bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation and clinical practice of pathogens and antimicrobial resistance genes of BioFire FilmArray Pneumonia panel in lower respiratory tract infections
Authors: Gong Jinru , Yang Jiasheng , Liu Lihong , Chen Xiaoxuan , Yang Guangyu , He Yaowei , Sun Ruilin
Published: December 2023

Background

Existing panels for lower respiratory tract infections (LRTIs) are slow and lack quantification of important pathogens and antimicrobial resistance, which are not solely responsible for their complex etiology and antibiotic resistance. BioFire FilmArray Pneumonia (PN) panels may provide rapid information on their etiology.

Methods

The bronchoalveolar lavage fluid of 187 patients with LRTIs was simultaneously analyzed using a PN panel and cultivation, and the impact of the PN panel on clinical practice was assessed. The primary endpoint was to compare the consistency between the PN panel and conventional microbiology in terms of etiology and drug resistance, as well as to explore the clinical significance of the PN panel. The secondary endpoint was pathogen detection using the PN panel in patients with community-acquired pneumonia (CAP) or hospital-acquired pneumonia (HAP).

Results

Fifty-seven patients with HAP and 130 with CAP were included. The most common pathogens of HAP were Acinetobacter baumannii and Klebsiella pneumoniae, with the most prevalent antimicrobial resistance (AMR) genes being CTX-M and KPC. For CAP, the most common pathogens were Haemophilus influenzae and Staphylococcus aureus, with the most frequent AMR genes being CTX-M and VIM. Compared with routine bacterial culture, the PN panel demonstrated an 85% combined positive percent agreement (PPA) and 92% negative percent agreement (NPA) for the qualitative identification of 13 bacterial targets. PN detection of bacteria with higher levels of semi-quantitative bacteria was associated with more positive bacterial cultures. Positive concordance between phenotypic resistance and the presence of corresponding AMR determinants was 85%, with 90% positive agreement between CTX-M-type extended-spectrum beta-lactamase gene type and phenotype and 100% agreement for mecA/C and MREJ. The clinical benefit of the PN panel increased by 25.97% compared with traditional cultural tests.

Conclusion

The bacterial pathogens and AMR identified by the PN panel were in good agreement with conventional cultivation, and the clinical benefit of the PN panel increased by 25.97% compared with traditional detection. Therefore, the PN panel is recommended for patients with CAP or HAP who require prompt pathogen diagnosis and resistance identification.
Component test for the assessment of delayed hydrogen-assisted cracking in thick-walled SAW joints for offshore applications
Authors: Rhode Michael , Kromm Arne , Mente Tobias , Brackrock Daniel , Czeskleba Denis , Kannengiesser Thomas
Published: December 2023

Offshore wind turbines continuously increase in size and weight and demand adequate offshore foundations concepts like monopiles, tripods, or jackets. These components are typically constructed using submerged arc welding (SAW) with high-strength thick steel plates like the S420ML. During welding, the occurrence of delayed hydrogen-assisted cracking (HAC) must be anticipated. HAC is a critical combination of the local hydrogen concentration within a susceptible microstructure under certain mechanical load, i.e., the occurring (welding) residual stresses. The welding sequence of the thick-walled plates complicates the residual stress distribution due to the necessary repeated thermal cycling, i.e., welding seam/layer deposition to fill the joint. For that purpose, SAW with two-wire-technique was used to weld a specially designed and prototype-like mock-up of a real component with a thickness of 50 mm, filled with over 20 passes and a seam length of 1000 mm. Additional welded stiffeners simulated the effect of a high restraint, to achieve critical HAC conditions. The necessity of a minimum waiting time (MWT) before the NDT can be conducted (to exclude HAC) was critically verified by the application of ultrasonic testing of the welded joint at different time-steps of the NDT of up to 48 h after the completion welding. The residual stresses were determined by a robot XRD goniometer. Tensile residual stresses up to the yield limit are found both in the weld metal and in the heat-affected zone. Numerical modeling allowed the qualitative estimation of the hydrogen diffusion in the weld. No noticeable HAC occurrence was identified and confirms the high cracking resistance of the investigated material. Finally, the applicability of the MWT concept should be critically discussed.
Properties oriented WAAM—microstructural and geometrical control in WAAM of low-alloy steel
Authors: Treutler Kai , Gehling Tobias , Scheck Maxim , Richter Andreas , Bohn Christian , Ehlers Rüdiger , Rembe Christian , Wesling Volker
Published: December 2023

Today, arc-based additive manufacturing has great potential for industrial application due to new developments in robotics, welding technology, and computer-aided manufacturing. Two issues are currently the focus of research. One is the accurate generation of geometry with respect to the design, e.g., geometry fidelity, defined roughness, and shape deviations within the tolerances. Here, there are still open questions, particularly with regard to path planning and the dependence of the geometry on the selected process variables. The second topic is the adjustment or determination of the achievable mechanical and microstructural properties, as these are of crucial importance for the use of the technology in industry. The combination of both areas into a geometry- and property-oriented approach to additive manufacturing has been little discussed in the literature for arc-based welding processes. The correlations between cooling conditions and emerging properties can serve as a starting point for such a consideration. The temperature history depends on three key factors: the energy input, the interpass temperature (which in additive manufacturing is determined by the time to over-weld), and the heat transfer conditions, which are determined by the part geometry. The melt pool size or volume also depends on these three constraints. In this study, an approach is presented to realize property-oriented additive manufacturing from the interaction of property-oriented path planning and a melt pool size control system. By controlling the melt pool size, the cooling of the material can be adjusted within certain limits, and consequently, a local adjustment of the microstructure can be achieved, which greatly influences the local mechanical properties. This work demonstrates this approach for a low-alloy filler metal (DIN EN ISO 14341-A G 50 7 M21 4Mo/A5.28 ER80S-D2). Gas metal arc welding was carried out using an M21 shielding gas (82% Ar, 18% CO2). Finally, microstructural characterization will show that different microstructural morphologies and properties can be achieved in a component by combining property-oriented path planning and the use of a control loop to regulate the melt pool size.
Covid-19 Vaccine Hesitancy and Under-Vaccination among Marginalized Populations in the United States and Canada: A Scoping Review
Authors: Newman Peter A. , Dinh Duy A. , Nyoni Thabani , Allan Kate , Fantus Sophia , Williams Charmaine C. , Tepjan Suchon , Reid Luke , Guta Adrian
Published: December 2023

Background

Amid persistent disparities in Covid-19 vaccination and burgeoning research on vaccine hesitancy (VH), we conducted a scoping review to identify multilevel determinants of Covid-19 VH and under-vaccination among marginalized populations in the U.S. and Canada.

Methods

Using the scoping review methodology developed by the Joanna Briggs Institute, we designed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020–October 25, 2022. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 VH and under-vaccination among marginalized populations.

Results

The search captured 11,374 non-duplicated records, scoped to 103 peer-reviewed articles. Among 14 marginalized populations identified, African American/Black, Latinx, LGBTQ+, American Indian/Indigenous, people with disabilities, and justice-involved people were the predominant focus. Thirty-two factors emerged as influencing Covid-19 VH, with structural racism/stigma and institutional mistrust (structural)(n = 71) most prevalent, followed by vaccine safety (vaccine-specific)(n = 62), side effects (vaccine-specific)(n = 50), trust in individual healthcare provider (social/community)(n = 38), and perceived risk of infection (individual)(n = 33). Structural factors predominated across populations, including structural racism/stigma and institutional mistrust, barriers to Covid-19 vaccine access due to limited supply/availability, distance/lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally- and linguistically-appropriate information.

Discussion

We identified multilevel and complex drivers of Covid-19 under-vaccination among marginalized populations. Distinguishing vaccine-specific, individual, and social/community factors that may fuel decisional ambivalence, more appropriately defined as VH, from structural racism/structural stigma and systemic/institutional barriers to vaccination access may better support evidence-informed interventions to promote equity in access to vaccines and informed decision-making among marginalized populations.
Two-Dimensional Cr5Te8@Graphite Heterostructure for Efficient Electromagnetic Microwave Absorption
Authors: Qin Liyuan , Guo Ziyang , Zhao Shuai , Kong Denan , Jiang Wei , Liu Ruibin , Lv Xijuan , Zhou Jiadong , Shu Qinghai
Published: December 2023

Two-dimensional (2D) transition metal chalcogenides (TMCs) hold great promise as novel microwave absorption materials owing to their interlayer interactions and unique magnetoelectric properties. However, overcoming the impedance mismatch at the low loading is still a challenge for TMCs due to the restricted loss pathways caused by their high-density characteristic. Here, an interface engineering based on the heterostructure of 2D Cr5Te8 and graphite is in situ constructed via a one-step chemical vapor deposit to modulate impedance matching and introduce multiple attenuation mechanisms. Intriguingly, the Cr5Te8@EG (ECT) heterostructure exhibits a minimum reflection loss of up to − 57.6 dB at 15.4 GHz with a thin thickness of only 1.4 mm under a low filling rate of 10%. The density functional theory calculations confirm that the splendid performance of ECT heterostructure primarily derives from charge redistribution at the abundant intimate interfaces, thereby reinforcing interfacial polarization loss. Furthermore, the ECT coating displays a remarkable radar cross section reduction of 31.9 dB m2, demonstrating a great radar microwave scattering ability. This work sheds light on the interfacial coupled stimulus response mechanism of TMC-based heterogeneous structures and provides a feasible strategy to manipulate high-quality TMCs for excellent microwave absorbers.
Synthesis and Optimisation of an Integrated Renewable Energy and Greenhouse Network
Authors: Godlonton Alice , Borain Candice M. , Isafiade Adeniyi J. , Möller Klaus , Chitsiga Takudzwa
Published: December 2023

This paper presents a study on the synthesis and optimisation of a renewable energy and resource supply chain network (SCN) to satisfy agricultural greenhouse resource and energy demands. This is motivated by the high costs and emissions to run greenhouses due to the resources and energy required for optimal growth conditions. The investigation aims to contribute to the growing area of research on circular practices in the agricultural sector. The SCN includes biomass from agricultural waste transported to a utility hub, consisting of water and carbon dioxide (CO2) as resource supplies, as well as a boiler and steam turbine-generator and solar photovoltaic (PV), as energy conversion technologies. The resources and energy are distributed to greenhouses. The objectives are to minimise both the total annualised costs (TAC) and environmental impact (EI), calculated as CO2 emissions of the integrated network. Multi-periodicity accounts for the monthly and daily variation in constraints on the system, such as feedstock and solar radiation availability and energy limitations. The model is applied to a case study of an agro-industrial zone in Kwa-Zulu Natal (KZN) province, South Africa. The network meets greenhouse demands at a minimum TAC and EI of 8.052 $$\times {10}^{6}$$

×

10

6

R/y and 14,370 tCO2e/y, respectively. The biomass supply chain (BSC) contributes most significantly to the TAC at 43.7% while biomass combustion makes up 99.8% of the EI. Additional key results include bagasse and corn stover being selected as the only feedstocks and rail as the transport mode. The 26,560 MWh/y of electricity supplied to the greenhouses is made up by 71.4% from the boiler and turbine-generator with the remainder from solar PV. The potential of solar PV as a clean and low-cost energy source is demonstrated by the model selection at its full capacity. The study confirms that holistic modelling and optimisation of renewable energy SCNs for greenhouses is necessary to meet a trade-off between the network costs and CO2 emissions.
Racial Inequality in Firearm Homicide Victimization—but not Other Types of US Violence
Authors: Piquero Alex R.
Published: December 2023

Research Question

Is violent crime victimization among US minority groups higher than for White Americans in general, or is there a distinct failure of equal protection by race with respect to firearm homicide?

Data

This analysis examines per capita rates of violent victimization for Blacks, Hispanics, and Whites as reported in recent years in the National Crime Victimization Survey (NCVS), as well as the firearms homicide data collected from local and state death certificates by the US Center for Disease Control (CDC).

Method

The analysis compares the extent of disparity between White and minority victimization rates for different kinds of violent crimes. The framework is to calculate the ratio of minority victimization rates to the White rates for the same offense categories.

Findings

While there are very small differences in victimization rates by race/ethnicity for most types of violent crime, and while Whites report higher victimization rates than minorities do for some kinds of violent crimes, there is a massive ratio for rates of firearms homicides. Black Americans of all ages, for example, suffer firearm homicides at a rate that is 12 times higher per capita than for Whites. Hispanic Americans are twice as likely to be victimized by firearm homicide than Whites.

Conclusions

Policing strategies often fail to distinguish different types of violence, even when discussing racial disparity in policing actions. The evidence of this report provides the most direct support for police increasing the precision of their focus on crime prevention efforts that can reduce homicide as the most important racial disparity in criminal victimization, and, in the US context, firearm homicide in particular.
Exploring the advantages and applications of nanocomposites produced via vat photopolymerization in additive manufacturing: A review
Authors: Colorado Henry A. , Gutierrez-Velasquez Elkin I. , Gil León D. , de Camargo Italo Leite
Published: December 2023

Additive manufacturing (AM) also known as 3D printing (3DP) has become a popular technology with a wide range of applications, from which vat photopolymerization is a technique for producing nanocomposites with controlled mechanical, thermal, and electrical properties. This technology uses a UV light laser to cure a liquid resin into a solid object, layer by layer, allowing complex three-dimensional (3D) objects with intricate details of manufacturing and excellent finishing. Nanocomposites produced by vat photopolymerization have been used in aerospace, automotive, and medical industries, due to their superior mechanical strength and dimensional accuracy. In this article, we will discuss the advantages and other aspects of nanocomposites made with vat photopolymerization, exploring potential applications, and discuss the research by different areas, such as their AM technologies and materials properties.

Graphical abstract

This review deals with nanocomposites made by additive manufacturing (3D printing), presenting a systematic on vat photopolymerization technology, including the technologies, materials, and properties.
Understanding the progress and challenges in the fields of thermo-catalysis and electro-catalysis for the CO2 conversion to fuels
Authors: Yadav V. S. K. , Al-Marri Mohammed J. , Saad Mohammed A. H. S. , Kumar Anand
Published: December 2023

The need to limit anthropogenic CO2 emissions and lower the atmospheric CO2 concentration makes CO2 conversion an imminent requirement. Availability of suitable facilities and prior understanding how electro and thermal catalysis work renders them as appealing platforms for conversion of CO2. Catalysts play a crucial part in the conversion of CO2 to chemicals in both processes. Catalysis is a process initiated by the interaction of reactants, intermediates, and products produced on the catalyst’s surface. Generally, higher temperatures in thermo-catalytic process or electrical potentials in electrocatalytic process are used to increase the reaction rate to get the desired results and to overcome the kinetic barrier. Several studies have been reported in both the processes with a desire to decrease the atmospheric CO2 concentration by stopping CO2 emissions at the site of generation itself. The viability of catalytic performance in both situations for the large-scale conversion of CO2 is still up for debate. In this review, we intend to focus on recent developments in CO2 conversion aided by diverse catalysts by analyzing and comparing proof-of-principle investigations on applied conditions, catalyst activity and stability for thermocatalytic and electrocatalytic CO2 conversions. The most common catalyst synthesis techniques employed in both experiments were analyzed. Primary goal of this review is to draw connections between the two fields in order to generate fresh insights that will lead to a more efficient and integrated CO2 conversion process.
Using ScrutinAI for visual inspection of DNN performance in a medical use case
Authors: Görge Rebekka , Haedecke Elena , Mock Michael
Published: December 2023

Our Visual Analytics (VA) tool ScrutinAI supports human analysts to investigate interactively model performance and data sets. Model performance depends on labeling quality to a large extent. In particular in medical settings, generation of high quality labels requires in depth expert knowledge and is very costly. Often, data sets are labeled by collecting opinions of groups of experts. We use our VA tool to analyze the influence of label variations between different experts on the model performance. ScrutinAI facilitates to perform a root cause analysis that distinguishes weaknesses of deep neural network (DNN) models caused by varying or missing labeling quality from true weaknesses. We scrutinize the overall detection of intracranial hemorrhages and the more subtle differentiation between subtypes in a publicly available data set.
The emergence of geo-economic institutions: observations on European and Chinese development cooperation in Ukraine, Georgia, and Moldova 2014 – 2020
Authors: Kruger Angelo , Strosser Jack
Published: December 2023

The emergence of China as a major provider of development finance has garnered considerable scholarly debate. Chinese investments and their impact on recipient states have been extensively studied, mainly focusing on the Belt and Road Initiative (BRI). In response to the BRI, the European Commission recently announced its connectivity strategy, the Global Gateway initiative. In this context, and even before the announcement, little work has been done to map Chinese state capitalist development finance side by side with the European Union’s (EU) market-led, public-private partnership-oriented strategies, especially within Europe’s own neighborhood. Additionally, the literature insufficiently explains why development institutions (agents) would act geo-economically to enforce their most powerful member states’ (principals) international agendas. This lack of theoretical explanatory power poses a serious puzzle. Thus, we ask, how has EU and Chinese institutional investment cooperation developed (legally and financially) in the EU’s Eastern Partnership (EaP) region in the previous EU Multiannual Financial Framework (MFF) from 2014 to 2020? We argue that development institutions have acted in accordance with their principal’s policy goals by facilitating investment and institutional agreements and by offering beneficial cooperation conditions, so that the EU and China can direct investment in a geo-economic manner if they choose to do so. In the following, we find that European investment in the EaP countries Ukraine, Moldova, and Georgia, has been huge in absolute terms (amount invested) and strong in relative terms––through deeper economic cooperation––when compared to Chinese investment activity in the same countries. This development supports the EU’s aim of countering China’s increasing economic presence in the region. However, we find that this gap has been closing in total terms. Our study suggests that while China has not matched EU investment in the EaP region for the previous MFF, further research is needed to unpack individual sectors and their geo-economic implications for official development institutions and their respective states.
The Life after Life of the 2006 Transnistrian Sovereignty Referendum
Authors: Kosienkowski Marcin
Published: December 2023

In 2006, the authorities of the de facto state of Transnistria unilaterally held a sovereignty referendum. Almost all voters supported Transnistria gaining internationally recognized independence and subsequently integrating/associating with Russia. Despite such clear results, the poll was not recognized internationally and, consequently, not implemented. However, this was not a problem for the Transnistrian leadership, since the primary objective of the referendum was not to reallocate sovereignty, but to domestically empower Transnistria’s President Igor Smirnov. Based on the discourse of Transnistria’s next president, Yevgeniy Shevchuk, this article argues that the referendum was not placed in the dustbin of history. Analysis of the official Transnistrian news published during his presidency from 2011–2016 shows that Shevchuk re-exploited the 2006 sovereignty referendum. His aim was not to reallocate sovereignty either, but to reach the following goals: 1. procure legitimacy of the Transnistrian sovereignty cause internationally; 2. empower Transnistria vis-à-vis its parent state, Moldova; 3. boost relations with Transnistria’s patron, Russia; and 4. empower himself domestically. Arguably, the argument about the strategic use of past unilateral sovereignty referendums also works in cases of other de facto states, which can be analyzed using the analytical framework presented in this article.
“Junge Mädchen” and “Daughters of the Sky”: Transatlantic Changes in the Construction of Femininity after 1930
Authors: Hung Jochen
Published: December 2023

The difference between the representation of German femininity in the 1920s and the 1930s is striking: while glamorous flappers with bob haircuts ruled the beginning of the interwar period, its end is characterized by serious and earnest—and often longhaired—young women. Rather than taking the obvious route of relating this change to the political changes in Germany, most importantly the rise of the Nazis, this article argues that the changing representation of interwar femininity in Germany was always embedded in a transnational, transatlantic process. The transformation of flappers into humble girls started well before the Nazis came to power and was fueled by a wide variety of voices, from communist to bourgeois actors.
Forty-two years of computer-assisted language learning research: A scientometric study of hotspot research and trending issues
Authors: Mohsen Mohammed Ali , Althebi Sultan , Alsagour Rawan , Alsalem Albatool , Almudawi Amjad , Alshahrani Abdulaziz
Published: December 2023

For years, computer-assisted language learning (CALL) has thrived as an interdisciplinary subfield, linking applied linguistics and educational technology. Despite its significance and a number of syntheses, CALL research has not yet undergone a comprehensive scientometric synthesis. This study synthesizes CALL research over a period of 42 years by employing a scientometric analysis of sources and document co-citation analyses. Scopus was used to retrieve original articles with a timespan limit from 1980 to 2021. Our records identified 4,631 articles representing CALL-based research, which were published in 63 peer-reviewed journals and collectively contained 186,589 references. The findings indicate that CALL research is supported by robust theoretical frameworks, grounded in socio-cultural and second language acquisition theories. Our research findings have revealed several significant clusters of interest within the realm of CALL, with a pronounced focus on writing among CALL scholars. Additionally, the study identified emerging research areas such as mobile-assisted language learning, synchronous computer-mediated communication, and data-driven learning in CALL literature. Notably, “CALL-core” journals exhibited high productivity, with Language Learning & Technology, Computer Assisted Language Learning, and Computers & Education standing out as top-ranked journals in terms of the Hirsch index (h-index) and co-citation. Suggestions for future research are outlined in the conclusion.
Diversity analyses of chickpea (Cicer arietinum L.) through agro-morphological traits
Authors: Dehbaoui Nasser Eddine , Gentzbittel Laurent , Drevon Jean Jacques , Lazali Mohamed
Published: December 2023

The limited genetic resource of chickpea (Cicer arietinum L.) is one of the most critical issue impeding its improvement and production. Collection and characterization of chickpea for agronomic traits is prerequisite to build a successful breeding programme through expanding chickpea's genepool to fulfil the needs of farmers and breeders, such as grain size and yield which supply food to a world rising population. To reach such an objective, numerous collection missions were carried out in Algeria, covering the northern agro-ecological environments, this allows us to gather 56 national and international genotypes that report a phenotypic variability and may provide a valuable diversity of useful features. Characterization experiments of 19 agro-morphological traits were set up at the Technical Institute of Field Crops over two successive seasons 2020 and 2021. All traits were statistically significant and the cluster analysis classified the genotypes into three major group, where local and improved accessions revealed an interesting outcome in terms of seed yield and resistance to Ascochyta blight. In general, the current study's findings clearly demonstrated that plant and seed morphological characteristics could be used to distinguish and identify chickpea genotypes. More often, it might participate as a source of variation in breeding programmes to meet the desirable improvement targets.
Evaluating cognitive and physical work performance: A comparative study of an active and passive industrial back-support exoskeleton
Authors: Govaerts Renée , Turcksin Tom , Vanderborght Bram , Roelands Bart , Meeusen Romain , De Pauw Kevin , De Bock Sander
Published: December 2023

Occupational back-support exoskeletons, categorized as active or passive, hold promise for mitigating work-related musculoskeletal disorders. However, their impact on combined physical and cognitive aspects of industrial work performance remains inadequately understood, especially regarding potential differences between exoskeleton categories. A randomized, counterbalanced cross-over study was conducted, comparing the active CrayX, passive Paexo Back, and a no exoskeleton condition. A 15-min dual task was used to simulate both cognitive and physical aspects of industrial work performance. Cognitive workload parameters included reaction time, accuracy, and subjective measures. Physical workload included movement duration, segmented in three phases: (1) walking to and grabbing the box, (2) picking up, carrying, and putting down the box, and (3) returning to the starting point. Comfort of both devices was also surveyed. The Paexo significantly increased movement duration in the first segment compared to NoExo (Paexo = 1.55 ± 0.19 s; NoExo = 1.32 ± 0.17 s; p < .01). Moreover, both the Paexo and CrayX increased movement duration for the third segment compared to NoExo (CrayX = 1.70 ± 0.27 s; Paexo = 1.74 ± 0.27 s, NoExo = 1.54 ± 0.23 s; p < .01). No significant impact on cognitive outcomes was observed. Movement Time 2 was not significantly affected by both exoskeletons. Results of the first movement segment suggest the Paexo may hinder trunk bending, favoring the active device for dynamic movements. Both devices may have contributed to a higher workload as the movement duration in the third segment increased compared to NoExo.
Audio‐Magnetotelluric Survey for Groundwater Investigation in the Al‐Jaww Plain in Eastern Abu Dhabi, Al‐Ain, United Arab Emirates
Authors: Saibi H. , Ali M. Y. , Cherkose B. A. , Alaran A. , Ullah S. , Tsuji T.
Published: December 2023

The United Arab Emirates (UAE), located in an arid climate zone with low rainfall, relies on shallow aquifers for freshwater. Understanding the depth and extent of such aquifers is crucial for meeting water supply needs. The UAE's hydrogeology is influenced by neighboring mountains in Oman. The Al‐Jaww Plain in southeast of Al‐Ain city is an essential groundwater source, characterized by a large, flat area of gravel and sand deposits from the Oman Mountains. This study aims to map groundwater aquifers in the Al‐Jaww Plain by integrating the audio‐magnetotelluric (AMT) method, seismic reflection profiling, and borehole data. AMT data were collected along an 11‐km ENE–WSW profile and a 2D resistivity model was generated. The resulting model delineates three distinct geo‐electrical zones from the surface to a depth of 5 km. First, a shallow layer with low resistivity (0–15 Ωm) represents the Quaternary and Pliocene aquifers, in addition to the Upper Cretaceous Simsima and Tertiary groundwater aquifer zone, extending to a depth of 1.5 km. Second, a moderately resistive layer (15–250 Ωm) is recorded beneath the first layer, corresponding to the Upper Cretaceous Aruma foreland basin sequence. Finally, a high‐resistivity region (>250 Ωm) at depths exceeding 3 km is attributed to the allochthonous Hawasina thrust sheet, which is associated with Late Cretaceous obduction of the Semail ophiolite. These findings have practical implications for managing groundwater resources in Al‐Ain.
Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities
Authors: Birnbaum Rebecca
Published: December 2023

Tandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
Mechanical control of neural plate folding by apical domain alteration
Authors: Matsuda Miho , Rozman Jan , Ostvar Sassan , Kasza Karen E. , Sokol Sergei Y.
Published: December 2023

Vertebrate neural tube closure is associated with complex changes in cell shape and behavior, however, the relative contribution of these processes to tissue folding is not well understood. At the onset ofXenopusneural tube folding, we observed alternation of apically constricted and apically expanded cells. This apical domain heterogeneity was accompanied by biased cell orientation along the anteroposterior axis, especially at neural plate hinges, and required planar cell polarity signaling. Vertex models suggested that dispersed isotropically constricting cells can cause the elongation of adjacent cells. Consistently, in ectoderm, cell-autonomous apical constriction was accompanied by neighbor expansion. Thus, a subset of isotropically constricting cells may initiate neural plate bending, whereas a ‘tug-of-war’ contest between the force-generating and responding cells reduces its shrinking along the body axis. This mechanism is an alternative to anisotropic shrinking of cell junctions that are perpendicular to the body axis. We propose that apical domain changes reflect planar polarity-dependent mechanical forces operating during neural folding.
Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin
Authors: Yamashiro Sawako , Rutkowski David M. , Lynch Kelli Ann , Liu Ying , Vavylonis Dimitrios , Watanabe Naoki
Published: December 2023

Force transmission at integrin-based adhesions is important for cell migration and mechanosensing. Talin is an essential focal adhesion (FA) protein that links F-actin to integrins. F-actin constantly moves on FAs, yet how Talin simultaneously maintains the connection to F-actin and transmits forces to integrins remains unclear. Here we show a critical role of dynamic Talin unfolding in force transmission. Using single-molecule speckle microscopy, we found that the majority of Talin are bound only to either F-actin or the substrate, whereas 4.1% of Talin is linked to both structures via elastic transient clutch. By reconstituting Talin knockdown cells with Talin chimeric mutants, in which the Talin rod subdomains are replaced with the stretchable β-spectrin repeats, we show that the stretchable property is critical for force transmission. Simulations suggest that unfolding of the Talin rod subdomains increases in the linkage duration and work at FAs. This study elucidates a force transmission mechanism, in which stochastic molecular stretching bridges two cellular structures moving at different speeds.
Building synthetic chromosomes from natural DNA
Authors: Coradini Alessandro L. V. , Ville Christopher Ne , Krieger Zachary A. , Roemer Joshua , Hull Cara , Yang Shawn , Lusk Daniel T. , Ehrenreich Ian M.
Published: December 2023

De novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We use CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment reveals that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.
Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome
Authors: Aupič Jana , Borišek Jure , Fica Sebastian M. , Galej Wojciech P. , Magistrato Alessandra
Published: December 2023

Cleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large cellular machineries composed of both protein and RNA. Long thought to rely on a two-metal-ion mechanism for catalysis, structure comparisons revealed many contain highly spatially conserved second-shell monovalent cations, whose precise function remains elusive. A recent high-resolution structure of the spliceosome, essential for pre-mRNA splicing in eukaryotes, revealed a potassium ion in the active site. Here, we employ biased quantum mechanics/ molecular mechanics molecular dynamics to elucidate the function of this monovalent ion in splicing. We discover that the K+ ion regulates the kinetics and thermodynamics of the first splicing step by rigidifying the active site and stabilizing the substrate in the pre- and post-catalytic state via formation of key hydrogen bonds. Our work supports a direct role for the K+ ion during catalysis and provides a mechanistic hypothesis likely shared by other nucleic acid processing enzymes.
Amino acid catabolite markers for early prognostication of pneumonia in patients with COVID-19
Authors: Maeda Rae , Seki Natsumi , Uwamino Yoshifumi , Wakui Masatoshi , Nakagama Yu , Kido Yasutoshi , Sasai Miwa , Taira Shu , Toriu Naoya , Yamamoto Masahiro , Matsuura Yoshiharu , Uchiyama Jun , Yamaguchi Genki , Hirakawa Makoto , Kim Yun-Gi , Mishima Masayo , Yanagita Motoko , Suematsu Makoto , Sugiura Yuki
Published: December 2023

Effective early-stage markers for predicting which patients are at risk of developing SARS-CoV-2 infection have not been fully investigated. Here, we performed comprehensive serum metabolome analysis of a total of 83 patients from two cohorts to determine that the acceleration of amino acid catabolism within 5 days from disease onset correlated with future disease severity. Increased levels of de-aminated amino acid catabolites involved in the de novo nucleotide synthesis pathway were identified as early prognostic markers that correlated with the initial viral load. We further employed mice models of SARS-CoV2-MA10 and influenza infection to demonstrate that such de-amination of amino acids and de novo synthesis of nucleotides were associated with the abnormal proliferation of airway and vascular tissue cells in the lungs during the early stages of infection. Consequently, it can be concluded that lung parenchymal tissue remodeling in the early stages of respiratory viral infections induces systemic metabolic remodeling and that the associated key amino acid catabolites are valid predictors for excessive inflammatory response in later disease stages.
Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment
Authors: Lu Xiaojian , Luo Yanwei , Nie Xichen , Zhang Bailing , Wang Xiaoyan , Li Ran , Liu Guangmin , Zhou Qianyin , Liu Zhizhong , Fan Liqing , Hotaling James M. , Zhang Zhe , Bo Hao , Guo Jingtao
Published: December 2023

Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.
Synaptic density affects clinical severity via network dysfunction in syndromes associated with frontotemporal lobar degeneration
Authors: Whiteside David J. , Holland Negin , Tsvetanov Kamen A. , Mak Elijah , Malpetti Maura , Savulich George , Jones P. Simon , Naessens Michelle , Rouse Matthew A. , Fryer Tim D. , Hong Young T. , Aigbirhio Franklin I. , Mulroy Eoin , Bhatia Kailash P. , Rittman Timothy , O’Brien John T. , Rowe James B.
Published: December 2023

There is extensive synaptic loss from frontotemporal lobar degeneration, in preclinical models and human in vivo and post mortem studies. Understanding the consequences of synaptic loss for network function is important to support translational models and guide future therapeutic strategies. To examine this relationship, we recruited 55 participants with syndromes associated with frontotemporal lobar degeneration and 24 healthy controls. We measured synaptic density with positron emission tomography using the radioligand [11C]UCB-J, which binds to the presynaptic vesicle glycoprotein SV2A, neurite dispersion with diffusion magnetic resonance imaging, and network function with task-free magnetic resonance imaging functional connectivity. Synaptic density and neurite dispersion in patients was associated with reduced connectivity beyond atrophy. Functional connectivity moderated the relationship between synaptic density and clinical severity. Our findings confirm the importance of synaptic loss in frontotemporal lobar degeneration syndromes, and the resulting effect on behaviour as a function of abnormal connectivity.
Reassessing endothelial-to-mesenchymal transition in mouse bone marrow: insights from lineage tracing models
Authors: Cao Jia , Jin Ling , Yan Zi-Qi , Wang Xiao-Kai , Li You-You , Wang Zun , Liu Yi-Wei , Li Hong-Ming , Guan Zhe , He Ze-Hui , Gong Jiang-Shan , Liu Jiang-Hua , Yin Hao , Tan Yi-Juan , Hong Chun-Gu , Feng Shi-Kai , Zhang Yan , Wang Yi-Yi , Qi Lu-Yue , Chen Chun-Yuan , Liu Zheng-Zhao , Wang Zhen-Xing , Xie Hui
Published: December 2023

Endothelial cells (ECs) and bone marrow stromal cells (BMSCs) play crucial roles in supporting hematopoiesis and hematopoietic regeneration. However, whether ECs are a source of BMSCs remains unclear. Here, we evaluate the contribution of endothelial-to-mesenchymal transition to BMSC generation in postnatal mice. Single-cell RNA sequencing identifies ECs expressing BMSC markers Prrx1 and Lepr; however, this could not be validated using Prrx1-Cre and Lepr-Cre transgenic mice. Additionally, only a minority of BMSCs are marked by EC lineage tracing models using Cdh5-rtTA-tetO-Cre or Tek-CreERT2. Moreover, Cdh5+ BMSCs and Tek+ BMSCs show distinct spatial distributions and characteristic mesenchymal markers, suggestive of their origination from different progenitors rather than CDH5+ TEK+ ECs. Furthermore, myeloablation induced by 5-fluorouracil treatment does not increase Cdh5+ BMSCs. Our findings indicate that ECs hardly convert to BMSCs during homeostasis and myeloablation-induced hematopoietic regeneration, highlighting the importance of using appropriate genetic models and conducting careful data interpretation in studies concerning endothelial-to-mesenchymal transition.
Machine learning for automated experimentation in scanning transmission electron microscopy
Authors: Kalinin Sergei V. , Mukherjee Debangshu , Roccapriore Kevin , Blaiszik Benjamin J. , Ghosh Ayana , Ziatdinov Maxim A. , Al-Najjar Anees , Doty Christina , Akers Sarah , Rao Nageswara S. , Agar Joshua C. , Spurgeon Steven R.
Published: December 2023

Machine learning (ML) has become critical for post-acquisition data analysis in (scanning) transmission electron microscopy, (S)TEM, imaging and spectroscopy. An emerging trend is the transition to real-time analysis and closed-loop microscope operation. The effective use of ML in electron microscopy now requires the development of strategies for microscopy-centric experiment workflow design and optimization. Here, we discuss the associated challenges with the transition to active ML, including sequential data analysis and out-of-distribution drift effects, the requirements for edge operation, local and cloud data storage, and theory in the loop operations. Specifically, we discuss the relative contributions of human scientists and ML agents in the ideation, orchestration, and execution of experimental workflows, as well as the need to develop universal hyper languages that can apply across multiple platforms. These considerations will collectively inform the operationalization of ML in next-generation experimentation.
Large-scale fully printed “Lego Bricks” type wearable sweat sensor for physical activity monitoring
Authors: Ji Wenhui , Liu Huanzhuan , Liu Yadong , Zhang Wei , Zhou Tong , Liu Xinxin , Tao Chao , Dai Jiangxuan , Zha Baoli , Xie Ruijie , Wu Jiansheng , Wu Qiong , Zhang Weina , Li Lin , Huo Fengwei
Published: December 2023

Wearable sweat sensors are becoming increasingly popular for their robust capabilities in non-invasive, dynamic, and continuous real-time monitoring of biological information. Real-time monitoring of large-scale samples is crucial for realizing intelligent health. A major bottleneck for enabling large-scale sweat elucidation is the fabrication of wearable sensors equipped with microfluidic devices and flexible electrodes in a cost-effective, homogeneous performance and rapid large-scale way. Herein, a “Screen+Wax”-printing technique was introduced to prepare these components and construct “Lego Bricks” type wearable sweat sensor sensor to monitor sweat Na+ and K+. Flexible electrode arrays and paper-based microfluidic layers (they act as building blocks) were fabricated on polyethylene terephthalate and paper surfaces, respectively, using screen printing and wax printing. Gold nanoparticles and Na+/K+ ion-selective membranes were modified on the electrode surfaces by electrodeposition and drop coating, respectively. In this work, we highlight the excellent performance of the “Lego Bricks” type wearable sweat sensor in testing the Na+ and K+ imbalance of sweat from different body regions during exercise and, more significantly, to track the physical activity during prolonged exercise under different interventions. Furthermore, the prepared “Lego Bricks” wearable sweat ion electrochemical sensor is demonstrated to be capable of large-scale samples elucidation with outstanding performance and cost-effectiveness, which is expected to deeply integrate sweat monitoring into physical activity, providing an important tool for intelligent health.