB1 are valuable biomarkers for disease risk assessment, estimating host neuropathy following T. multiceps (c. cerebralis) exposure, and providing a new therapeutic target. This is the first study to show that HMGB1 and ADAMTS-13 are expressed in reactive cells and are associated with neuroimmunopathology in coenurosis.
Graphene oxide immobilized 2-morpholinoethanamine as a versatile acid–base catalyst for synthesis of some heterocyclic compounds and molecular docking study
Authors: Amiri-Zirtol Leila , Ahooie Tahereh Solymani , Riazimontazer Elham , Amrollahi Mohammad Ali , Mirjalili Bibi-Fatemeh
Published: October 2023

In this study, a new heterogeneous catalyst was synthesized based on graphene oxide (GO) as a natural material. On the surface of nanosheet graphene oxide, 2-Morpholinoethanamine was immobilized using a non-toxic, green, and simple method. This resulted in the preparation of a bifunctional acid–base nanocatalyst. The synthesized composite was fully characterized using various methods, including Fourier transform infrared spectrometry (FT-IR), scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDS), mapping, Raman spectroscopy, X-ray diffractometry (XRD), thermogravimetric analysis (TGA), and CHN elemental analysis. The catalytic reactivity of GO-mor was investigated in the one-pot synthesis of some benzo[b]pyran, pyrano[3,2-c]chromene, and polyhydroquinoline derivatives, yielding good efficiency and short reaction times. In addition, several recent studies have shown that some derivatives of pyran, chromene, and quinoline have remarkable anti COVID activity. Particularly, COVID-19 3CLpro/Mpro is considered a potential target for the treatment of this virus. For this purpose, docking models were constructed using the corresponding crystal structures with the synthesized derivatives. Based on the docking score and similarity of the binding mode to remdesivir and elvitegravir (the only approved drugs for the treatment of COVID-19), A2, B1, and C4 were selected as promising candidates for further research.
Lemon peel essential oil and its nano-formulation to control Agrotis ipsilon (Lepidoptera: Noctuidae)
Authors: Ahmed Habiba A. , Nassrallah Amr A. , Abdel-Raheem M. A. , Elbehery Huda H.
Published: October 2023

Due to excessive use of synthetic pesticides the pest resistance developed along with pesticide residues accumulation in crops. Therefore, many nations are switching from chemical-based agriculture to “green” agriculture for pest control. The destructive pest black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae), is a polyphagous species that economically lead to extensive loss of a broad range of crops including corn, cotton, wheat, and many vegetables through the damage of foliar and roots. In this study, lemon peel essential oil (LPEO) was subjected to nano-formulation using polyethylene glycol as nanocarrier. The lethal activity of LPEO and its nano-form (LPEO-NPs) were tested against A. ipsilon second larval instar using feeding bioassay at different concentrations. Growth and developmental parameters, including larval and pupal duration, larval and pupal mortality, malformations % and adult emergence were evaluated. Results showed that LPEO exhibited insecticidal activity and causes different levels of effects on the development of A. ipsilon according to its concentration and formulation. In addition, at 75 mg/ml LPEO and LPEO-NPs significantly increased the larval mortality to 80.00% and 90.00%, respectively. The overall data revealed that insecticidal toxicity of LPEO was increased by nano-formulation.
Acoustic emission-based intelligent identification of piston aero-engine ignition advance angle anomalies
Authors: Yang Yanhe , Bi Xiaoyang , Lee Alamusi , Ma Teng , Sun Yinghui , Kong Wei , Hu Wei , Hu Ning
Published: October 2023

Ignition advance angle is one of the important factors affecting the performance of the engine, when it occurs abnormally will make the engine power and economy worse, and even cause serious damage to the engine. Therefore, it is very necessary to recognize the abnormal ignition advance angle of the engine. However, the engine system is closed and has a complex structure, which makes traditional diagnostic methods difficult. This paper proposes an intelligent identification method based on acoustic emission (AE) signals, which collects the AE signals from the engine surface and divides their spectra into equal parts, and selects the frequency bands with high contribution to the classification based on the minimum distance method to construct feature maps, which is used as the input to the convolutional neural network (CNN). The extracted frequency band features of this method can better characterize the AE signals, and the constructed feature maps make the fault information more obvious. Experiments show that the accuracy of this method for abnormal ignition advance angle under normal operating conditions of piston aero-engine is 100%, which is better than the traditional methods. In addition, the recognition accuracies under the other two operating conditions are 99.75% and 98.5%, respectively, indicating that the method has a certain universality.
White targeted chromatographic screening method of Molnupiravir and its metabolite with degradation kinetics characterization and in-silico toxicity
Authors: Aboras Sara I. , Megahed Ahmed A. , El-Yazbi Fawzy , Maher Hadir M.
Published: October 2023

SARS-CoV-2 virus triggered a worldwide crisis, with world nations putting up massive efforts to halt its spread. Molnupiravir (MLN) was the first oral, direct-acting antiviral drug approved for nasopharyngeal SARS-CoV-2 infection with favorable safety and tolerability profile. This study aims at determination of MLN and N4-hydroxycytidine (NHC), its main degradation product and its main metabolite, using sensitive, simple, and green HPLC–DAD method. Moreover, under different stress conditions using NaOH, HCl, neutral, H2O2, dry heat and sun light, the method was applied for MLN assay along with kinetics degradation investigation. The linearity range for MLN and NHC were both 0.1–100 µg/mL with LOD and LOQ of 0.013 & 0.043 and 0.003 & 0.011 µg/mL, for MLN and NHC, respectively. MLN was found to be extremely vulnerable to alkali hydrolysis compared with acid and dry heat degradation. In contrast, MLN was stable under conditions of oxidative, neutral, and sunlight-induced deterioration. Acid and alkali-induced degradation followed pseudo first-order kinetics model. In addition, LC–MS-UV was used to suggest the mechanism of the stress-induced degradation route and to characterize the eluted degradation products. Toxicities of both MLN and its degradation products were evaluated using ProTox-II and they were found to be negligibly harmful. The proposed HPLC–DAD was effectively used for the analysis of MLN in commercial pharmaceutical formulations. The proposed method for MLN determination after greenness and whiteness appraisal was found to be superior compared to the reported methods for MLN analysis.
Small RNA sequencing provides insights into molecular mechanism of flower development in Rhododendron pulchrum Sweet
Authors: Fang Bo , Huang Zhiwei , Sun Yirong , Zhang Wanjing , Yu Jiaojun , Zhang Jialiang , Dong Hongjin , Wang Shuzhen
Published: October 2023

Rhododendron pulchrum sweet, a member of the Ericaceae family possessing valuable horticultural properties, is widely distributed in the temperate regions. Though serving as bioindicator of metal pollution, the molecular mechanism regulating flowering in R. pulchrum is very limited. Illumina sequencing was performed to identify critical miRNAs in the synthesis of flavonoids at different developmental stages. Totally, 722 miRNAs belonging to 104 families were screened, and 84 novel mature miRNA sequences were predicted. The miR166, miR156, and miR167-1 families were dominant. In particular, 126 miRNAs were significantly differentially expressed among four different flowering stages. Totally, 593 genes were differentially regulated by miRNAs during the flower development process, which were mostly involved in “metabolic pathways”, “plant hormone signal transduction”, and “mitosis and regulation of biosynthetic processes”. In pigment biosynthesis and signal transduction processes, gra-miR750 significantly regulated the expression of flavonoid 3’,5’-hydroxylase; aof-miR171a, aof-miR171b, aof-miR171c, cas-miR171a-3p, and cas-miR171c-3p could regulate the expression of DELLA protein; aof-miR390, aof-miR396b, ath-miR3932b-5p, cas-miR171a-3p, aof-miR171a, and aof-miR171b regulated BAK1 expression. This research showed great potentials for genetic improvement of flower color traits for R. pulchrum and other Rhododendron species.
A unified approach of detecting phase transition in time-varying complex networks
Authors: Znaidi Mohamed Ridha , Sia Jayson , Ronquist Scott , Rajapakse Indika , Jonckheere Edmond , Bogdan Paul
Published: October 2023

Deciphering the non-trivial interactions and mechanisms driving the evolution of time-varying complex networks (TVCNs) plays a crucial role in designing optimal control strategies for such networks or enhancing their causal predictive capabilities. In this paper, we advance the science of TVCNs by providing a mathematical framework through which we can gauge how local changes within a complex weighted network affect its global properties. More precisely, we focus on unraveling unknown geometric properties of a network and determine its implications on detecting phase transitions within the dynamics of a TVCN. In this vein, we aim at elaborating a novel and unified approach that can be used to depict the relationship between local interactions in a complex network and its global kinetics. We propose a geometric-inspired framework to characterize the network’s state and detect a phase transition between different states, to infer the TVCN’s dynamics. A phase of a TVCN is determined by its Forman–Ricci curvature property. Numerical experiments show the usefulness of the proposed curvature formalism to detect the transition between phases within artificially generated networks. Furthermore, we demonstrate the effectiveness of the proposed framework in identifying the phase transition phenomena governing the training and learning processes of artificial neural networks. Moreover, we exploit this approach to investigate the phase transition phenomena in cellular re-programming by interpreting the dynamics of Hi-C matrices as TVCNs and observing singularity trends in the curvature network entropy. Finally, we demonstrate that this curvature formalism can detect a political change. Specifically, our framework can be applied to the US Senate data to detect a political change in the United States of America after the 1994 election, as discussed by political scientists.
Elevational characteristics of soil bacterial community and their responses to soil translocation at a mountainside in northwest Sichuan, China
Authors: Wang Xuemei , Huang Tianzhi , Li Yunyun , Zhao Guang , Zhao Jixia
Published: October 2023

How the soil bacterial communities vary with elevation is context-dependent, and the effect of soil translocation between elevations on bacterial community structure and metabolic function was not fully understood yet. Here, the bacterial community composition and diversity at five elevations along a 1600–3000 m elevation gradient on a mountainside in northwest Sichuan were characterized, and the responses of soil bacterial community to simulated climate changes were further studied by soil translocation reciprocally at three elevations for 12 months. Significant differences were found in soil temperature and moisture at different elevations, but there was no observed change in bacterial alpha diversity. The relative abundance of bacterial phyla was significantly different among the five elevations except for Proteobacteria (the dominant bacterial phyla in five elevation), and most bacterial phyla correlated with soil temperature, moisture, pH and soil bulk density. The direct effect of soil properties (pH, soil nutrients and soil bulk density) on soil bacterial community was stronger than the direct effect of temperature and moisture. Soil translocation changed the relative abundance of some bacterial phyla, and taxonomic groups with significant changes were mainly non-dominant phyla rather than the dominant phyla. Metabolism was the primary function of bacterial community at all elevations, which accounted for ~ 80% of relative abundance, and soil translocation had little effect on metabolic function. These findings indicated that soil bacterial dominant taxa and soil bacterial metabolic functions are relatively stable, which contribute to the stability of the ecosystem when response to the climate change in the future.
The combination of cigarette smoke and solar rays causes effects similar to skin aging in a bilayer skin model
Authors: Grenier Alexe , Morissette Mathieu C. , Rochette Patrick J. , Pouliot Roxane
Published: October 2023

Skin aging is a multifactorial process influenced by internal and external factors. The contribution of different environmental factors has been well established individually in the last few years. On the one hand, man is rarely exposed to a single factor, and on the other hand, there is very little knowledge about how these extrinsic factors may interact with each other or even how the skin may react to chronic exposure. This study aimed to evaluate the effect on skin aging of a chronic co-exposure of tissue-engineered skin substitutes to cigarette smoke extract (CSE) and solar simulator light (SSL). Skin substitutes were reconstructed according to the self-assembly method and then exposed to CSE followed by irradiation with SSL simultaneously transmitting UVA1, visible light and infrared. When skin substitutes were chronically exposed to CSE and SSL, a significant decrease in procollagen I synthesis and the inhibition of Smad2 phosphorylation of the TGF-β signaling pathway were observed. A 6.7-fold increase in MMP-1 activity was also observed when CSE was combined with SSL, resulting in a decrease in collagen III and collagen IV protein expression. The secretory profile resulting from the toxic synergy was investigated and several alterations were observed, notably an increase in the quantities of pro-inflammatory cytokines. The results also revealed the activation of the ERK1/2 (3.4-fold) and JNK (3.3-fold) pathways. Taken together, the results showed that a synergy between the two environmental factors could provoke premature skin aging.
Synthetic complex Weyl superconductors, chiral Josephson effect and synthetic half-vortices
Authors: Faraei Zahra , Jafari Seyed Akbar
Published: October 2023

We show that the most generic form of spin-singlet superconducting order parameter for chiral fermions in systems with broken time reversal symmetry and inversion symmetry is of the $$\Delta _s+i\gamma ^5\Delta _5$$

Δ
s

+
i

γ
5

Δ
5

where $$\Delta _s$$

Δ
s

is the usual order parameter and $$\Delta _5$$

Δ
5

is the pseudo-scalar order parameter. After factoring out the U(1) phase $$e^{i\phi }$$

e

i
ϕ

, this form of superconductivity admits yet additional complex structure in the plane of $$(\Delta _s,\Delta _5)$$

(

Δ
s

,

Δ
5

)

. The polar angle $$\chi $$
χ
in this plane, which we call the chiral angle, can be controlled by the external flux bias. We present a synthetic setup based on stacking of topological insulators (TIs) and superconductors (SCs). Alternatively flux biasing the superconductors with a fluxes $$\pm \Phi $$

±
Φ

leads to $$\Delta _5=\Delta _0 \sin (\chi )$$

Δ
5

=

Δ
0

sin

(
χ
)

, where $$\Delta _0$$

Δ
0

is the superconducting order parameter of the SC layers, and the chiral angle $$\chi ={2\pi }\Phi /\Phi _0$$

χ
=

2
π

Φ
/

Φ
0

is directly given by the flux $$\Phi $$
Φ
in units of the flux quantum $$\Phi _0=h/(2e)$$

Φ
0

=
h
/

(
2
e
)

. This can be used as a building block to construct a two-dimensional Josephson array. In this setup $$\chi $$
χ
will be a background field defining a pseudoscalar $$\Delta _5$$

Δ
5

that can be tuned to desired configuration. While in a uniform background field $$\Delta _5$$

Δ
5

the dynamics of $$\phi $$
ϕ
is given by standard XY model and its associated vortices, a staggered background $$\pm \Delta _5$$

±

Δ
5

(or equivalently $$\chi $$
χ
and $$\chi +\pi $$

χ
+
π

in alternating lattice sites) creates a new set of minima for the $$\phi $$
ϕ
field that will support half-vortex excitations. An isolated single engineered “half-vortex” in the $$\chi $$
χ
field in an otherwise uniform background will bind a $$\phi $$
ϕ
-half-vortex. This is similar to the way a p-wave superconducting vortex core binds a Majorana fermion.
Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision
Authors: Pattelli Olivia N. , Diec Dinh Dinh Ly , Guo Wanting , Russi Silvia , Fernandez Daniel
Published: October 2023

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.
Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis
Authors: Al Bataineh Mohammad Tahseen , Künstner Axel , Dash Nihar Ranjan , Alsafar Habiba S. , Ragab Mohab , Schmelter Franziska , Sina Christian , Busch Hauke , Ibrahim Saleh Mohamed
Published: October 2023

Type 2 Diabetes Mellitus has reached epidemic levels globally, and several studies have confirmed a link between gut microbial dysbiosis and aberrant glucose homeostasis among people with diabetes. While the assumption is that abnormal metabolomic signatures would often accompany microbial dysbiosis, the connection remains largely unknown. In this study, we investigated how diet changed the gut bacteriome, mycobiome and metabolome in people with and without type 2 Diabetes.1 Differential abundance testing determined that the metabolites Propionate, U8, and 2-Hydroxybutyrate were significantly lower, and 3-Hydroxyphenyl acetate was higher in the high fiber diet compared to low fiber diet in the healthy control group. Next, using multi-omics factor analysis (MOFA2), we attempted to uncover sources of variability that drive each of the different groups (bacterial, fungal, and metabolite) on all samples combined (control and DM II). Performing variance decomposition, ten latent factors were identified, and then each latent factor was tested for significant correlations with age, BMI, diet, and gender. Latent Factor1 was the most significantly correlated. Remarkably, the model revealed that the mycobiome explained most of the variance in the DM II group (12.5%) whereas bacteria explained most of the variance in the control group (64.2% vs. 10.4% in the DM II group). The latent Factor1 was significantly correlated with dietary intake (q < 0.01). Further analyses of the impact of bacterial and fungal genera on Factor1 determined that the nine bacterial genera (Phocaeicola, Ligilactobacillus, Mesosutterella, Acidaminococcus, Dorea A, CAG-317, Caecibacter, Prevotella and Gemmiger) and one fungal genus (Malassezia furfur) were found to have high factor weights (absolute weight > 0.6). Alternatively, a linear regression model was fitted per disease group for each genus to visualize the relationship between the factor values and feature abundances, showing Xylose with positive weights and Propionate, U8, and 2-Hydroxybutyrate with negative weights. This data provides new information on the microbially derived changes that influence metabolic phenotypes in response to different diets and disease conditions in humans.
A perspective of randomness in a clinical test of olfactory performance
Authors: Lötsch Jörn , Hummel Thomas , Ultsch Alfred
Published: October 2023

Random walks describe stochastic processes characterized by a sequence of unpredictable changes in a random variable with no correlation to past changes. This report describes the random walk component of a clinical sensory test of olfactory performance. The precise definition of this stochastic process allows the establishment of precise diagnostic cut-offs for the identification of olfactory loss. Within the Sniffin`Sticks olfactory test battery, odor discrimination (D) and odor identification (I) are assessed by four- and three-alternative forced-choice designs, respectively. Meanwhile, the odor threshold (T) test integrates a three-alternative forced-choice paradigm within a staircase paradigm with seven turning points. We explored this paradigm through computer simulations and provided a formal description. The odor threshold assessment test consists of two sequential components, the first of which sets the starting point for the second. Both parts can be characterized as biased random walks with significantly different probabilities of moving to higher (11%) or lower (89%) values. The initial odor concentration step for the first phase of the test and the length of the subsequent random walk in the second phase significantly affect the probability of randomly achieving high test scores. Changing the odor concentration from where the starting point determination for the second test part begins has raised the current cut-off for anosmia, represented as T + D + I < 16, from the 87th quantile of random test scores to the 97th quantile. Analogous findings are likely applicable to other sensory tests that use the staircase paradigm characterized as random walk.
Sensorimotor memories influence movement kinematics but not associated tactile processing
Authors: Beyvers Marie C. , Voudouris Dimitris , Fiehler Katja
Published: October 2023

When interacting with objects, we often rely on visual information. However, vision is not always the most reliable sense for determining relevant object properties. For example, when the mass distribution of an object cannot be inferred visually, humans may rely on predictions about the object’s dynamics. Such predictions may not only influence motor behavior but also associated processing of movement-related afferent information, leading to reduced tactile sensitivity during movement. We examined whether predictions based on sensorimotor memories influence grasping kinematics and associated tactile processing. Participants lifted an object of unknown mass distribution and reported whether they detected a tactile stimulus on their grasping hand during the lift. In Experiment 1, the mass distribution could change from trial to trial, whereas in Experiment 2, we intermingled longer with shorter parts of constant and variable mass distributions, while also providing implicit or explicit information about the trial structure. In both experiments, participants grasped the object by predictively choosing contact points that would compensate the mass distribution experienced in the previous trial. Tactile suppression during movement, however, was invariant across conditions. These results suggest that predictions based on sensorimotor memories can influence movement kinematics but not associated tactile perception.
XRF online analyzer for measurements of P2O5 content in phosphate slurry
Authors: Ben Amar Ismail , Thomas Andrew , Bachmann Claus , Hafnaoui Anass , Griguer Hafid , Miled Amine , Messaddeq Younès
Published: October 2023

Online X-ray Fluorescence (XRF) setup was constructed and optimized for analysing the P2O5 content in phosphate slurry (PS). Serval samples were analysed using two configurations of the setup, one with low and vertical flow and another with high and horizontal flow. The mean absolute error achieved through the first configuration was 0.87% and 0.38% using the second configuration. Reference samples were analyzed using the two configurations to construct the calibration curves. The curves cover a concentration range of P2O5 from 13.50 to 18.50% when considering the horizontal flow configuration, and a range of 14.00–15.60% when considering the vertical flow setup. An experimental study was conducted in order to optimize the measurement parameters for the online measurement of P2O5 in the phosphate slurry using the horizontal flow setup. A good signal-to-noise ratio (SNR) of $$P\left(K\alpha \right)$$

P

K
α

was attained using an excitation energy of 20 kV or 25 kV, an excitation current of 600 µA, a distance of 18 mm between the sample and the detector, a measurement time of 60 s per spectrum and the use of an Aluminum filter between the X-ray tube and the measurement window. Online X-ray fluorescence analysis of P entails some challenges due to the low characteristic energy of P, the phosphate slurry matrix and the online analysis mode. However, the outcomes of this study indicate that XRF is a promising technology to meet the requirement for digitalization of chemical analysis of phosphate products.
Renal impairment as a risk factor for trifluridine/tipiracil-induced adverse events in metastatic colorectal cancer patients from the REGOTAS study
Authors: Shiroyama Mamiko , Fukuoka Shota , Masuishi Toshiki , Takashima Atsuo , Kumekawa Yosuke , Kajiwara Takeshi , Yamazaki Kentaro , Shimada Yasuhiro , Esaki Taito , Makiyama Akitaka , Moriwaki Toshikazu
Published: October 2023

Renal impairment may be associated with an increased risk of hematologic events (AEs) in patients undergoing treatment with trifluridine/tipiracil (FTD/TPI). This study aimed to investigate the specific types of AEs linked to renal impairment in patients with metastatic colorectal cancer (mCRC) receiving FTD/TPI, using real-world data. Among the patients included in the REGOTAS study (a retrospective study of FTD/TPI versus regorafenib), those treated with FTD/TPI were evaluated. Creatinine clearance values of < 30, 30–60, 60–90, and > 90 mL/min were defined as severe, moderate, mild renal impairment, and normal renal function, respectively. Renal impairment was analyzed as a risk factor for grade 3 or higher AEs using a logistic regression model. Overall survival (OS) and progression-free survival (PFS) based on renal impairment were evaluated. A total of 309 patients were included in the analysis, with 124, 130, and 55 patients divided into the normal, mild, and moderate-to-severe groups, respectively. The risk of grade 3 or higher neutropenia was significantly higher in the moderate-to-severe group (odds ratio 3.47; 95% confidence interval 1.45–8.30; P = 0.005), but there was no significant increase in the risk of non-hematologic AEs in any of the groups. The OS and PFS of patients in the mild and moderate-to-severe groups were comparable to those in the normal group. Patients with mCRC and moderate/severe renal impairment receiving FTD/TPI therapy may develop severe neutropenia; however, FTD/TPI remains a viable treatment option due to its clinical benefit.
Binding affinity predictions with hybrid quantum-classical convolutional neural networks
Authors: Domingo L. , Djukic M. , Johnson C. , Borondo F.
Published: October 2023

Central in drug design is the identification of biomolecules that uniquely and robustly bind to a target protein, while minimizing their interactions with others. Accordingly, precise binding affinity prediction, enabling the accurate selection of suitable candidates from an extensive pool of potential compounds, can greatly reduce the expenses associated to practical experimental protocols. In this respect, recent advances revealed that deep learning methods show superior performance compared to other traditional computational methods, especially with the advent of large datasets. These methods, however, are complex and very time-intensive, thus representing an important clear bottleneck for their development and practical application. In this context, the emerging realm of quantum machine learning holds promise for enhancing numerous classical machine learning algorithms. In this work, we take one step forward and present a hybrid quantum-classical convolutional neural network, which is able to reduce by 20% the complexity of the classical counterpart while still maintaining optimal performance in the predictions. Additionally, this results in a significant cost and time savings of up to 40% in the training stage, which means a substantial speed-up of the drug design process.