bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic representation of many-body quantum states
Authors: Atanasova Hristiana , Bernheimer Liam , Cohen Guy 
Published: June 2023

AbstractThe quantum many-body problem is ultimately a curse of dimensionality: the state of a system with many particles is determined by a function with many dimensions, which rapidly becomes difficult to efficiently store, evaluate and manipulate numerically. On the other hand, modern machine learning models like deep neural networks can express highly correlated functions in extremely large-dimensional spaces, including those describing quantum mechanical problems. We show that if one represents wavefunctions as a stochastically generated set of sample points, the problem of finding ground states can be reduced to one where the most technically challenging step is that of performing regression—a standard supervised learning task. In the stochastic representation the (anti)symmetric property of fermionic/bosonic wavefunction can be used for data augmentation and learned rather than explicitly enforced. We further demonstrate that propagation of an ansatz towards the ground state can then be performed in a more robust and computationally scalable fashion than traditional variational approaches allow.
Resource-aware construct design in mammalian cells
Authors: Di Blasi Roberto , Pisani Mara , Tedeschi Fabiana , Marbiah Masue M. , Polizzi Karen , Furini Simone , Siciliano Velia , Ceroni Francesca 
Published: June 2023

AbstractResource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report the quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits and optimise the co-expression of transfected cassettes, shedding light on how this can be useful for bioproduction and biotherapeutic applications. This work provides the scientific community with a framework to consider resource demand when designing mammalian constructs to achieve robust and optimised gene expression.
Understanding capacity fade in organic redox-flow batteries by combining spectroscopy with statistical inference techniques
Authors: Modak Sanat Vibhas , Shen Wanggang , Singh Siddhant , Herrera Dylan , Oudeif Fairooz , Goldsmith Bryan R. , Huan Xun , Kwabi David G. 
Published: June 2023

AbstractOrganic redox-active molecules are attractive as redox-flow battery (RFB) reactants because of their low anticipated costs and widely tunable properties. Unfortunately, many lab-scale flow cells experience rapid material degradation (from chemical and electrochemical decay mechanisms) and capacity fade during cycling (>0.1%/day) hindering their commercial deployment. In this work, we combine ultraviolet-visible spectrophotometry and statistical inference techniques to elucidate the Michael attack decay mechanism for 4,5-dihydroxy-1,3-benzenedisulfonic acid (BQDS), a once-promising positive electrolyte reactant for aqueous organic redox-flow batteries. We use Bayesian inference and multivariate curve resolution on the spectroscopic data to derive uncertainty-quantified reaction orders and rates for Michael attack, estimate the spectra of intermediate species and establish a quantitative connection between molecular decay and capacity fade. Our work illustrates the promise of using statistical inference to elucidate chemical and electrochemical mechanisms of capacity fade in organic redox-flow battery together with uncertainty quantification, in flow cell-based electrochemical systems.
Structure and antigenicity of divergent Henipavirus fusion glycoproteins
Authors: Isaacs Ariel , Low Yu Shang , Macauslane Kyle L. , Seitanidou Joy , Pegg Cassandra L. , Cheung Stacey T. M. , Liang Benjamin , Scott Connor A. P. , Landsberg Michael J. , Schulz Benjamin L. , Chappell Keith J. , Modhiran Naphak , Watterson Daniel 
Published: June 2023

AbstractIn August 2022, a novel henipavirus (HNV) named Langya virus (LayV) was isolated from patients with severe pneumonic disease in China. This virus is closely related to Mòjiāng virus (MojV), and both are divergent from the bat-borne HNV members, Nipah (NiV) and Hendra (HeV) viruses. The spillover of LayV is the first instance of a HNV zoonosis to humans outside of NiV and HeV, highlighting the continuing threat this genus poses to human health. In this work, we determine the prefusion structures of MojV and LayV F proteins via cryogenic electron microscopy to 2.66 and 3.37 Å, respectively. We show that despite sequence divergence from NiV, the F proteins adopt an overall similar structure but are antigenically distinct as they do not react to known antibodies or sera. Glycoproteomic analysis revealed that while LayV F is less glycosylated than NiV F, it contains a glycan that shields a site of vulnerability previously identified for NiV. These findings explain the distinct antigenic profile of LayV and MojV F, despite the extent to which they are otherwise structurally similar to NiV. Our results carry implications for broad-spectrum HNV vaccines and therapeutics, and indicate an antigenic, yet not structural, divergence from prototypical HNVs.
Sexual selection for both diversity and repetition in birdsong
Authors: Sierro Javier , de Kort Selvino R. , Hartley Ian R. 
Published: June 2023

AbstractFrom fiddler crabs to humans, animals perform repetitive displays showing neuromotor skill and vigour. Consistent repetition of identical notes (vocal consistency) facilitates the assessment of neuromotor skills and is important in communication in birds. Most birdsong research has focused on song diversity as a signal of individual quality, which seems contradictory as repetition is extremely common in most species. Here we show that consistent repetition within songs is positively correlated with reproductive success in male blue tits (Cyanistes caeruleus). A playback experiment shows that females are sexually aroused by male songs with high levels of vocal consistency, which also peaks seasonally during the fertile period of the female, supporting the role of vocal consistency in mate choice. Male vocal consistency also increases with subsequent repetitions of the same song type (a warm-up effect) which conflicts with the fact that females habituate to repeated song, showing decreased arousal. Importantly, we find that switching song types elicits significant dishabituation within the playback, supporting the habituation hypothesis as an evolutionary mechanism driving song diversity in birds. An optimal balance between repetition and diversity may explain the singing style of many bird species and displays of other animals.
Ratiometric measurement of MAM Ca2+ dynamics using a modified CalfluxVTN
Authors: Cho Eunbyul , Woo Youngsik , Suh Yeongjun , Suh Bo Kyoung , Kim Soo Jeong , Nhung Truong Thi My , Yoo Jin Yeong , Nghi Tran Diem , Lee Su Been , Mun Dong Jin , Park Sang Ki 
Published: June 2023

AbstractMitochondria-associated ER membrane (MAM) is a structure where these calcium-regulating organelles form close physical contact sites for efficient Ca2+crosstalk. Despite the central importance of MAM Ca2+dynamics in diverse biological processes, directly and specifically measuring Ca2+concentrations inside MAM is technically challenging. Here, we develop MAM-Calflux, a MAM-specific BRET-based Ca2+indicator. The successful application of the bimolecular fluorescence complementation (BiFC) concept highlights Ca2+-responsive BRET signals in MAM. The BiFC strategy imparts dual functionality as a Ca2+indicator and quantitative structural marker specific for MAM. As a ratiometric Ca2+indicator, MAM-Calflux estimates steady-state MAM Ca2+levels. Finally, it enables the visualization of uneven intracellular distribution of MAM Ca2+and the elucidation of abnormally accumulated MAM Ca2+from the neurons of Parkinson’s disease mouse model in both steady-state and stimulated conditions. Therefore, we propose that MAM-Calflux can be a versatile tool for ratiometrically measuring dynamic inter-organellar Ca2+communication.
Tunable CO2 electroreduction to ethanol and ethylene with controllable interfacial wettability
Authors: Lin Yan , Wang Tuo , Zhang Lili , Zhang Gong , Li Lulu , Chang Qingfeng , Pang Zifan , Gao Hui , Huang Kai , Zhang Peng , Zhao Zhi-Jian , Pei Chunlei , Gong Jinlong 
Published: June 2023

AbstractThe mechanism of how interfacial wettability impacts the CO2 electroreduction pathways to ethylene and ethanol remains unclear. This paper describes the design and realization of controllable equilibrium of kinetic-controlled *CO and *H via modifying alkanethiols with different alkyl chain lengths to reveal its contribution to ethylene and ethanol pathways. Characterization and simulation reveal that the mass transport of CO2 and H2O is related with interfacial wettability, which may result in the variation of kinetic-controlled *CO and *H ratio, which affects ethylene and ethanol pathways. Through modulating the hydrophilic interface to superhydrophobic interface, the reaction limitation shifts from insufficient supply of kinetic-controlled *CO to that of *H. The ethanol to ethylene ratio can be continuously tailored in a wide range from 0.9 to 1.92, with remarkable Faradaic efficiencies toward ethanol and multi-carbon (C2+) products up to 53.7% and 86.1%, respectively. A C2+ Faradaic efficiency of 80.3% can be achieved with a high C2+ partial current density of 321 mA cm−2, which is among the highest selectivity at such current densities.
Chromatin remodeling by Pol II primes efficient Pol III transcription
Authors: Yague-Sanz Carlo , Migeot Valérie , Larochelle Marc , Bachand François , Wéry Maxime , Morillon Antonin , Hermand Damien 
Published: June 2023

AbstractThe packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is coupled with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here a mechanism where RNA Polymerase II (Pol II) transcription is required to prime and maintain nucleosome depletion at Pol III loci and contributes to efficient Pol III recruitment upon re-initiation of growth from stationary phase in Fission yeast. The Pcr1 transcription factor participates in the recruitment of Pol II, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These data expand the central role of Pol II in gene expression beyond mRNA synthesis.
A short dasatinib and quercetin treatment is sufficient to reinstate potent adult neuroregenesis in the aged killifish
Authors: Van houcke Jolien , Mariën Valerie , Zandecki Caroline , Ayana Rajagopal , Pepermans Elise , Boonen Kurt , Seuntjens Eve , Baggerman Geert , Arckens Lutgarde 
Published: June 2023

AbstractThe young African turquoise killifish has a high regenerative capacity, but loses it with advancing age, adopting several aspects of the limited form of mammalian regeneration. We deployed a proteomic strategy to identify pathways that underpin the loss of regenerative power caused by aging. Cellular senescence stood out as a potential brake on successful neurorepair. We applied the senolytic cocktail Dasatinib and Quercetin (D + Q) to test clearance of chronic senescent cells from the aged killifish central nervous system (CNS) as well as rebooting the neurogenic output. Our results show that the entire aged killifish telencephalon holds a very high senescent cell burden, including the parenchyma and the neurogenic niches, which could be diminished by a short-term, late-onset D + Q treatment. Reactive proliferation of non-glial progenitors increased substantially and lead to restorative neurogenesis after traumatic brain injury. Our results provide a cellular mechanism for age-related regeneration resilience and a proof-of-concept of a potential therapy to revive the neurogenic potential in an already aged or diseased CNS.
Ontogenetic transitions, biomechanical trade-offs and macroevolution of scyphozoan medusae swimming patterns
Authors: von Montfort Guilherme M. , Costello John H. , Colin Sean P. , Morandini André C. , Migotto Alvaro E. , Maronna Maximiliano M. , Reginato Marcelo , Miyake Hiroshi , Nagata Renato M. 
Published: June 2023

AbstractEphyrae, the early stages of scyphozoan jellyfish, possess a conserved morphology among species. However, ontogenetic transitions lead to morphologically different shapes among scyphozoan lineages, with important consequences for swimming biomechanics, bioenergetics and ecology. We used high-speed imaging to analyse biomechanical and kinematic variables of swimming in 17 species of Scyphozoa (1 Coronatae, 8 “Semaeostomeae” and 8 Rhizostomeae) at different developmental stages. Swimming kinematics of early ephyrae were similar, in general, but differences related to major lineages emerged through development. Rhizostomeae medusae have more prolate bells, shorter pulse cycles and higher swimming performances. Medusae of “Semaeostomeae”, in turn, have more variable bell shapes and most species had lower swimming performances. Despite these differences, both groups travelled the same distance per pulse suggesting that each pulse is hydrodynamically similar. Therefore, higher swimming velocities are achieved in species with higher pulsation frequencies. Our results suggest that medusae of Rhizostomeae and “Semaeostomeae” have evolved bell kinematics with different optimized traits, rhizostomes optimize rapid fluid processing, through faster pulsations, while “semaeostomes” optimize swimming efficiency, through longer interpulse intervals that enhance mechanisms of passive energy recapture.
A global perspective on the intrinsic dimensionality of COVID-19 data
Authors: Varghese Abhishek , Santos-Fernandez Edgar , Denti Francesco , Mira Antonietta , Mengersen Kerrie 
Published: June 2023

AbstractWe develop a novel global perspective of the complexity of the relationships between three COVID-19 datasets, the standardised per-capita growth rate of COVID-19 cases and deaths, and the Oxford Coronavirus Government Response Tracker COVID-19 Stringency Index (CSI) which is a measure describing a country’s stringency of lockdown policies. We use a state-of-the-art heterogeneous intrinsic dimension estimator implemented as a Bayesian mixture model, called Hidalgo. Our findings suggest that these highly popular COVID-19 statistics may project onto two low-dimensional manifolds without significant information loss, suggesting that COVID-19 data dynamics are generated from a latent mechanism characterised by a few important variables. The low dimensionality imply a strong dependency among the standardised growth rates of cases and deaths per capita and the CSI for countries over 2020–2021. Importantly, we identify spatial autocorrelation in the intrinsic dimension distribution worldwide. The results show how high-income countries are more prone to lie on low-dimensional manifolds, likely arising from aging populations, comorbidities, and increased per capita mortality burden from COVID-19. Finally, the temporal stratification of the dataset allows the examination of the intrinsic dimension at a more granular level throughout the pandemic.
Photo-elasticity of silk fibroin harnessing whispering gallery modes
Authors: Korakas Nikolaos , Vurro Davide , Tsilipakos Odysseas , Vasileiadis Thomas , Graczykowski Bartlomiej , Cucinotta Annamaria , Selleri Stefano , Fytas George , Iannotta Salvatore , Pissadakis Stavros 
Published: June 2023

AbstractSilk fibroin is an important biomaterial for photonic devices in wearable systems. The functionality of such devices is inherently influenced by the stimulation from elastic deformations, which are mutually coupled through photo-elasticity. Here, we investigate the photo-elasticity of silk fibroin employing optical whispering gallery mode resonation of light at the wavelength of 1550 nm. The fabricated amorphous (Silk I) and thermally-annealed semi-crystalline structure (Silk II) silk fibroin thin film cavities display typical Q-factors of about 1.6 × 104. Photo-elastic experiments are performed tracing the TE and TM shifts of the whispering gallery mode resonances upon application of an axial strain. The strain optical coefficient K’ for Silk I fibroin is found to be 0.059 ± 0.004, with the corresponding value for Silk II being 0.129 ± 0.004. Remarkably, the elastic Young’s modulus, measured by Brillouin light spectroscopy, is only about 4% higher in the Silk II phase. However, differences between the two structures are pronounced regarding the photo-elastic properties due to the onset of β-sheets that dominates the Silk II structure.
Effect of light intensity in the nest site on eggshell pigmentation in a hole-nesting passerine
Authors: Malinowska Katarzyna , Szala Klaudia , Podkowa Paweł , Surmacki Adrian 
Published: June 2023

AbstractDaylight is an important factor necessary for the proper embryonic development of birds, which raises the question, what happens when birds nest in relatively dim sites? The study experimentally tested whether there is a relationship between light conditions at the nesting site and the protoporphyrin-based pigmentation in the eggshell of the Great Tit (Parus major). We hypothesised that at lower light levels, eggs are less pigmented to increase the amount of light reaching the embryo. Our study system consisted of two types of nest boxes: "dark", in which the only source of light was the entrance hole, and "bright", which had two additional side windows. Photographs of clutches taken during the incubation period were used to quantify eggshell pigmentation. Multispectral image analyses were performed to measure variables correlating with protoporphyrin content, such as spot brightness, average spot size, spotting coverage, and spot red chroma. Repeatability analysis indicated that eggshell colouration characteristics were significantly and moderately repeatable between eggs from a single clutch, which suggests that they are under genetic and environmental control. However, none of the pigmentation traits differed significantly between the two types of nest boxes. We speculate about other ecological aspects that might have influenced the observed variability in eggshell pigmentation.
X-ray source arrays for volumetric imaging during radiotherapy treatment
Authors: Dillon Owen , Reynolds Tess , O’Brien Ricky T. 
Published: June 2023

AbstractThis work presents a novel hardware configuration for radiotherapy systems to enable fast 3D X-ray imaging before and during treatment delivery. Standard external beam radiotherapy linear accelerators (linacs) have a single X-ray source and detector located at ± 90° from the treatment beam respectively. The entire system can be rotated around the patient acquiring multiple 2D X-ray images to create a 3D cone-beam Computed Tomography (CBCT) image before treatment delivery to ensure the tumour and surrounding organs align with the treatment plan. Scanning with a single source is slow relative to patient respiration or breath holds and cannot be performed during treatment delivery, limiting treatment delivery accuracy in the presence of patient motion and excluding some patients from concentrated treatment plans that would be otherwise expected to have improved outcomes. This simulation study investigated whether recent advances in carbon nanotube (CNT) field emission source arrays, high frame rate (60 Hz) flat panel detectors and compressed sensing reconstruction algorithms could circumvent imaging limitations of current linacs. We investigated a novel hardware configuration incorporating source arrays and high frame rate detectors into an otherwise standard linac. We investigated four potential pre-treatment scan protocols that could be achieved in a 17 s breath hold or 2–10 1 s breath holds. Finally, we demonstrated for the first time volumetric X-ray imaging during treatment delivery by using source arrays, high frame rate detectors and compressed sensing. Image quality was assessed quantitatively over the CBCT geometric field of view as well as across each axis through the tumour centroid. Our results demonstrate that source array imaging enables larger volumes to be imaged with acquisitions as short as 1 s albeit with reduced image quality arising from lower photon flux and shorter imaging arcs.
Sitagliptin ameliorates busulfan-induced pulmonary and testicular injury in rats through antioxidant, anti-inflammatory, antifibrotic, and antiapoptotic effects
Authors: Ali Eman A. , Tayel Sara G. , Abbas Mona A. 
Published: June 2023

AbstractBusulfan (BUS) is an anticancer agent with serious adverse effects on various body organs, including the lung and testis. Sitagliptin was proven to have antioxidant, anti-inflammatory, antifibrotic, and antiapoptotic effects. This study aims to evaluate whether sitagliptin, a DPP4I, ameliorates BUS-induced pulmonary and testicular injury in rats. Male Wistar rats were split into control, sitagliptin (10 mg/kg), BUS (30 mg/kg), and sitagliptin + BUS groups. Weight change, lung and testis indices, serum testosterone, sperm parameters, markers of oxidative stress [malondialdehyde (MDA) and reduced glutathione (GSH)], inflammation [tumor necrosis factor-alpha (TNF-α)], and relative expression of sirtuin1 (SIRT1) and forkhead box protein type O1 (FOXO1) genes were estimated. Histopathological examination of lung and testicular tissues was done to detect architectural changes [Hematoxylin & Eosin (H&E)], fibrosis (Masson’s trichrome), and apoptosis (caspase-3). Sitagliptin treatment reduced body weight loss, lung index, lung and testis MDA, serum TNF-α and sperm abnormal morphology, and increased testis index, lung and testis GSH, serum testosterone, sperm count, viability and motility. SIRT1/FOXO1 balance was restored. Also, sitagliptin attenuated fibrosis and apoptosis in lung and testicular tissues via reducing collagen deposition and caspase-3 expression. Accordingly, sitagliptin ameliorated BUS-induced pulmonary and testicular damage in rats via attenuating oxidative stress, inflammation, fibrosis, and apoptosis.