bluuebunny/crossref_metadata_2025 huggingface dataset:
Delineating the drought vulnerability zones in Bangladesh
Authors: Sarkar Showmitra Kumar , Das Swadhin , Rudra Rhyme Rubayet , Ekram Khondaker Mohammed Mohiuddin , Haydar Mafrid , Alam Edris , Islam Md Kamrul , Islam Abu Reza Md. Towfiqul
Published: October 2024

The research aims to explore the vulnerability of Bangladesh to drought by considering a comprehensive set of twenty-four factors, classified into four major categories: meteorological, hydrological, agricultural, and socioeconomic vulnerability. To achieve this, the study utilized a knowledge-based multi-criteria method known as the Analytic Hierarchy Process (AHP) to delineate drought vulnerability zones across the country. Weight estimation was accomplished by creating pairwise comparison matrices for factors and different types of droughts, drawing on relevant literature, field experience, and expert opinions. Additionally, online-based interviews and group discussions were conducted with 30 national and foreign professionals, researchers, and academics specializing in drought-related issues in Bangladesh. Results from overall drought vulnerability map shows that the eastern hills region displays a notably high vulnerability rate of 56.85% and an extreme low vulnerability rate of 0.03%. The north central region shows substantial vulnerability at high levels (35.85%), while the north east exhibits a significant proportion (41.68%) classified as low vulnerability. The north west region stands out with a vulnerability rate of 40.39%, emphasizing its importance for drought management strategies. The River and Estuary region displays a modest vulnerability percentage (38.44%), suggesting a balanced susceptibility distribution. The south central and south east regions show significant vulnerabilities (18.99% and 39.60%, respectively), while the south west region exhibits notable vulnerability of 41.06%. The resulting model achieved an acceptable level of performance, as indicated by an area under the curve value of 0.819. Policymakers and administrators equipped with a comprehensive vulnerability map can utilize it to develop and implement effective drought mitigation strategies, thereby minimizing the losses associated with drought.
Patterns of sperm swimming behaviour depend on male mating tactic and spawning environment in chinook salmon
Authors: Rosengrave Patrice C. , Lymbery Rowan A. , Evans Jonathan P.
Published: October 2024

Many species exhibit alternative mating tactics (ARTs), with larger socially dominant males competing for females and smaller males adopting “sneaker” strategies to exploit fertilisation opportunities without competition or courtship. Females typically prefer larger socially dominant males, but their ability to manipulate mating or fertilisation outcomes is largely unknown. Here, using chinook salmon Oncorhynchus tshawytscha, we examined whether the female’s ovarian fluid (OF) differentially influences the temporal patterns of sperm swimming traits in ejaculates from non-preferred sneaker (‘parr’) and preferred (dominant) males. Results demonstrate that OF improves sperm swimming speed and linearity compared to river water, regardless of male mating tactic. We report a novel tactic-specific difference in sperm linearity in which parr male sperm initially maintain straighter trajectories in river water, compared to dominant males, but then rapidly change to less linear and more circular paths over time. Intriguingly, we show that OF counteracts this change in sperm linearity in parr males so that patterns become indistinguishable from dominants when parr sperm swim in OF. Together, these results show that male chinook salmon exhibit differential sperm trait investment strategies depending on reproductive tactic.
Unique brood ester profile in a Varroa destructor resistant population of European honey bee (Apis mellifera)
Authors: Scaramella Nicholas , Glinwood Robert , Locke Barbara
Published: October 2024

Varroa destructor is one of the greatest threats to Apis mellifera worldwide and if left untreated will kill a colony in less than three years. A Varroa-resistant population from Gotland, Sweden, has managed to survive for 25 years with little to no Varroa treatment by reducing the mite’s reproductive success. The underlying mechanisms of this trait is currently not known, though previous research indicates that it is the honey bee brood, and not adult bee influence, that contributes to this phenotype. As the mite’s own reproduction is synchronized with the brood’s development though the interception of brood pheromones, it is possible that a change in pheromone profile would disrupt the mite’s reproductive timing. To investigate this, we characterized the brood ester pheromone (BEP) profile of our resistant Gotland population compared to a non-resistant control. This was done by extracting and analyzing key cuticular compounds of the BEP using gas chromatography. A significant difference was found immediately after brood capping, indicating a divergence in their pheromonal production at this time point. This is an important step to understanding the mechanisms of the Gotland population’s Varroa-resistance and contributes to our global understanding of Varroa destructor infestation and survival.
Exploring current conduction dynamics in multiferroic BiFeO3 thin films prepared via modified chemical solution method
Authors: Wani Waseem Ahmad , Venkataraman Harihara , Ramaswamy Kannan
Published: October 2024

The current study describes current conduction mechanisms in BiFeO3 thin films prepared by using a modified chemical solution-based technique. In particular, in these films, X-ray photoelectron spectroscopy revealed that the defect causing Fe2+ ions reduced by about 18% compared to the solution-based synthesis methods reported before, indicating better film quality. The leakage current density was measured to be 1.7 × 10–6 A/cm2 at an applied voltage of 1.5 V, which is one order of magnitude less than the previously reported work in a similar system. Oxygen annealing was found to be effective in further reducing the current conduction, making these films a suitable choice for device applications. The current–voltage curves exhibited three different behaviours of current conduction mechanisms in these films. In particular, when the applied electric field was increased, a transition from Ohmic conduction to trap-filled space charge limited conduction was observed. The presented investigations demonstrate the importance of deposition methods in determining the suitability of thin films for device applications.
18-Years of single-centre DNA testing in over 7000 index cases with inherited retinal dystrophies and optic neuropathies
Authors: Kiel Christina , Biasella Fabiola , Stöhr Heidi , Rating Philipp , Spital Georg , Kellner Ulrich , Hufendiek Karsten , Huchzermeyer Cord , Jaegle Herbert , Ruether Klaus , Weber Bernhard H. F.
Published: October 2024

Inherited retinal dystrophies (IRDs) and inherited optic neuropathies (IONs) are characterized by distinct genetic causes and molecular mechanisms that can lead to varying degrees of visual impairment. The discovery of pathogenic variants in numerous genes associated with these conditions has deepened our understanding of the molecular pathways that influence both vision and disease manifestation and may ultimately lead to novel therapeutic approaches. Over the past 18 years, our DNA diagnostics unit has been performing genetic testing on patients suspected of having IRD or ION, using state-of-the-art mutation detection technologies that are continuously updated. This report presents a retrospective analysis of genetic data from 6237 IRD and 780 ION patients. Out of these, 3054 IRD patients (49.0%) and 211 ION patients (27.1%) received a definitive molecular diagnosis, with disease-causing variants identified in 139 different genes. The genes most implicated in disease pathologies are ABCA4, accounting for 23.8% of all IRD/ION index cases, followed by BEST1 (7.8%), USH2A (6.2%), PRPH2 (5.7%), RPGR (5.6%), RS1 (5.5%), OPA1 (4.3%), and RHO (3.1%). Our study has compiled the most extensive dataset in combined IRD/ION diagnostics to date and offers valuable insights into the frequencies of mutant alleles and the efficiency of mutation detection in various inherited retinal conditions.
Successful non-invasive imaging of the coronary artery IMT in pediatric patients with Kawasaki disease using high-resolution echocardiography
Authors: Gerling Stephan , Dalla-Pozza Robert , Michel Holger , Jakob André , Melter Michael , Dechant Markus Johannes
Published: October 2024

Kawasaki Disease (KD) is a multisystemic vasculitis of medium- and small-sized arteries. Abnormal intimal thickening may develop in the involved arterial area after regression of coronary artery aneurysm (CAA). Intimal dysfunction may induce local stenosis or arteriosclerosis in the future. In this case–control study, we investigated 29 consecutive KD patients [20 male, median current age, 7.9 years; median follow-up duration, 5.7 years] and a group of 29 healthy matched controls (CON) [19 male, median current age, 10.8 years]. They were assesed and compared for CAA, LVFS, GCS, GLS, coronary artery (CA) Z scores, carotid intima-media thickness (IMT) and coronary artery IMT by high-resolution transthoracic echocardiography (hrTTE). Coronary artery IMT (caIMT) was significantly higher in patients with a maximal CA Z score > 2.5 in acute KD than in CON: KD caIMT: 0.62 mm [IQR, 0.57–0.72 mm] vs. 0.53 mm [0.51–0.60 mm], p = 0.043. CAAs were found in 15 (51.7%) patients with acute KD. The maximal median LCA Z score in acute KD was 2.57z [IQR, 1.93—3.2z] and in follow-up −0.39z [IQR, −1.25 to −0.36z]. There was no significant difference in carotid IMT between KD patients and CON. Signs of CA intima-media thickening were detected by hrTTE in patients with a maximal CA Z score > 2.5 in acute KD. These data indicate that these patients may be at risk for cardiovascular sequale even in the absence of permanent CA luminal abnormalities. Therefore long-term follow-up of this group of KD patients may be required.
Double exchange interaction in Mn-based topological kagome ferrimagnet
Authors: Wang Jiameng , Ernst Arthur , Antonov Victor N. , Jiang Qi , Qian Haoji , Wang Deyang , Cao Jiefeng , Zhu Fangyuan , Qiao Shan , Ye Mao
Published: October 2024

Recently discovered Mn-based kagome materials, such as RMn6Sn6 (R = rare-earth element), exhibit the coexistence of topological electronic states and long-range magnetic order, offering a platform for studying quantum phenomena. However, understanding the electronic and magnetic properties of these materials remains incomplete. Here, we investigate the electronic structure and magnetic properties of GdMn6Sn6 using x-ray magnetic circular dichroism, photoemission spectroscopy, and theoretical calculations. We observe localized electronic states from spin frustration in the Mn-based kagome lattice and induced magnetic moments in the nonmagnetic element Sn experimentally, which originate from the Sn-$$p$$
p
and Mn-$$d$$
d
orbital hybridization. Our calculations also reveal ferromagnetic coupling within the kagome Mn-Mn layer, driven by double exchange interaction. This work provides insights into the mechanisms of magnetic interaction and magnetic tuning in the exploration of topological quantum materials.
Social threat avoidance depends on action-outcome predictability
Authors: Sequestro Matteo , Serfaty Jade , Grèzes Julie , Mennella Rocco
Published: October 2024

Avoiding threatening individuals is pivotal for adaptation to our social environment. Yet, it remains unclear whether social threat avoidance is subtended by goal-directed processes, in addition to stimulus-response associations. To test this, we manipulated outcome predictability during spontaneous approach/avoidance decisions from avatars displaying angry facial expressions. Across three virtual reality experiments, we showed that participants avoided more often when they could predict the outcome of their actions, indicating goal-directed processes. However, above-chance avoidance rate when facing unpredictable outcomes suggested that stimulus-response associations also played a role. We identified two latent classes of participants: the “goal-directed class” showed above-chance avoidance only in the predictable condition, while the “stimulus-response class” showed no credible difference between conditions but had a higher overall avoidance rate. The goal-directed class exhibited greater cardiac deceleration in the predictable condition, associated with better value integration in decision-making. Computationally, this class had an increased drift-rate in the predictable condition, reflecting increased value estimation of threat avoidance. In contrast, the stimulus-response class showed higher responsiveness to threat, indicated by increased drift-rate for avoidance and increased muscular activity at response time. These results support the central role of goal-directed processes in social threat avoidance and reveal its physiological and computational correlates.
Electron-delocalization catalyzers for high performance, low-temperature Li–S batteries
Authors: Zhang Jing , Li Lin , Yang Mannan , Cheng Chen , Tian Na , Zhang Yongzheng , Jiao Dongmao , Lin Hongzhen , Wang Jian
Published: October 2024

An electron-delocalization strategy to strengthen electron hybridization between catalyst and sulfur species has been proposed to enhance Li+ transformation kinetics for a fast redox reaction at 0 or −10 °C, enabling a high-capacity retention of 85%.
The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation
Authors: Wei Fenfen , Jiang Huibin , Zhu Chuang , Zhong Lingyue , Lin Zihan , Wu Yan , Song Lihua
Published: October 2024

A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions.
Terrylene on monolayer WS2: coverage-dependent molecular re-orientation and interfacial electronic energy levels
Authors: Wang Qiang , You Sifan , Kobin Björn , Amsalem Patrick , Zu Fengshuo , Wang Rongbin , Opitz Andreas , Hecht Stefan , Chi Lifeng , Koch Norbert
Published: October 2024

Molecular orientation and energy level alignment at interfaces between terrylene and monolayer WS2 change substantially as a function of molecular coverage.
Spider-silk inspired ultrafast alkali-induced molecular aggregation for 3D printing arbitrary tubular hydrogels
Authors: Lyu Yang , Ji Zhongying , Liu Di , Xu Xinqiang , Guo Rui , Shi Xinyan , Wang Xiaolong
Published: October 2024

Fabricating tubular hydrogel models with arbitrary structural complexity and controllable diameters using an ultrafast, facile yet universal method is desirable for vascular prototypes yet still a great challenge.
Injectable pH-responsive polypeptide hydrogels for local delivery of doxorubicin
Authors: Guo Yijun , Chen Yong , Wu Yiqun , Zhu Ying , Luo Shiyao , Shen Juan , Luo Yongjun
Published: October 2024

Cancer, as a global health threat, is often treated with chemotherapy, but its effect is limited, especially the drugs such as doxorubicin (DOX) are limited by their non-specificity and side effects.
Electron-deficient Pd nanoparticles on nitrogen-doped carbon nanofibers for high selectivity alkyne transfer semi-hydrogenation
Authors: Li Huaike , Li Shuai , Yue Guichu , Gao Songwei , Zhang Xuefeng , Zhu Keping , Yang Tingting , Zhang Ziyue , Wang Nü , Bai Jie , Cui Zhimin , Zhao Yong
Published: October 2024

The catalytic activity and stability of Pd nanoparticles on nitrogen-doped carbon nanofibers for the semi-hydrogenation of phenylacetylene.
Normal‐mode planar meander‐line antenna array with bidirectional broadside radiation pattern
Authors: Liu Meicheng , Jin Peiqi , Hou Yuefeng
Published: October 2024

In this letter, a normal‐mode planar bidirectional broadside antenna array with the merits of high gain, broadband, low aerodynamic drag, and high assembly robustness is proposed. First, the bidirectional antenna array is implemented based on a novel design strategy. The expected radiation field generated by currents along the same direction is superimposed while the unexpected radiation field is offset due to the out‐of‐phase currents, achieving a normal‐mode high‐gain bidirectional pattern. Then, the bidirectional antenna array is designed with two metallic meander lines, featuring low aerodynamic drag and cost‐efficiency. Moreover, a simple feed structure using an impedance transformer parallel strip line is adopted for a wide bandwidth. Besides, the bidirectional antenna array exhibits a stable impedance when the array scale increases. The stable impedance is also observed when the antenna array is bent to different angles, ensuring ease of installation and high assembly robustness. To validate the design strategy, a prototype with an aperture length of 5.8λ at 2.4 GHz is fabricated. The proposed antenna array is designed to operate from 2.2 to 2.6 GHz, with a maximum gain of 13 dBi around the center of frequency, which can be a promising candidate in long and narrow communication scenarios.
Failure to oxygenate during cardiopulmonary bypass; treatment options and intervention algorithm
Authors: Matte Gregory S. , Regan William L. , Gadille Sarah I. , Connor Kevin R. , Boyle Sharon L. , Fynn-Thompson Francis E.
Published: October 2024

Membrane oxygenator failure remains a concern for perfusion teams. Successful outcomes for this low-frequency, high-risk intervention are predicated on having written institutional protocols for both the oxygenator change-out procedure as well as how often the procedure is practiced by staff perfusionists. A recent review of peer-reviewed journal articles, textbooks and online resources revealed a lack of a unified intervention algorithm for failure to oxygenate during cardiopulmonary bypass (CPB). While an oxygenator change-out procedure may still be considered the gold standard for a confirmed device failure, temporizing measures exist that, in select cases, can afford time to the clinical team and even obviate the need for an oxygenator change-out procedure. We now consider the venous piggyback technique sourcing blood from the venous limb of the circuit a first-line intervention to afford enhanced patient safety while the clinical team decides on required interventions when oxygenator failure presents during CPB.
Computational hermeneutics of emotion: a comparative study of emotional landscapes in the Dostoevsky’s novel “Crime and Punishment”
Authors: Picca Davide , Schnyder Antonin , Romele Alberto
Published: October 2024

This study employs computational hermeneutics to explore emotional representations in Fyodor Dostoevsky’sCrime and Punishment. Using advanced Natural Language Processing (NLP) techniques, including sentiment analysis powered by the BERT model and other tools, we examine the emotional and existential aspects embedded in the narrative. Our approach combines computational tools with traditional hermeneutic methods to deconstruct the emotional journey of the protagonist, Rodion Raskolnikov. We quantitatively analyze his emotional evolution before and after the pivotal crime, mapping his psychological transition from detachment to engagement. The study focuses on four key emotional dimensions: Attitude, Introspection, Sensitivity, and Temper. By transforming qualitative textual data into a quantitative framework, we provide a novel illustration of Raskolnikov’s psychological progression from a state of depersonalization to full emotional contact. This computational analysis is contextualized within a broader philosophical interpretation, drawing on concepts such as Stoicapatheiaand HeideggerianSorge. Our research serves a dual purpose: it enhances our understanding of Dostoevsky’s work while demonstrating the potential of computational methods in literary analysis. By bridging digital humanities and traditional literary criticism, this study contributes to the growing field of digital hermeneutics and opens new avenues for interdisciplinary research in literature, philosophy, and computational linguistics.
Envelope Inversion with Source encoding for Ultrasound Computed Tomography
Authors: Zhang Nuomin , Zhou Naixin , Yuan Yu , Shen Yi , Zhao Yue
Published: October 2024

Ultrasound computed tomography (USCT) is a noninvasive and non-ionizing imaging technique for soft tissue and limb bones. Full waveform inversion (FWI) has received increased interest due to its high resolution. The difficulties in FWI are twofold: high computational burden and poor convergence. To address these issues, an envelope inversion with source coding (EI-SE) algorithm is proposed in this paper. The envelope-based objective function measures the matching degree between the predicted and measured envelopes. It can provide the low-frequency components of the signal that are not available to FWI. Therefore, the EI can provide an accurate solution even when the initial model is far from the ground truth and low-frequency data are missing. The simulations are conducted to demonstrate the validity of the proposed algorithm. The root mean squared error (RMSE) of the proposed algorithm is much smaller than that of conventional FWI. The results show that EI-SE is effective in avoiding cycle skipping.
Comparison between experimental and numerical results for piezoelectric signals generated in water-saturated cancellous bone by ultrasound irradiation
Authors: Hosokawa A
Published: October 2024

The bone formation is considered to be accompanied by the piezoelectric effects in bone. Therefore, the piezoelectric effect under ultrasound irradiation should be elucidated to realize the effective healing. Then, the piezoelectric properties in cancellous bone have been attempted to clarify by complementing experiments and simulations with each other. In this paper, the piezoelectric signals generated in water-saturated cancellous bone by ultrasound irradiation were experimentally and numerically observed, and the effect of the trabecular orientation was investigated. The experimental observation was performed by the piezoelectric cell (PE-cell), which corresponds to an ultrasound receiver using the cancellous bone specimen as a piezoelectric element. The numerical observation was performed by the piezoelectric finite-difference time-domain (PE-FDTD) method, which is an elastic FDTD method with piezoelectric constitutive equations. In both the experimental and simulated results, the piezoelectric signal amplitude increased with the mean intercept lengths (MILs) of the trabecular elements and the pore spaces or the strength of the trabecular orientation. From the fact that the ultrasound propagation in water-saturated cancellous bone can depend on the trabecular orientation, it was considered that the ultrasound properties could be largely associated with the piezoelectric properties.
Investigation on the fatigue properties of adhesives for acoustic transducers in deep logging wells
Authors: Wei Qian , Liu Bin , Cong Jiansheng
Published: October 2024

Deep well exploration of oil and gas resources requires acoustic transducers that can withstand temperatures above 200 degrees. It is particularly important to overcome the key technology of high-temperature dipole transmitters. The bonding strength of the dipole transmitters with a tri-laminar structure is studied numerically and experimentally. Transducers were prepared using structural adhesives. The aging and fatigue test is conducted at a high temperature of 200 degrees. The aging lasted for 15 hours and the strong electric field fatigue cycle number reached up to 36000. The conductivity curve remains almost unchanged after the high-temperature test. The work provides an application basis for deep acoustic logging technology.
Theoretical analysis of the dimensionality of ultrasonic attenuation in polycrystalline materials with elongated grains
Authors: Victoria Giraldo Juan Camilo , Tie Bing , Laurent Jérôme , Lhémery Alain , Solas Denis
Published: October 2024

In the present work, the grain scattering-induced attenuation coefficient is obtained for longitudinal bulk waves in untextured cubic polycrystalline materials with elongated grains using proposed 2D and 3D theoretical models. These models are obtained based on previously developed 2D and 3D models for equiaxed grains. Comparison of the 2D and 3D models allows an analysis of the dimensionality of grain scattering-induced attenuation, which involves more complex mechanisms with elongated grains. In the higher stochastic scattering regime, both 3D and 2D longitudinal attenuations are found to be dependent on the grain size parallel to the wave propagation. In the Rayleigh scattering regime the 3D attenuation is volume dependent and in contrast, the 2D longitudinal attenuation is found to be cross-section dependent and is therefore helpful for identifying the 3D grain shape/rotation.
Signal de-noising based on ICEEMDAN for delamination detection by phased array ultrasonic testing
Authors: Zhang PH , Ma SW , Huang KH , Pan YD
Published: October 2024

Aiming at the problem of clutter noise of inter-layer reflections that occurs in multilayer heterogeneous medium such as hybrid fibre composites during ultrasonic inspection, a signal de-noising method based on the improved complete ensemble empirical mode decomposition with adaptive noise (ICEEMDAN) is proposed in this paper. In the method, the cross-correlation coefficient is utilized to identify the intrinsic mode function (IMF) that is related to raw ultrasonic signal. Particularly, the root mean square error (RMSE), as selection criterions, are employed conjunctively to sift the optimal IMF among selected decomposition signals. Hilbert transform is used to extract the envelope of the signal after removing the interlayer reflection noise. Experimental results show that, the proposed method can adaptively decompose the non-stationary ultrasonic signal into several IMFs with different spectrum so as to dealing with clutter noises. For delaminate detection by phased array ultrasonic testing for hybrid fibre composites, structural noises are significantly suppressed in the reconstructed signal that retains the distinct echo characteristics of a delaminated defect.
TLR4 promotes smooth muscle cell-derived foam cells formation by inducing receptor-independent macropinocytosis
Authors: Chen Xue , Kang Yulai , Tang Chunhua , Zhang Lili , Guo Lu
Published: October 2024

Foam cells are primarily formed through scavenger receptors that mediate the uptake of various modified low-density lipoproteins (LDL) into cells. In addition to the receptor-dependent pathway, macropinocytosis is an essential nonreceptor endocytic pathway for vascular smooth muscle cells (VSMCs) to take up lipids. However, the molecular mechanisms underlying this process remain unclear. Primary cultured VSMCs were stimulated with 200 ng/mL lipopolysaccharide (LPS) and 200 µg/mL native LDL (nLDL). We observed a significant increase in Toll-like receptor 4 (TLR4) protein expression and a significant activation of macropinocytosis, which correlated with the highest uptake of nLDL and intracellular lipid deposition in WT VSMCs. However, macropinocytosis was inhibited and lipid accumulation decreased after treatment with macropinocytosis inhibitors and Syk inhibitors in WT VSMCs. Consistently, TLR4 knockout significantly suppressed macropinocytosis and lipid droplets accumulation in VSMCs. Taken together, our findings suggest a critical role of TLR4/Syk signaling in promoting receptor-independent macropinocytosis leading to VSMC-derived foam cells formation.
Urban sensory conditions alter rival interactions and mate choice in urban and forest túngara frogs
Authors: Smit Judith A H , Thijssen Vera , Cronin Andrew D , Ellers Jacintha , Halfwerk Wouter
Published: October 2024

Sexual communication often takes place in networks with multiple competing signalers being simultaneously assessed by mate choosers. Altered sensory conditions, such as noise and light pollution, can affect communication by altering signal production and perception. While evidence of sensory pollution affecting sexual signaling is widespread, few studies assess impacts on sexual signaling during rival interactions as well as mate choice, let alone whether urban and non-urban populations have diverged in their response. Here, we investigate the effects of urban sensory conditions on sexual communication in urban and forest túngara frogs (Engystomops pustulosus). We recorded dyadic vocal rival interactions and assessed mate choice with and without noise and light pollution in the lab. We show that urban sensory conditions can directly impact the intensity of rival interactions, differences between rivals, and mate choice, though changes were often in opposite directions for frogs of urban and forest origins. Moreover, we demonstrate that urban-induced changes in rival interactions can also indirectly affect how females choose between potential mates. Our study reveals origin-dependent direct and indirect effects of noise and light pollution and suggests local adaptation of sexual communication in urban populations.
arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact storage and fast access
Authors: Le Roux Julien , Sade Julien
Published: October 2024

The arcMS R package addresses the challenges posed by proprietary and open-source high-resolution mass spectrometry data formats by providing functions to collect MSE data from the Waters UNIFI software and store it in the efficient Apache Parquet format, facilitating fast, easy access, and compatibility with various programming environments. This solution facilitates the manipulation of complex mass spectrometry data, including ion mobility or other additional dimensions, enabling potential integration into efficient and open-source workflows.

Availability and implementation

arcMS is an open-source R package and is available on GitHub at https://github.com/leesulab/arcMS. The complete documentation, including details on UNIFI configuration and tutorials for data conversion, access to Parquet files, and filtration of data, is available at https://leesulab.github.io/arcMS. An R/Shiny companion application is also provided for visualization of Parquet data and demonstration of data filtering with the Arrow library https://github.com/leesulab/arcms-dataviz.
Addressing the antibody germline bias and its effect on language models for improved antibody design
Authors: Olsen Tobias H , Moal Iain H , Deane Charlotte M
Published: October 2024

Motivation

The versatile binding properties of antibodies have made them an extremely important class of biotherapeutics. However, therapeutic antibody development is a complex, expensive, and time-consuming task, with the final antibody needing to not only have strong and specific binding but also be minimally impacted by developability issues. The success of transformer-based language models in protein sequence space and the availability of vast amounts of antibody sequences, has led to the development of many antibody-specific language models to help guide antibody design. Antibody diversity primarily arises from V(D)J recombination, mutations within the CDRs, and/or from a few nongermline mutations outside the CDRs. Consequently, a significant portion of the variable domain of all natural antibody sequences remains germline. This affects the pre-training of antibody-specific language models, where this facet of the sequence data introduces a prevailing bias toward germline residues. This poses a challenge, as mutations away from the germline are often vital for generating specific and potent binding to a target, meaning that language models need be able to suggest key mutations away from germline.

Results

In this study, we explore the implications of the germline bias, examining its impact on both general-protein and antibody-specific language models. We develop and train a series of new antibody-specific language models optimized for predicting nongermline residues. We then compare our final model, AbLang-2, with current models and show how it suggests a diverse set of valid mutations with high cumulative probability.

Availability and implementation

AbLang-2 is trained on both unpaired and paired data, and is freely available at https://github.com/oxpig/AbLang2.git.
Collapsible tree: interactive web app to present collapsible hierarchies
Authors: Gao Yuan , Patro Rob , Jiang Peng
Published: October 2024

Motivation

A crucial component of intuitive data visualization is presenting a hierarchical tree structure with interactive functions. For example, single-cell transcriptomics studies may generate gene expression values with developmental trajectories or cell lineage structures. Two common visualization methods, t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), require two separate figures to depict the distribution of cell types and gene expression data, with low-dimension projections that may not capture the hierarchical structures among cells.

Results

Here, we present a JavaScript framework and an interactive web app named Collapsible Tree, which presents values jointly with interactive, expandable, and collapsible lineage structures. For example, the Collapsible Tree presents cellular states and gene expression from single-cell transcriptomics within a single hierarchical plot, enabling comparisons of gene expression across lineages and subtle patterns between sub-lineages. Our framework can facilitate the exploration of complicated value patterns that are not evident in UMAP or t-SNE plots.

Availability and implementation

The Collapsible Tree web interface is available at https://collapsibletree.data2in.net. The JavaScript library source code is available at https://github.com/data2intelligence/collapsible_tree.
Genital coupling and copulatory wounding in the Drosophila rufa species complex: comparison with the D. auraria species complex (Diptera: Drosophilidae)
Authors: Omiya Haruka , Onuma Moe , Awasaki Takeshi , Kamimura Yoshitaka , Sawamura Kyoichi
Published: October 2024

In sexually reproducing animals, genital morphology is usually divergent among closely related species, which can lead to a mismatch of genital coupling (i.e. mechanical isolation). The montium species group of the subgenus Sophophora is the largest clade in Drosophila and is a useful model in which to study the evolution of genital morphology. This group includes a pair of sister clades, i.e. the Drosophila auraria and Drosophila rufa species complexes. The former includes four species with overlapping distributions, and the latter consists of five species that are almost allopatric. The previous study on the D. auraria complex suggested genital co-evolution between sexes (female structures accepting for or protecting from male structures). To test the generality, we analysed the D. rufa complex and three outgroup species. In the D. rufa complex, we detected genital structures corresponding between sexes, and copulatory wounds with species-specific positions. Given that approximately the same number of evolutionary changes in the genital traits were detected in both sexes of the two clades, we conclude that selection pressure to avoid interspecific mating (reproductive character displacement) is not a prerequisite for rapid genital co-evolution.
A rapid and inexpensive 96-well DNA-extraction method from blood using silicon dioxide powder (Glassmilk)
Authors: Vásquez Bonilla Maria Mercedes , Guerrero-Freire Mónica Salome , Ledesma Yanua , Laglaguano Juan Carlos , de Waard Jacobus H
Published: October 2024

We present a rapid high-throughput DNA extraction method for use with EDTA-anticoagulated blood using silicon dioxide (SiO2) powder in a guanidine–HCl solution, hereinafter referred to as “Glassmilk.” The method utilizes a 96-well deep-well plate, enabling DNA extraction from 96 samples in under 3 h. The method integrates cell lysis, washing, elution, and DNA storage within the same well, eliminating the need for DNA transfer. The Glassmilk extraction method is cost-effective and fast, and it avoids expensive or toxic reagents by using only basic lab equipment. The method yielded approximately 40 μg of high-quality DNA from 200 μl of blood. The DNA yield of the Glassmilk method was about 50% higher, and the purity of the DNA was comparable to those obtained using two commercial column-based extraction kits that were used for comparison. The cost per sample was around $1, with the most expensive item being the filter pipette tips, which account for about $0.80 per sample. As we show, the extracted DNA is suitable for downstream applications such as polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism analysis, and qPCR. The method can be adapted for various sample types, including biopsies, fecal samples, cultured cells, and bacteria (see “subprotocols” section), and can also be applied in individual Eppendorf tubes. Our protocol may be useful for basic molecular research in laboratories having limited funds.
Telecoupling cannot be ignored for the forest-based carbon market
Authors: Williams Brooke A , Metzger Jean-Paul , Cho Frankie , Phelan Anya , López-Cubillos Sofía , Bentley Lily K , Fu Bojie , Zhang Yangjian , Liu Yanxu , Johnson Justin , Rhodes Jonathan R
Published: October 2024

Telecoupling interactions between social–ecological systems across large, often global distances drive negative impacts from the forest-based carbon market. However, these negative impacts have been underreported and, therefore, have likely been vastly underestimated. We identify how these unintended negative impacts may occur and provide recommendations for the forest-based carbon market to better account for externalities by prioritizing positive social impact, expanding comprehensive ecological outcomes, and improving the transparency of investments. We call for a carbon market that is designed to account for its global interconnectedness.
An update on pancreatic cancer imaging, staging, and use of the PACT-UK radiology template pre- and post-neoadjuvant treatment
Authors: Corallo Carmelo , Al-Adhami Abdullah S , Jamieson Nigel , Valle Juan , Radhakrishna Ganesh , Moir John , Albazaz Raneem
Published: October 2024

Pancreatic ductal adenocarcinoma continues to have a poor prognosis, although recent advances in neoadjuvant treatments (NATs) have provided some hope. Imaging assessment of suspected tumours can be challenging and requires a specific approach, with pancreas protocol CT being the primary imaging modality for staging with other modalities used as problem-solving tools to facilitate appropriate management. Imaging assessment post NAT can be particularly difficult due to a current lack of robust radiological criteria to predict response and differentiate treatment induced fibrosis/inflammation from residual tumour. This review aims to provide an update of pancreatic ductal adenocarcinoma with particular focus on three points: tumour staging pre- and post-NAT including vascular assessment, structured reporting with introduction of the PAncreatic Cancer reporting Template—UK (PACT-UK) radiology template, and the potential future role of artificial intelligence in the diagnosis and staging of pancreatic cancer.
CACNA1A haploinsufficiency leads to reduced synaptic function and increased intrinsic excitability
Authors: Hommersom Marina P , Doorn Nina , Puvogel Sofía , Lewerissa Elly I , Mordelt Annika , Ciptasari Ummi , Kampshoff Franziska , Dillen Lieke , van Beusekom Ellen , Oudakker Astrid , Kogo Naoki , Dolga Amalia M , Frega Monica , Schubert Dirk , van de Warrenburg Bart P C , Nadif Kasri Nael , van Bokhoven Hans
Published: October 2024

Haploinsufficiency of CACNA1A, encoding the pore-forming α1 subunit of P/Q-type voltage-gated calcium channels, is associated with a clinically variable phenotype ranging from cerebellar ataxia to neurodevelopmental syndromes with epilepsy and intellectual disability.

To understand the pathological mechanisms of CACNA1A loss-of-function variants, we characterized a human neuronal model for CACNA1A haploinsufficiency by differentiating isogenic induced pluripotent stem cell lines into glutamatergic neurons and investigated the effect of CACNA1A haploinsufficiency on mature neuronal networks through a combination of electrophysiology, gene expression analysis and in silico modelling.

We observed an altered network synchronization in CACNA1A+/− networks alongside synaptic deficits, notably marked by an augmented contribution of GluA2 subunit-lacking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Intriguingly, these synaptic perturbations coexisted with increased non-synaptically driven activity, as characterized by inhibition of N-methyl-D-aspartate and AMPA receptors on micro-electrode arrays. Single-cell electrophysiology and gene expression analysis corroborated this increased intrinsic excitability through reduced potassium channel function and expression. Moreover, we observed partial mitigation of the CACNA1A+/− network phenotype by 4-aminopyridine, a therapeutic intervention for episodic ataxia type 2. Positive modulation of small conductance calcium-activated potassium channels could reverse the CACNA1A+/− network electrophysiological phenotype.

In summary, our study pioneers the characterization of a human induced pluripotent stem cell-derived neuronal model for CACNA1A haploinsufficiency and has unveiled new mechanistic insights. Beyond showcasing synaptic deficits, this neuronal model exhibited increased intrinsic excitability mediated by diminished potassium channel function, underscoring its potential as a therapeutic discovery platform with predictive validity.
Eosinophilic dermatosis of haematological malignancy
Authors: Nallathamby Kasthuri , Moss Kat , Khirwadkar Nitin , Azurdia Richard
Published: October 2024

This report is about a 71-year-old woman with a background of chronic lymphocytic leukaemia (CLL) diagnosed in 2017, managed conservatively with active surveillance under haematology. Presented to dermatology 5 years ago with a non-resolving insect bite-like rash on her chest. Multiple biopsies were taken over the years due to the diagnostic challenge. The biopsies usually demonstrated perivascular inflammation, heavy eosinophilic infiltrate along with lymphocytes and histiocytes, without evidence of a frank vasculitis. Following multidisciplinary team discussion with clinical and pathological correlation, a diagnosis of eosinophilic dermatosis of haematological malignancy mimicking insect bites was made.
The Substantial Role of Sleep, Stress, and Physical Activity in Persistent High Levels of Fatigue in Patients With Inflammatory Bowel Disease: A Longitudinal Trajectory Study
Authors: Bredero Quirine M , Fleer Joke , Blom Denise M , Bourgonje Arno R , Dijkstra Gerard , Schroevers Maya J
Published: October 2024

Background and Aims

Fatigue is a common and burdensome problem for patients with inflammatory bowel disease (IBD). Previous studies lack insight into the individual variability in fatigue severity and course over time, and the characteristics of patients at risk of severe and persistent fatigue. This study aimed to identify distinct groups of IBD patients based on their level and course of fatigue over 5 years. Subsequently, we examined the relationship between these trajectories, patient characteristics, and trajectories of perceived stress, sleep, and physical activity.

Methods

This longitudinal cohort study used prospectively collected data from the myIBDcoach telemedicine monitoring tool, including 320 IBD patients who completed 3 or more online consultations between 2016 and 2021. Latent class growth analyses were performed to identify distinct trajectories.

Results

We found 5 subgroups with distinct trajectories of fatigue, differing in level and course over time, with 33% of patients experiencing chronic stable and high levels of fatigue. Few differences in patient characteristics were found between trajectories, yet the chronic high fatigue subgroup was more likely to report persistent stable sleep problems, perceived stress, and little physical activity over time compared to the other groups.

Conclusions

Distinct subgroups of IBD patients can be identified based on longitudinal fatigue trajectories. The relatively stable levels of fatigue, stress, sleep, and physical activity suggest that a one-time screening of patients on these topics may be sufficient to identify those at risk. Interventions aiming to reduce fatigue should target persistent stress, sleep problems, and low levels of physical activity.
Response of hibiscus mealybug (Hemiptera: Pseudococcidae) to citrus volatiles induced by mechanical injury
Authors: Olabiyi David , Diepenbrock Lauren M , Martini Xavier , Stelinski Lukasz L
Published: October 2024

Hibiscus mealybug, Nipaecoccus viridis (Newstead) (Hemiptera: Pseudococcidae), is a recent invasive pest of citrus and many other crops in Florida. Nipaecoccus viridis attacks all above ground parts of citrus trees and heavy infestation can cause leaf drop and premature abortion of developing fruits. We quantified greater captures of N. viridis in cardboard band traps on areas of citrus trees that were intentionally injured by mechanical rasping of epidermal tissues as compared with similar but uninjured citrus branches. Direct field collection of headspace volatiles from mechanically injured or intact citrus branches revealed both qualitative and quantitative differences. Certain volatiles (γ-terpinene, citronellal, citronellyl acetate, β-E-farnesene, α-humulene, and α-E-E-farnesene) were only present in samples from damaged citrus branches. Behavioral assays using a laboratory Y-tube olfactometer revealed attraction of N. viridis to volatiles associated with mechanical damage of citrus including synthetic β-ocimene, γ-terpinene, sabinene, isomers of farnesene, and citronellal when loaded into lures at either of 2 concentrations (0.01 or 0.1 µg/µl). Subsequent field trapping experiments confirmed increased captures of various life stages of N. viridis in cardboard band traps baited with a 10.0 µg/µl concentration of farnesene:ocimene:sabinene blend (in 7:13:17 ratio), as well as those releasing either farnesene or ocimene alone at this same concentration, as compared with the mineral oil (diluent) negative control. Our results indicate that common plant related terpenes released by citrus following mechanical damage may be useful for development of an effective monitoring trap for N. viridis.
Entrepreneurial Reluctance: Talent and Firm Creation in China
Authors: Bai Chong-En , Jia Ruixue , Li Hongbin , Wang Xin
Published: October 2024

This paper examines the correlation between cognitive ability and firm creation. Drawing on administrative college admission data and firm registration records in China, we investigate who had created firms by their mid-thirties. We find a clear pattern of entrepreneurial reluctance: given the same backgrounds, individuals with higher college entrance exam scores are less likely to create firms. Through an exploration of firm performance, alternative career trajectories and variations across regions, we propose an explanation: the ability represented by exam scores is useful across occupations, yet higher-scoring individuals are attracted to waged jobs, particularly those of the state sector.