bluuebunny/crossref_metadata_2025 huggingface dataset:
Recall Bias in Client-Reported Outcomes in Canine Orthopaedic Patients Using Clinical Metrology Instruments
Authors: Pappa Eirini , Maddox Thomas W. , Crystal Edward , Comerford Eithne J. , Tomlinson Andrew W.
Published: July 2023

Objective The aim of this study was to determine the accuracy of client recollection of their dogs' preconsultation status using clinical metrology instruments such as the Liverpool Osteoarthritis in Dogs (LOAD) and Canine Brief Pain Inventory (CBPI) questionnaires in dogs presenting to a referral orthopaedic clinic.

Study Design This is a longitudinal prospective cohort study of client-owned dogs presenting for investigations of lameness (n = 217). LOAD and CBPI questionnaires were completed by the owners at the first consultation (T0). Owners were contacted at 2 (T1), 6 (T2), and 12 (T3) months and asked to recall their dogs' T0 status by completing another LOAD and CBPI questionnaire. The agreement between the T0 and recalled LOAD and CBPI scores was determined using the two-way mixed effects intraclass correlation coefficient (ICC). The Wilcoxon signed-rank test was used to determine the difference between scores.

Results For the LOAD scores, there was moderate agreement between T0 and T1 (ICC: 0.64) and T0 and T2 (ICC: 0.53) scores and poor agreement between T0 and T3 (ICC: 0.496). For the CBPI Pain Severity Scores, there was poor agreement between T0 and all three subsequent time points (ICC < 0.5). For the CBPI Pain Interference Scores, there was moderate agreement between T0 and T1 (ICC: 0.57) and T2 (ICC: 0.56) scores and poor agreement between T0 and T3 (ICC: 0.43).

Conclusion The LOAD and CBPI questionnaires are subject to recall bias. Studies reporting retrospectively acquired CMI data should be interpreted with caution.
The price and income elasticities of natural gas demand in Azerbaijan: Is there room to export more?
Authors: Gurbanov Sarvar , Mikayilov Jeyhun I. , Mukhtarov Shahriyar , Maharramli Shahin
Published: July 2023

Natural gas is frequently introduced as a “transitional fuel”. Because burning natural gas emits less carbon dioxide emissions than burning either oil or coal. Additionally, the intermittent nature of low-carbon electricity generation creates imperative for using natural gas for power generation. The role of natural gas is currently under scrutiny as climate change transforms into a climate crisis. Meanwhile, share of natural gas in the primary energy consumption of Azerbaijan is 69%, while 94% of the country’s electricity is currently being generated in natural gas-fired power plants. In this manner, this paper estimates income and price elasticities of natural gas demand for the Azerbaijan case. In this study, various sets of estimation techniques are utilized. By modeling natural gas demand with different estimation methods, including Autoregressive Distributed Lagged Structural Time Series Modeling, Dynamic Ordinary Least Squares Method, Fully Modified Ordinary Least Squares, Canonical Cointegrating Regression, and General to Specific under Autometrics multi-path search machine learning algorithm, we try to find if there is room for the country to export more. All these utilized estimation methods confirmed the long-run income elasticity to be around 0.8, while the long-run price elasticity is around −0.1. Both estimations provide insights in terms of energy security and electricity security for policymakers during the implementation process of climate, energy, and environmental policy. Findings of this study classify natural as a necessity and normal good for the Azerbaijan case. The main policy implication of this study is that policymakers must enable and facilitate the availability of close renewable substitutes for residential and commercial customers. Estimated elasticities suggest that with rising national income, demand for natural gas will keep increasing, and efficient consumption will not be attainable with increasing prices. In the pursuit of export potential, findings suggest that it is more relevant to free up natural gas allocated from power generation by substituting it with renewable energy sources.
Transferability evaluation of the deep potential model for simulating water-graphene confined system
Authors: Liu Dongfei , Wu Jianzhong , Lu Diannan
Published: July 2023

Machine learning potentials (MLPs) are poised to combine the accuracy of ab initio predictions with the computational efficiency of classical molecular dynamics (MD) simulation. While great progress has been made over the last two decades in developing MLPs, there is still much to be done to evaluate their model transferability and facilitate their development. In this work, we construct two deep potential (DP) models for liquid water near graphene surfaces, Model S and Model F, with the latter having more training data. A concurrent learning algorithm (DP-GEN) is adopted to explore the configurational space beyond the scope of conventional ab initio MD simulation. By examining the performance of Model S, we find that an accurate prediction of atomic force does not imply an accurate prediction of system energy. The deviation from the relative atomic force alone is insufficient to assess the accuracy of the DP models. Based on the performance of Model F, we propose that the relative magnitude of the model deviation and the corresponding root-mean-square error of the original test dataset, including energy and atomic force, can serve as an indicator for evaluating the accuracy of the model prediction for a given structure, which is particularly applicable for large systems where density functional theory calculations are infeasible. In addition to the prediction accuracy of the model described above, we also briefly discuss simulation stability and its relationship to the former. Both are important aspects in assessing the transferability of the MLP model.
Surface phonon localization and heat flux regulation in nanophononic metamaterials
Authors: Zhang Jian , Zhang Haochun , Chen Shuai , Zhang Gang
Published: July 2023

Nanophononic metamaterials (NPM) have received surging research attention for thermal conductivity modification. The local resonance hybridization mechanism of NPM is of great significance to the performance optimization of heat flux regulation devices. In this Letter, using silicon nanofilm with a periodic array of nanopillars as example, we systemically studied the phonon localization effect and heat flux regulation. The results demonstrate that the phonon localization effect produced by the nanopillars is mainly concentrated in the region close to surface layer. Moreover, the effects of nanopillar height, spacing, and atomic mass of atoms in the nanopillars on the localization are also explored. Finally, the relationship between phonon localization and heat flux density is demonstrated through non-equilibrium molecular dynamics calculations. This study provides not only the better understanding of the phonon resonance hybridization mechanism in nanophononic metamaterials but also useful guidelines for the design of nanoscale heat flux regulation devices.
Mpemba effect in a Langevin system: Population statistics, metastability, and other exact results
Authors: Biswas Apurba , Rajesh R. , Pal Arnab
Published: July 2023

The Mpemba effect is a fingerprint of the anomalous relaxation phenomenon wherein an initially hotter system equilibrates faster than an initially colder system when both are quenched to the same low temperature. Experiments on a single colloidal particle trapped in a carefully shaped double well potential have demonstrated this effect recently [A. Kumar and J. Bechhoefer, Nature 584, 64 (2020)]. In a similar vein, here, we consider a piece-wise linear double well potential that allows us to demonstrate the Mpemba effect using an exact analysis based on the spectral decomposition of the corresponding Fokker–Planck equation. We elucidate the role of the metastable states in the energy landscape as well as the initial population statistics of the particles in showcasing the Mpemba effect. Crucially, our findings indicate that neither the metastability nor the asymmetry in the potential is a necessary or a sufficient condition for the Mpemba effect to be observed.
Nodal-line symmetry breaking induced colossal anomalous Hall and Nernst effects in Cu2CoSn Heusler compound
Authors: Shukla Gaurav K. , Modanwal Ujjawal , Singh Sanjay
Published: July 2023

The presence of topological band crossings near the Fermi energy is essential for the realization of large anomalous transport properties in the materials. The topological semimetals host such properties owing to their unique topological band structure, such as Weyl points or nodal lines (NLs), those are protected by certain symmetries of the crystal. When the NLs break out in the system, a large Berry curvature arises in the surrounding area of the gapped NL. In the present work, we studied anomalous transport properties of Cu2CoSn compound, which has a cubic Heusler crystal structure (space group: Fm3¯m). Cu2CoSn full Heusler compound possesses NLs at the Fermi level that is protected by mirror reflection symmetries of the lattice. Upon introducing the spin–orbit coupling in the Hamiltonian and by setting the magnetization axis along the [001] direction, we found that the NLs are gapped out and large Berry curvature arises in the system. The integral of Berry curvature gives the intrinsic anomalous Hall conductivity (AHC) about 1003 S/cm and the anomalous Nernst conductivity (ANC) about 3.98 A/m K at the Fermi level. These values of AHC and ANC are comparable to the largest reported values for the Co2MnGa Heusler compound. Therefore, Cu2CoSn becomes a newborn member of the family of full Heusler compounds, which possesses giant AHC and ANC that can be useful for the spintronics application.
The influence of MoS2 on perpendicular magnetic anisotropy and spin–orbit torque of Pt/Co/Pt multilayer
Authors: Li Chexin , Xu Xiaoguang , Zhang Tanzhao , Zhu Zhiqiang , Liu Qianbiao , Song Linxuan , Wu Yong , Meng Kangkang , Chen Jikun , Wang Wenhong , Jiang Yong
Published: July 2023

Two-dimensional (2D) materials provide a wide choice for the next-generation spintronic devices at the post-Moore era. Here, we reveal the effect of the 2D transition metal dichalcogenide MoS2 on the perpendicular magnetic anisotropy (PMA) and spin–orbit torque (SOT) of the Pt/Co/Pt multilayer. MoS2 can distinctly enhance the PMA of Pt/Co/Pt multilayer, which shows no obvious dependence on the thickness of MoS2. Moreover, the magnetization of monolayer MoS2/Pt/Co/Pt can be switched under a small external magnetic field around 300 Oe and maintained up to 4000 Oe, verifying the enhanced PMA by MoS2. Interestingly, the SOT efficiency can also be increased about 9.65% by monolayer MoS2, which can be attributed to the spin absorption at the MoS2/Pt interface. Comparing the SOT behaviors of devices with different MoS2 thickness, the monolayer MoS2 is proved to be an ideal candidate for high-performance SOT devices.
Concentration and cavitation in the vanishing pressure limit of solutions to the relativistic Euler equations with the logarithmic equation of state
Authors: Lei Zhoutong , Shao Zhiqiang
Published: July 2023

In this paper, we constructively solve the Riemann problem for the relativistic Euler equations with the logarithmic equation of state. The concentration and cavitation phenomena are observed and analyzed during the process of vanishing pressure in the Riemann solutions. It is rigorously proved that, as the pressure vanishes, they tend to the two kinds of Riemann solutions to the zero-pressure relativistic Euler equations, which include a delta shock formed by a weighted δ-measure and a vacuum state.
Scanning tunneling microscopy under chemical reaction at solid–liquid and solid–gas interfaces
Authors: Kim Yongman , Kim Young Jae , Park Jeong Young
Published: July 2023

The task of bridging the pressure gap between ideal ultrahigh vacuum conditions and more realistic reaction conditions involving gas and liquid phases is crucial in surface and interfacial chemistry. Scanning tunneling microscopy (STM) has played a key role in addressing this challenge by enabling atomic-scale probing of the interface. STM enabled us to study surface structure, electronic structure, atomic manipulation, dynamics of molecules and atoms, and chemical properties of the surface at the atomic scale. Over the past four decades, the field of STM has undergone explosive growth. This review article focuses on recent advances in operando STM, specifically in the study of solid–liquid and solid–gas interfaces. It highlights the latest works in ambient-pressure STM, which has enabled the observation of atomic features under various gas and reaction conditions. This information sheds light on the surface mobility of adsorbates and atomic structures of reaction intermediates. The review also addresses research on electrochemical STM, which investigates the evolution of surface morphology under electrochemical processes and provides insights into atomic-scale reaction mechanisms. Finally, the article outlines future challenges and perspectives for operando STM techniques.
An mCherry biolaser based on microbubble cavity with ultra-low threshold
Authors: Ma Jiyang , Zhao Shuoying , Peng Xubiao , Li Gaoshang , Wang Yuanjin , Zhang Bo , Zhao Qing
Published: July 2023

Biolasers show considerable potential in the biomedical field. Fluorescent protein (FP) is a type of biomaterial with good luminescence efficiency that can be used as the luminescent gain medium in biolasers. Due to the higher cell/tissue permeability, lower cell phototoxicity, and relatively less background fluorescence than other fluorescent proteins, the red fluorescent protein is more suitable in biological applications. MCherry is the most extensively used high-quality red fluorescent protein because of its short maturation time and stable luminescence properties. In this study, using mCherry and microbubble cavity, we realize a highly stable mCherry fluorescent protein laser. The laser resonator achieves a quality factor of 108, which is the highest Q factor among the currently available FP lasers. Moreover, this laser exhibits a low threshold of 1.15 μJ/mm2, which can effectively protect the luminescent material from being damaged by pump light. The prepared laser shows excellent stability in a wide pH range with good photobleaching resistance and can be stored at 4 °C for 30 days. Also, the laser can serve as a high-sensitivity molecular concentration detector with mCherry as biomarker, owing to its lasing threshold behavior.
Traveling internal waves in a two-layer shallow medium with variable bathymetry and current: Surface and near-bottom flows
Authors: Churilov S. M.
Published: July 2023

In the linear approximation, we examine the one-dimensional problem of long internal wave propagation without reflection in a stationary two-layer flow with a free boundary in a channel of variable depth and width, in the limiting cases of surface and near-bottom currents. We use the shallow-water approximation and assume that liquids in the layers are ideal, immiscible, and having a small relative density difference, and that the flow is only in one of the layers. To filter fast processes (such as surface gravity waves), the flow velocity is assumed to have the same order of magnitude as the speed of internal waves. Both surface and near-bottom flows are divided into three classes, in accordance with conditions providing wave propagation without reflection. The properties of the flows in each of the classes are examined, and it is shown that the global reflectionless near-bottom flows do exist. The main results and conclusions are illustrated by a few particular solutions. A detailed comparison with the first part of the study concerning the flows with currents in both layers made it possible to clarify and refine some of the results obtained there, and to formulate questions for further investigation. The results obtained may be of interest for understanding of those natural processes in surface and near-bottom flows, which are significantly influenced by internal waves.
A conservation-significant threatened mammal uses fire exclusions and shifts ranges in the presence of prescribed burning
Authors: Povh Leticia F. , Willers Nicole , Shephard Jill M. , Fleming Patricia A.
Published: July 2023

Background Understanding how animals change their use of space following prescribed burning is essential for effective conservation management, particularly a threatened species such as the quokka (Setonix brachyurus). Aims To determine how individual quokkas change their home ranges following burns. Methods The movement patterns of 20 quokkas were tracked before and after prescribed burns between 2018 and 2020. Home-range area was calculated for each individual, and behavioural change point analysis was carried out to determine whether they changed their space use after the burns. Key results Six quokkas that had previously resided in areas that were prescribed burned, shifted their ranges and moved into the fire exclusions, avoiding the burn areas for an average of 105 ± 65 days. After 3 months, these quokkas spent no more than 2% of their time in the burn areas. By contrast, quokkas inhabiting fire exclusion and control sites did not show any change in their space use. Conclusions This study highlights the importance and proximity of appropriately sized fire exclusions to ensure that populations of species dependent on dense vegetation can be retained. Implications Fire exclusion areas are an important part of the planning of prescribed burns to retain habitat for fauna species that rely on dense cover for refuge and food.
Large-scale land acquisitions exacerbate local farmland inequalities in Tanzania
Authors: Sullivan Jonathan A. , Samii Cyrus , Brown Daniel G. , Moyo Francis , Agrawal Arun
Published: July 2023

Land inequality stalls economic development, entrenches poverty, and is associated with environmental degradation. Yet, rigorous assessments of land-use interventions attend to inequality only rarely. A land inequality lens is especially important to understand how recent large-scale land acquisitions (LSLAs) affect smallholder and indigenous communities across as much as 100 million hectares around the world. This paper studies inequalities in land assets, specifically landholdings and farm size, to derive insights into the distributional outcomes of LSLAs. Using a household survey covering four pairs of land acquisition and control sites in Tanzania, we use a quasi-experimental design to characterize changes in land inequality and subsequent impacts on well-being. We find convincing evidence that LSLAs in Tanzania lead to both reduced landholdings and greater farmland inequality among smallholders. Households in proximity to LSLAs are associated with 21.1% (
P
= 0.02) smaller landholdings while evidence, although insignificant, is suggestive that farm sizes are also declining. Aggregate estimates, however, hide that households in the bottom quartiles of farm size suffer the brunt of landlessness and land loss induced by LSLAs that combine to generate greater farmland inequality. Additional analyses find that land inequality is not offset by improvements in other livelihood dimensions, rather farm size decreases among households near LSLAs are associated with no income improvements, lower wealth, increased poverty, and higher food insecurity. The results demonstrate that without explicit consideration of distributional outcomes, land-use policies can systematically reinforce existing inequalities.
Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins
Authors: Malinverni Duccio , Zamuner Stefano , Rebeaud Mathieu E. , Barducci Alessandro , Nillegoda Nadinath B. , De Los Rios Paolo
Published: July 2023

The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.
Behavioral signatures of face perception emerge in deep neural networks optimized for face recognition
Authors: Dobs Katharina , Yuan Joanne , Martinez Julio , Kanwisher Nancy
Published: July 2023

Human face recognition is highly accurate and exhibits a number of distinctive and well-documented behavioral “signatures” such as the use of a characteristic representational space, the disproportionate performance cost when stimuli are presented upside down, and the drop in accuracy for faces from races the participant is less familiar with. These and other phenomena have long been taken as evidence that face recognition is “special”. But why does human face perception exhibit these properties in the first place? Here, we use deep convolutional neural networks (CNNs) to test the hypothesis that all of these signatures of human face perception result from optimization for the task of face recognition. Indeed, as predicted by this hypothesis, these phenomena are all found in CNNs trained on face recognition, but not in CNNs trained on object recognition, even when additionally trained to detect faces while matching the amount of face experience. To test whether these signatures are in principle specific to faces, we optimized a CNN on car discrimination and tested it on upright and inverted car images. As we found for face perception, the car-trained network showed a drop in performance for inverted vs. upright cars. Similarly, CNNs trained on inverted faces produced an inverted face inversion effect. These findings show that the behavioral signatures of human face perception reflect and are well explained as the result of optimization for the task of face recognition, and that the nature of the computations underlying this task may not be so special after all.
Engineered calprotectin-sensing probiotics for IBD surveillance in humans
Authors: Xia Jonathan Y. , Hepler Chelsea , Tran Peter , Waldeck Nathan J. , Bass Joseph , Prindle Arthur
Published: July 2023

Inflammatory bowel disease (IBD) is a spectrum of autoimmune diseases affecting the gastrointestinal tract characterized by a relapsing and remitting course of gut mucosal inflammation. Disease flares can be difficult to predict, and the current practice of IBD disease activity surveillance through endoscopy is invasive and requires medical expertise. Recent advancements in synthetic biology raise the possibility that symbiotic microbes can be engineered to selectively detect disease biomarkers used in current clinical practice. Here, we introduce an engineered probiotic capable of detecting the clinical gold standard IBD biomarker, calprotectin, with sensitivity and specificity in IBD patients. Specifically, we identified a bacterial promoter in the probiotic strain
Escherichia coli
Nissle 1917 (EcN) which exhibits a specific expression increase in the presence of calprotectin. Using murine models of colitis, we show that the reporter signal is activated in vivo during transit of the GI tract following oral delivery. Furthermore, our engineered probiotic can successfully discriminate human patients with active IBD from those in remission and without IBD using patient stool samples, where the intensity of reporter signal quantitatively tracks with clinical laboratory–measured levels of calprotectin. Our pilot study sets the stage for probiotics that can be engineered to detect fecal calprotectin for precise noninvasive disease activity monitoring in IBD patients.
Slow earthquake scaling reconsidered as a boundary between distinct modes of rupture propagation
Authors: Ide Satoshi , Beroza Gregory C.
Published: July 2023

The scaling law for slow earthquakes, which is a linear relationship between seismic moment and duration, was proposed 15 y ago and initiated a debate on the difference in physical processes governing slow vs. fast (ordinary) earthquakes. Based on new observations across a wide period range, we show that linear scaling of slow earthquakes remains valid, but as a well-defined upper bound on moment rate of ~10
13
Nm/s. The large gap in moment-rate between the scaling of slow and fast earthquakes remains unfilled. Slow earthquakes occur near the detectability threshold, such that we are unable to detect deformation events with lower moment rates. Observed trends within slow earthquake categories support the idea that this unobservable field is populated with events of lower moment rate. This suggests a change in perspective – that the proposed scaling should be considered as a bound, or speed limit, on slow earthquakes. We propose that slow earthquakes represent diffusional propagation, and that the bound on moment rate reflects an upper limit on the speed of those diffusional processes. Ordinary earthquakes, in contrast, occur as a coupled process between seismic wave propagation and fracture. Thus, even though both phenomena occur as shear slip, the difference of scaling reflects a difference in the physical process governing propagation.
NMDA-driven dendritic modulation enables multitask representation learning in hierarchical sensory processing pathways
Authors: Wybo Willem A. M. , Tsai Matthias C. , Tran Viet Anh Khoa , Illing Bernd , Jordan Jakob , Morrison Abigail , Senn Walter
Published: July 2023

While sensory representations in the brain depend on context, it remains unclear how such modulations are implemented at the biophysical level, and how processing layers further in the hierarchy can extract useful features for each possible contextual state. Here, we demonstrate that dendritic N-Methyl-D-Aspartate spikes can, within physiological constraints, implement contextual modulation of feedforward processing. Such neuron-specific modulations exploit prior knowledge, encoded in stable feedforward weights, to achieve transfer learning across contexts. In a network of biophysically realistic neuron models with context-independent feedforward weights, we show that modulatory inputs to dendritic branches can solve linearly nonseparable learning problems with a Hebbian, error-modulated learning rule. We also demonstrate that local prediction of whether representations originate either from different inputs, or from different contextual modulations of the same input, results in representation learning of hierarchical feedforward weights across processing layers that accommodate a multitude of contexts.
Air pollution, genetic susceptibility, and the risk of atrial fibrillation: A large prospective cohort study
Authors: Ma Yudiyang , Su Binbin , Li Dankang , Cui Feipeng , Tang Linxi , Wang Jianing , Tian Yaohua , Zheng Xiaoying
Published: July 2023

To date, no study has explored the extent to which genetic susceptibility modifies the effects of air pollutants on the risk of atrial fibrillation (AF). This study was designed to investigate the separate and joint effects of long-term exposure to air pollutants and genetic susceptibility on the risk of AF events. This study included 401,251 participants without AF at baseline from UK Biobank. We constructed a polygenic risk score and categorized it into three categories. Cox proportional hazards models were fitted to assess the separate and joint effects of long-term exposure to air pollutants and genetics on the risk of AF. Additionally, we further evaluated the effect modification of genetic susceptibility. The hazard ratios and corresponding 95% confidence intervals of incident AF for per interquartile range increase in particulate matter with an aerodynamic diameter smaller than 2.5 µm (PM
2.5
) or 10 µm (PM
10
), nitrogen dioxide (NO
2
), and nitrogen oxide (NO
x
) were 1.044 (1.025, 1.063), 1.063 (1.044, 1.083), 1.061 (1.042, 1.081), and 1.039 (1.023, 1.055), respectively. For the combined effects, participants exposed to high air pollutants levels and high genetic risk had approximately 149.2% (PM
2.5
), 181.7% (PM
10
), 170.2% (NO
2
), and 157.2% (NO
x
) higher risk of AF compared to those with low air pollutants levels and low genetic risk, respectively. Moreover, the significant additive interactions between PM
10
and NO
2
and genetic risk on AF risk were observed, with around 16.4% and 35.1% of AF risk could be attributable to the interactive effects. In conclusion, long-term exposure to air pollutants increases the risk of AF, particularly among individuals with high genetic susceptibility.
Quantifying common and distinct information in single-cell multimodal data with Tilted Canonical Correlation Analysis
Authors: Lin Kevin Z. , Zhang Nancy R.
Published: July 2023

Multimodal single-cell technologies profile multiple modalities for each cell simultaneously, enabling a more thorough characterization of cell populations. Existing dimension-reduction methods for multimodal data capture the “union of information,” producing a lower-dimensional embedding that combines the information across modalities. While these tools are useful, we focus on a fundamentally different task of separating and quantifying the information among cells that is shared between the two modalities as well as unique to only one modality. Hence, we develop Tilted Canonical Correlation Analysis (Tilted-CCA), a method that decomposes a paired multimodal dataset into three lower-dimensional embeddings—one embedding captures the “intersection of information,” representing the geometric relations among the cells that is common to both modalities, while the remaining two embeddings capture the “distinct information for a modality,” representing the modality-specific geometric relations. We analyze single-cell multimodal datasets sequencing RNA along surface antibodies (i.e., CITE-seq) as well as RNA alongside chromatin accessibility (i.e., 10x) for blood cells and developing neurons via Tilted-CCA. These analyses show that Tilted-CCA enables meaningful visualization and quantification of the cross-modal information. Finally, Tilted-CCA’s framework allows us to perform two specific downstream analyses. First, for single-cell datasets that simultaneously profile transcriptome and surface antibody markers, we show that Tilted-CCA helps design the target antibody panel to complement the transcriptome best. Second, for developmental single-cell datasets that simultaneously profile transcriptome and chromatin accessibility, we show that Tilted-CCA helps identify development-informative genes and distinguish between transient versus terminal cell types.
Clade-specific forebrain cytoarchitectures of the extinct Tasmanian tiger
Authors: Haines Elizabeth , Bailey Evan , Nelson John , Fenlon Laura R. , Suárez Rodrigo
Published: July 2023

The thylacine, or Tasmanian tiger, is the largest of modern-day carnivorous marsupials and was hunted to extinction by European settlers in Australia. Its physical resemblance to eutherian wolves is a striking example of evolutionary convergence to similar ecological niches. However, whether the neuroanatomical organization of the thylacine brain resembles that of canids and how it compares with other mammals remain unknown due to the scarcity of available samples. Here, we gained access to a century-old hematoxylin-stained histological series of a thylacine brain, digitalized it at high resolution, and compared its forebrain cellular architecture with 34 extant species of monotremes, marsupials, and eutherians. Phylogenetically informed comparisons of cortical folding, regional volumes, and cell sizes and densities across cortical areas and layers provide evidence against brain convergences with canids, instead demonstrating features typical of marsupials, and more specifically Dasyuridae, along with traits that scale similarly with brain size across mammals. Enlarged olfactory, limbic, and neocortical areas suggest a small-prey predator and/or scavenging lifestyle, similar to extant quolls and Tasmanian devils. These findings are consistent with a nonuniformity of trait convergences, with brain traits clustering more with phylogeny and head/body traits with lifestyle. By making this resource publicly available as rapid web-accessible, hierarchically organized, multiresolution images for perpetuity, we anticipate that additional comparative insights might arise from detailed studies of the thylacine brain and encourage researchers and curators to share, annotate, and preserve understudied material of outstanding biological relevance.
In situ electrogenerated Cu(III) triggers hydroxyl radical production on the Cu-Sb-SnO
2
electrode for highly efficient water decontamination
Authors: Lu Sen , Li Xuechuan , Cheng Yumeng , Zhou Jia , Zhang Guan
Published: July 2023

The electrochemical oxidation process has the unique advantage of in-situ •OH generation for deep mineralization of organic pollutants, which is expected to provide a solution for the globally decentralized wastewater treatment and reuse. However, it is still a great challenge to develop low-cost anodes with ultrahigh •OH yield and low energy consumption. Here, a low-cost and stable mixed metal oxide (MMO) anode (Cu-Sb-SnO
2
) developed by a simple and scalable preparation process presents extremely high organic pollutants degradation efficiency and low energy consumption. The tetracycline degradation kinetics constant of the Cu-Sb-SnO
2
system (0.362 min
−1
) was 9 to 45 times higher than that of other prepared anodes, which is superior to the existing anodes reported so far. The experimental results and theoretical calculations indicate that the Cu-Sb-SnO
2
has moderate oxygen evolution potential, larger water adsorption energy, and lower reaction energy barrier, which is conducive to selective water oxidation to generate •OH. Notably, it is systematically and comprehensively confirmed that the generation of •OH triggered by in situ electrogenerated Cu(III) increased •OH steady-state concentration by over four times. Furthermore, the doped Cu species can play a key role in promoting charge transfer as an “electronic porter” between Sn and Sb in the electrocatalytic process by adjusting the electronic structure of the Sb-SnO
2
electrode. This work paves the way for the development of MMO anodes utilizing the advantage of the Cu redox shuttle.
Sociocultural approaches to L2 digital collaborative
writing
Authors: Elola Idoia , Oskoz Ana
Published: July 2023

Whereas collaborative writing is an established
approach to second language (L2) education, the use of this approach
in the L2 classroom has now been bolstered by the ubiquity of
digital tools. Sociocultural theory (SCT) and activity theory (AT),
both frameworks that inform digital collaborative writing,
conceptualize writing as a holistic activity in which several key
elements interact dynamically, including participants, tools, and
outcomes. This chapter explores the value of knowledge sharing,
meaning negotiation, scaffolding, mediation, intersubjectivity, and
action completion – all pivotal tenets in collaborative writing –
through these frameworks. It also illustrates critical issues (e.g.,
knowledge co-construction and interaction) and concludes by
acknowledging unexplored areas of research and instructional
practices that could further advance digital collaborative
writing.
Examining the role of peer collaborative feedback processing and
task repetition in task-based L2 writing
Authors: Abrams Zsuzsanna
Published: July 2023

Grounded in research on task-based and
collaborative L2 writing, this quasi-experimental study examined the
impact of collaborative processing of instructor feedback during the
revision process. Forty-six intermediate learners of German in two
intact classes at a U.S. university completed two written summary
tasks, producing a draft and a revision for each, following feedback
from the instructor in-between. The two groups processed this
feedback individually and collaboratively, in a counterbalanced
design. All texts were analyzed for syntactic complexity, accuracy,
fluency, and lexical sophistication (i.e., lexical accuracy, choice,
richness). The results indicate that processing the instructor’s
feedback collaboratively with a peer primarily improved the lexical
domain, whereas the revision process itself led to improvements on
all linguistic features in diverse ways. The results offer
implications for research, methodology and pedagogy.
Use of digital technologies for collaborative writing
Authors: Gibbons John , Akoto Miriam
Published: July 2023

This chapter provides a brief overview of current
technologies for collaborative writing. We begin by sharing the
distinctive features of three commonly used platforms in
computer-mediated collaborative writing (i.e., Google Docs, wikis,
and Etherpad) which have been found to offer L2 learners a safe
space to freely work (Ware & Warschauer, 2006) and promote
co-authorship and collaboration (Li & Storch, 2017). Next, in
line with the increasing implementation of digital multimodal
writing tasks, we present another set of multimedia tools (i.e.,
Canva infographics and Plot storyboards) which allow L2 users to
incorporate multimodal publishing and collaboration during L2
writing practices (Krauss,
2012; Maamuujav et. al., 2019). We conclude with
pedagogical recommendations for instructors who intend to use any of
these tools.
Assessing collaborative writing
Authors: Storch Neomy , Knoch Ute
Published: July 2023

Over the past two decades, we have witnessed the
widespread use of collaborative writing tasks in second language
classes driven in part by advances in technology. These advances
have led to noticeable changes in the design and implementation of
these tasks as well as their inclusion in assessed classwork.
However, assessing collaborative writing is challenging because it
requires assessors to consider what aspects of the construct of
collaborative writing (product, process, nature of collaboration)
should be included in the assessment criteria, and how these aspects
can be reliably assessed. In this chapter we discuss these
challenges, consider some suggestions on how to assess collaborative
writing, and the pedagogical implications of assessing collaborative
writing. We conclude by outlining future research directions.
Otolin-1 as a biomarker for the evaluation of the effectiveness of betahistine treatment for benign paroxysmal positional vertigo
Authors: Cakmak Karaer Isil , Urhan Ayca , Akalin Yahya
Published: July 2023

Objective:

Benign paroxysmal positional vertigo (BPPV) is the most common vertigo disorder. Betahistine is the most commonly used drug in the treatment of vertigo, however its effect on the inner ear is not fully known. Otolin-1 is an inner ear-specific glycoprotein that can be identified in peripheral blood. The aim of the study was to determine the effect of treatment of betahistine for BPPV on serum otolin-1 levels.

Methods:

Thirty (30) patients with BPPV and 30 healthy controls were enrolled in the study. Serum otolin-1 levels were measured before and 14 days after perioral (po) betahistine treatment in the BPPV group, whereas otolin-1 level was examined once in controls. The efficacy of treatment was evaluated with Dizziness Handicap Index (DHI) and Visual Analog Scale (VAS) in the BPPV group.

Results:

Otolin-1 levels were statistically significantly higher in patients with BPPV than controls. In the BPPV group, serum otolin-1 level was found to be statistically significantly lower after betahistine treatment. There was a statistically significantly difference between pre-treatment and posttreatment groups regarding to both DHI and VAS scores.

Conclusion:

Serum otolin-1 can be used as a biomarker in monitoring the effectiveness of treatment of BPPV with betahistine as well as diagnosis of BPPV.
Alkali metal cations modulate the geometry of different binding sites in HCN4 selectivity filter for permeation or block
Authors: Krumbach Jan H. , Bauer Daniel , Sharifzadeh Atiyeh Sadat , Saponaro Andrea , Lautenschläger Rene , Lange Kristina , Rauh Oliver , DiFrancesco Dario , Moroni Anna , Thiel Gerhard , Hamacher Kay
Published: July 2023

Hyperpolarization-activated cyclic-nucleotide gated (HCN) channels are important for timing biological processes like heartbeat and neuronal firing. Their weak cation selectivity is determined by a filter domain with only two binding sites for K+ and one for Na+. The latter acts as a weak blocker, which is released in combination with a dynamic widening of the filter by K+ ions, giving rise to a mixed K+/Na+ current. Here, we apply molecular dynamics simulations to systematically investigate the interactions of five alkali metal cations with the filter of the open HCN4 pore. Simulations recapitulate experimental data like a low Li+ permeability, considerable Rb+ conductance, a block by Cs+ as well as a punch through of Cs+ ions at high negative voltages. Differential binding of the cation species in specific filter sites is associated with structural adaptations of filter residues. This gives rise to ion coordination by a cation-characteristic number of oxygen atoms from the filter backbone and solvent. This ion/protein interplay prevents Li+, but not Na+, from entry into and further passage through the filter. The site equivalent to S3 in K+ channels emerges as a preferential binding and presumably blocking site for Cs+. Collectively, the data suggest that the weak cation selectivity of HCN channels and their block by Cs+ are determined by restrained cation-generated rearrangements of flexible filter residues.
Unlocking the Potential of Two-Dimensional Janus Superlattices: Directly Visualizing Phonon Transitions
Authors: Liu Yingzhou , Yue Jincheng , Liu Yinong , Nian Lei-Lei , Hu Shiqian
Published: July 2023

Recent research has focused on using Anderson’s localization concept to modulate coherent phonon transport by introducing disorder into periodic structures. However, designing and identifying the disorder’s strength remain challenging, and visual evidence characterizing phonon localization is lacking. Here, we investigate the effect of disorder on coherent phonon transport in a two-dimensional Janus MoSSe/WSSe superlattice with a defined disorder strength. Using non-equilibrium molecular dynamics, we demonstrate that strong disorder can lead to strong phonon localization, as evidenced by smaller thermal conductivity and significantly different dependence on defect ratio in strongly disordered structures. Furthermore, we propose a novel defect engineering method to determine whether phonon localization occurs. Our work provides a unique platform for modulating coherent phonon transport and presents visual evidence of the phonon transition from localization to nonlocalization. These findings will contribute to development of phonon transport and even phononics, which are essential for thermoelectric and phononic applications.
Metasurface modulator of frequency diverse multi-mode OAM beams with equal divergence angle for coincidence imaging
Authors: Zhou Ningning , Tian Chunming , Zhu Shitao , Li Caipin , Zhao Mengran , Chen Xiaoming , Zhang Anxue
Published: July 2023

Traditional multi-mode orbital angular momentum (OAM) beams suffer from low energy efficiency in detection since the divergence angle tends to increase with increasing order of the OAM mode. Thus, OAM beams with equal divergence angle are highly desirable. In this paper, a frequency-diverse multi-mode (FDMM) OAM modulator with approximately equal divergence angle is proposed. The modulator is composed of an OAM modulation metasurface and a spatial filter (SF) with narrow passband. Firstly, the OAM modulation metasurface is designed based on multiple ring-like regions with different radii in the metasurface aperture. Each mode of OAM beam is generated at a corresponding frequency point in one region. Thus, the metasurface aperture can generate different modes of OAM beams at different frequencies (i.e., FDMM OAM beams) simultaneously. Then, the SF with narrow passband is proposed through synthesizing multi-layer frequency selective metasurfaces, aiming to reduce interferences between different modes of OAM beams. Finally, the FDMM OAM modulator is realized by superposing the SF on the OAM modulation metasurface. The FDMM OAM modulator can generate six modes of OAM beams (i.e.,

±
3

,

±
2

and

±
1

modes) at 12.5 GHz, 13.0 GHz and 13.6 GHz, respectively. A multi-mode OAM coincidence imaging model based on the FDMM OAM modulator is established. The simulation and experiment results show that the proposed FDMM OAM modulator can be used for target reconstruction and the coincidence imaging performance can be improved assisted by an optimization algorithm.
Performance benchmarking of an ultra-low vibration laboratory to host a commercial millikelvin scanning tunnelling microscope
Authors: Que Yande , Kumar Amit , Lodge Michael S , Tong Zhengjue , Lai Marcus Kar Fai , Tao Wei , Cui Zhenhao , Shivajirao Ranjith , Jia Junxiang , Lee Siew Eang , Weber Bent
Published: July 2023

Ultra-low temperature scanning tunnelling microscopy and spectroscopy (STM/STS) achieved by dilution refrigeration can provide unrivalled insight into the local electronic structure of quantum materials and atomic-scale quantum systems. Effective isolation from mechanical vibration and acoustic noise is critical in order to achieve ultimate spatial and energy resolution. Here, we report on the design and performance of an ultra-low vibration (ULV) laboratory hosting a customized but otherwise commercially available 40 mK STM. The design of the vibration isolation consists of a T-shaped concrete mass block (∼55t), suspended by actively controlled pneumatic springs, and placed on a foundation separated from the surrounding building in a ‘room-within-a-room’ design. Vibration levels achieved are meeting the VC-M vibration standard at >3 Hz, reached only in a limited number of laboratories worldwide. Measurement of the STM’s junction noise confirms effective vibration isolation on par with custom built STMs in ULV laboratories. In this tailored low-vibration environment, the STM achieves an energy resolution of 43 μeV (144 mK), promising for the investigation and control of quantum matter at atomic length scales.
Cramér distance and discretisations of circle expanding maps I: theory
Authors: Guihéneuf Pierre-Antoine , Monge Maurizio
Published: July 2023

This paper is aimed to study the ergodic short-term behaviour of discretisations of circle expanding maps. More precisely, we prove some asymptotics of the distance between the tth iterate of Lebesgue measure by the dynamics f and the tth iterate of the uniform measure on the grid of order N by the discretisation on this grid, when t is fixed and the order N goes to infinity. This is done under some explicit genericity hypotheses on the dynamics, and the distance between measures is measured by the mean of Cramér distance. The proof is based on a study of the corresponding linearised problem, where the problem is translated into terms of equirepartition on tori of dimension exponential in t. A numerical study associated to this work is presented in Guihéneuf and Monge (2022 arXiv:2206.08000).