bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding defects in glasses through machine learning
Authors: Ciarella Simone , Khomenko Dmytro , Berthier Ludovic , Mocanu Felix C. , Reichman David R. , Scalliet Camille , Zamponi Francesco 
Published: July 2023

AbstractStructural defects control the kinetic, thermodynamic and mechanical properties of glasses. For instance, rare quantum tunneling two-level systems (TLS) govern the physics of glasses at very low temperature. Due to their extremely low density, it is very hard to directly identify them in computer simulations. We introduce a machine learning approach to efficiently explore the potential energy landscape of glass models and identify desired classes of defects. We focus in particular on TLS and we design an algorithm that is able to rapidly predict the quantum splitting between any two amorphous configurations produced by classical simulations. This in turn allows us to shift the computational effort towards the collection and identification of a larger number of TLS, rather than the useless characterization of non-tunneling defects which are much more abundant. Finally, we interpret our machine learning model to understand how TLS are identified and characterized, thus giving direct physical insight into their microscopic nature.
Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma
Authors: Abbas Sujath , Pich Oriol , Devonshire Ginny , Zamani Shahriar A. , Katz-Summercorn Annalise , Killcoyne Sarah , Cheah Calvin , Nutzinger Barbara , Grehan Nicola , Lopez-Bigas Nuria ,   OCCAMS Consortium, Edwards Paul A. W. , Fidziukiewicz Elwira , Redmond Aisling M. , Freeman Adam , Smyth Elizabeth C. , O’Donovan Maria , Miremadi Ahmad , Malhotra Shalini , Tripathi Monika , Coles Hannah , Flint Conor , Eldridge Matthew , Jammula Sriganesh , Davies Jim , Crichton Charles , Carroll Nick , Hardwick Richard H. , Safranek Peter , Hindmarsh Andrew , Sujendran Vijayendran , Hayes Stephen J. , Ang Yeng , Sharrocks Andrew , Preston Shaun R. , Bagwan Izhar , Save Vicki , Skipworth Richard J. E. , Hupp Ted R. , O’Neill J. Robert , Tucker Olga , Beggs Andrew , Taniere Philippe , Puig Sonia , Contino Gianmarco , Underwood Timothy J. , Walker Robert C. , Grace Ben L. , Lagergren Jesper , Gossage James , Davies Andrew , Chang Fuju , Mahadeva Ula , Goh Vicky , Ciccarelli Francesca D. , Sanders Grant , Berrisford Richard , Chan David , Cheong Ed , Kumar Bhaskar , Sreedharan L. , Parsons Simon L. , Soomro Irshad , Kaye Philip , Saunders John , Lovat Laurence , Haidry Rehan , Scott Michael , Sothi Sharmila , Lishman Suzy , Hanna George B. , Peters Christopher J. , Moorthy Krishna , Grabowska Anna , Turkington Richard , McManus Damian , Coleman Helen , Petty Russell D. , Bartlett Freddie , Fitzgerald Rebecca C. , Secrier Maria 
Published: July 2023

AbstractA variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping oesophageal adenocarcinoma tumorigenesis in 997 instances comprising distinct stages of this malignancy, from Barrett Oesophagus to primary tumours and advanced metastatic disease. The mutational landscape is dominated by the C[T > C/G]T substitution enriched signatures SBS17a/b, which are linked withTP53mutations, increased proliferation, genomic instability and disease progression. The APOBEC mutagenesis signature is a weak but persistent signal amplified in primary tumours. We also identify prevalent alterations in DNA damage repair pathways, with homologous recombination, base and nucleotide excision repair and translesion synthesis mutated in up to 50% of the cohort, and surprisingly uncoupled from transcriptional activity. Among these, the presence of base excision repair deficiencies show remarkably poor prognosis in the cohort. In this work, we provide insights on the mutational aetiology and changes enabling the transition from pre-neoplastic to advanced oesophageal adenocarcinoma.
Structural basis for specific RNA recognition by the alternative splicing factor RBM5
Authors: Soni Komal , Jagtap Pravin Kumar Ankush , Martínez-Lumbreras Santiago , Bonnal Sophie , Geerlof Arie , Stehle Ralf , Simon Bernd , Valcárcel Juan , Sattler Michael 
Published: July 2023

AbstractThe RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains to cis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.
pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle
Authors: Berger Fiona , Gomez Guillermo M. , Sanchez Cecilia P. , Posch Britta , Planelles Gabrielle , Sohraby Farzin , Nunes-Alves Ariane , Lanzer Michael 
Published: July 2023

AbstractThe chloroquine resistance transporter, PfCRT, of the human malaria parasitePlasmodium falciparumis sensitive to acidic pH. Consequently, PfCRT operates at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs interfering with heme detoxification. Here we show by alanine-scanning mutagenesis that E207 is critical for pH sensing. The E207A mutation abrogates pH-sensitivity, while preserving drug substrate specificity. Substituting E207 with Asp or His, but not other amino acids, restores pH-sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can accept both protons and chloroquine in a partial noncompetitive manner, with increased proton concentrations decreasing drug transport. Further simulations reveal that E207 relocates from a peripheral to an engaged location during the transport cycle, forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor, facilitating transport cycle progression, with pH sensing as a by-product.
Long-term neurological outcome after COVID-19 using all SARS-CoV-2 test results and hospitalisations in Denmark with 22-month follow-up
Authors: Grønkjær Clara S. , Christensen Rune H. B. , Kondziella Daniel , Benros Michael E. 
Published: July 2023

AbstractHospitalisation with COVID-19 is associated with an increased risk of neurological sequelae; however, representative nationwide studies comparing to other infections with similar severity and also including milder SARS-CoV-2 infections have been lacking. Using the nationwide Danish registers including all SARS-CoV-2 PCR test results and hospitalisations between March 1, 2020, and December 31, 2021, we estimate the risk of any first neurological disorder diagnosed in inpatient, outpatient, or emergency room settings. We show that positive tests increase the rate of neurological disorders by a hazard ratio of 1.96 (95% confidence interval: 1.88–2.05) compared to individuals not tested and by a hazard ratio of 1.11 (95% confidence interval: 1.07-1.16) compared to individuals with negative tests only. However, there is no evidence that the risk of neurological disorders is higher for individuals who test positive compared to non-COVID-19 infections treated with anti-infective medication. The risk of neurological disorders is increased after COVID-19-hospitalisation compared to no COVID-19 hospital admission; however, these risks are comparable to hospitalisation with other respiratory infections (Pvalue 0.328). In conclusion, COVID-19 is associated with an increased risk of neurological disorders, but no more than that observed after other infections of similar severity.
Macroscopic photonic single crystals via seeded growth of DNA-coated colloids
Authors: Hensley Alexander , Videbæk Thomas E. , Seyforth Hunter , Jacobs William M. , Rogers W. Benjamin 
Published: July 2023

AbstractPhotonic crystals—a class of materials whose optical properties derive from their structure in addition to their composition—can be created by self-assembling particles whose sizes are comparable to the wavelengths of visible light. Proof-of-principle studies have shown that DNA can be used to guide the self-assembly of micrometer-sized colloidal particles into fully programmable crystal structures with photonic properties in the visible spectrum. However, the extremely temperature-sensitive kinetics of micrometer-sized DNA-functionalized particles has frustrated attempts to grow large, monodisperse crystals that are required for photonic metamaterial applications. Here we describe a robust two-step protocol for self-assembling single-domain crystals that contain millions of optical-scale DNA-functionalized particles: Monodisperse crystals are initially assembled in monodisperse droplets made by microfluidics, after which they are grown to macroscopic dimensions via seeded diffusion-limited growth. We demonstrate the generality of our approach by assembling different macroscopic single-domain photonic crystals with metamaterial properties, like structural coloration, that depend on the underlying crystal structure. By circumventing the fundamental kinetic traps intrinsic to crystallization of optical-scale DNA-coated colloids, we eliminate a key barrier to engineering photonic devices from DNA-programmed materials.
Strong bulk photovoltaic effect in engineered edge-embedded van der Waals structures
Authors: Liang Zihan , Zhou Xin , Zhang Le , Yu Xiang-Long , Lv Yan , Song Xuefen , Zhou Yongheng , Wang Han , Wang Shuo , Wang Taihong , Shum Perry Ping , He Qian , Liu Yanjun , Zhu Chao , Wang Lin , Chen Xiaolong 
Published: July 2023

AbstractBulk photovoltaic effect (BPVE), a second-order nonlinear optical effect governed by the quantum geometric properties of materials, offers a promising approach to overcome the Shockley-Quiesser limit of traditional photovoltaic effect and further improve the efficiency of energy harvesting. Here, we propose an effective platform, the nano edges embedded in assembled van der Waals (vdW) homo- or hetero-structures with strong symmetry breaking, low dimensionality and abundant species, for BPVE investigations. The BPVE-induced photocurrents strongly depend on the orientation of edge-embedded structures and polarization of incident light. Reversed photocurrent polarity can be observed at left and right edge-embedded structures. Our work not only visualizes the unique optoelectronic effect in vdW nano edges, but also provides an effective strategy for achieving BPVE in engineered vdW structures.
HIV-1 promotes ubiquitination of the amyloidogenic C-terminal fragment of APP to support viral replication
Authors: Gu Feng , Boisjoli Marie , Naghavi Mojgan H. 
Published: July 2023

AbstractHIV-1 replication in macrophages and microglia involves intracellular assembly and budding into modified subsets of multivesicular bodies (MVBs), which support both viral persistence and spread. However, the cellular factors that regulate HIV-1’s vesicular replication remain poorly understood. Recently, amyloid precursor protein (APP) was identified as an inhibitor of HIV-1 replication in macrophages and microglia via an unknown mechanism. Here, we show that entry of HIV-1 Gag into MVBs is blocked by the amyloidogenic C-terminal fragment of APP, “C99”, but not by the non-amyloidogenic product, “C83”. To counter this, Gag promotes multi-site ubiquitination of C99 which controls both exocytic sorting of MVBs and further processing of C99 into toxic amyloids. Processing of C99, entry of Gag into MVBs and release of infectious virus could be suppressed by expressing ubiquitination-defective C99 or by γ-secretase inhibitor treatment, suggesting that APP’s amyloidogenic pathway functions to sense and suppress HIV-1 replication in macrophages and microglia.
Location-selective immobilisation of single-atom catalysts on the surface or within the interior of ionic nanocrystals using coordination chemistry
Authors: Endo Kenichi , Saruyama Masaki , Teranishi Toshiharu 
Published: July 2023

AbstractSingle-atom catalysts dispersed on support materials show excellent heterogeneous catalytic properties that can be tuned using the interactions between the single atoms and the support. Such interactions depend on whether the single atoms are located on the surface or within the interior of the support. However, little is known about immobilising single atoms on the surface or within the interior of supports deliberately and selectively. Herein, such location-selective placement of single atoms is achieved through the choice of metal complex precursor, solvent, and workup procedure. Using CdSe nanoplatelets as a support, a cis-[PtCl2(SO(CH3)2)2] precursor in an aprotic solvent exclusively attaches single Pt atoms on the surface of the support. In contrast, a [PtCl4]2− precursor in a protic solvent followed by amine treatment places 60% of the single Pt atoms inside the support by cation substitution. The surface-adsorbed single Pt atoms show higher stability in photocatalytic hydrogen evolution than the substituted ones, and the preclusion of substitution as internal Pt maximises the activity. Thus, this study provides a viable strategy for the structurally precise synthesis and design of single-atom catalysts.
Potential-dependent transition of reaction mechanisms for oxygen evolution on layered double hydroxides
Authors: Wang Zeyu , Goddard William A. , Xiao Hai 
Published: July 2023

AbstractOxygen evolution reaction (OER) is of crucial importance to sustainable energy and environmental engineering, and layered double hydroxides (LDHs) are among the most active catalysts for OER in alkaline conditions, but the reaction mechanism for OER on LDHs remains controversial. Distinctive types of reaction mechanisms have been proposed for the O-O coupling in OER, yet they compose a coupled reaction network with competing kinetics dependent on applied potentials. Herein, we combine grand-canonical methods and micro-kinetic modeling to unravel that the nature of dominant mechanism for OER on LDHs transitions among distinctive types as a function of applied potential, and this arises from the interplay among applied potential and competing kinetics in the coupled reaction network. The theory-predicted overpotentials, Tafel slopes, and findings are in agreement with the observations of experiments including isotope labelling. Thus, we establish a computational methodology to identify and elucidate the potential-dependent mechanisms for electrochemical reactions.
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells
Authors: Barrena Naroa , Valcárcel Luis V. , Olaverri-Mendizabal Danel , Apaolaza Iñigo , Planes Francisco J. 
Published: July 2023

AbstractSynthetic lethality (SL) is a promising concept in cancer research. A wide array of computational tools has been developed to predict and exploit synthetic lethality for the identification of tumour-specific vulnerabilities. Previously, we introduced the concept of genetic Minimal Cut Sets (gMCSs), a theoretical approach to SL developed for genome-scale metabolic networks. The major challenge in our gMCS framework is to go beyond metabolic networks and extend existing algorithms to more complex protein-protein interactions. In this article, we take a step further and incorporate linear regulatory pathways into our gMCS approach. Extensive algorithmic modifications to compute gMCSs in integrated metabolic and regulatory models are presented in detail. Our extended approach is applied to calculate gMCSs in integrated models of human cells. In particular, we integrate the most recent genome-scale metabolic network, Human1, with 3 different regulatory network databases: Omnipath, Dorothea and TRRUST. Based on the computed gMCSs and transcriptomic data, we discovered new essential genes and their associated synthetic lethal for different cancer cell lines. The performance of the different integrated models is assessed with available large-scale in-vitro gene silencing data. Finally, we discuss the most relevant gene essentiality predictions based on published literature in cancer research.
Maternal and neonatal outcomes of COVID-19 vaccination during pregnancy, a systematic review and meta-analysis
Authors: Marchand Greg , Masoud Ahmed Taher , Grover Sandeep , King Alexa , Brazil Giovanna , Ulibarri Hollie , Parise Julia , Arroyo Amanda , Coriell Catherine , Goetz Sydnee , Moir Carmen , Govindan Malini , Moberly Atley , Proctor Anna , Sainz Katelyn , Blumrick Richard 
Published: July 2023

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is associated with increased pregnancy complications. Despite effective vaccination strategies for the general population, the evidence on the safety and efficacy of Coronavirus disease 2019 (COVID-19) vaccinations in pregnancy is limited due to a lack of well-powered studies. The present study compares the maternal, neonatal, and immunological outcomes between vaccinated pregnant and unvaccinated pregnant women using a systematic review and meta-analysis approach. We included 37 studies with a total of 141,107 pregnant women (36.8% vaccinated) spread across all outcomes. Our evidence indicates a higher rate of cesarean section in the 1898 vaccinated pregnant women compared to the 6180 women who did not receive vaccination (OR = 1.20, CI = (1.05, 1.38), P = 0.007, I2 = 45%). Regarding immunological outcomes, the risk of SARS-CoV-2 infection during pregnancy or postpartum was significantly reduced in 6820 vaccinated pregnant women compared to 17,010 unvaccinated pregnant women (OR = 0.25, CI = 0.13–0.48, P < 0.0001, I2 = 61%), as evident from qualitative assessment indicating significantly higher postpartum antibody titers compared to that observed in both unvaccinated mothers and mothers who have recently recovered from a SARS-CoV-2 infection. Our analysis represents high quality evidence showing that COVID-19 vaccination effectively raises antibody titers against SARS-CoV-2. This may confer protection against infection during pregnancy and the postpartum period. In addition to being protective against SARS-CoV-2, the vaccine was associated with decreased odds of preterm delivery. Furthermore, COVID-19 vaccination may also be associated with higher odds of cesarean section.
Distribution and abundance of Peleng Tarsier (Tarsius pelengensis) in Banggai Island group, Indonesia
Authors: Syahrullah Fakhri Naufal , Maddus Un , Mustari Abdul Haris , Gursky Sharon , Indrawan Mochamad 
Published: July 2023

AbstractThe Peleng tarsier (Tarsius pelengensis) is poorly known primate, with a range limited to Banggai island-group, Central Sulawesi, Indonesia. It was classified as “Endangered” by IUCN in 2017 based on extremely limited demographic and distributional data. The aim of this study was to collect and analyze data on the population and distribution of Peleng tarsiers. Surveys were conducted over approximately 5 months in 2017 and 2018 across Peleng and the neighboring islands of Banggai, Labobo, and Bangkurung. We determined that tarsiers only occur on Peleng and Banggai Island. The average population density in Peleng and Banggai was estimated to be 234 individuals/km2. This is comparable to the broad ranges of tarsier densities throughout Sulawesi and offshore islands. Peleng tarsiers were found in all elevations (0–937 m above sea level) and nearly all vegetated habitats in Peleng island. Using the IUCN criteria for determining conservation status, in conjunction with our new data, we believe that the Peleng tarsier population should be classified as “Vulnerable”.
Decoding information about cognitive health from the brainwaves of sleep
Authors: Adra Noor , Dümmer Lisa W. , Paixao Luis , Tesh Ryan A. , Sun Haoqi , Ganglberger Wolfgang , Westmeijer Mike , Da Silva Cardoso Madalena , Kumar Anagha , Ye Elissa , Henry Jonathan , Cash Sydney S. , Kitchener Erin , Leveroni Catherine L. , Au Rhoda , Rosand Jonathan , Salinas Joel , Lam Alice D. , Thomas Robert J. , Westover M. Brandon 
Published: July 2023

AbstractSleep electroencephalogram (EEG) signals likely encode brain health information that may identify individuals at high risk for age-related brain diseases. Here, we evaluate the correlation of a previously proposed brain age biomarker, the “brain age index” (BAI), with cognitive test scores and use machine learning to develop and validate a series of new sleep EEG-based indices, termed “sleep cognitive indices” (SCIs), that are directly optimized to correlate with specific cognitive scores. Three overarching cognitive processes were examined: total, fluid (a measure of cognitive processes involved in reasoning-based problem solving and susceptible to aging and neuropathology), and crystallized cognition (a measure of cognitive processes involved in applying acquired knowledge toward problem-solving). We show that SCI decoded information about total cognition (Pearson’s r = 0.37) and fluid cognition (Pearson’s r = 0.56), while BAI correlated only with crystallized cognition (Pearson’s r = − 0.25). Overall, these sleep EEG-derived biomarkers may provide accessible and clinically meaningful indicators of neurocognitive health.
A perceptual field test in object experts using gaze-contingent eye tracking
Authors: Hagen Simen , Vuong Quoc C. , Jung Liandra , Chin Michael D. , Scott Lisa S. , Tanaka James W. 
Published: July 2023

AbstractA hallmark of expert object recognition is rapid and accurate subordinate-category recognition of visually homogenous objects. However, the perceptual strategies by which expert recognition is achieved is less known. The current study investigated whether visual expertise changes observers’ perceptual field (e.g., their ability to use information away from fixation for recognition) for objects in their domain of expertise, using a gaze-contingent eye-tracking paradigm. In the current study, bird experts and novices were presented with two bird images sequentially, and their task was to determine whether the two images were of the same species (e.g., two different song sparrows) or different species (e.g., song sparrow and chipping sparrow). The first study bird image was presented in full view. The second test bird image was presented fully visible (full-view), restricted to a circular window centered on gaze position (central-view), or restricted to image regions beyond a circular mask centered on gaze position (peripheral-view). While experts and novices did not differ in their eye-movement behavior, experts’ performance on the discrimination task for the fastest responses was less impaired than novices in the peripheral-view condition. Thus, the experts used peripheral information to a greater extent than novices, indicating that the experts have a wider perceptual field to support their speeded subordinate recognition.