bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferon-γ couples CD8+ T cell avidity and differentiation during infection
Authors: Uhl Lion F. K. , Cai Han , Oram Sophia L. , Mahale Jagdish N. , MacLean Andrew J. , Mazet Julie M. , Piccirilli Theo , He Alexander J. , Lau Doreen , Elliott Tim , Gerard Audrey 
Published: October 2023

AbstractEffective responses to intracellular pathogens are characterized by T cell clones with a broad affinity range for their cognate peptide and diverse functional phenotypes. How T cell clones are selected throughout the response to retain a breadth of avidities remains unclear. Here, we demonstrate that direct sensing of the cytokine IFN-γ by CD8+ T cells coordinates avidity and differentiation during infection. IFN-γ promotes the expansion of low-avidity T cells, allowing them to overcome the selective advantage of high-avidity T cells, whilst reinforcing high-avidity T cell entry into the memory pool, thus reducing the average avidity of the primary response and increasing that of the memory response. IFN-γ in this context is mainly provided by virtual memory T cells, an antigen-inexperienced subset with memory features. Overall, we propose that IFN-γ and virtual memory T cells fulfil a critical immunoregulatory role by enabling the coordination of T cell avidity and fate.
Neuro-inspired optical sensor array for high-accuracy static image recognition and dynamic trace extraction
Authors: Huang Pei-Yu , Jiang Bi-Yi , Chen Hong-Ji , Xu Jia-Yi , Wang Kang , Zhu Cheng-Yi , Hu Xin-Yan , Li Dong , Zhen Liang , Zhou Fei-Chi , Qin Jing-Kai , Xu Cheng-Yan 
Published: October 2023

AbstractNeuro-inspired vision systems hold great promise to address the growing demands of mass data processing for edge computing, a distributed framework that brings computation and data storage closer to the sources of data. In addition to the capability of static image sensing and processing, the hardware implementation of a neuro-inspired vision system also requires the fulfilment of detecting and recognizing moving targets. Here, we demonstrated a neuro-inspired optical sensor based on two-dimensional NbS2/MoS2 hybrid films, which featured remarkable photo-induced conductance plasticity and low electrical energy consumption. A neuro-inspired optical sensor array with 10 × 10 NbS2/MoS2 phototransistors enabled highly integrated functions of sensing, memory, and contrast enhancement capabilities for static images, which benefits convolutional neural network (CNN) with a high image recognition accuracy. More importantly, in-sensor trajectory registration of moving light spots was experimentally implemented such that the post-processing could yield a high restoration accuracy. Our neuro-inspired optical sensor array could provide a fascinating platform for the implementation of high-performance artificial vision systems.
Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir
Authors: Prévost Jérémie , Chen Yaozong , Zhou Fei , Tolbert William D. , Gasser Romain , Medjahed Halima , Nayrac Manon , Nguyen Dung N. , Gottumukkala Suneetha , Hessell Ann J. , Rao Venigalla B. , Pozharski Edwin , Huang Rick K. , Matthies Doreen , Finzi Andrés , Pazgier Marzena 
Published: October 2023

AbstractThe HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this, temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveals that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad antiviral activity.
Staphylococcus aureus sacculus mediates activities of M23 hydrolases
Authors: Razew Alicja , Laguri Cedric , Vallet Alicia , Bougault Catherine , Kaus-Drobek Magdalena , Sabala Izabela , Simorre Jean-Pierre 
Published: October 2023

AbstractPeptidoglycan, a gigadalton polymer, functions as the scaffold for bacterial cell walls and provides cell integrity. Peptidoglycan is remodelled by a large and diverse group of peptidoglycan hydrolases, which control bacterial cell growth and division. Over the years, many studies have focused on these enzymes, but knowledge on their action within peptidoglycan mesh from a molecular basis is scarce. Here, we provide structural insights into the interaction between short peptidoglycan fragments and the entire sacculus with two evolutionarily related peptidases of the M23 family, lysostaphin and LytM. Through nuclear magnetic resonance, mass spectrometry, information-driven modelling, site-directed mutagenesis and biochemical approaches, we propose a model in which peptidoglycan cross-linking affects the activity, selectivity and specificity of these two structurally related enzymes differently.
A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint
Authors: Sánchez Humberto , Liu Zhaowei , van Veen Edo , van Laar Theo , Diffley John F. X. , Dekker Nynke H. 
Published: October 2023

AbstractChromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.
Activation of coagulation and proinflammatory pathways in thrombosis with thrombocytopenia syndrome and following COVID-19 vaccination
Authors: Aid Malika , Stephenson Kathryn E. , Collier Ai-ris Y. , Nkolola Joseph P. , Michael James V. , McKenzie Steven E. , Barouch Dan H. 
Published: October 2023

AbstractThrombosis with thrombocytopenia syndrome (TTS) is a rare but potentially severe adverse event following immunization with adenovirus vector-based COVID-19 vaccines such as Ad26.COV2.S (Janssen) and ChAdOx1 (AstraZeneca). However, no case of TTS has been reported in over 1.5 million individuals who received a second immunization with Ad26.COV2.S in the United States. Here we utilize transcriptomic and proteomic profiling to compare individuals who receive two doses of Ad26.COV2.S with those vaccinated with BNT162b2 or mRNA-1273. Initial Ad26.COV2.S vaccination induces transient activation of platelet and coagulation and innate immune pathways that resolve by day 7; by contrast, patients with TTS show robust upregulation of these pathways on days 15–19 following initial Ad26.COV2.S vaccination. Meanwhile, a second immunization or a reduced initial dose of Ad26.COV2.S induces lower activation of these pathways than does the full initial dose. Our data suggest a role of coagulation and proinflammatory pathways in TTS pathogenesis, which may help optimize vaccination regimens to reduce TTS risk.
Efficient screening framework for organic solar cells with deep learning and ensemble learning
Authors: Wang Hongshuai , Feng Jie , Dong Zhihao , Jin Lujie , Li Miaomiao , Yuan Jianyu , Li Youyong 
Published: October 2023

AbstractOrganic photovoltaics have attracted worldwide interest due to their unique advantages in developing low-cost, lightweight, and flexible power sources. Functional molecular design and synthesis have been put forward to accelerate the discovery of ideal organic semiconductors. However, it is extremely expensive to conduct experimental screening of the wide organic compound space. Here we develop a framework by combining a deep learning model (graph neural network) and an ensemble learning model (Light Gradient Boosting Machine), which enables rapid and accurate screening of organic photovoltaic molecules. This framework establishes the relationship between molecular structure, molecular properties, and device efficiency. Our framework evaluates the chemical structure of the organic photovoltaic molecules directly and accurately. Since it does not involve density functional theory calculations, it makes fast predictions. The reliability of our framework is verified with data from previous reports and our newly synthesized organic molecules. Our work provides an efficient method for developing new organic optoelectronic materials.
Forest composition change and biophysical climate feedbacks across boreal North America
Authors: Massey Richard , Rogers Brendan M. , Berner Logan T. , Cooperdock Sol , Mack Michelle C. , Walker Xanthe J. , Goetz Scott J. 
Published: October 2023

AbstractDeciduous tree cover is expected to increase in North American boreal forests with climate warming and wildfire. This shift in composition has the potential to generate biophysical cooling via increased land surface albedo. Here we use Landsat-derived maps of continuous tree canopy cover and deciduous fractional composition to assess albedo change over recent decades. We find, on average, a small net decrease in deciduous fraction from 2000 to 2015 across boreal North America and from 1992 to 2015 across Canada, despite extensive fire disturbance that locally increased deciduous vegetation. We further find near-neutral net biophysical change in radiative forcing associated with albedo when aggregated across the domain. Thus, while there have been widespread changes in forest composition over the past several decades, the net changes in composition and associated post-fire radiative forcing have not induced systematic negative feedbacks to climate warming over the spatial and temporal scope of our study.
Chase-away evolution maintains imperfect mimicry in a brood parasite–host system despite rapid evolution of mimics
Authors: Dixit Tanmay , Lund Jess , Fulford Anthony J. C. , Apostol Andrei L. , Chen Kuan-Chi , Tong Wenfei , Feeney William E. , Hamusikili Lazaro , Colebrook-Robjent John F. R. , Town Christopher P. , Spottiswoode Claire N. 
Published: October 2023

AbstractWe studied a brood parasite–host system (the cuckoo finch Anomalospiza imberbis and its host, the tawny-flanked prinia Prinia subflava) to test (1) the fundamental hypothesis that deceptive mimics evolve to resemble models, selecting in turn for models to evolve away from mimics (‘chase-away evolution’) and (2) whether such reciprocal evolution maintains imperfect mimicry over time. Over only 50 years, parasites evolved towards hosts and hosts evolved away from parasites, resulting in no detectible increase in mimetic fidelity. Our results reflect rapid adaptive evolution in wild populations of models and mimics and show that chase-away evolution in models can counteract even rapid evolution of mimics, resulting in the persistence of imperfect mimicry.
Effective prediction finite element model of pull-out capacity for cast-in-place anchor in high strain rate effects
Authors: Bao Quoc To , Lee Kihak , An Hyoseo , Lee Do Hyung , Shin Jiuk 
Published: October 2023

AbstractCast-in-place anchors are being increasingly used in many applications including building construction, bridge, and power plants. The anchorage to concrete systems are subjected to tensile, shear and combined loads from a variety of loading circumstances including static, dynamic, and shock loading. Despite extensive studies on these systems, reliable numerical models for predicting the behavior of these anchors are still limited. Therefore, this paper investigated the tensile behavior of cast-in-place anchorage to concrete systems, to propose an effective model for reproducing anchorage behavior using finite element (FE) methods. Experiments and code-based models for the anchorage system in tension were used to evaluate the numerical models for cast-in-place anchors in concrete, and the most suitable model, with advantages in accuracy and saving analysis time, was chosen. Finally, the FE model was used to study the tensile capacity and related dynamic increase factor for various strain rates, anchor diameters, and embedment depths.
The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot
Authors: Viver T. , López-Causapé C. , Ribot-Fraile P. , Pérez-Mazón C. , López-Solé D. , Jiménez-Guerra G. , Taltavull B. , López-López A. 
Published: October 2023

AbstractThe public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequencing in resource-limited hospitals, other PCR-based strategies could be applied to efficiently monitor the circulating variants without the need to greatly expand the sequencing capacity. In our case, overpassing the technical limitations inherent to a second level hospital, we were able to characterize the weekly distribution of SARS-CoV-2 by the RT-qPCR amplification patterns visualization, single nucleotide polymorphism genotyping, and sequencing of randomly selected samples. All these molecular approaches allowed us to trace the epidemiology of SARS-CoV-2 viruses circulating in Ibiza and Formentera (Balearic Islands, Spain) during the third to the sixth pandemic waves (January 2021–July 2022), in which three major lineages that were considered as VOCs (Alpha, Delta, and Omicron), and many other non-VOC variants were detected and tracked.
Superior performance of biofilm versus planktonic Limosilactobacillus reuteri in protection of the intestines and brain in a piglet model of necrotizing enterocolitis
Authors: Wala Samantha J. , Sajankila Nitin , Ragan Mecklin V. , Duff Audrey F. , Wickham Joseph , Volpe Samuel G. , Wang Yijie , Conces Miriam , Dumbauld Zachary , Purayil Nanditha , Narayanan Siddharth , Rajab Adrian , Mihi Belgacem , Bailey Michael T. , Goodman Steven D. , Besner Gail E. 
Published: October 2023

AbstractNecrotizing enterocolitis (NEC) is the leading cause of gastrointestinal-related death in premature infants. Its etiology is multifactorial, with intestinal dysbiosis playing a major role. Probiotics are a logical preventative therapy for NEC, however their benefits have been inconsistent. We previously developed a novel probiotic delivery system in which planktonic (free-living) Limosilactobacillus reuteri (Lr) is incubated with biocompatible dextranomer microspheres (DM) loaded with maltose (Lr-DM-maltose) to induce biofilm formation. Here we have investigated the effects of Lr-DM-maltose in an enteral feed-only piglet model of NEC. We found a significant decrease in the incidence of Definitive NEC (D-NEC), death associated with D-NEC, and activated microglia in the brains of piglets treated with Lr-DM-maltose compared to non-treated piglets. Microbiome analyses using 16S rRNA sequencing of colonic contents revealed a significantly different microbial community composition between piglets treated with Lr-DM-maltose compared to non-treated piglets, with an increase in Lactobacillaceae and a decrease in Clostridiaceae in Lr-DM-maltose-treated piglets. Furthermore, there was a significant decrease in the incidence of D-NEC between piglets treated with Lr-DM-maltose compared to planktonic Lr. These findings validate our previous results in rodents, and support future clinical trials of Lr in its biofilm state for the prevention of NEC in premature neonates.
Three-dimensional solitons in Rydberg-dressed cold atomic gases with spin–orbit coupling
Authors: Zhao Yuan , Hu Heng-Jie , Zhou Qian-Qian , Qiu Zhang-Cai , Xue Li , Xu Si-Liu , Zhou Qin , Malomed Boris A. 
Published: October 2023

AbstractWe present numerical results for three-dimensional (3D) solitons with symmetries of the semi-vortex (SV) and mixed-mode (MM) types, which can be created in spinor Bose–Einstein condensates of Rydberg atoms under the action of the spin–orbit coupling (SOC). By means of systematic numerical computations, we demonstrate that the interplay of SOC and long-range spherically symmetric Rydberg interactions stabilize the 3D solitons, improving their resistance to collapse. We find how the stability range depends on the strengths of the SOC and Rydberg interactions and the soft-core atomic radius.
Effectiveness of exercise interventions to improve long-term outcomes in people living with mild cognitive impairment: a systematic review and meta-analysis
Authors: Dieckelmann Mirjam , González-González Ana I. , Banzer Winfried , Berghold Andrea , Jeitler Klaus , Pantel Johannes , Pregartner Gudrun , Schall Arthur , Tesky Valentina A. , Siebenhofer Andrea 
Published: October 2023

AbstractAlthough exercise guidelines now recommend exercise for patients with MCI, the long-term effects of exercise in patients with MCI has not been reviewed systematically. The aim was to assess (1) the effectiveness of exercise and physical activity (EXPA) interventions in improving long-term patient-relevant cognitive and non-cognitive outcomes in people with mild cognitive impairment, (2) how well the included trials reported details of the intervention, and (3) the extent to which reported endpoints were in line with patient preferences that were assessed in patient workshops. Following PRISMA guidelines, we performed a systematic review and meta-analysis including randomized controlled trials. A total of ten studies were included after searching in six electronic sources from 1995 onwards. There is a trend that 6 + -month EXPA interventions improve global cognition 12 months after initiation. Evidence on long-term effects of EXPA interventions on non-cognitive health outcomes could not be meaningfully pooled and the individual studies reported mixed results. Workshop participants considered freedom from pain and stress, mood, motivation and self-efficacy to be important, but these outcomes were rarely addressed. Too little information is available on intervention details for EXPA programs to be replicated and confidently recommended for patients with MCI. PROSPERO registration in December, 2021 (CRD42021287166).
Telephone-based evaluation of cognitive impairment and mood disorders in cardiac arrest survivors with good neurologic outcomes: a retrospective cohort study
Authors: Kim June-sung , Kim Youn-Jung , Ryoo Seung Mok , Ahn Shin , Kim Won Young 
Published: October 2023

AbstractThis study determined the occurrence of cognitive impairment and mood disorders in out-of-hospital cardiac arrest (OHCA) survivors with good neurologic outcomes. We performed a retrospective, cross-sectional, single-center study with a total of 97 patients. We evaluated cognitive dysfunction via the Montreal Cognitive Assessment and Alzheimer’s disease-8 mood disorders via the Patient Health Questionnaire-9 and the Hospital Anxiety and Depression Scale. We measured quality of life with the European Quality of Life 5-Dimension 5-Levels questionnaire. Cognitive impairment and mood disorders were common among patients with good neurologic recovery. There were 23 patients who experienced cognitive impairments (23.7%) and 28 who suffered from mood disorders (28.9%). Age (adjusted OR 1.07, 95% CI 1.02–1.12), mood disorders (adjusted OR 22.80, 95% CI 4.84–107.49) and hospital length of stay (adjusted OR 1.05, 95% CI 1.02–1.09) were independent risk factors for cognitive impairment. The occurrence of cognitive impairments (adjusted OR 9.94, 95% CI 2.83–35.97) and non-cardiac causes of cardiac arrest (adjusted OR 11.51, 95% CI 3.15–42.15) were risk factors for mood disorders. Quality of life was significantly lower in the OHCA survivors with each disorder than the healthy individuals. Routine screening and intervention are needed for OHCA survivors.
Differences in race history by distance of recreational endurance runners from The NURMI Study (Step 2)
Authors: Knechtle Beat , Tanous Derrick , Thuany Mabliny , Motevalli Mohamad , Wirnitzer Gerold , Leitzmann Claus , Weiss Katja , Rosemann Thomas , Wirnitzer Katharina 
Published: October 2023

AbstractFew studies were developed to understand the relationship between running characteristics and motivation. The purpose of this study was to assess the relationship between running event history, running experience, and best race performances in recreational distance runners. We used a web survey to obtain information regarding running experience, racing history, and periodization training routines/exercise habits, including weekly volumes and daily mileage and duration across periods and conditions. Associations between variables were conducted with the Chi-square test (χ2; nominal scale) and Wilcoxon test. Multiple linear regression analysis and multivariate linear regression were performed. Concerning the participants’ motive for exercising, a significant difference was identified between the race distance subgroups (p < 0.001), where 58% of M/UM runners exercised for performance (n = 38) and 64% of HM runners (n = 57) and 57% of 10 km runners (n = 52) exercised for recreational purposes. A significant difference was found in the number of years of running completed without taking a break (p = 0.004), with marathoners/ultramarathoners reporting the most years. Runners competing in different race distances such as 10 km, half-marathon, marathon, and ultra-marathon presented differences in training background and habits according to the distance of preference.
High-performance grating couplers on 220-nm thick silicon by inverse design for perfectly vertical coupling
Authors: Yang Mingxiang , Yan Yunjie , Wu Zhenlin , Gu YiYing , Zhao Shiyuan , Morthier Geert , Zhao Mingshan 
Published: October 2023

AbstractEfficient grating couplers (GCs) for perfectly vertical coupling are difficult to realize due to the second-order back reflection. In this study, apodized GCs (AGCs) are presented for achieving perfectly-vertical coupling to 220 nm thick silicon-on-insulator (SOI) waveguides in the C-band. We compare the performance of the AGCs to that of uniform GCs (UGCs) and demonstrate the superiority of the former. The AGCs were obtained through inverse design using gradient-based optimization and were found to effectively suppress back reflection and exhibit better matching to the Gaussian beam profile. The design and measurement results show that AGCs have a 3 dB lower coupling loss than UGCs. We fabricated focusing AGCs by electron beam lithography with a single, 70 nm shallow etch and a minimum feature size of 100 nm, which makes them compatible with CMOS technology. The AGCs achieved a coupling efficiency of −5.86 dB for perfectly vertical coupling. Overall, our results demonstrate the potential of AGCs for achieving high-performance coupling in the C-band on the SOI platform.