bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deterministic photon source interfaced with a programmable silicon-nitride integrated circuit
Authors: Wang Ying , Faurby Carlos F. D. , Ruf Fabian , Sund Patrik I. , Nielsen Kasper , Volet Nicolas , Heck Martijn J. R. , Bart Nikolai , Wieck Andreas D. , Ludwig Arne , Midolo Leonardo , Paesani Stefano , Lodahl Peter 
Published: September 2023

AbstractWe develop a quantum photonic platform that interconnects a high-quality quantum dot single-photon source and a low-loss photonic integrated circuit made in silicon nitride. The platform is characterized and programmed to demonstrate various multiphoton applications, including bosonic suppression laws and photonic entanglement generation. The results show a promising technological route forward to scale-up photonic quantum hardware.
Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns
Authors: Walter Katharine S. , Altamirano Jonathan , Huang ChunHong , Carrington Yuan J. , Zhou Frank , Andrews Jason R. , Maldonado Yvonne 
Published: September 2023

AbstractThere is an increasing burden of circulating vaccine-derived polioviruses (cVDPVs) due to the continued use of oral poliovirus vaccine (OPV). However, the informativeness of routine OPV VP1 sequencing for the early identification of viruses carrying virulence-associated reversion mutations has not been directly evaluated in a controlled setting. We prospectively collected 15,331 stool samples to track OPV shedding from children receiving OPV and their contacts for ten weeks following an immunization campaign in Veracruz State, Mexico and sequenced VP1 genes from 358 samples. We found that OPV was genetically unstable and evolves at an approximately clocklike rate that varies across serotypes and by vaccination status. Overall, 61% (11/18) of OPV-1, 71% (34/48) OPV-2, and 96% (54/56) OPV-3 samples with available data had evidence of a reversion at the key 5’ UTR attenuating position and 28% (13/47) of OPV-1, 12% (14/117) OPV-2, and 91% (157/173) OPV-3 of Sabin-like viruses had ≥1 known reversion mutations in the VP1 gene. Our results are consistent with previous work documenting rapid reversion to virulence of OPV and underscores the need for intensive surveillance following OPV use.
Allometrically scaling tissue forces drive pathological foreign-body responses to implants via Rac2-activated myeloid cells
Authors: Padmanabhan Jagannath , Chen Kellen , Sivaraj Dharshan , Henn Dominic , Kuehlmann Britta A. , Kussie Hudson C. , Zhao Eric T. , Kahn Anum , Bonham Clark A. , Dohi Teruyuki , Beck Thomas C. , Trotsyuk Artem A. , Stern-Buchbinder Zachary A. , Than Peter A. , Hosseini Hadi S. , Barrera Janos A. , Magbual Noah J. , Leeolou Melissa C. , Fischer Katharina S. , Tigchelaar Seth S. , Lin John Q. , Perrault David P. , Borrelli Mimi R. , Kwon Sun Hyung , Maan Zeshaan N. , Dunn James C. Y. , Nazerali Rahim , Januszyk Michael , Prantl Lukas , Gurtner Geoffrey C. 
Published: September 2023

AbstractSmall animals do not replicate the severity of the human foreign-body response (FBR) to implants. Here we show that the FBR can be driven by forces generated at the implant surface that, owing to allometric scaling, increase exponentially with body size. We found that the human FBR is mediated by immune-cell-specific RAC2 mechanotransduction signalling, independently of the chemistry and mechanical properties of the implant, and that a pathological FBR that is human-like at the molecular, cellular and tissue levels can be induced in mice via the application of human-tissue-scale forces through a vibrating silicone implant. FBRs to such elevated extrinsic forces in the mice were also mediated by the activation of Rac2 signalling in a subpopulation of mechanoresponsive myeloid cells, which could be substantially reduced via the pharmacological or genetic inhibition of Rac2. Our findings provide an explanation for the stark differences in FBRs observed in small animals and humans, and have implications for the design and safety of implantable devices.
The interface of condensates of the hnRNPA1 low-complexity domain promotes formation of amyloid fibrils
Authors: Linsenmeier Miriam , Faltova Lenka , Morelli Chiara , Capasso Palmiero Umberto , Seiffert Charlotte , Küffner Andreas M. , Pinotsi Dorothea , Zhou Jiangtao , Mezzenga Raffaele , Arosio Paolo 
Published: September 2023

AbstractThe maturation of liquid-like protein condensates into amyloid fibrils has been associated with several neurodegenerative diseases. However, the molecular mechanisms underlying this liquid-to-solid transition have remained largely unclear. Here we analyse the amyloid formation mediated by condensation of the low-complexity domain of hnRNPA1, a protein involved in amyotrophic lateral sclerosis. We show that phase separation and fibrillization are connected but distinct processes that are modulated by different regions of the protein sequence. By monitoring the spatial and temporal evolution of amyloid formation we demonstrate that the formation of fibrils does not occur homogeneously inside the droplets but is promoted at the interface of the condensates. We further show that coating the interface of the droplets with surfactant molecules inhibits fibril formation. Our results reveal that the interface of biomolecular condensates of hnRNPA1 promotes fibril formation, therefore suggesting interfaces as a potential novel therapeutic target against the formation of aberrant amyloids mediated by condensation.
Climate extremes likely to drive land mammal extinction during next supercontinent assembly
Authors: Farnsworth Alexander , Lo Y. T. Eunice , Valdes Paul J. , Buzan Jonathan R. , Mills Benjamin J. W. , Merdith Andrew S. , Scotese Christopher R. , Wakeford Hannah R. 
Published: September 2023

AbstractMammals have dominated Earth for approximately 55 Myr thanks to their adaptations and resilience to warming and cooling during the Cenozoic. All life will eventually perish in a runaway greenhouse once absorbed solar radiation exceeds the emission of thermal radiation in several billions of years. However, conditions rendering the Earth naturally inhospitable to mammals may develop sooner because of long-term processes linked to plate tectonics (short-term perturbations are not considered here). In ~250 Myr, all continents will converge to form Earth’s next supercontinent, Pangea Ultima. A natural consequence of the creation and decay of Pangea Ultima will be extremes in $$p_{\mathrm{CO}_2}$$

p

CO

2

due to changes in volcanic rifting and outgassing. Here we show that increased $$p_{\mathrm{CO}_2}$$

p

CO

2

, solar energy (F⨀; approximately +2.5% W m−2 greater than today) and continentality (larger range in temperatures away from the ocean) lead to increasing warming hostile to mammalian life. We assess their impact on mammalian physiological limits (dry bulb, wet bulb and Humidex heat stress indicators) as well as a planetary habitability index. Given mammals’ continued survival, predicted background $$p_{\mathrm{CO}_2}$$

p

CO

2

levels of 410–816 ppm combined with increased F⨀ will probably lead to a climate tipping point and their mass extinction. The results also highlight how global landmass configuration, $$p_{\mathrm{CO}_2}$$

p

CO

2

and F⨀ play a critical role in planetary habitability.
Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers
Authors: Koch Caroline , Reilly-O’Donnell Benedict , Gutierrez Richard , Lucarelli Carla , Ng Fu Siong , Gorelik Julia , Ivanov Aleksandar P. , Edel Joshua B. 
Published: September 2023

AbstractThere is an unmet need to develop low-cost, rapid and highly multiplexed diagnostic technology platforms for quantitatively detecting blood biomarkers to advance clinical diagnostics beyond the single biomarker model. Here we perform nanopore sequencing of DNA-barcoded molecular probes engineered to recognize a panel of analytes. This allows for highly multiplexed and simultaneous quantitative detection of at least 40 targets, such as microRNAs, proteins and neurotransmitters, on the basis of the translocation dynamics of each probe as it passes through a nanopore. Our workflow is built around a commercially available MinION sequencing device, offering a one-hour turnaround time from sample preparation to results. We also demonstrate that the strategy can directly detect cardiovascular disease-associated microRNA from human serum without extraction or amplification. Due to the modularity of barcoded probes, the number and type of targets detected can be significantly expanded.
Distinguishing features of long COVID identified through immune profiling
Authors: Klein Jon , Wood Jamie , Jaycox Jillian R. , Dhodapkar Rahul M. , Lu Peiwen , Gehlhausen Jeff R. , Tabachnikova Alexandra , Greene Kerrie , Tabacof Laura , Malik Amyn A. , Silva Monteiro Valter , Silva Julio , Kamath Kathy , Zhang Minlu , Dhal Abhilash , Ott Isabel M. , Valle Gabrielee , Peña-Hernández Mario , Mao Tianyang , Bhattacharjee Bornali , Takahashi Takehiro , Lucas Carolina , Song Eric , McCarthy Dayna , Breyman Erica , Tosto-Mancuso Jenna , Dai Yile , Perotti Emily , Akduman Koray , Tzeng Tiffany J. , Xu Lan , Geraghty Anna C. , Monje Michelle , Yildirim Inci , Shon John , Medzhitov Ruslan , Lutchmansingh Denyse , Possick Jennifer D. , Kaminski Naftali , Omer Saad B. , Krumholz Harlan M. , Guan Leying , Dela Cruz Charles S. , van Dijk David , Ring Aaron M. , Putrino David , Iwasaki Akiko 
Published: September 2023

AbstractPost-acute infection syndromes may develop after acute viral disease1. Infection with SARS-CoV-2 can result in the development of a post-acute infection syndrome known as long COVID. Individuals with long COVID frequently report unremitting fatigue, post-exertional malaise, and a variety of cognitive and autonomic dysfunctions2–4. However, the biological processes that are associated with the development and persistence of these symptoms are unclear. Here 275 individuals with or without long COVID were enrolled in a cross-sectional study that included multidimensional immune phenotyping and unbiased machine learning methods to identify biological features associated with long COVID. Marked differences were noted in circulating myeloid and lymphocyte populations relative to the matched controls, as well as evidence of exaggerated humoral responses directed against SARS-CoV-2 among participants with long COVID. Furthermore, higher antibody responses directed against non-SARS-CoV-2 viral pathogens were observed among individuals with long COVID, particularly Epstein–Barr virus. Levels of soluble immune mediators and hormones varied among groups, with cortisol levels being lower among participants with long COVID. Integration of immune phenotyping data into unbiased machine learning models identified the key features that are most strongly associated with long COVID status. Collectively, these findings may help to guide future studies into the pathobiology of long COVID and help with developing relevant biomarkers.
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments
Authors: Oosterheert Wout , Blanc Florian E. C. , Roy Ankit , Belyy Alexander , Sanders Micaela Boiero , Hofnagel Oliver , Hummer Gerhard , Bieling Peter , Raunser Stefan 
Published: September 2023

AbstractThe release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying Pi release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a ‘molecular backdoor’. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why Pi escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated Pi release and filaments with drastically shortened ADP-Pi caps. Our results provide the molecular basis for Pi release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament.
Thermodynamic flow of radiative induced magneto modified Maxwell Sutterby fluid model at stretching sheet/cylinder
Authors: Abbas Nadeem , Shatanawi Wasfi , Hasan Fady , Mustafa Zead 
Published: September 2023

AbstractA steady flow of Maxwell Sutterby fluid is considered over a stretchable cylinder. The magnetic Reynolds number is considered very high and induced magnetic and electric fields are applied on the fluid flow. Joule heating and radiation impacts are studied under the temperature-dependent properties of the liquid. Having the above assumptions, the mathematical model has been evolving via differential equations. The differential equations are renovated in the dimensionless form of ordinary differential equations using the appropriate transformations. The numerical results have been developed employing numerical techniques on the ordinary differential equations. The impact of involving physical factors on velocity, induced magneto hydrodynamic, and temperature function is debated in graphical and tabular form. The velocity profile is boosted by thicker momentum boundary layers, which are caused by higher values of the magnetic field factor. So, the fluid flow becomes higher velocity due to enlarging values of the magnetic field factor. Heat transfer factor and friction at surface factor boosted up for increment of $${\gamma }_{0}$$

γ
0

(Magnetic field factor). The $${\gamma }_{0}$$

γ
0

(Magnetic field factor) is larger which better-quality of heat transfer at surface and also offered the results of friction factor boosting up in both cases of stretching sheet/cylinder. The $${\lambda }_{0}$$

λ
0

(Magnetic Prandtl number) increased which provided better-quality of heat transfer at surface.
Neural mechanism facilitating PM2.5-related cardiac arrhythmias through cardiovascular autonomic and calcium dysregulation in a rat model
Authors: Tsai Tsung-Ying , Lo Li-Wei , Lin Wei-Lun , Chou Yu-Hui , Cheng Wen-Han , Liu Shin-Hui , Yang Cheryl C. H. , Kuo Terry B. J. , Chen Shih-Ann 
Published: September 2023

AbstractParticulate matter < 2.5 μm (PM2.5) exposure is associated with increased arrhythmia events and cardiovascular mortality, but the detailed mechanism remained elusive. In the current study, we aimed to investigate the autonomic alterations in a rodent model after acute exposure to PM2.5. Twelve male WKY rats were randomized to control and PM2.5 groups. All were treated with 2 exposures of oropharyngeal aerosol inhalations (1 μg PM2.5 per gram of body weight in 100 μL normal saline for the PM2.5 group) separately by 7 days. Polysomnography and electrocardiography were surgically installed 7 days before oropharyngeal inhalation and monitored for 7 days after each inhalation. Physiologic monitors were used to define active waking (AW), quiet sleep (QS), and paradoxical sleep (PS). Autonomic regulations were measured by heart rate variability (HRV). The protein expression of ventricular tissue of the 2 groups was compared at the end of the experiment. In sleep pattern analysis, QS interruption of the PM2.5 group was significantly higher than the control group (0.52 ± 0.13 events/min, 0.35 ± 0.10 events/min, p = 0.002). In HRV analysis, the LF/HF was significantly higher for the PM2.5 group than the control group (1.15 ± 0.16, 0.64± 0.30, p = 0.003), largely driven by LF/HF increase during the QS phase. Ionic channel protein expression from Western blots showed that the PM2.5 group had significantly lower L-type calcium channel and higher SERCA2 and rectifier potassium channel expressions than the control group, respectively. Our results showed that acute PM2.5 exposure leads to interruption of QS, sympathetic activation, and recruitment of compensatory calcium handling proteins. The autonomic and calcium dysregulations developed after PM 2.5 exposure may explain the risk of sleep disturbance and sleep-related arrhythmia.
Extrusion and characterization of recycled polyethylene terephthalate (rPET) filaments compounded with chain extender and impact modifiers for material-extrusion additive manufacturing
Authors: Rashwan Ola , Koroneos Zachary , Townsend Trent G. , Caputo Matthew P. , Bylone Robert J. , Wodrig Brennan , Cantor Kirk 
Published: September 2023

AbstractThe continuous growth of annual production and consumption of polyethylene terephthalate (PET) is coined with increasing waste that leaks into the environment, landfills and oceans as microplastics and nano plastics fragments. Upcycling the recycled PET to make a feedstock for the fast-growing material-extrusion additive manufacturing (MEX-AM) technology can contribute to the solution and supports the concept of sustainable materials. In this work, extrudable filaments comprising recycled polyethylene terephthalate (rPET) with low-cost additives, such as pyromellitic dianhydride (PMDA) as a chain extender, styrene-ethylene-butylene-styrene terpolymer functionalized with maleic anhydride (SEBS-g-MA), a thermal modifier and toughening agent, ethylene-ethyl acrylate-glycidyl methacrylate terpolymer (E-EA-GMA), a functional reactive elastomeric impact modifier and ethylene-ethyl-acrylate (EEA), a non-reactive elastomeric impact modifier, have been fabricated using the twin-screw extruder. The optimum extrusion process parameters for producing uniform filaments of different rPET compounded formulations have been identified, this includes the extrusion die temperature of 280 °C and the screw speed of 150 ± 3 rpm. The compounded filaments are then printed into standard ASTM test specimens for thermal characterization and mechanical characterization, including glass transition and melting temperatures, crystallinity and crystallization temperature, tensile strength, tensile modulus, ductility, flexural strength, and Izod impact energy. Furthermore, the melt flow index for the filaments was measured. More significantly, the experimental data showed that compounding rPET with such additives in the reactive twin-screw extrusion process results in uniform filaments that display advantageous thermal and mechanical properties and can be used as a feedstock in the MEX-AM technology. This study suggests that compounding the recycled PET pellets with low-cost additives while extruding them into filaments for MEX-AM offers excellent potential to make high-value-added customized products from a sustainable polymer feedstock, such as prototyping, tooling, testing components or end-use internal components for small machines and cars.
The chloroplast protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix
Authors: Guerra-Guimarães Leonor , Pinheiro Carla , Oliveira Ana Sofia F. , Mira-Jover Andrea , Valverde Javier , Guedes Fernanda A. de F. , Azevedo Herlander , Várzea Vitor , Muñoz Pajares Antonio Jesús 
Published: September 2023

AbstractTo explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid “Híbrido de Timor”. Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
Loss of HES1 expression is associated with extracellular matrix remodeling and tumor immune suppression in KRAS mutant colon adenocarcinomas
Authors: Wang Lei , Gu Wenchao , Zou Bingqing , Kalady Matthew , Xin Wei , Zhou Lan 
Published: September 2023

AbstractThe loss of HES1, a canonical Notch signaling target, may cooperate with KRAS mutations to remodel the extracellular matrix and to suppress the anti-tumor immune response. While HES1 expression is normal in benign hyperplastic polyps and normal colon tissue, HES1 expression is often lost in sessile serrated adenomas/polyps (SSAs/SSPs) and colorectal cancers (CRCs) such as those right-sided CRCs that commonly harbor BRAF or KRAS mutations. To develop a deeper understanding of interaction between KRAS and HES1 in colorectal carcinogenesis, we selected microsatellite stable (MSS) and KRAS mutant or KRAS wild type CRCs that show aberrant expression of HES1 by immunohistochemistry. By comparing the transcriptional landscapes of microsatellite stable (MSS) CRCs with or without nuclear HES1 expression, we investigated differentially expressed genes and activated pathways. We identified pathways and markers in the extracellular matrix and immune microenvironment that are associated with mutations in KRAS. We found that loss of HES1 expression positively correlated with matrix remodeling and epithelial-mesenchymal transition but negatively correlated with tumor cell proliferation. Furthermore, loss of HES1 expression in KRAS mutant CRCs correlates with a higher M2 macrophage polarization and activation of IL6 and IL10 immunosuppressive signature. Identifying these HES1-related markers may be useful for prognosis stratification and developing treatment for KRAS-mutant CRCs.
Cracking and damage analysis of a masonry structure based on joint masonry model caused by a obliquely undercrossing tunnel
Authors: Jin Junwei , Zhang Qinglong , Fu Boyi , Chen Jian , Li Mingyu , Jin Qianqian 
Published: September 2023

AbstractThe damage variation of a masonry structure during shield tunneling has been investigated. Furthermore, the damage degree of the masonry building has been investigated by combining the field measurement, finite element method results, and theoretical method. The results show that compared with the theoretical calculation method LSTM, the method provide by this paper can give the detail damage location of the masonry structure caused by shield construction. Due to the existence of door and window openings, the result of JMM is larger than LSTM result, the differences can be modified by concept of “characteristic tensile strain”. The wall of the masonry building encounter the shield face first suffers more damage than the later ones. At the beginning of tunnlling, the damage were generated from a small area at the bottom for wall 1, but a larger area at the top of the building for wall 2. The damage area increase more at the top of the building as tunneling advanced, but the maximum damage occurred at the bottom of the building.