bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRAND: a platform for closed-loop experiments with deep network models
Authors: Ali Yahia H , Bodkin Kevin , Rigotti-Thompson Mattia , Patel Kushant , Card Nicholas S , Bhaduri Bareesh , Nason-Tomaszewski Samuel R , Mifsud Domenick M , Hou Xianda , Nicolas Claire , Allcroft Shane , Hochberg Leigh R , Au Yong Nicholas , Stavisky Sergey D , Miller Lee E , Brandman David M , Pandarinath Chethan 
Published: April 2024

Abstract

Objective. Artificial neural networks (ANNs) are state-of-the-art tools for modeling and decoding neural activity, but deploying them in closed-loop experiments with tight timing constraints is challenging due to their limited support in existing real-time frameworks. Researchers need a platform that fully supports high-level languages for running ANNs (e.g. Python and Julia) while maintaining support for languages that are critical for low-latency data acquisition and processing (e.g. C and C++). Approach. To address these needs, we introduce the Backend for Realtime Asynchronous Neural Decoding (BRAND). BRAND comprises Linux processes, termed nodes, which communicate with each other in a graph via streams of data. Its asynchronous design allows for acquisition, control, and analysis to be executed in parallel on streams of data that may operate at different timescales. BRAND uses Redis, an in-memory database, to send data between nodes, which enables fast inter-process communication and supports 54 different programming languages. Thus, developers can easily deploy existing ANN models in BRAND with minimal implementation changes. Main results. In our tests, BRAND achieved <600 microsecond latency between processes when sending large quantities of data (1024 channels of 30 kHz neural data in 1 ms chunks). BRAND runs a brain-computer interface with a recurrent neural network (RNN) decoder with less than 8 ms of latency from neural data input to decoder prediction. In a real-world demonstration of the system, participant T11 in the BrainGate2 clinical trial (ClinicalTrials.gov Identifier: NCT00912041) performed a standard cursor control task, in which 30 kHz signal processing, RNN decoding, task control, and graphics were all executed in BRAND. This system also supports real-time inference with complex latent variable models like Latent Factor Analysis via Dynamical Systems. Significance. By providing a framework that is fast, modular, and language-agnostic, BRAND lowers the barriers to integrating the latest tools in neuroscience and machine learning into closed-loop experiments.
Extending the understanding of Shannon’s safe stimulation limit for platinum electrodes: biphasic charge-balanced pulse trains in unbuffered saline at pH = 1 to pH = 12
Authors: Niederhoffer Thomas , Vanhoestenberghe Anne , Lancashire Henry T 
Published: April 2024

Abstract

Objective. In neural electrical stimulation, safe stimulation guidelines are essential to deliver efficient treatment while avoiding neural damage and electrode degradation. The widely used Shannon’s limit, k, gives conditions on the stimulation parameters to avoid neural damage, however, underlying damage mechanisms are not fully understood. Moreover, the translation from bench testing to in vivo experiments still presents some challenges, including the increased polarisation observed, which may influence charge-injection mechanisms. In this work, we studied the influence on damage mechanisms of two electrolyte parameters that are different in vivo compared to usual bench tests: solution pH and electrolyte gelation. Approach. The potential of a platinum macroelectrode was monitored in a three-electrode setup during current-controlled biphasic charge-balanced cathodic-first pulse trains. Maximum anodic and cathodic potential excursions during pulse trains were projected on cyclic voltammograms to infer possible electrochemical reactions. Main results. In unbuffered saline of pH ranging from 1 to 12, the maximum anodic potential was systematically located in the oxide formation region, while the cathodic potential was located the molecular oxygen and oxide reduction region when k approached Shannon’s damage limit, independent of solution pH. The results support the hypothesis that Shannon’s limit corresponds to the beginning of platinum dissolution following repeated cycles of platinum oxidation and reduction, for which the cathodic excursion is a key tipping point. Despite similar potential excursions between solution and gel electrolytes, we found a joint influence of pH and gelation on the cathodic potential alone, while we observed no effect on the anodic potential. We hypothesise that gelation creates a positive feedback loop exacerbating the effects of pH ; however, the extent of that influence needs to be examined further. Significance. This work supports the hypothesis of charge injection mechanisms associated with stimulation-induced damage at platinum electrodes. The validity of a major hypothesis explaining stimulation-induced damage was tested and supported on a range of electrolytes representing potential electrode environments, calling for further characterisation of platinum dissolution during electrical stimulation in various testing conditions.
Towards ASSR-based hearing assessment using natural sounds
Authors: Sergeeva Anna , Christensen Christian Bech , Kidmose Preben 
Published: April 2024

Abstract

Objective. The auditory steady-state response (ASSR) allows estimation of hearing thresholds. The ASSR can be estimated from electroencephalography (EEG) recordings from electrodes positioned on both the scalp and within the ear (ear-EEG). Ear-EEG can potentially be integrated into hearing aids, which would enable automatic fitting of the hearing device in daily life. The conventional stimuli for ASSR-based hearing assessment, such as pure tones and chirps, are monotonous and tiresome, making them inconvenient for repeated use in everyday situations. In this study we investigate the use of natural speech sounds for ASSR estimation. Approach. EEG was recorded from 22 normal hearing subjects from both scalp and ear electrodes. Subjects were stimulated monaurally with 180 min of speech stimulus modified by applying a 40 Hz amplitude modulation (AM) to an octave frequency sub-band centered at 1 kHz. Each 50 ms sub-interval in the AM sub-band was scaled to match one of 10 pre-defined levels (0–45 dB sensation level, 5 dB steps). The apparent latency for the ASSR was estimated as the maximum average cross-correlation between the envelope of the AM sub-band and the recorded EEG and was used to align the EEG signal with the audio signal. The EEG was then split up into sub-epochs of 50 ms length and sorted according to the stimulation level. ASSR was estimated for each level for both scalp- and ear-EEG. Main results. Significant ASSRs with increasing amplitude as a function of presentation level were recorded from both scalp and ear electrode configurations. Significance. Utilizing natural sounds in ASSR estimation offers the potential for electrophysiological hearing assessment that are more comfortable and less fatiguing compared to existing ASSR methods. Combined with ear-EEG, this approach may allow convenient hearing threshold estimation in everyday life, utilizing ambient sounds. Additionally, it may facilitate both initial fitting and subsequent adjustments of hearing aids outside of clinical settings.
Peripheral direct current reduces naturally evoked nociceptive activity at the spinal cord in rodent models of pain
Authors: Su Tom F , Hamilton Jack D , Guo Yiru , Potas Jason R , Shivdasani Mohit N , Moalem-Taylor Gila , Fridman Gene Y , Aplin Felix P 
Published: April 2024

Abstract

Objective. Electrical neuromodulation is an established non-pharmacological treatment for chronic pain. However, existing devices using pulsatile stimulation typically inhibit pain pathways indirectly and are not suitable for all types of chronic pain. Direct current (DC) stimulation is a recently developed technology which affects small-diameter fibres more strongly than pulsatile stimulation. Since nociceptors are predominantly small-diameter Aδ and C fibres, we investigated if this property could be applied to preferentially reduce nociceptive signalling. Approach. We applied a DC waveform to the sciatic nerve in rats of both sexes and recorded multi-unit spinal activity evoked at the hindpaw using various natural stimuli corresponding to different sensory modalities rather than broad-spectrum electrical stimulus. To determine if DC neuromodulation is effective across different types of chronic pain, tests were performed in models of neuropathic and inflammatory pain. Main results. We found that in both pain models tested, DC application reduced responses evoked by noxious stimuli, as well as tactile-evoked responses which we suggest may be involved in allodynia. Different spinal activity of different modalities were reduced in naïve animals compared to the pain models, indicating that physiological changes such as those mediated by disease states could play a larger role than previously thought in determining neuromodulation outcomes. Significance. Our findings support the continued development of DC neuromodulation as a method for reduction of nociceptive signalling, and suggests that it may be effective at treating a broader range of aberrant pain conditions than existing devices.
Moiré-enabled topological superconductivity in twisted bilayer graphene
Authors: Khosravian Maryam , Bascones Elena , Lado Jose L 
Published: April 2024

Abstract
Twisted van der Waals materials have risen as highly tunable platforms for realizing unconventional superconductivity. Here we demonstrate how a topological superconducting state can be driven in a twisted graphene multilayer at a twist angle of approximately 1.6 degrees proximitized to other 2D materials. We show that an encapsulated twisted bilayer subject to induced Rashba spin–orbit coupling, s-wave superconductivity, and exchange field generates a topological superconducting state enabled by the moiré pattern. We demonstrate the emergence of a variety of topological states with different Chern numbers, that are highly tunable through doping, strain, and bias voltage. Our proposal does not depend on fine-tuning the twist angle, but solely on the emergence of moiré minibands and is applicable for twist angles between 1.3 and 3 degrees. Our results establish the potential of twisted graphene bilayers to create topological superconductivity without requiring ultraflat dispersions.
Dislocations in twistronic heterostructures
Authors: Enaldiev V V 
Published: April 2024

Abstract
Long-period moiré superlattices at the twisted interface of van der Waals heterostructures relax into preferential stacking domains separated by dislocation networks. Here, we develop a mesoscale theory for dislocations in networks formed in twistronic bilayers with parallel (P) and antiparallel (AP) alignment of unit cells across the twisted interface. For P bilayers we find an exact analytical displacement field across partial dislocations and determine analytic dependences of energy per unit length and width on the orientation and microscopic model parameters. For AP bilayers we formulate a semi-analytical approximation for displacement fields across perfect dislocations, establishing parametric dependences for their widths and energies per unit length. In addition, we find regions in the parametric space of crystal thicknesses and Moiré periods for strong and weak relaxation of the Moiré pattern in multilayered twistronic heterostructures.
Gay for pay: homocapitalism and LGBTQ employees in the transnational corporate landscape
Authors: Mowlabocus Sharif 
Published: April 2024

Abstract
In this forum piece, I utilize Rahul Rao’s concept of “homocapitalism” (2020) as an analytical lens through which to evaluate the corporate support of lesbian, gay, bisexual, transgender and queer (LGBTQ) rights. Affinity groups, including those designed to support LGBTQ employees, have become a regular feature of most Fortune 500 companies. These groups seek to represent the interests of particular employee audiences, while also helping the company to advance its profit-driven goals. Drawing on interviews with queer professionals working for multinational technology companies, I signpost the promises and limitations of LGBTQ activism when it becomes (re)located within the context of a corporation.
Simultaneous Screening of 172 Veterinary Drugs by Modified QuEChERS-LC–MS/MS in TCM Galli Gigerii Endothelium Corneum
Authors: Hu Qing , Sun Jian , Yu Hong , Feng Rui , Zhang Jingxian , Zhou Heng , Ji Shen 
Published: April 2024

Abstract
An analytical method was developed for the screening of 172 veterinary drugs in traditional Chinese medicine Galli Gigerii Endothelium Corneum by high-performance liquid chromatography tandem mass spectrometry. The samples were pretreated by a modified QuEChERS method. A Zorbax Eclipse plus C18 column (1.8 μm, 3.0 × 150 mm2, Agilent) was used for the separation of analytes by gradient elution. All analytes were detected by electrospray ionization mass spectrometry with multiple reaction monitoring mode. Good linearity with R ≥ 0.99 was exhibited for all analytes within the respective range. The recoveries of all monitored analytes ranged from 55.4 to 127.6% at three spiked levels (limit of quantitation—LOQ, 2-fold LOQ, 10-fold LOQ), with relative standard deviations &lt;17.8%. The estimated LOQ levels were 0.2–20 μg/kg. The application of this method provides a reference for the safety control of traditional Chinese medicines.
Novel echocardiographic pixel intensity quantification method for differentiating transthyretin cardiac amyloidosis from light chain cardiac amyloidosis and other phenocopies
Authors: Slostad Brody , Appadurai Vinesh , Narang Akhil , Hale Sarah , Lehrer Susan , Kline Adrienne , Bavishi Aakash , Okwuosa Ike , Jankowski Madeline , Weinberg Richard , Kansal Mayank , Thomas James D , Shah Sanjiv 
Published: April 2024

Abstract

Aims
Differentiating cardiac amyloidosis (CA) subtypes is important considering the significantly different therapies for transthyretin (ATTR)-CA and light chain (AL)-CA. Therefore, an echocardiographic method to distinguish ATTR-CA from AL-CA would provide significant value. We assessed a novel echocardiographic pixel intensity method to quantify myocardial calcification to differentiate ATTR-CA from phenocopies of CA and from AL-CA, specifically.

Methods and results
167 patients with ATTR-CA (n = 53), AL-CA (n = 32), hypertrophic cardiomyopathy (n = 37), and advanced chronic kidney disease (n = 45) were retrospectively evaluated. The septal reflectivity ratio (SRR) was measured as the average pixel intensity of the visible anterior septal wall divided by the average pixel intensity of the visible posterior lateral wall. SRR and other myocardial strain-based echocardiographic measures were evaluated with receiver operator characteristic analysis to evaluate accuracy in distinguishing ATTR-CA from AL-CA and other forms of left ventricular hypertrophy. Mean SRR was significantly higher in the ATTR-CA cohort compared to the other cohorts (P &lt; 0.001). SRR demonstrated the largest area under the curve (AUC) (0.91, P &lt; 0.001) for distinguishing ATTR from all other cohorts and specifically for distinguishing ATTR-CA from AL-CA (AUC = 0.90, P &lt; 0.001, specificity 96%, and sensitivity 63%). There was excellent inter- and intra-operator reproducibility with an ICC of 0.91 (P &lt; 0.001) and 0.89 (P &lt; 0.001), respectively.

Conclusion
The SRR is a reproducible and robust parameter for differentiating ATTR-CA from other phenocopies of CA and specifically ATTR-CA from AL-CA.
Sse1, Hsp110 chaperone of yeast, controls the cellular fate during endoplasmic reticulum stress
Authors: Jha Mainak Pratim , Kumar Vignesh , Ghosh Asmita , Mapa Koyeli 
Published: April 2024

Abstract
Sse1 is a cytosolic Hsp110 molecular chaperone of yeast, Saccharomyces cerevisiae. Its multifaceted roles in cellular protein homeostasis as a nucleotide exchange factor (NEF), as a protein-disaggregase and as a chaperone linked to protein synthesis (CLIPS) are well documented. In the current study, we show that SSE1 genetically interacts with IRE1 and HAC1, the endoplasmic reticulum-unfolded protein response (ER-UPR) sensors implicating its role in ER protein homeostasis. Interestingly, the absence of this chaperone imparts unusual resistance to tunicamycin-induced ER stress which depends on the intact Ire1-Hac1 mediated ER-UPR signaling. Furthermore, cells lacking SSE1 show inefficient ER-stress-responsive reorganization of translating ribosomes from polysomes to monosomes that drive uninterrupted protein translation during tunicamycin stress. In consequence, the sse1Δ strain shows prominently faster reversal from ER-UPR activated state indicating quicker restoration of homeostasis, in comparison to the wild-type (WT) cells. Importantly, Sse1 plays a critical role in controlling the ER-stress-mediated cell division arrest, which is escaped in sse1Δ strain during chronic tunicamycin stress. Accordingly, sse1Δ strain shows significantly higher cell viability in comparison to WT yeast imparting the stark fitness following short-term as well as long-term tunicamycin stress. These data, all together, suggest that cytosolic chaperone Sse1 is an important modulator of ER stress response in yeast and it controls stress-induced cell division arrest and cell death during overwhelming ER stress induced by tunicamycin.
The impact of differential transposition activities of autonomous and nonautonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata
Authors: Hatanaka Ryuhei , Tamagawa Katsunori , Haruta Nami , Sugimoto Asako 
Published: April 2024

Abstract
Transposable elements are DNA sequences capable of moving within genomes and significantly influence genomic evolution. The nematode Caenorhabditis inopinata exhibits a much higher transposable element copy number than its sister species, Caenorhabditis elegans. In this study, we identified a novel autonomous transposable element belonging to the hAT superfamily from a spontaneous transposable element-insertion mutant in C. inopinata and named this transposon Ci-hAT1. Further bioinformatic analyses uncovered 3 additional autonomous hAT elements—Ci-hAT2, Ci-hAT3, and Ci-hAT4—along with over 1,000 copies of 2 nonautonomous miniature inverted-repeat transposable elements, mCi-hAT1 and mCi-hAT4, likely derived from Ci-hAT1 and Ci-hAT4 through internal deletion. We tracked at least 3 sequential transpositions of Ci-hAT1 over several years. However, the transposition rates of the other 3 autonomous hAT elements were lower, suggesting varying activity levels. Notably, the distribution patterns of the 2 miniature inverted-repeat transposable element families differed significantly: mCi-hAT1 was primarily located in the chromosome arms, a pattern observed in the transposable elements of other Caenorhabditis species, whereas mCi-hAT4 was more evenly distributed across chromosomes. Additionally, interspecific transcriptome analysis indicated that C. inopinata genes with upstream or intronic these miniature inverted-repeat transposable element insertions tend to be more highly expressed than their orthologous genes in C. elegans. These findings highlight the significant role of de-silenced transposable elements in driving the evolution of genomes and transcriptomes, leading to species-specific genetic diversity.
A Recql5 mutant facilitates complex CRISPR/Cas9-mediated chromosomal engineering in mouse zygotes
Authors: Iwata Satoru , Nagahara Miki , Ido Risako , Iwamoto Takashi 
Published: April 2024

Abstract
Complex chromosomal rearrangements (CCRs) are often observed in clinical samples from patients with cancer and congenital diseases but are difficult to induce experimentally. Here, we report the first success in establishing animal models for CCRs. Mutation in Recql5, a crucial member of the DNA helicase RecQ family involved in DNA replication, transcription, and repair, enabled CRISPR/Cas9-mediated CCRs, establishing a mouse model containing triple fusion genes and megabase-sized inversions. Some of these structural features of individual chromosomal rearrangements use template switching and microhomology-mediated break-induced replication mechanisms and are reminiscent of the newly described phenomenon “chromoanasynthesis.” These data show that Recql5 mutant mice could be a powerful tool to analyze the pathogenesis of CCRs (particularly chromoanasynthesis) whose underlying mechanisms are poorly understood. The Recql5 mutants generated in this study are to be deposited at key animal research facilities, thereby making them accessible for future research on CCRs.
SlGAD2 is the target of SlTHM27, positively regulates cold tolerance by mediating anthocyanin biosynthesis in tomato
Authors: Wang Jingrong , Zhang Yong , Wang Junzheng , Khan Abid , Kang Zheng , Ma Yongbo , Zhang Jiarui , Dang Haoran , Li Tianlai , Hu Xiaohui 
Published: April 2024

Abstract
Cold stress significantly limits the yield and quality of tomato. Deciphering the key genes related to cold tolerance is important for selecting and breeding superior cold-tolerant varieties. γ-aminobutyric acid (GABA) responds to various types of stress by rapidly accumulating in plant. In this study, glutamic acid decarboxylase (GAD2) was a positive regulator to enhance cold stress tolerance of tomato. Overexpression of SlGAD2 decreased the extent of cytoplasmic membrane damage and increased the endogenous GABA content, antioxidant enzyme activities, and reactive oxygen species (ROS) scavenging capacity in response to cold stress, whereas Slgad2 mutant plants showed the opposite trend. In addition, SlGAD2 induced anthocyanin biosynthesis in response to cold stress by increasing the content of endogenous GABA. Further study revealed that SlGAD2 expression was negatively regulated by the transcription factor SlTHM27. However, the transcript levels of SlTHM27 were repressed under cold stress. Antioxidant enzyme activities, SlGAD2 transcript levels, GABA and anthocyanin contents were significantly increased in Slthm27 mutant plants. Further, our study demonstrated that SlTHM27 decreases SlGAD2-promoted cold resistance in tomato by repressing SlGAD2 transcription. Overall, our results showed that the SlTHM27-SlGAD2 model regulates the cold tolerance in tomato by regulating GABA and anthocyanin.