bluuebunny/crossref_metadata_2025 huggingface dataset:
Language Teachers' Social Cognition
Authors: Xu Hao
Published: May 2024

This Element aims to elucidate the theories of social cognition and to delineate their implications for the professional development of language teachers in primary and secondary schools. We first explore the concept of social cognition. The three key dimensions, that is, representation of social reality, social cognitive processing, and social mental abilities, of the social cognition theories are further elaborated with examples closely associated with language teaching and teacher development. We continue with more specific issues such as impression, attitude, emotion, and self-efficacy, which arise and develop as language teachers code, store, and retrieve information from social situations. We then discuss how social cognition influences teacher learning and development as observed and promoted within different social realities, and we end this Element with a call for a social-cognitive perspective on understanding language teachers' learning and development situated in diverse and changing contexts in and out of schools.
Onset of absolute instability on a pitching aerofoil
Authors: Kern J.S. , Negi P.S. , Hanifi A. , Henningson D.S.
Published: May 2024

A global transient linear stability analysis of the three-dimensional time-dependent flow around an aerofoil undergoing small-amplitude pitching motion is performed using the optimally time-dependent (OTD) framework. The most salient linear instabilities associated with the instantaneous basic state are computed and tracked over time. The resulting OTD modes reflect the variations in the basic state and can be used as predictors of its spatial and temporal evolution, including the formation of a laminar separation bubble and its gradual spanwise modulation via primary global instability, leading to secondary instability and finally rapid breakdown to turbulence. The study confirms and expands upon earlier stability analyses of the same case based on the local properties of spanwise averaged velocity profiles in the bubble that predicted the onset of absolute instability soon followed by rapid breakdown of the separation bubble. The three-dimensional structure of the most unstable OTD mode is extracted, which compares well with both the locally absolutely unstable mode and the evolution of the basic state itself.
NOTES ON PLUTARCH, ALEXANDER
Authors: Sansone David
Published: May 2024

Notes on the text and interpretation of passages in Plutarch's Life of Alexander.
Hören im Alter: Perspektiven von Mitarbeitenden auf die Hörversorgung in stationären Pflegeeinrichtungen
Authors: Branding Melina , Fleischmann Nina , Wittland Michael
Published: May 2024

Zusammenfassung: Hintergrund: Hörbeeinträchtigungen im Alter sind weit verbreitet. Mehr als jede_r Zweite über 80 Jahre gilt als hochgradig hörbeeinträchtigt, nur wenige in dieser Altersgruppe können noch gut hören. Teilhabe wie auch die pflegerische Versorgung sind durch Hörminderungen wesentlich beeinträchtigt. Ziel: Im Rahmen dieser Erhebung werden die Auswirkungen von Hörbeeinträchtigungen auf den Alltag von Mitarbeitenden und Bewohnenden stationärer Pflegeeinrichtungen untersucht. Zudem wird erfasst, wie Mitarbeitende die Hörversorgung erleben und welche Verbesserungspotenziale gesehen werden. Methode: Dieses Teilvorhaben eines Verbundprojektes umfasst leitfadengestützte Fokusgruppen mit Mitarbeitenden stationärer Pflegeeinrichtungen. Das Sample setzt sich aus sechs Fokusgruppen mit Mitarbeitenden aus Pflege und Alltagsbegleitung zusammen (n = 42). Die erhobenen Daten wurden mittels qualitativer Inhaltsanalyse ausgewertet. Ergebnisse: Hörbeeinträchtigungen erschweren die partizipative Gestaltung des Pflegeprozesses und die Alltagskommunikation. Hörbeeinträchtigte Bewohnende nehmen weniger an Gruppenangeboten teil und ziehen sich zurück. Der Zugang zu Leistungen der Hörversorgung ist für Bewohnende mit teils unüberwindbaren Hürden verbunden. Schlussfolgerungen: Optimierte Versorgungsstrukturen, zielgruppengerechte Hilfsmittel und Schulungsangebote für Mitarbeitende könnten eine nachhaltige Hörversorgung sicherstellen.
Development of Fear of Falling after proximal femoral fracture
Authors: Baltes Marion , Stephan Astrid , Andrich Silke , Meyer Gabriele
Published: May 2024

Abstract: Background: Proximal femoral fracture is common in older people. Beyond a long recovery process and significant permanent functional limitations, older people often experience subsequent Fear of Falling. The phenomenon of Fear of Falling is not fully understood; qualitative research is underrepresented but can provide insights into the experience of those affected. Objectives: We aimed to explore the experiences of Fear of Falling development and to what extent it affects peoples’ life after proximal femoral fracture. Methods: We conducted semi-structured, in-depth interviews with nine older people, aged between 61 and 88, who participated in a prospective observational study. Interview data were analysed through inductive content analysis. Results: Six major themes emerged: The development of Fear of Falling; the effect of FoF and hope for recovery; alternating between moments of fear and security; fear of helplessness and of losing independence; strategies for dealing with Fear of Falling and maintaining independence; need of support by health care professionals. Conclusion: To identify and support older people in coping with Fear of Falling (after proximal femoral fracture), strategies for dealing with Fear of Falling across occupational groups and all healthcare settings should be implemented. Nurses have a key role in this process.
Meta-Analysis of the Effects of Computerized Adaptive Testing on the Motivation and Emotion of Examinees
Authors: Frey Andreas , Liu Tuo , Fink Aron , König Christoph
Published: May 2024

Abstract: Findings on the motivational and emotional effects of computerized adaptive testing (CAT) compared to nonadaptive testing (NCAT) have been heterogeneous and inconclusive so far. This meta-analysis aims to determine the specific effects of CAT better by analyzing several moderator variables related to the test, the examinee, and the test setting. To be included in the meta-analysis, studies needed to be original, correlational, quasi-experimental, or experimental studies in English, German, or Chinese, and they needed to compare CAT to NCAT regarding motivational and/or emotional states. A three-level random-effects model with motivation, negative emotion, and positive emotion as dependent variables was estimated. The risk of bias and publication bias were examined. Twenty-seven studies with a total of 190 effect sizes were analyzed. The overall effect of CAT was not significant for motivation and negative emotion and significant for positive emotion after publication bias correction. The moderator analysis showed significant moderator effects for “test speededness” on motivation and positive emotion, “instantaneous feedback on given responses” and “possibility of response revision” on positive emotion, and “average difficulty of presented items” on negative emotion. For CAT configurations, it is recommended to avoid speededness, present easy items, allow for response revision, and provide feedback.
Global Distribution of EMIC Waves and Its Association to Subauroral Proton Precipitation During the 27 May 2017 Storm: Modeling and Multipoint Observations
Authors: Shreedevi P. R. , Yu Yiqun , Miyoshi Yoshizumi , Tian Xingbin , Zhu Minghui , Jordanova Vania K. , Nakamura Satoko , Jun Chae‐Woo , Kumar Sandeep , Shiokawa Kazuo , Connors Martin , Hori T. , Shoji Masafumi , Shinohara I. , Yokota S. , Kasahara S. , Keika K. , Matsuoka A. , Kadokura Akira , Tsuchiya Fuminori , Kumamoto Atsushi , Kasahara Yoshiya
Published: May 2024

Recent simulation studies using the RAM‐SCB model showed that proton precipitation contributes significantly to the total energy flux deposited into the subauroral ionosphere thereby affecting the magnetosphere‐ionosphere coupling. In this study, we use the BATS‐R‐US + RAM‐SCB model to understand the evolution of ElectroMagnetic Ion Cyclotron (EMIC) waves in the inner magnetosphere, their correspondence to the proton precipitation into the subauroral ionosphere, and to assess the performance of the model in reproducing the EMIC wave‐particle interactions. During the 27 May 2017 storm, Arase and RBSP‐A satellites observed typical signatures of EMIC waves in the inner magnetosphere. Within this interval, Defense Meteorological Satellite Program (DMSP) and National Oceanic and Atmospheric Administration (NOAA)/MetOp satellites observed significant proton precipitation in the dusk‐midnight sector. Simulation results show that H‐ and He‐band EMIC waves are excited within regions of strong temperature anisotropy near the plasmapause. The simulated growth rates of EMIC waves show a similar trend to that of the EMIC wave power observed by the Arase and RBSP‐A satellites, suggesting that the model can reproduce the EMIC wave activity qualitatively. The simulated H‐band waves in the dusk sector are stronger than He‐band waves possibly due to the presence of excess protons in the boundary conditions obtained from the BATS‐R‐US code. The precipitating proton fluxes reproduced by the simulation with EMIC waves are found to agree reasonably well with the DMSP and NOAA/MetOp satellite observations. It is suggested that EMIC wave scattering of ring current ions can account for proton precipitation observed by the DMSP and MetOp satellites during the 27 May 2017 storm.
An Air Quality Model That Is Evolving with the Times
Authors: Huang Min , Carmichael Gregory , Bowman Kevin
Published: May 2024

The pioneering Sulfur Transport and Deposition Model, initially designed to simulate atmospheric sulfur, continues to find new applications and value in environmental science and policymaking.
Brittle Damage Processes Around Equi‐Dimensional Pores or Cavities in Rocks: Implications for the Brittle‐Ductile Transition
Authors: Bernabé Yves , Peč Matěj
Published: May 2024

In the Earth's upper crust, rocks deform mostly by means of brittle fracturing processes. At the micro‐scale these processes involve the formation and growth of microcracks in the vicinity of defects such as open fissures, pores and other cavities. Large defects can produce strong enough perturbations of the stress field to activate and/or intensify brittle damage around them. Here we considered the ideal cases of smooth cylindrical and spherical pores inside an infinite solid body subjected to remote triaxial compressive stresses (i.e., the intermediate and minimum principal stresses are assumed equal). We first established the resulting local stress field around one of those large pores and then verified whether certain brittle damage processes could be activated in these conditions. We mainly considered the formation of tensile microcracks and micro shear bands. The former requires the presence of tensile stresses in some regions around the pore, while the latter needs sufficiently large shear stresses on pre‐existing optimally inclined microcracks to overcome their frictional resistance to sliding. We find that shear driven deformation remains localized in the vicinity of the pore. On the other hand, dilatational, tensile cracks can propagate large distances away from the pore but cannot form at and above some threshold ratio of the least to the largest principal stresses. Faulting associated with interacting tensile cracks is therefore suppressed with increasing depth. Our analysis leads to conclusions generally consistent with published experimental observations and provides some clues to discuss the physical cause of the brittle‐ductile transition in rocks.
Frequency of personal care product use among reproductive-aged Black individuals and associations with socio-demographic characteristics
Authors: Taylor Kyla W. , Co Caroll A. , Gaston Symielle A. , Jackson Chandra L. , Harmon Quaker , Baird Donna D.
Published: May 2024

Background

Compared to White women, Black women in the United States are more likely to use personal care products (PCPs) with higher concentrations of endocrine-disrupting chemicals (EDCs) and harsher chemical formulations. This may contribute to differential health outcomes in Black women such as increased risk of breast cancer, cardiometabolic outcomes, adverse birth outcomes, and uterine fibroids.

Objective

Classify distinct PCP use patterns across multiple types of products and examine how patterns vary by socio-demographic characteristics.

Methods

The Study of Environment, Lifestyle and Fibroids is a cohort study of reproductive-aged Black individuals living around Detroit, Michigan. Using self-reported data on frequency of PCP collected between 2013–2018, we employed latent class analysis to identify distinct groups of participants with similar PCP use. Socio-demographic characteristics were compared across latent classes.

Results

Among 1562 participants, we identified 6 latent classes: Lower Overall; Higher Nailcare; Higher Skincare; Moderate Overall; Higher Makeup/Haircare/Skincare; Higher Overall. Makeup and nailcare usage were the most predictive for classifying participants into groups. Participants in classes with less frequent use of all PCPs and those with only high use of nailcare products, were more likely to report lower socio-economic status (SES), be current smokers, have a body mass index of ≥35 kg/m2, and have ≥3 births. In comparison, participants in classes with average and more frequent use of PCPs were more likely to report higher SES, be non-smokers, be nulliparous, and have ever used oral contraceptives.

Impact statement

This study is one of the first detailed assessments of PCP usage among a large cohort of young adult Black women that considers multiple product categories including makeup, hair, skin, nail, and vaginal products. Latent class analysis was used to capture complex patterns of PCP use and identify distinct groups of individuals with similar product use. Although the latent classes are specific to this study population, the identified socio-demographic characteristics or behaviors associated with latent classes may inform targeted and impactful exposure reduction strategies in similar populations.
Natural evidence of coronaviral 2′-O-methyltransferase activity affecting viral pathogenesis via improved substrate RNA binding
Authors: Deng Jikai , Yang Shimin , Li Yingjian , Tan Xue , Liu Jiejie , Yu Yanying , Ding Qiang , Fan Chengpeng , Wang Hongyun , Chen Xianyin , Liu Qianyun , Guo Xiao , Gong Feiyu , Zhou Li , Chen Yu
Published: May 2024

Previous studies through targeted mutagenesis of K-D-K-E motif have demonstrated that 2′-O-MTase activity is essential for efficient viral replication and immune evasion. However, the K-D-K-E catalytic motif of 2′-O-MTase is highly conserved across numerous viruses, including flaviviruses, vaccinia viruses, coronaviruses, and extends even to mammals. Here, we observed a stronger 2′-O-MTase activity in SARS-CoV-2 compared to SARS-CoV, despite the presence of a consistently active catalytic center. We further identified critical residues (Leu-36, Asn-138 and Ile-153) which served as determinants of discrepancy in 2′-O-MTase activity between SARS-CoV-2 and SARS-CoV. These residues significantly enhanced the RNA binding affinity of 2′-O-MTase and boosted its versatility toward RNA substrates. Of interest, a triple substitution (Leu36 → Ile36, Asn138 → His138, Ile153 → Leu153, from SARS-CoV-2 to SARS-CoV) within nsp16 resulted in a proportional reduction in viral 2′-O-methylation and impaired viral replication. Furthermore, it led to a significant upregulation of type I interferon (IFN-I) and proinflammatory cytokines both in vitro and vivo, relying on the cooperative sensing of melanoma differentiation-associated protein 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). In conclusion, our findings demonstrated that alterations in residues other than K-D-K-E of 2′-O-MTase may affect viral replication and subsequently influence pathogenesis. Monitoring changes in nsp16 residues is crucial as it may aid in identifying and assessing future alteration in viral pathogenicity resulting from natural mutations occurring in nsp16.
Network analysis of comorbid aggressive behavior and testosterone among bipolar disorder patients: a cross-sectional study
Authors: Liu Yi , Cai Hong , Han Tian , Wang Yi-Fan , Li Juan , Xie Xiao-meng , Ji Xiao
Published: May 2024

Testosterone has complex effects on psychological traits and behavior; it is associated with social dominance and competition and is a potential human sex pheromone. This study aimed to investigate the associations between testosterone levels, aggressive behavior, and manic symptoms using a network analysis among bipolar disorder (BD) patients in psychiatric emergency departments (PED). Data from January 2021 and March 2022 BD patients in PED were analyzed. Manic symptoms were assessed using the Young Mania Rating Scale (YMRS). Aggression was assessed with subscale of the PANSS scale (PANSS-AG). The undirected network structures of testosterone levels, aggressive behavior, and manic symptoms were estimated, and centrality and bridge centrality indices were examined. Network stability was examined using the case-dropping procedure. The Network Comparison Test (NCT) was conducted to evaluate whether network characteristics differed by gender. We recruited a total of 898 BD patients, with the mean YMRS score as 13.30 ± 9.58. The prevalence of level II aggression was 35.6% (95%CI = 32.5%–38.7%), level III aggression was 29.5% (95%CI = 26.3%–32.6%), and level VI aggression was 7.0% (95%CI = 5.4%–8.8%). The male participants had a mean testosterone level of 391.71 (Standard Deviation (SD):223.39) compared to 36.90 (SD:30.50) for female participants in the whole sample. Through network analysis, “Increased motor activity-energy” emerged as the central symptom, with the highest centrality expected influence, followed by “Emotional Instability” and “Disruptive/aggression behavior”. Notably, “Emotional Instability” appeared to be the bridge symptom linking manic symptoms to aggressive behavior. Within the flow network model, “Speech rate and amount” exhibited the strongest positive correlation with testosterone levels, followed closely by “Disruptive/aggression behavior”. The constructed network model demonstrated robust stability, with gender showing no significant impact on the structure. In this study, “Increased motor activity-energy” stood out as the most influential symptom, and “Speech rate and amount” acted as the main bridge symptom linking testosterone levels, aggressive behavior, and manic symptoms. Targeting the central and bridge symptoms may improve the outcomes of aggression interventions implemented among BD patients in psychiatric emergency care.
GRP94 is an IGF-1R chaperone and regulates beta cell death in diabetes
Authors: Kim Do-Sung , Song Lili , Gou Wenyu , Kim Jisun , Liu Bei , Wei Hua , Muise-Helmericks Robin C. , Li Zihai , Wang Hongjun
Published: May 2024

High workload-induced cellular stress can cause pancreatic islet β cell death and dysfunction, or β cell failure, a hallmark of type 2 diabetes mellitus. Thus, activation of molecular chaperones and other stress-response genes prevents β cell failure. To this end, we have shown that deletion of the glucose-regulated protein 94 (GRP94) in Pdx1+ pancreatic progenitor cells led to pancreas hypoplasia and reduced β cell mass during pancreas development in mice. Here, we show that GRP94 was involved in β cell adaption and compensation (or failure) in islets from leptin receptor-deficient (db/db) mice in an age-dependent manner. GRP94-deficient cells were more susceptible to cell death induced by various diabetogenic stress conditions. We also identified a new client of GRP94, insulin-like growth factor-1 receptor (IGF-1R), a critical factor for β cell survival and function that may mediate the effect of GRP94 in the pathogenesis of diabetes. This study has identified essential functions of GRP94 in β cell failure related to diabetes.
Combined inhibition of class 1-PI3K-alpha and delta isoforms causes senolysis by inducing p21WAF1/CIP1 proteasomal degradation in senescent cells
Authors: Neuwahl Judith , Neumann Chantal A. , Fitz Annika C. , Biermann Anica D. , Magel Maja , Friedrich Annabelle , Sellin Lorenz , Stork Björn , Piekorz Roland P. , Proksch Peter , Budach Wilfried , Jänicke Reiner U. , Sohn Dennis
Published: May 2024

The targeted elimination of radio- or chemotherapy-induced senescent cells by so-called senolytic substances represents a promising approach to reduce tumor relapse as well as therapeutic side effects such as fibrosis. We screened an in-house library of 178 substances derived from marine sponges, endophytic fungi, and higher plants, and determined their senolytic activities towards DNA damage-induced senescent HCT116 colon carcinoma cells. The Pan-PI3K-inhibitor wortmannin and its clinical derivative, PX-866, were identified to act as senolytics. PX-866 potently induced apoptotic cell death in senescent HCT116, MCF-7 mammary carcinoma, and A549 lung carcinoma cells, independently of whether senescence was induced by ionizing radiation or by chemotherapeutics, but not in proliferating cells. Other Pan-PI3K inhibitors, such as the FDA-approved drug BAY80-6946 (Copanlisib, Aliqopa®), also efficiently and specifically eliminated senescent cells. Interestingly, only the simultaneous inhibition of both PI3K class I alpha (with BYL-719 (Alpelisib, Piqray®)) and delta (with CAL-101 (Idelalisib, Zydelig®)) isoforms was sufficient to induce senolysis, whereas single application of these inhibitors had no effect. On the molecular level, inhibition of PI3Ks resulted in an increased proteasomal degradation of the CDK inhibitor p21WAF1/CIP1 in all tumor cell lines analyzed. This led to a timely induction of apoptosis in senescent tumor cells. Taken together, the senolytic properties of PI3K-inhibitors reveal a novel dimension of these promising compounds, which holds particular potential when employed alongside DNA damaging agents in combination tumor therapies.
Pancreatic beta-cell IL-22 receptor deficiency induces age-dependent dysregulation of insulin biosynthesis and systemic glucose homeostasis
Authors: Sajiir Haressh , Wong Kuan Yau , Müller Alexandra , Keshvari Sahar , Burr Lucy , Aiello Elena , Mezza Teresa , Giaccari Andrea , Sebastiani Guido , Dotta Francesco , Ramm Grant A. , Macdonald Graeme A. , McGuckin Michael A. , Prins Johannes B. , Hasnain Sumaira Z.
Published: May 2024

The IL-22RA1 receptor is highly expressed in the pancreas, and exogenous IL-22 has been shown to reduce endoplasmic reticulum and oxidative stress in human pancreatic islets and promote secretion of high-quality insulin from beta-cells. However, the endogenous role of IL-22RA1 signaling on these cells remains unclear. Here, we show that antibody neutralisation of IL-22RA1 in cultured human islets leads to impaired insulin quality and increased cellular stress. Through the generation of mice lacking IL-22ra1 specifically on pancreatic alpha- or beta-cells, we demonstrate that ablation of murine beta-cell IL-22ra1 leads to similar decreases in insulin secretion, quality and islet regeneration, whilst increasing islet cellular stress, inflammation and MHC II expression. These changes in insulin secretion led to impaired glucose tolerance, a finding more pronounced in female animals compared to males. Our findings attribute a regulatory role for endogenous pancreatic beta-cell IL-22ra1 in insulin secretion, islet regeneration, inflammation/cellular stress and appropriate systemic metabolic regulation.
An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm
Authors: Grau-Bové Xavier , Subirana Lucie , Meister Lydvina , Soubigou Anaël , Neto Ana , Elek Anamaria , Naranjo Silvia , Fornas Oscar , Gomez-Skarmeta Jose Luis , Tena Juan J. , Irimia Manuel , Bertrand Stéphanie , Sebé-Pedrós Arnau , Escriva Hector
Published: May 2024

The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis.
Multivariate extremes in lakes
Authors: Woolway R. Iestyn , Tong Yan , Feng Lian , Zhao Gang , Dinh Dieu Anh , Shi Haoran , Zhang Yunlin , Shi Kun
Published: May 2024

Extreme within-lake conditions have the potential to exert detrimental effects on lakes. Here we use satellite observations to investigate how the occurrence of multiple types of extremes, notably algal blooms, lake heatwaves, and low lake levels, have varied in 2724 lakes since the 1980s. Our study, which focuses on bloom-affected lakes, suggests that 75% of studied lakes have experienced a concurrent increase in at least two of the extremes considered (27% defined as having a notable increase), with 25% experiencing an increase in frequency of all three extremes (5% had a notable increase). The greatest increases in the frequency of these extremes were found in regions that have experienced increases in agricultural fertilizer use, lake warming, and a decline in water availability. As extremes in lakes become more common, understanding their impacts must be a primary focus of future studies and they must be carefully considered in future risk assessments.
Data-driven optimization and machine learning analysis of compatible molecules for halide perovskite material
Authors: Wang Shaojun , Huang Yiru , Hu Wenguang , Zhang Lei
Published: May 2024

Optoelectronic stability of halide perovskite material in hostile conditions such as water is rather limited, preventing them from further industrial deployment. Here, we optimize and perform machine learning analysis on CH3NH3PbI3 materials with additives, solvents and post-treatment molecules using combined experimental and data-driven methods. A champion system consisting of a compatible tertiary molecular combination ‘calcein+PbBr2 + DMSO’ active at diverse surfaces is identified, delivering a large aqueous photoelectrochemical (PEC) photocurrent of 10-5 A/cm2 and an improved aqueous stability of 92.5%. Subsequently, machine interpretation is provided to decouple the multi-molecule contributions with the assistance of genetic programming (GP) and extra-trees (ET) machine learning models, highlighting the intricate molecular features for the target outputs. The post-hoc density functional theory (DFT) calculation suggests the presence of multiple hydrogen bond and anion··π surface interactions to stabilize the interfacial structures. The present ‘PEC + GP + ET + DFT’ approach is suggested to be an effective approach to design and comprehensively evaluate molecule-modified materials.
Analysis of cell free DNA to predict outcome to bevacizumab therapy in colorectal cancer patients
Authors: Venken Tom , Miller Ian S. , Arijs Ingrid , Thomas Valentina , Barat Ana , Betge Johannes , Zhan Tianzuo , Gaiser Timo , Ebert Matthias P. , O’Farrell Alice C. , Prehn Jochen , Klinger Rut , O’Connor Darran P. , Moulton Brian , Murphy Verena , Serna Garazi , Nuciforo Paolo G. , McDermott Ray , Bird Brian , Leonard Gregory , Grogan Liam , Horgan Anne , Schulte Nadine , Moehler Markus , Lambrechts Diether , Byrne Annette T.
Published: May 2024

To predict outcome to combination bevacizumab (BVZ) therapy, we employed cell-free DNA (cfDNA) to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients. Low-coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples, collected from 74 mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444), and analysed for CIN and NFs. A validation cohort of plasma samples from the University Medical Center Mannheim (UMM) was similarly profiled. 61 AC-ANGIOPREDICT plasma samples collected before and following BVZ treatment were selected for targeted methylation sequencing. Using cfDNA CIN profiles, AC-ANGIOPREDICT samples were subtyped with 92.3% accuracy into low and high CIN clusters, with good concordance observed between matched plasma and tumor. Improved survival was observed in CIN-high patients. Plasma-based CIN clustering was validated in the UMM cohort. Methylation profiling identified differences in CIN-low vs. CIN high (AUC = 0.87). Moreover, significant methylation score decreases following BVZ was associated with improved outcome (p = 0.013). Analysis of CIN, NFs and methylation profiles from cfDNA in plasma samples facilitates stratification into CIN clusters which inform patient response to treatment.
The art of modeling gene regulatory circuits
Authors: Gómez-Schiavon Mariana , Montejano-Montelongo Isabel , Orozco-Ruiz F. Sophia , Sotomayor-Vivas Cristina
Published: May 2024

The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame and develop our understanding of their properties. Here, we present some fundamental considerations to develop and analyze a model of a gene regulatory circuit of interest, either representing a natural, synthetic, or theoretical system. A mathematical model allows us to effectively evaluate the logical implications of our hypotheses. Using our models to systematically perform in silico experiments, we can then propose specific follow-up assessments of the biological system as well as to reformulate the original assumptions, enriching both our knowledge and our understanding of the system. We want to invite the community working on different aspects of gene regulatory circuits to explore the power and benefits of mathematical modeling in their system.
Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder
Authors: Nieto César , Vargas-García César Augusto , Pedraza Juan Manuel , Singh Abhyudai
Published: May 2024

Under ideal conditions, Escherichia coli cells divide after adding a fixed cell size, a strategy known as the adder. This concept applies to various microbes and is often explained as the division that occurs after a certain number of stages, associated with the accumulation of precursor proteins at a rate proportional to cell size. However, under poor media conditions, E. coli cells exhibit a different size regulation. They are smaller and follow a sizer-like division strategy where the added size is inversely proportional to the size at birth. We explore three potential causes for this deviation: degradation of the precursor protein and two models where the propensity for accumulation depends on the cell size: a nonlinear accumulation rate, and accumulation starting at a threshold size termed the commitment size. These models fit the mean trends but predict different distributions given the birth size. To quantify the precision of the models to explain the data, we used the Akaike information criterion and compared them to open datasets of slow-growing E. coli cells in different media. We found that none of the models alone can consistently explain the data. However, the degradation model better explains the division strategy when cells are larger, whereas size-related models (power-law and commitment size) account for smaller cells. Our methodology proposes a data-based method in which different mechanisms can be tested systematically.
Shift away from Nile incision at Luxor ~4,000 years ago impacted ancient Egyptian landscapes
Authors: Peeters Jan , Graham Angus , Toonen Willem H. J. , Pennington Benjamin T. , Durcan Julie A. , Winkels Timotheus G. , Barker Dominic S. , Masson-Berghoff Aurélia , Adamson Kathryn , Emery Virginia L. , Strutt Kristian D. , Millet Marie , Sollars Luke H. , Ghazala Hosni H.
Published: May 2024

Although the Nile is one of the largest rivers in the world and played a central role in ancient Egyptian life, little is known about its response to climatic change during the Holocene. Here we present a framework for the evolution of the Egyptian Nile, demonstrating how climatic and environmental changes have shaped the landscape of the Egyptian Nile Valley over the past 11,500 years, including the civilization of ancient Egypt (~5,000 to 2,000 years ago). Using data from over 80 sediment cores drilled in a transect spanning the Nile Valley near Luxor, pinned in time by 48 optically stimulated luminescence ages, we reconstruct the dynamics of the Nile River during the Holocene in the vicinity of UNESCO World Heritage sites such as Karnak and Luxor temples. According to our reconstruction, valley incision occurred from the start of the record until approximately 4,000 years ago and then rapidly shifted to massive floodplain aggradation. We argue that this relatively abrupt change in the riverine landscape near Luxor from the Middle to Late Holocene was linked to a shift towards a drier regional hydroclimate around this time. Such a dramatic change in river sediment dynamics could have had local agro-economic consequences.
The chromosome-level genome assembly of the dwarfing apple interstock Malus hybrid ‘SH6’
Authors: Li Jinrong , Cai Huacheng , Peng Haixu , Deng Yulin , Zhou Shijie , Tian Ji , Zhang Jie , Hu Yujing , Qin Xiaoxiao , Yao Yuncong , Zheng Yi , Wang Sen
Published: May 2024

Malus hybrid ‘SH6’ (M. honanensis × M. domestica)is a commonly used apple interstock in China, known for its excellent dwarfing characteristics and cold tolerance. In this study, a combined strategy utilizing PacBio HiFi, Hi-C and parental resequencing data were employed to assemble two haploid genomes for ‘SH6’. After chromosome anchoring, the final hapH genome size was 596.63 Mb, with a contig N50 of 34.38 Mb. The hapR genome was 649.37 Mb, with a contig N50 of 36.84 Mb. Further analysis predicted that repeated sequences made up 59.69% and 62.52% of the entire genome, respectively. Gene annotations revealed 45,435 genes for hapH and 48,261 genes for hapR. Combined with genomic synteny we suggest that the hapR genome originates from its maternal parent M. domestica cv. Ralls Janet, while the hapH genome comes from its paternal parent, M. honanensis. The assembled genome significantly contributes to the discovery of genes associated with apple dwarfing and the molecular mechanisms governing them.
A multimodal machine learning model for predicting dementia conversion in Alzheimer’s disease
Authors: Lee Min-Woo , Kim Hye Weon , Choe Yeong Sim , Yang Hyeon Sik , Lee Jiyeon , Lee Hyunji , Yong Jung Hyeon , Kim Donghyeon , Lee Minho , Kang Dong Woo , Jeon So Yeon , Son Sang Joon , Lee Young-Min , Kim Hyug-Gi , Kim Regina E. Y. , Lim Hyun Kook
Published: May 2024

Alzheimer’s disease (AD) accounts for 60–70% of the population with dementia. Mild cognitive impairment (MCI) is a diagnostic entity defined as an intermediate stage between subjective cognitive decline and dementia, and about 10–15% of people annually convert to AD. We aimed to investigate the most robust model and modality combination by combining multi-modality image features based on demographic characteristics in six machine learning models. A total of 196 subjects were enrolled from four hospitals and the Alzheimer’s Disease Neuroimaging Initiative dataset. During the four-year follow-up period, 47 (24%) patients progressed from MCI to AD. Volumes of the regions of interest, white matter hyperintensity, and regional Standardized Uptake Value Ratio (SUVR) were analyzed using T1, T2-weighted-Fluid-Attenuated Inversion Recovery (T2-FLAIR) MRIs, and amyloid PET (αPET), along with automatically provided hippocampal occupancy scores (HOC) and Fazekas scales. As a result of testing the robustness of the model, the GBM model was the most stable, and in modality combination, model performance was further improved in the absence of T2-FLAIR image features. Our study predicts the probability of AD conversion in MCI patients, which is expected to be useful information for clinician’s early diagnosis and treatment plan design.
A recurrent Gaussian quantum network for online processing of quantum time series
Authors: De Prins Robbe , Van der Sande Guy , Bienstman Peter
Published: May 2024

Over the last decade, researchers have studied the interplay between quantum computing and classical machine learning algorithms. However, measurements often disturb or destroy quantum states, requiring multiple repetitions of data processing to estimate observable values. In particular, this prevents online (real-time, single-shot) processing of temporal data as measurements are commonly performed during intermediate stages. Recently, it was proposed to sidestep this issue by focusing on tasks with quantum output, eliminating the need for detectors. Inspired by reservoir computers, a model was proposed where only a subset of the internal parameters are trained while keeping the others fixed at random values. Here, we also process quantum time series, but we do so using a Recurrent Gaussian Quantum Network (RGQN) of which all internal interactions can be trained. As expected, this increased flexibility yields higher performance in benchmark tasks. Building on this, we show that the RGQN can tackle two quantum communication tasks, while also removing some hardware restrictions of the currently available methods. First, our approach is more resource efficient to enhance the transmission rate of quantum channels that experience certain memory effects. Second, it can counteract similar memory effects if they are unwanted, a task that could previously only be solved when redundantly encoded input signals could be provided. Finally, we run a small-scale version of the last task on Xanadu’s photonic processor Borealis.
Projected patterns of land uses in Africa under a warming climate
Authors: Yahaya Ibrahim , Xu Runhong , Zhou Jian , Jiang Shan , Su Buda , Huang Jinlong , Cheng Jing , Dong Zhibo , Jiang Tong
Published: May 2024

Land-use change is a direct driver of biodiversity loss, projection and future land use change often consider a topical issue in response to climate change. Yet few studies have projected land-use changes over Africa, owing to large uncertainties. We project changes in land-use and land-use transfer under future climate for three specified time periods: 2021–2040, 2041–2060, and 2081–2100, and compares the performance of various scenarios using observational land-use data for the year 2020 and projected land-use under seven Shared Socioeconomic Pathways Scenarios (SSP): SSP1-1.9, SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0 and SSP5-8.5 from 2015 to 2100 in Africa. The observational land-use types for the year 2020 depict a change and show linear relationship between observational and simulated land-use with a strong correlation of 0.89 (P < 0.01) over Africa. Relative to the reference period (1995–2014), for (2021–2040), (2041–2060), (2081–2100), barren land and forest land are projected to decrease by an average of (6%, 11%, 16%), (9%, 19%, 38%) respectively, while, crop land, grassland and urban land area are projected to increase by (36%, 58%, and 105%), (4%, 7% and 11%), and (139%, 275% and 450%) respectively. Results show a substantial variations of land use transfer between scenarios with major from barren land to crop land, for the whole future period (2015–2100). Although SSP4-3.4 project the least transfer. Population and GDP show a relationship with cropland and barren land. The greatest conversion of barren land to crop land could endanger biodiversity and have negative effects on how well the African continent's ecosystem’s function.
Distribution and pathogen prevalence of field-collected ticks from south-western Korea: a study from 2019 to 2022
Authors: Kim Kwang gon , Hwang Da jeong , Park Jung wook , Ryu Mi geum , Kim Yujin , Yang So-Jin , Lee Ji-Eun , Lee Gi seong , Lee Ju Hye , Park Ji sun , Seo Jung mi , Kim Sun-hee
Published: May 2024

Hard ticks are known vectors of various pathogens, including the severe fever with thrombocytopenia syndrome virus, Rickettsia spp., Coxiella burnetii, Borrelia spp., Anaplasma phagocytophilum, and Ehrlichia spp. This study aims to investigate the distribution and prevalence of tick-borne pathogens in southwestern Korea from 2019 to 2022. A total of 13,280 ticks were collected during the study period, with H. longicornis accounting for 86.1% of the collected ticks. H. flava, I. nipponensis and A. testudinarium comprised 9.4%, 3.6%, and 0.8% of the ticks, respectively. Among 983 pools tested, Rickettsia spp. (216 pools, 1.6% MIR) were the most prevalent pathogens across all tick species, with R. japonica and R. monacensis frequently detected in I. nipponensis and Haemaphysalis spp., respectively. Borrelia spp. (28 pools, 0.2% MIR) were predominantly detected in I. nipponensis (27 pools, 13.8% MIR, P < 0.001). Co-infections, mainly involving Rickettsia monacensis and Borrelia afzelii, were detected in I. nipponensis. Notably, this study identified R. monacensis for the first time in A. testudinarium in South Korea. These findings offer valuable insights into the tick population and associated pathogens in the region, underscoring the importance of tick-borne disease surveillance and prevention measures.
The development of an extended Weibull model with applications to medicine, industry and actuarial sciences
Authors: Imran Muhammad , Alsadat Najwan , Tahir M. H. , Jamal Farrukh , Elgarhy Mohammed , Ahmad Hijaz , Johannssen Arne
Published: May 2024

This paper delves into the theoretical and practical exploration of the complementary Bell Weibull (CBellW) model, which serves as an analogous counterpart to the complementary Poisson Weibull model. The study encompasses a comprehensive examination of various statistical properties of the CBellW model. Real data applications are carried out in three different fields, namely the medical, industrial and actuarial fields, to show the practical versatility of the CBellW model. For the medical data segment, the study utilizes four data sets, including information on daily confirmed COVID-19 cases and cancer data. Additionally, a Group Acceptance Sampling Plan (GASP) is designed by using the median as quality parameter. Furthermore, some actuarial risk measures for the CBellW model are obtained along with a numerical illustration of the Value at Risk and the Expected Shortfall. The research is substantiated by a comprehensive numerical analysis, model comparisons, and graphical illustrations that complement the theoretical foundation.
Cerebrovascular disease emerges with age and Alzheimer’s disease in adults with Down syndrome
Authors: Lao Patrick , Edwards Natalie , Flores-Aguilar Lisi , Alshikho Mohamad , Rizvi Batool , Tudorascu Dana , Rosas H. Diana , Yassa Michael , Christian Bradley T. , Mapstone Mark , Handen Benjamin , Zimmerman Molly E. , Gutierrez Jose , Wilcock Donna , Head Elizabeth , Brickman Adam M.
Published: May 2024

Adults with Down syndrome have a genetic form of Alzheimer’s disease (AD) and evidence of cerebrovascular disease across the AD continuum, despite few systemic vascular risk factors. The onset and progression of AD in Down syndrome is highly age-dependent, but it is unknown at what age cerebrovascular disease emerges and what factors influence its severity. In the Alzheimer’s Biomarker Consortium-Down Syndrome study (ABC-DS; n = 242; age = 25–72), we estimated the age inflection point at which MRI-based white matter hyperintensities (WMH), enlarged perivascular spaces (PVS), microbleeds, and infarcts emerge in relation to demographic data, risk factors, amyloid and tau, and AD diagnosis. Enlarged PVS and infarcts appear to develop in the early 30s, while microbleeds, WMH, amyloid, and tau emerge in the mid to late 30s. Age-residualized WMH were higher in women, in individuals with dementia, and with lower body mass index. Participants with hypertension and APOE-ε4 had higher age-residualized PVS and microbleeds, respectively. Lifespan trajectories demonstrate a dramatic cerebrovascular profile in adults with Down syndrome that appears to evolve developmentally in parallel with AD pathophysiology approximately two decades prior to dementia symptoms.
Identity and inequality misperceptions, demographic determinants and efficacy of corrective measures
Authors: Arin K. Peren , Mazrekaj Deni , Thum Marcel , Lacomba Juan A. , Lagos Francisco
Published: May 2024

By conducting two waves of large-scale surveys in the United Kingdom and Germany, we investigate the determinants of identity and inequality misperceptions. We first show that people substantially overestimate the share of immigrants, Muslims, people under the poverty line, and the income share of the richest. Moreover, women, lower-income, and lower-educated respondents generally have higher misperceptions. Only income share misperceptions are associated more with people who place themselves on the left of the political spectrum. In contrast, the other three misperceptions are more prevalent among those who place themselves to the right. We then attempt to correct misperceptions by conducting a classic controlled experiment. Specifically, we randomly assign respondents into a treatment group informed about their initial misperceptions and a control group left uninformed. Our results indicate that information treatments had some corrective effects on misperceptions in Germany but were ineffective in the United Kingdom. Moreover, information treatments in Germany were more effective for men, centrists, and highly educated respondents. There is also no evidence of spill-over effects: correcting one misperception does not have corrective effects for the other misperceptions.
Molecular evidence for a new endemic species of Acartia (Copepoda, Calanoida) from the Southeast Pacific coast
Authors: Mesas Andrés , Aguilera Víctor M. , González Carolina E. , Giesecke Ricardo , Escribano Rubén , Vargas Cristian A.
Published: May 2024

The loss of biodiversity in marine populations is one of the consequences of the increased events of extreme environmental conditions in the oceans, which can condition the persistence of populations to future scenarios of climate change. Therefore, it is extremely necessary to explore and monitor the genetic diversity of natural populations. In the Southeast Pacific Ocean (SEPO), specifically on the coast of Chile, the presence of the copepod Acartia tonsa has been indicated solely using morphological evidence, due to the absence of genetic information. In the present work, the genetic diversity, population structure and phylogenetic position within the genus Acartia, of populations identified morphologically as A. tonsa, was evaluated by amplification of the mitochondrial cytochrome c oxidase subunit I and nuclear marker 18 s. Our results showed that the populations identified as A. tonsa correspond to a new monophyletic group endemic to SEPO (GMYC = 1.00; PTP = 0.95). The populations showed moderate to high genetic diversity with an incipient structuring between populations and biogeographic zones. Our results suggest that despite the homogenizing effect of the Humboldt Current, isolation by distance and contrasting environmental conditions at different geographic scales have an important influence on the genetic diversity of zooplankton in the SEPO region.