bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum coherence tomography of light-controlled superconductivity
Authors: Luo L. , Mootz M. , Kang J. H. , Huang C. , Eom K. , Lee J. W. , Vaswani C. , Collantes Y. G. , Hellstrom E. E. , Perakis I. E. , Eom C. B. , Wang J. 
Published: December 2022

AbstractThe coupling between superconductors and oscillation cycles of light pulses, i.e., lightwave engineering, is an emerging control concept for superconducting quantum electronics. Although progress has been made towards terahertz-driven superconductivity and supercurrents, the interactions able to drive non-equilibrium pairing are still poorly understood, partially due to the lack of measurements of high-order correlation functions. In particular, the sensing of exotic collective modes that would uniquely characterize light-driven superconducting coherence, in a way analogous to the Meissner effect, is very challenging but much needed. Here we report the discovery of parametrically driven superconductivity by light-induced order-parameter collective oscillations in iron-based superconductors. The time-periodic relative phase dynamics between the coupled electron and hole bands drives the transition to a distinct parametric superconducting state out-of-equalibrium. This light-induced emergent coherence is characterized by a unique phase–amplitude collective mode with Floquet-like sidebands at twice the Higgs frequency. We measure non-perturbative, high-order correlations of this parametrically driven superconductivity by separating the terahertz-frequency multidimensional coherent spectra into pump–probe, Higgs mode and bi-Higgs frequency sideband peaks. We find that the higher-order bi-Higgs sidebands dominate above the critical field, which indicates the breakdown of susceptibility perturbative expansion in this parametric quantum matter.
Cohesin and CTCF control the dynamics of chromosome folding
Authors: Mach Pia , Kos Pavel I. , Zhan Yinxiu , Cramard Julie , Gaudin Simon , Tünnermann Jana , Marchi Edoardo , Eglinger Jan , Zuin Jessica , Kryzhanovska Mariya , Smallwood Sebastien , Gelman Laurent , Roth Gregory , Nora Elphège P. , Tiana Guido , Giorgetti Luca 
Published: December 2022

AbstractIn mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.
Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint
Authors: Tamman Hedvig , Ernits Karin , Roghanian Mohammad , Ainelo Andres , Julius Christina , Perrier Anthony , Talavera Ariel , Ainelo Hanna , Dugauquier Rémy , Zedek Safia , Thureau Aurelien , Pérez Javier , Lima-Mendez Gipsi , Hallez Régis , Atkinson Gemma C. , Hauryliuk Vasili , Garcia-Pino Abel 
Published: December 2022

AbstractStringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of ‘long’-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis.
Defectronics based photoelectrochemical properties of Cu2+ ion doped hematite thin film
Authors: Kim Chang Woo , Pawar Amol U. , Hawari Thomi , Ahn Na Hyeon , Lee Don Keun , Yang Long , Sivasankaran Ramesh Poonchi , Tang Jun , Zhuo Zhongbiao , Kang Young Soo 
Published: December 2022

AbstractThe concentration of guest elements (dopants) into host materials play an important role in changing their intrinsic electrical and optical properties. The existence of hetero-element induce defect in crystal structure, affecting conductivity. In the current work, we report Cu2+ ion into hematite in the defectronics point of view and their photoelectrochemical properties. Crystal distortion in the structure of hematite is observed as the amount of dopant increases. Among 1, 3 and 5 mol% of Cu2+ doped hematite, the existence of 1 mol% of Cu2+ ion into hematite crystal structure produce photocurrent value of 0.15 mA/cm2, IPCE value of ~ 4.7% and EIS value of ~ 2000 Ω/cm2 as best performances. However, further increasing dopants increases the number of interstitial defects, which cause the deformation of intrinsic lattice structure.
Impacts of climate variability and land use on the blue and green water resources in a subtropical basin of China
Authors: Liu Meibing , Wang Di , Chen Xingwei , Chen Ying , Gao Lu , Deng Haijun 
Published: December 2022

AbstractWater scarcity has become a global severe challenge over the past few decades. Quantifying the impact of climate variability and land use on water resource availability is crucial for integrated water resource management. Many studies have focused on blue water but ignored green water which is important in the terrestrial ecosystem, especially on different temporal scales. In this study, we selected the Shanmei Reservoir, the most import drinking water resource for a rapidly development city of Southeast China, as a case for analysis of these impacts for the entire basin. We adopted the Soil and Water Assessment Tool (SWAT) to investigate the spatial and temporal distributions of blue water (BW), green water flow (GWF) and green water storage (GWS) in the Shanmei Reservoir Basin (SRB). The results of the blue and green water components (BW and GW) revealed that SRB is dominated by BW, accounting for 52.6% of the total water resources, while GW accounted for 47.4%. There was an insignificant upward trend of BW and a significant upward trend of GWF, with a tendency rate of 1.125 mm a−1. Precipitation was the key factor affecting BW on annual and monthly scales. The GWF was more sensitive to temperature at both the annual and monthly scales. The GWS was significantly correlated with precipitation at the monthly scale, while insignificant correlation occurred at the annual scale. The spatial distribution of BW was largely dominated by precipitation, and land-use types led to the differentiation of GW. It indicates that the BW of paddy fields is greater than that of forests, while the GWS of forests is greater than that of orchards and rainfed croplands.
Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors
Authors: Kim Hoshin , Hauner Darin , Laureanti Joseph A. , Agustin Kruel , Raugei Simone , Kumar Neeraj 
Published: December 2022

AbstractTargeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (MPRO), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against MPRO. Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of MPRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient MPRO inhibitors.
5-HT-dependent synaptic plasticity of the prefrontal cortex in postnatal development
Authors: Higa Guilherme Shigueto Vilar , Francis-Oliveira José , Carlos-Lima Estevão , Tamais Alicia Moraes , Borges Fernando da Silva , Kihara Alexandre Hiroaki , Shieh Ianê Carvalho , Ulrich Henning , Chiavegatto Silvana , De Pasquale Roberto 
Published: December 2022

AbstractImportant functions of the prefrontal cortex (PFC) are established during early life, when neurons exhibit enhanced synaptic plasticity and synaptogenesis. This developmental stage drives the organization of cortical connectivity, responsible for establishing behavioral patterns. Serotonin (5-HT) emerges among the most significant factors that modulate brain activity during postnatal development. In the PFC, activated 5-HT receptors modify neuronal excitability and interact with intracellular signaling involved in synaptic modifications, thus suggesting that 5-HT might participate in early postnatal plasticity. To test this hypothesis, we employed intracellular electrophysiological recordings of PFC layer 5 neurons to study the modulatory effects of 5-HT on plasticity induced by theta-burst stimulation (TBS) in two postnatal periods of rats. Our results indicate that 5-HT is essential for TBS to result in synaptic changes during the third postnatal week, but not later. TBS coupled with 5-HT2A or 5-HT1A and 5-HT7 receptors stimulation leads to long-term depression (LTD). On the other hand, TBS and synergic activation of 5-HT1A, 5-HT2A, and 5-HT7 receptors lead to long-term potentiation (LTP). Finally, we also show that 5-HT dependent synaptic plasticity of the PFC is impaired in animals that are exposed to early-life chronic stress.
Prevalence and associated risk factors of tinnitus among adult Palestinians: a cross-sectional study
Authors: Al-Lahham Saad , Nazzal Zaher , Massarweh Ahmad , Saymeh Diana , Al-abed Sojoud , Muhammad Donia , Alawni Raghda , Bouzya Noor , Alqub Malik , Ghanim Mustafa , Ellahham Nael 
Published: December 2022

AbstractTinnitus is a common complaint with potentially negative impact on quality of life. Prevalence of tinnitus ranges from 5 to 43% worldwide. This variation could be due to the heterogeneity of tinnitus assessment. This has limited the progress in understanding tinnitus. Therefore, we employed a standardized and a validated assessment method to determine the prevalence and related risk factors of tinnitus among Palestinians for the first time. This is a cross-sectional study in which we questioned a representative sample of 618 subjects in one-to-one interviews. The prevalence of any tinnitus was 30.6% among adult Palestinians. Participants from the oldest age group were almost five times more likely to have tinnitus. Moreover, participants with head and neck pain syndrome, severe hearing impairment, sleeping disorders or frequent complaints of vertigo were approximately two times more likely to have tinnitus. Our study provides novel information regarding tinnitus in Palestine and improves our understanding of tinnitus. This will improve the diagnosis and consequently will contribute in reducing the prevalence and perhaps in preventing tinnitus. As tinnitus still has no known cure, further investigations of modifiable risk factors and causes of tinnitus are crucial to prevent it in the future.
Identification of three new ‘Candidatus Liberibacter solanacearum’ haplotypes in four psyllid species (Hemiptera: Psylloidea)
Authors: Grimm Kylie D. Swisher , Horton David R. , Lewis Tamera M. , Garczynski Stephen F. , Jensen Andrew S. , Charlton Brian A. 
Published: December 2022

AbstractEleven haplotypes of the bacterium, ‘Candidatus Liberibacter solanacearum’, have been identified worldwide, several of which infect important agricultural crops. In the United States, haplotypes A and B are associated with yield and quality losses in potato, tomato, and other crops of the Solanaceae. Both haplotypes are vectored by potato psyllid, Bactericera cockerelli. Recently, a third haplotype, designated F, was identified in southern Oregon potato fields. To identify the vector of this haplotype, psyllids of multiple species were collected from yellow sticky cards placed near potato fields during two growing seasons. Over 2700 specimens were tested for ‘Ca. L. solanacearum’ by polymerase chain reaction. Forty-seven psyllids harbored the bacterium. The infected specimens comprised four psyllid species in two families, Aphalaridae and Triozidae (Hemiptera: Psylloidea). Nucleic acid and/or amino acid sequence analysis of the ‘Ca. L. solanacearum’ 16S ribosomal RNA, 50S ribosomal proteins L10/L12, and outer membrane protein identified three new haplotypes of the bacterium, designated as Aph1, Aph2 and Aph3, including two variants of Aph2 (Aph2a and Aph2b). The impact of these new haplotypes on solanaceous or other crops is not known. The vector of ‘Ca. L. solanacearum’ haplotype F was not detected in this study.
Decoding the cognitive states of attention and distraction in a real-life setting using EEG
Authors: Kaushik Pallavi , Moye Amir , Vugt Marieke van , Roy Partha Pratim 
Published: December 2022

AbstractLapses in attention can have serious consequences in situations such as driving a car, hence there is considerable interest in tracking it using neural measures. However, as most of these studies have been done in highly controlled and artificial laboratory settings, we want to explore whether it is also possible to determine attention and distraction using electroencephalogram (EEG) data collected in a natural setting using machine/deep learning. 24 participants volunteered for the study. Data were collected from pairs of participants simultaneously while they engaged in Tibetan Monastic debate, a practice that is interesting because it is a real-life situation that generates substantial variability in attention states. We found that attention was on average associated with increased left frontal alpha, increased left parietal theta, and decreased central delta compared to distraction. In an attempt to predict attention and distraction, we found that a Long Short Term Memory model classified attention and distraction with maximum accuracy of 95.86% and 95.4% corresponding to delta and theta waves respectively. This study demonstrates that EEG data collected in a real-life setting can be used to predict attention states in participants with good accuracy, opening doors for developing Brain-Computer Interfaces that track attention in real-time using data extracted in daily life settings, rendering them much more usable.
Dominant phytoplankton groups as the major source of polyunsaturated fatty acids for hilsa (Tenualosa ilisha) in the Meghna estuary Bangladesh
Authors: Shaha Dinesh Chandra , Hasan Jahid , Kundu Sampa Rani , Yusoff Fatimah Md. , Salam Mohammad Abdus , Khan Murshida , Haque Farhana , Ahmed Minhaz , Rahman Mohammad Jalilur , Wahab Md. Abdul 
Published: December 2022

AbstractThe tropical estuarine ecosystem is fascinating for studying the dynamics of water quality and phytoplankton diversity due to its frequently changing hydrological conditions. Most importantly, phytoplankton is the main supplier of ω3 polyunsaturated fatty acids (PUFA) in the coastal food web for fish as they could not synthesize PUFA. This study evaluated seasonal variations of water quality parameters in the Meghna River estuary (MRE), explored how phytoplankton diversity changes according to hydro-chemical parameters, and identified the major phytoplankton groups as the main source of PUFA for hilsa fish. Ten water quality indicators including temperature, dissolved oxygen, pH, salinity, dissolved inorganic nitrogen (DIN = nitrate, nitrite, ammonia) and phosphorus, dissolved silica and chlorophyll-a were evaluated. In addition, phytoplankton diversity was assessed in the water and hilsa fish gut. Principal component analysis (PCA) was used to analyze the spatio-temporal changes in the water quality conditions, and the driving factors in the MRE. Four main components were extracted and explained 75.4% variability of water quality parameters. The most relevant driving factors were dissolved oxygen, salinity, temperature, and DIN (nitrate, nitrite and ammonia). These variabilities in physicochemical parameters and dissolved inorganic nutrients caused seasonal variations in two major groups of phytoplankton. Peak abundance of Chlorophyta (green algae) occurred in water in nutrient-rich environments (nitrogen and phosphorus) during the wet (36%) season, while Bacillariophyta (diatoms) were dominant during the dry (32%) season that depleted dissolved silica. Thus, the decrease of green algae and the increase of diatoms in the dry season indicated the potential link to seasonal changes of hydro-chemical parameters. The green algae (53.7%) were the dominant phytoplankton group in the hilsa gut content followed by diatoms (22.6%) and both are contributing as the major source of PUFAs for hilsa fish according to the electivity index as they contain the highest amounts of PUFAs (60 and 28% respectively).
Vector coding reveals the underlying balance control strategies used by humans during translational perturbation
Authors: Taleshi Naser , Brownjohn James M. W. , Lamb Sarah E. , Zivanovic Stana , Williams Genevieve K. R. 
Published: December 2022

AbstractPostural control research has focused on standing balance experiments on platforms moving with relatively large amplitudes (0.1–0.2 m). This study investigated balance strategies while standing on a platform moving 4 mm in anterior-posterior direction with frequency scaled linearly from 0.4 to 6 Hz. Platform motion and kinematic and kinetic information for nine healthy participants were recorded using motion capture and force plate systems. Coordination between hip, knee and ankle joint torque, and centre of mass (COM) and centre of pressure (COP) motion was quantified by vector coding. Significant main effect of platform frequency for knee-ankle and COP-COM phase relationship was observed (p = 0.023, p = 0.016). At frequencies below 2.11 and 2.34 Hz, ankle strategy was recruited. With ankle strategy, in-phase COP-COM motion with COP dominancy occurred at frequencies below 2.19 and 2.23 Hz during scaling up and down, respectively. As platform frequency passed these values, COM dominated over COP which was followed by anti-phase knee-ankle torque, called a knee strategy, and anti-phase motion between the COP and COM that allowed COP to regain dominance over COM. Collectively, we reveal knee strategy as a new and relevant strategy in real-life settings, and transition between ankle and knee strategies that underpinned transition between COP-COM relative motion.
The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool
Authors: Wilkinson Melanie J. , Yamashita Risa , James Maddie E. , Bally Ian S. E. , Dillon Natalie L. , Ali Asjad , Hardner Craig M. , Ortiz-Barrientos Daniel 
Published: December 2022

AbstractGenomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
Disease-associated H58Y mutation affects the nuclear dynamics of human DNA topoisomerase IIβ
Authors: Morotomi-Yano Keiko , Hiromoto Yukiko , Higaki Takumi , Yano Ken-ichi 
Published: December 2022

AbstractDNA topoisomerase II (TOP2) is an enzyme that resolves DNA topological problems and plays critical roles in various nuclear processes. Recently, a heterozygous H58Y substitution in the ATPase domain of human TOP2B was identified from patients with autism spectrum disorder, but its biological significance remains unclear. In this study, we analyzed the nuclear dynamics of TOP2B with H58Y (TOP2B H58Y). Although wild-type TOP2B was highly mobile in the nucleus of a living cell, the nuclear mobility of TOP2B H58Y was markedly reduced, suggesting that the impact of H58Y manifests as low protein mobility. We found that TOP2B H58Y is insensitive to ICRF-187, a TOP2 inhibitor that halts TOP2 as a closed clamp on DNA. When the ATPase activity of TOP2B was compromised, the nuclear mobility of TOP2B H58Y was restored to wild-type levels, indicating the contribution of the ATPase activity to the low nuclear mobility. Analysis of genome-edited cells harboring TOP2B H58Y showed that TOP2B H58Y retains sensitivity to the TOP2 poison etoposide, implying that TOP2B H58Y can undergo at least a part of its catalytic reactions. Collectively, TOP2 H58Y represents a unique example of the relationship between a disease-associated mutation and perturbed protein dynamics.