bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of shallow underground targets using electrical resistivity tomography and the implications in civil/environmental engineering
Authors: Alao Joseph Omeiza , Lawal Kolawole Muideen , Dewu Bala Bello Muhammad , Raimi Jimoh
Published: August 2024

Applying the electrical resistivity tomography (ERT) technique in detecting very near-surface targets is quite challenging in geophysical investigation, especially in civil and environmental engineering for adequate planning and designing of structural foundations, contributing to the overall safety and efficiency of construction projects. However, locating the exact position and depth of underground targets such as faults, underground utilities, and contaminants is more challenging. Therefore, this study is aimed at examining the geophysical response of various buried targets and evaluating the ability of ERT to detect buried targets in terms of locations and depths of occurrence in the context of engineering investigation and environmental studies. A laboratory test was conducted on the targets to determine their electrical conductivity and resistivity before burial. The two-dimensional (2D) ERT survey was performed on thirteen targets buried at the site using both Wenner and dipole–dipole (DD) arrays. Both arrays captured the metallic targets with a low electrical resistivity contrast (< 0.1 Ωm) corresponding to the laboratory results. In comparison, the positions of the non-metallic buried targets were found to have a high resistivity contrast greater than 3000 Ωm, matching the laboratory results. The modelled pipes and the car engine block captured by both DD and Wenner arrays on 1.0 m electrode spacing were relatively smeared and poorly resolved in shapes, sizes and geometries, while some were not captured. The electrode spacing of 0.25 m and 0.50 m was explored on undetected targets, which provide a better resolution with sizes and depths compared to 1.0 m spacing but did not produce satisfactory results in some cases. The success and failure of ERT to detect a few targets were discussed alongside the environmental and engineering implications. The effectiveness of both arrays was assessed by their sensitivity in mapping the change in subsurface resistivity values. The DD array shows sensitivity to horizontal variations in resistivity values with low signal. In contrast, the Wenner array shows a good signal strength with a good change in the horizontal and vertical resistivity values. In addition, both arrays show capacity in mapping the geophysical signature of the buried targets and subsurface structures, which has significant application in engineering and environmental investigations.
Unravelling the tissue regenerative nature of marine polysaccharide chitosan embedded halloysite reinforced poly (vinyl alcohol) nanocomposite films
Authors: Shabeena M. , Kouser Sabia , Prabhu Ashwini , Warale Deepali , Manasa D. J. , Nagaraja G. K.
Published: August 2024

The study focuses on developing the poly (vinyl alcohol) (PVA) nanocomposite films reinforced with Halloysite Nano-Tubes (HNT) which were surface functionalised with chitosan forming a Schiff base structure. The work was aimed to traverse its way in tissue engineering. Modification of halloysite with sea polysaccharide chitosan enhanced its ability to bind to the PVA matrix. The modification was assisted by FTIR, XRD, FESEM, TEM, AFM and DSC-TGA techniques. The films could withstand a higher temperature and exhibited high ranges of tensile strength and Young’s modulus. In addition, biocompatible studies such as in-vitro swelling, enzymatic degradation, water contact angle and hemolysis presented extremely well compatibilities proving it to be viable in physiological pH (in phosphate buffered saline). The cell adhesion and proliferation studies conducted on NIH3T3 mouse fibroblasts revealed the cell proliferation and tissue regeneration properties of the films. Both the tests performed for cell growth- Trypan blue dye exclusion and Acridine Orange Ethidium bromide assays showed a doubled rate of cell growth on the films which proves its biomedical nature.

Graphical Abstract
Equally spaced squares and some impossible identities
Authors: Jameson G.J.O.
Published: August 2024

Consecutive squares are, of course, not equally spaced: the gap increases by 2 each time. However, it is quite possible to select three equally spaced squares, for example 1, 25, 49. Actually, such triples correspond to Pythagorean triples in a pleasantly simple way, which we will describe.
Pythagorean triples using the relativistic velocity addition formula
Authors: Sporn Howard
Published: August 2024

In the special theory of relativity, there is an unusual formula for addition of velocities. We will use this formula to generate Pythagorean triples. We define a Pythagorean triple in the usual manner as a triple of positive integers (a, b, c) such that a2 + b2 = c2. The numbers a and b are called legs, and c is called the hypotenuse. Later, we will allow b to take on the value of any integer. A primitive Pythagorean triple is a Pythagorean triple for which a, b and c are relatively prime.
A provocative tale of unwinding
Authors: De Subhranil
Published: August 2024

One fine spring morning, at some point, I was simply tearing a few sheets of paper towel off a fresh roll. As the sheets came off and the roll rotated about the vertical axle of the holder (Figure 1), I lazily pondered the geometry lurking in the situation. I realised that sometimes I would let the roll rotate as the unwound part moved straight until tearing, while at other times, I might hold the roll in place and unwind the sheets around the roll. More often, it would be some spontaneous combination of the two modes of unwinding.
Narayana’s integer sequence revisited
Authors: Crilly Tony
Published: August 2024

An essential feature of the Fibonacci sequence (Fn): 1, 1, 2, 3, 5, 8, … is an explicit expression for its nth term Fn (Binet’s formula) and the corollary that is the golden ratio and {x} is the nearest integer to x.
More variations on Nagel and Gergonne analogues of the Steiner-Lehmus theorem
Authors: Abu-Saymeh Sadi , Hajja Mowaffaq
Published: August 2024

The celebrated Steiner-Lehmus theorem states that if the internal bisectors of two angles of a triangle are equal then the corresponding sides have equal lengths. That is to say if P is the incentre of ΔABC and if BP and CP meet the sides AC and AB at B′ and C′, respectively, then

An elegant proof of this theorem appeared in [1] and is reproduced in [2].
Digitale Hoffnungsträger?
Authors: Kohl Simon H. , Henn Alina T. , Fendel Johannes C. , Luttermann Alfred , van Noort Betteke Maria , Konrad Kerstin
Published: August 2024

Zusammenfassung: Mit dem Digitale-Versorgung-Gesetz hat Deutschland einen entscheidenden Schritt zur Förderung qualitativ hochwertiger, evidenzbasierter digitaler Gesundheitsanwendungen (DiGAs) unternommen. Zugleich besteht in weiten Teilen Deutschlands eine deutliche Versorgungslücke im Bereich psychischer Störungen, von der Kinder und Jugendliche, insbesondere infolge der Corona-Pandemie, besonders stark betroffen sind. DiGAs bieten als niedrigschwellige, orts- und zeitunabhängige therapeutische Angebote eine zusätzliche Möglichkeit, auf diese Unterversorgung zu reagieren. Insbesondere in der heranwachsenden Generation von Digital Natives besteht eine große Nachfrage nach digitalen therapeutischen Angeboten. Trotz des wachsenden DiGA-Angebots für Erwachsene fehlen bisher zugelassene DiGAs für Kinder und Jugendliche mit psychischen Störungen. Die Versorgungsnachfrage wird damit einem unübersichtlichen und unregulierten Markt internet- und mobilbasierter Interventionen überlassen, deren Evidenzbasierung, Sicherheit und Qualität nicht gewährleistet sind. Diese Diskrepanz zwischen Angebot und Nachfrage könnte in den spezifischen Herausforderungen und Risiken sowie einem daraus resultierenden geringen Anreiz begründet sein, DiGAs für diese besonders schutzbedürftige Zielgruppe zu entwickeln. Dazu gehören: (1) limitierte Evidenzgrundlage, (2) hohe Komplexität bei der Studiendurchführung, (3) hohe Komplexität bei der Entwicklung, (4) spezifische, wenig erforschte Risiken und (5) hohe regulatorische Anforderungen. In diesem Artikel sollen diese Herausforderungen diskutiert und Perspektiven für eine hochwertige, sichere und evidenzbasierte digitale mentale Gesundheitsversorgung von Kindern und Jugendlichen durch DiGAs aufgezeigt werden.
Opportunities for use of neuroimaging in de-risking drug development and improving clinical outcomes in psychiatry: an industry perspective
Authors: Etkin Amit , Powell Jessica , Savitz Adam J.
Published: August 2024

Neuroimaging, across positron emission tomography (PET), electroencephalography (EEG), and magnetic resonance imaging (MRI), has been a mainstay of clinical neuroscience research for decades, yet has penetrated little into psychiatric drug development beyond often underpowered phase 1 studies, or into clinical care. Simultaneously, there is a pressing need to improve the probability of success in drug development, increase mechanistic diversity, and enhance clinical efficacy. These goals can be achieved by leveraging neuroimaging in a precision psychiatry framework, wherein effects of drugs on the brain are measured early in clinical development to understand dosing and indication, and then in later-stage trials to identify likely drug responders and enrich clinical trials, ultimately improving clinical outcomes. Here we examine the key variables important for success in using neuroimaging for precision psychiatry from the lens of biotechnology and pharmaceutical companies developing and deploying new drugs in psychiatry. We argue that there are clear paths for incorporating different neuroimaging modalities to de-risk subsequent development phases in the near to intermediate term, culminating in use of select neuroimaging modalities in clinical care for prescription of new precision drugs. Better outcomes through neuroimaging biomarkers, however, require a wholesale commitment to a precision psychiatry approach and will necessitate a cultural shift to align biopharma and clinical care in psychiatry to a precision orientation already routine in other areas of medicine.
TAGLN2 induces resistance signature ISGs by activating AKT-YBX1 signal with dual pathways and mediates the IFN-related DNA damage resistance in gastric cancer
Authors: Zhuo Huiqin , Hou Jingjing , Hong Zhijun , Yu Shuqi , Peng Huifang , Zhang Lihua , Xie Wen , Hong Xuehui
Published: August 2024

Recently, various cancer types have been identified to express a distinct subset of Interferon-stimulated genes (ISGs) that mediate therapy resistance. The mechanism through which cancer cells maintain prolonged Interferon stimulation effects to coordinate resistance remains unclear. Our research demonstrated that aberrant upregulation of TAGLN2 is associated with gastric cancer progression, and inhibiting its expression renders gastric cancer cells more susceptible to chemotherapy and radiation. We uncovered a novel role for TAGLN2 in the upregulation of resistance signature ISGs by enhancing YBX1-associated ssDNA aggregation and cGAS-STING pathway activation. TAGLN2 modulates YBX1 by recruiting c-Myc and SOX9 to YBX1 promoter region and directly interacting with AKT-YBX1, thereby enhancing YBX1 phosphorylation and nuclear translocation. Significantly, targeted downregulation of key proteins, inhibition of the TAGLN2-YBX1-AKT interaction (using Fisetin or MK2206) or disruption of the cGAS-STING pathway substantially reduced ssDNA accumulation, subsequent ISGs upregulation, and therapy resistance. The combination of Cisplatin with MK2206 displayed a synergistic effect in the higher TAGLN2-expressing xenograft tumors. Clinical analysis indicated that a derived nine-gene set effectively predicts therapeutic sensitivity and long-term prognosis in gastric cancer patients. These findings suggest that TAGLN2, YBX1 and induced ISGs are novel predictive markers for clinical outcomes, and targeting this axis is an attractive therapeutic sensitization strategy.
Small RNA activation of CDH13 expression overcome BCR-ABL1-independent imatinib-resistance and their signaling pathway studies in chronic myeloid leukemia
Authors: Su Rui , Wen Ziqi , Zhan Xingri , Long Yiling , Wang Xiuyuan , Li Chuting , Su Yubin , Fei Jia
Published: August 2024

BCR-ABL1-independent resistance to imatinib has no effective treatment due to its complexity and diversity. We previously reported that the CDH13 oncogene was expressed at low levels in BCR-ABL1-independent resistant CML cell lines. However, its effects on CML resistant cells and mechanisms remain unknown. This study investigated the effects of saRNA-based CDH13 activation on BCR-ABL1-independent imatinib resistance in CML and its underlying mechanism, and proposes a unique treatment method to overcome imatinib resistance. Specifically, this study demonstrated that using the DSIR (Designer of Small Interfering RNA) website tool, saRNAs targeting the CDH13 promoter region were generated and validated using qPCR and western blotting. Among the predicted sequences, C2 and C3 efficiently elevated CDH13 mRNA and protein expression, as well as inhibited the relative vitality of cells and the ability to form clones. After promoting CDH13 expression in K562-IMR cells, it inhabited the NF-κB signaling pathway and induced apoptosis in imatinib-resistant CML cells. LNP-saRNA (C3) was also observed to limit the growth of K562-IMR cells in vivo. From the above, the activation of CDH13 expression by saRNA promotes cell apoptosis by inhibiting the NF-κB signaling pathway to overcome to BCR-ABL1-independent resistance to imatinib in patients with CML.
Structural basis of the bacterial flagellar motor rotational switching
Authors: Tan Jiaxing , Zhang Ling , Zhou Xingtong , Han Siyu , Zhou Yan , Zhu Yongqun
Published: August 2024

The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body–hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the αtorque helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
Inferring histology-associated gene expression gradients in spatial transcriptomic studies
Authors: Kueckelhaus Jan , Frerich Simon , Kada-Benotmane Jasim , Koupourtidou Christina , Ninkovic Jovica , Dichgans Martin , Beck Juergen , Schnell Oliver , Heiland Dieter Henrik
Published: August 2024

Spatially resolved transcriptomics has revolutionized RNA studies by aligning RNA abundance with tissue structure, enabling direct comparisons between histology and gene expression. Traditional approaches to identifying signature genes often involve preliminary data grouping, which can overlook subtle expression patterns in complex tissues. We present Spatial Gradient Screening, an algorithm which facilitates the supervised detection of histology-associated gene expression patterns without prior data grouping. Utilizing spatial transcriptomic data along with single-cell deconvolution from injured mouse cortex, and TCR-seq data from brain tumors, we compare our methodology to standard differential gene expression analysis. Our findings illustrate both the advantages and limitations of cluster-free detection of gene expression, offering more profound insights into the spatial architecture of transcriptomes. The algorithm is embedded in SPATA2, an open-source framework written in R, which provides a comprehensive set of tools for investigating gene expression within tissue.
Molecular hydrogen in the N-doped LuH3 system as a possible path to superconductivity
Authors: Tresca Cesare , Forcella Pietro Maria , Angeletti Andrea , Ranalli Luigi , Franchini Cesare , Reticcioli Michele , Profeta Gianni
Published: August 2024

The discovery of ambient superconductivity would mark an epochal breakthrough long-awaited for over a century, potentially ushering in unprecedented scientific and technological advancements. The recent findings on high-temperature superconducting phases in various hydrides under high pressure have ignited optimism, suggesting that the realization of near-ambient superconductivity might be on the horizon. However, the preparation of hydride samples tends to promote the emergence of various metastable phases, marked by a low level of experimental reproducibility. Identifying these phases through theoretical and computational methods entails formidable challenges, often resulting in controversial outcomes. In this paper, we consider N-doped LuH3 as a prototypical complex hydride: By means of machine-learning-accelerated force-field molecular dynamics, we have identified the formation of H2 molecules stabilized at ambient pressure by nitrogen impurities. Importantly, we demonstrate that this molecular phase plays a pivotal role in the emergence of a dynamically stable, low-temperature, experimental-ambient-pressure superconductivity. The potential to stabilize hydrogen in molecular form through chemical doping opens up a novel avenue for investigating disordered phases in hydrides and their transport properties under near-ambient conditions.
Palmitoylation of ULK1 by ZDHHC13 plays a crucial role in autophagy
Authors: Tabata Keisuke , Imai Kenta , Fukuda Koki , Yamamoto Kentaro , Kunugi Hayato , Fujita Toshiharu , Kaminishi Tatsuya , Tischer Christian , Neumann Beate , Reither Sabine , Verissimo Fatima , Pepperkok Rainer , Yoshimori Tamotsu , Hamasaki Maho
Published: August 2024

Autophagy is a highly conserved process from yeast to mammals in which intracellular materials are engulfed by a double-membrane organelle called autophagosome and degrading materials by fusing with the lysosome. The process of autophagy is regulated by sequential recruitment and function of autophagy-related (Atg) proteins. Genetic hierarchical analyses show that the ULK1 complex comprised of ULK1-FIP200-ATG13-ATG101 translocating from the cytosol to autophagosome formation sites as a most upstream ATG factor; this translocation is critical in autophagy initiation. However, how this translocation occurs remains unclear. Here, we show that ULK1 is palmitoylated by palmitoyltransferase ZDHHC13 and translocated to the autophagosome formation site upon autophagy induction. We find that the ULK1 palmitoylation is required for autophagy initiation. Moreover, the ULK1 palmitoylated enhances the phosphorylation of ATG14L, which is required for activating PI3-Kinase and producing phosphatidylinositol 3-phosphate, one of the autophagosome membrane’s lipids. Our results reveal how the most upstream ULK1 complex translocates to the autophagosome formation sites during autophagy.
Time-of-day effects of cancer drugs revealed by high-throughput deep phenotyping
Authors: Ector Carolin , Schmal Christoph , Didier Jeff , De Landtsheer Sébastien , Finger Anna-Marie , Müller-Marquardt Francesca , Schulte Johannes H. , Sauter Thomas , Keilholz Ulrich , Herzel Hanspeter , Kramer Achim , Granada Adrián E.
Published: August 2024

The circadian clock, a fundamental biological regulator, governs essential cellular processes in health and disease. Circadian-based therapeutic strategies are increasingly gaining recognition as promising avenues. Aligning drug administration with the circadian rhythm can enhance treatment efficacy and minimize side effects. Yet, uncovering the optimal treatment timings remains challenging, limiting their widespread adoption. In this work, we introduce a high-throughput approach integrating live-imaging and data analysis techniques to deep-phenotype cancer cell models, evaluating their circadian rhythms, growth, and drug responses. We devise a streamlined process for profiling drug sensitivities across different times of the day, identifying optimal treatment windows and responsive cell types and drug combinations. Finally, we implement multiple computational tools to uncover cellular and genetic factors shaping time-of-day drug sensitivity. Our versatile approach is adaptable to various biological models, facilitating its broad application and relevance. Ultimately, this research leverages circadian rhythms to optimize anti-cancer drug treatments, promising improved outcomes and transformative treatment strategies.
Effect of vitamin E on energy metabolism indicators and gill tissue structure of crucian carp (Carassius auratus) under cooling stress
Authors: Tang Jiaming , Li Gongyan , Chen Dongjie , Jiang Lexia , Huang Baosheng , Jiang Peihong , Zhang Changfeng , Qin Xiaoming
Published: August 2024

The aim of this work is to examine the effects of vitamin E addition to water on the structure of the gill tissue and energy metabolism of crucian carp (Carassius auratus) under cooling stress. The crucian carp were chilled using a cold acclimation intelligent chilling equipment from 20 °C to 5 °C. They were divided into three groups: the control group (E1), the negative control group (E2), and the 100 mg/L vitamin E (E3) solution. Three different temperature points (20 °C, 10 °C, and 5 °C) were used to collect, test, and analyze the samples. The findings demonstrated that in the E3 treatment group, phosphoenolpyruvate carboxykinase, acetyl coenzyme A carboxylase, total cholesterol, urea nitrogen, triglyceride, and fatty acid synthase contents were significantly lower under cooling stress than those in the E1 and E2 treatment groups (P < 0.05). The E3 therapy group had significantly greater blood glucose, glycogen, and glycogen synthase levels than the E1 and E2 treatment groups (P < 0.05). The levels of pyruvate kinase in the E1, E2, and E3 treatment groups did not differ significantly. Crucian carp's gill tissue changed under cooling stress, including capillary dilatation, and the E3 treatment group experienced less damage overall than the E1 and E2 treatment groups. In conclusion, supplementing water with vitamin E to treat crucian carp can decrease damage, improve the body's ability to withstand cold, and slow down the stress response brought on by cooling stress. This provides a theoretical basis for supplementing water with vitamin E to fish stress relief.
Evaluating the Duke Criteria for infectious endocarditis in a single-center retrospective study
Authors: d’Almeida Sascha , Reischmann Kathrin , Andreß Stefanie , Felbel Dominik , Stephan Tilman , Hay Birgit , Rohlmann Friederike , Buckert Dominik , Rottbauer Wolfgang , Markovic Sinisa
Published: August 2024

The Duke Criteria have shaped the way infectious endocarditis (IE) is diagnosed in the last 30 years. This study aims to evaluate their current validity and importance in the diagnostic of IE. A retrospective cohort study was conducted on 163 consecutive patients who presented at the University Hospital in Ulm (Germany) with clinical suspicion of IE between 2009 and 2019. With patients’ medical records we differentiated between definitive endocarditis (DIE), possible endocarditis (PIE) and rejected endocarditis (RIE) and assessed the validity of the Duke Criteria in comparison to the final discharge diagnosis. We then tried to identify new potential parameters as an addition to the current valid Duke Criteria. The validity of the Duke Criteria improves with the length of hospitalization (especially cardiac imaging criterion, RIE 33.3%, PIE 31.6% and DIE 41.9%, p = 0.622 at admission and RIE 53.3%, PIE 68.4%, DIE 92.2%, p < 0.001 at discharge). At admission, overall sensitivity and specificity were respectively 29.5 and 91.2% in the DIE group. At discharge, sensitivity in the DIE group rose to 77.5% and specificity decreased to 79.4%. Of all screened metrics, microhematuria (p = 0.124), leukocyturia, (p = 0.075), younger age (p = 0.042) and the lack of rheumatoid disease (p = 0.011) showed a difference in incidence (p < 0.2) when comparing DIE and RIE group. In multivariate regression only microhematuria qualified as a potential sixth minor criterion at admission. Even with the latest technological breakthroughs our findings suggest that the Duke Criteria continue to hold value in the accurate assessment of IE. Future efforts must shorten the time until diagnosis.
Harnessing the acceptor substrate promiscuity of Clostridium botulinum Maf glycosyltransferase to glyco-engineer mini-flagellin protein chimeras
Authors: Sunsunwal Sonali , Khairnar Aasawari , Subramanian Srikrishna , Ramya T.N.C.
Published: August 2024

Several bacterial flagellins are O-glycosylated with nonulosonic acids on surface-exposed Serine/Threonine residues by Maf glycosyltransferases. The Clostridium botulinum Maf glycosyltransferase (CbMaf) displays considerable donor substrate promiscuity, enabling flagellin O-glycosylation with N-acetyl neuraminic acid (Neu5Ac) and 3-deoxy-D-manno-octulosonic acid in the absence of the native nonulosonic acid, a legionaminic acid derivative. Here, we have explored the sequence/structure attributes of the acceptor substrate, flagellin, required by CbMaf glycosyltransferase for glycosylation with Neu5Ac and KDO, by co-expressing C. botulinum flagellin constructs with CbMaf glycosyltransferase in an E. coli strain producing cytidine-5’-monophosphate (CMP)-activated Neu5Ac, and employing intact mass spectrometry analysis and sialic acid-specific flagellin biotinylation as readouts. We found that CbMaf was able to glycosylate mini-flagellin constructs containing shortened alpha-helical secondary structural scaffolds and reduced surface-accessible loop regions, but not non-cognate flagellin. Our experiments indicated that CbMaf glycosyltransferase recognizes individual Ser/Thr residues in their local surface-accessible conformations, in turn, supported in place by the secondary structural scaffold. Further, CbMaf glycosyltransferase also robustly glycosylated chimeric proteins constructed by grafting cognate mini-flagellin sequences onto an unrelated beta-sandwich protein. Our recombinant engineering experiments highlight the potential of CbMaf glycosyltransferase in future glycoengineering applications, especially for the neo-O-sialylation of proteins, employing E. coli strains expressing CMP-Neu5Ac (and not CMP-KDO).
An integrated coupled oscillator network to solve optimization problems
Authors: Graber Markus , Hofmann Klaus
Published: August 2024

Solving combinatorial optimization problems is essential in scientific, technological, and engineering applications, but can be very time and energy-consuming using classical algorithms executed on digital processors. Oscillator-based Ising machines offer a promising alternative by exploiting the analog coupling between electrical oscillators to solve such optimization problems more efficiently. Here we present the design and the capabilities of our scalable approach to solve Ising and quadratic unconstrained binary optimization problems. This approach includes routable oscillator connections to simplify the time-consuming embedding of the problem into the oscillator network. Our manufactured silicon chip, featuring 1440 oscillators implemented in a 28 nm technology, demonstrates the ability to solve optimization problems in 950 ns while consuming typically 319 μW per node. A frequency, phase, and delay calibration ensures robustness against manufacturing variations. The system is evaluated with multiple sets of benchmark problems to analyze the sensitivity for parameters such as the coupling strength or frequency.
Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes
Authors: Ghiaci Payam , Jouhten Paula , Martyushenko Nikolay , Roca-Mesa Helena , Vázquez Jennifer , Konstantinidis Dimitrios , Stenberg Simon , Andrejev Sergej , Grkovska Kristina , Mas Albert , Beltran Gemma , Almaas Eivind , Patil Kiran R , Warringer Jonas
Published: August 2024

Adaptive Laboratory Evolution (ALE) of microorganisms can improve the efficiency of sustainable industrial processes important to the global economy. However, stochasticity and genetic background effects often lead to suboptimal outcomes during laboratory evolution. Here we report an ALE platform to circumvent these shortcomings through parallelized clonal evolution at an unprecedented scale. Using this platform, we evolved 104 yeast populations in parallel from many strains for eight desired wine fermentation-related traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum leading to improved wine yeasts unencumbered by unwanted side effects. At the genomic level, evolutionary gains in metabolic characteristics often coincided with distinct chromosome amplifications and the emergence of side-effect syndromes that were characteristic of each selection niche. Several high-performing ALE strains exhibited desired wine fermentation kinetics when tested in larger liquid cultures, supporting their suitability for application. More broadly, our high-throughput ALE platform opens opportunities for rapid optimization of microbes which otherwise could take many years to accomplish.
Bio-inspired copper complexes with Cu2S cores: (solvent) effects on oxygen reduction reactions
Authors: Mangue Jordan , Wehrung Iris , Pécaut Jacques , Ménage Stéphane , Orio Maylis , Torelli Stéphane
Published: August 2024

A new mixed-valent Cu complex (6) allows for the systematic study of oxygen reduction reactions in acetonitrile/acetone and comparison with its parent (1). Kinetics and selectivity are influenced, suggesting changes at the chemical structure of (6).
Enhanced sodium ion mobility in sodium tellurosilicates and crystal structures of Na4SiTe4 and Na10Si2Te9 with isolated [SiTe4]4− tetrahedra and isolated Te2− anions
Authors: Kamm Franziska , Pielnhofer Florian , Schlosser Marc , Pfitzner Arno
Published: August 2024

The sodium tellurosilicates Na4SiTe4, Na10Si2Te9, Na6Si2Te6 and Na8Si4Te10 were synthesized by ball milling and subsequent high temperature solid state reactions and analyzed by electrochemical impedance spectroscopy.
The bioavailability of polyphenols following acute consumption of pigmented barley and wheat
Authors: Ed Nignpense Borkwei , Francis Nidhish , Blanchard Christopher , Santhakumar Abishek
Published: August 2024

Polyphenols from pigmented cereal grains exert health-promoting effects but data on their bioavailability are limited.
Sensory improvement and antioxidant enhancement in silver carp hydrolysate using prebiotic oligosaccharides: insights from the Maillard reaction
Authors: Dou Peipei , Wang Kai , Ding Ning , Zheng Yanyan , Hong Hui , Liu Huaigao , Tan Yuqing , Luo Yongkang
Published: August 2024

The sensory properties and antioxidant activities of SCH can be improved by using prebiotic oligosaccharides via the Maillard reaction, providing a theoretical basis for the development of new functional foods, and more possibilities for the sustainable development of the silver carp industry.
A proton-coupled electron transfer process from functionalized carbon dots to molecular substrates: the role of pH
Authors: Sayyad Umarfaruk S. , Waghmare Sapna , Mondal Somen
Published: August 2024

Multiple electron and proton transfers in nanomaterials pose significant demands and challenges across various fields such as renewable energy, chemical processes, biological applications, and photophysics.
Atomic scale insights into NaCl nucleation in nanoconfined environments
Authors: Wang Ruiyu , Tiwary Pratyush
Published: August 2024

Nanoconfinement stabilizes the solid phase of NaCl in aqueous solutions.
Bit‐Based Evaluation of Lightweight Block Ciphers SLIM, LBC‐IoT, and SLA by Mixed Integer Linear Programming
Authors: Sugio Nobuyuki
Published: August 2024

Many lightweight block ciphers have been proposed for IoT devices that have limited resources. SLIM, LBC‐IoT, and SLA are lightweight block ciphers developed for IoT systems. The designer of SLIM presented a 7‐round differential distinguisher and an 11‐round linear trail using a heuristic method. We have comprehensively sought the longest distinguisher for linear cryptanalysis, zero‐correlation linear cryptanalysis, impossible differential attack, and integral attack using the mixed integer linear Programming (MILP) on SLIM, LBC‐IoT, and SLA. The search led to discovery of a 16‐round linear trail on SLIM, which is 5‐round longer than the earlier result. We have also discovered 7‐, 7‐, and 9‐round distinguishers for zero‐correlation linear cryptanalysis, impossible differential attack, and integral attack, which are new results for SLIM. We have revealed 9‐, 8‐, and 11‐round distinguishers on LBC‐IoT for zero‐correlation linear cryptanalysis, impossible differential attack, and integral attack. We have presented full‐round distinguishers on SLA for integral attack using only two chosen plaintexts. We performed a key recovery attack on 16‐round SLIM with an experimental verification. This verification took 106 s with a success rate of 93%. Moreover, we present a key recovery attack on 19‐round SLIM using 16‐round linear trail with correlation 2−15: the necessary number of known plaintext–ciphertext pairs is 231; the time complexity is 264.4 encryptions; and the memory complexity is 238 bytes. Results show that this is the current best key recovery attack on SLIM. Because the recommended number of rounds is 32, SLIM is secure against linear cryptanalysis, as demonstrated herein.
Enhancing network attack detection across infrastructures: An automatic labeling method and deep learning model with an attention mechanism
Authors: Vu Dinh‐Minh , La Thi Ha , Nguyen Gia Bach , Huh Eui‐Nam , Tran Hoang Hai
Published: August 2024

In the era of industry 4.0 and the widespread use of digital devices, the number of cyber attacks poses an escalating and diverse threat, jeopardizing users' online activities. Intrusion detection systems (IDS) emerge as pivotal solutions, playing a crucial role in detecting anomalous signals within network systems. To counter novel attack patterns, IDS systems require periodic rule updates for effective identification of unusual signals. Typically, these policies are updated based on rule‐based or deep learning algorithms to enhance detection performance. However, the insufficient number of labeled samples remains a challenge for real‐world deployment. In this article, an automated labeling method is presented that has shown high effectiveness, requiring minimal hardware resources, and applicable to IDS systems. Additionally, the approach utilizes transfer learning combined with attention mechanisms to boost the efficiency of abnormal signal detection. The results from the approach are compared with those of a reference model, illustrating an overall improvement of nearly 10% in our model's performance compared to the reference model. This underscores the effectiveness of automating rule adjustments for IDS, contributing significantly to reducing associated financial costs. The research addresses the challenges in deploying IDS in real‐world scenarios and provides a valuable contribution to enhancing cyber threat detection capabilities.

A preprint has previously been published [11].
Two efficient three‐mode control strategies for four‐switch buck‐boost converters
Authors: Zhang Da , Gu Yu , Zhang Donglai , Zhang Xiaofeng , Li Haijin , Li Anshou
Published: August 2024

The bidirectional DC‐DC conversion, as an important application scenario, places certain requirements on the topology structure. The four‐switch buck‐boost (FSBB) converter has received widespread attention due to its simple structure, flexible control and state switchability. However, the traditional control strategy makes it difficult to meet the requirements of high performance, high stability and high security at the same time. Furthermore, the control methods commonly adopted in domestic and international practical applications rely heavily on analogue control, which cannot maintain efficiency over a wide stability range. The use of digital control methods allows for optimized control algorithms, maintaining stable system operation and improving efficiency. Therefore, it is very important to use the digital control method to further improve the smoothness and steady‐state efficiency of the system multi‐mode switching while maintaining a wide input and output range, based on this, this study proposes two new three‐mode control modes: interleaved bias control mode and dual‐edge bias control mode.
Dynamical accretion flows
Authors: Wells M. R. A. , Beuther H. , Molinari S. , Schilke P. , Battersby C. , Ho P. , Sánchez-Monge Á. , Jones B. , Scheuck M. B. , Syed J. , Gieser C. , Kuiper R. , Elia D. , Coletta A. , Traficante A. , Wallace J. , Rigby A. J. , Klessen R. S. , Zhang Q. , Walch S. , Beltrán M. T. , Tang Y. , Fuller G. A. , Lis D. C. , Möller T. , van der Tak F. , Klaassen P. D. , Clarke S. D. , Moscadelli L. , Mininni C. , Zinnecker H. , Maruccia Y. , Pezzuto S. , Benedettini M. , Soler J. D. , Brogan C. L. , Avison A. , Sanhueza P. , Schisano E. , Liu T. , Fontani F. , Rygl K. L. J. , Wyrowski F. , Bally J. , Walker D. L. , Ahmadi A. , Koch P. , Merello M. , Law C. Y. , Testi L.
Published: August 2024

Context. Investigating the flow of material along filamentary structures towards the central core can help provide insights into high-mass star formation and evolution.

Aims. Our main motivation is to answer the question of what the properties of accretion flows are in star-forming clusters. We used data from the ALMA Evolutionary Study of High Mass Protocluster Formation in the Galaxy (ALMAGAL) survey to study 100 ALMAGAL regions at a ∼1″ resolution, located between ∼2 and 6 kpc.

Methods. Making use of the ALMAGAL ∼1.3 mm line and continuum data, we estimated flow rates onto individual cores. We focus specifically on flow rates along filamentary structures associated with these cores. Our primary analysis is centered around position velocity cuts in H2CO (30, 3–20, 2), which allow us to measure the velocity fields surrounding these cores. Combining this work with column density estimates, we were able to derive the flow rates along the extended filamentary structures associated with cores in these regions.

Results. We selected a sample of 100 ALMAGAL regions, covering four evolutionary stages from quiescent to protostellar, young stellar objects (YSOs), and HII regions (25 each). Using a dendrogram and line analysis, we identify a final sample of 182 cores in 87 regions. In this paper, we present 728 flow rates for our sample (4 per core), analysed in the context of evolutionary stage, distance from the core, and core mass. On average, for the whole sample, we derived flow rates on the order of ∼10−4 M⊙ yr−1 with estimated uncertainties of ±50%. We see increasing differences in the values among evolutionary stages, most notably between the less evolved (quiescent and protostellar) and more evolved (YSO and HII region) sources and we also see an increasing trend as we move further away from the centre of these cores. We also find a clear relationship between the calculated flow rates and core masses ∼M2/3, which is in line with the result expected from the tidal-lobe accretion mechanism. The significance of these relationships is tested with Kolmogorov–Smirnov and Mann-Whitney U tests.

Conclusions. Overall, we see an increasing trend in the relationships between the flow rate and the three investigated parameters, namely: evolutionary stage, distance from the core, and core mass.
Effects of sodium hypochlorite cleaning on microbial diversity and phenotype of fresh-cut onions based on high-throughput sequencing
Authors: Yang Xi , Chen Dan , Chen Chichang , Zou Yao , Feng Lu , Zhang Xuan , Ren Juan
Published: August 2024

Fresh onion was used as raw material, sodium hypochlorite cleaning was used as the treatment group, and water cleaning was used as the control group. Stored at 4℃, high-throughput sequencing technology was used to compare the microbial succession and phenotype prediction of fresh-cut onion at the 1st, 3rd and 5th day, and to explore the effects of sodium hypochlorite cleaning on the microflora structure and phenotype of fresh-cut onion during storage. The results showed that at the level of family and genus, sodium hypochlorite cleaning had a significant inhibitory effect on Enterobacteriaceae, Enterobacter, Pantoea and Kosakonia. Compared with the control group, the relative abundance of facultative anaerobic, gramnegative and potential pathogenic phenotypes of bacteria in fresh-cut onion after sodium hypochlorite cleaning decreased, while the relative abundance of aerobic, anaerobic and gram-positive phenotypes increased. After cleaning with sodium hypochlorite, it could to some extent reduce the contamination of pathogenic bacteria in fresh-cut onion, thereby improving the quality and safety of fresh-cut onion.
Research Progress on the Antioxidant Activity of Oolong Tea
Authors: Zeng Jingxian
Published: August 2024

Oolong tea, a unique type of semi-fermented tea, has garnered widespread attention in recent years due to its distinctive production process and nutritional composition. Particularly, its antioxidant capacity has become a focal point for numerous researchers. This study systematically reviews the latest research advances in antioxidant compounds in oolong tea, discusses their potential applications in food preservation, processing, and functional food development, and anticipates future developments in the antioxidant activity of oolong tea.
Study on the Structure and Evolution of WOX Genes in the Populus trichocarpa Genome
Authors: Zhou Xueqing , Xing Zhen
Published: August 2024

The WOX gene family, a group of plant transcription factors, regulates growth, development, metabolism, and hormone signaling. This study employed bioinformatics to predict members and sequence characteristics of the Populus trichocarpa WOX gene family. By aligning the Populus trichocarpa genome with Arabidopsis and rice WOX genes, protein and nucleic acid sequences were obtained. Protein homology analysis identified all members, visualized with TBtools. Using MEGA11, an evolutionary tree of Populus trichocarpa and Arabidopsis WOX genes was constructed, revealing 18 predicted Populus trichocarpa WOX genes. Analysis of protein properties showed stability, and the evolutionary tree classified genes into branches, suggesting a close relationship between Populus trichocarpa and Arabidopsis WOX genes. Gene structure analysis revealed sequence variation and diversity.
Efficacy of Danshen Chuanxiongqin Injection Combined with Standard Western Therapy in Acute Coronary Syndrome: A Prospective Cohort Study
Authors: Zhang Xinsheng , Lansing Meryl Grace
Published: August 2024

This prospective cohort study evaluates the clinical efficacy of Danshen Chuanxiongqin (DSCXQ) injection, a Traditional Chinese Medicine (TCM) when used in conjunction with standard Western medical therapy in patients with Acute Coronary Syndrome (ACS). Conducted at Jinan Fuyuan Rehabilitation Hospital, China, the study involved 140 ACS patients randomized into two groups: treatment (n=70) receiving DSCXQ and standard therapy, and control (n=70) receiving only standard therapy. The primary outcomes measured were changes in serum levels of D-Dimer, BNP, Troponin, and cardiac ejection fraction (EF). The results revealed significant improvements in all primary biomarkers and EF in the treatment group compared to controls, with notable enhancements by day 5. However, elevated liver and kidney function markers in the treatment group suggest a need for careful monitoring. This study demonstrates the potential of integrating DSCXQ with conventional treatments to improve ACS management, although further research is necessary to establish long-term safety and efficacy.
Study on the Correlation Between the Genetics of Circadian Rhythms and Neurodegenerative Diseases
Authors: Yin Yueci
Published: August 2024

In the context of global population aging, the increasing incidence of neurodegenerative diseases presents a serious challenge to healthcare systems worldwide. This article meticulously reviews the genetic links between circadian rhythms and neurodegenerative diseases, revealing their complex interactions and potential implications for disease management and prevention. The foundational mechanisms of circadian rhythms, the roles of related genes, and the genetic basis of neurodegenerative diseases are explored. The relationship between circadian rhythm gene variations and neurodegenerative diseases is thoroughly discussed, and the risks posed by disruptions in the Circadian Rhythms are elucidated. Understanding the influence of circadian rhythms on neurodegenerative diseases may provide new directions for the development of therapeutic strategies, marking a step towards alleviating the burden of these diseases.
Immune Response to SARS-CoV-2 Infection
Authors: Cai Fengji
Published: August 2024

SARS-CoV-2 is a positive RNA virus which is responsible for the COVID-19 epidemic in 2020. This article provides an overview of this novel coronavirus, including its genome, proteins, receptor recognition, and synthesizes research on the immune responses and marker events triggered by the novel coronavirus. It emphasizes the critical roles of immune cells, specifically T cells and B cells, in the immune response. The article also highlights the virus’s ability to replicate within lung-resident macrophages and variations in immune responses among different patients. The discussion regarding the persistence of immune protection is ongoing, but studies indicate that prior infection may offer protection for at least ten months, even though reinfection remains possible. These findings are of significant importance for understanding the immune mechanisms of COVID-19, assessing disease severity, and devising effective treatment strategies.
The interplay between breast cancer and the nervous system during the progression of breast cancer and implications for its targeted therapy
Authors: Cai Guocui , Songa Feiyang
Published: August 2024

Breast cancer ranks as a leading cause of cancer-related deaths in women globally. Current treatments often fall short in eradicating it completely, posing challenges in managing its incidence and mortality rates. The nervous system significantly influences breast cancer initiation, progression, and metastasis. The review highlights how the hypothalamic-pituitary-adrenal axis in the central nervous system and peripheral nerves, such as parasympathetic and sympathetic nerves, can either promote or inhibit cancer development through neurotransmitter release. Understanding these mechanisms offers new therapeutic targets, potentially improving breast cancer diagnosis and treatment strategies.