bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimated human-induced warming from a linear temperature and atmospheric CO2 relationship
Authors: Jarvis Andrew , Forster Piers M. 
Published: November 2024

AbstractAssessing compliance with the human-induced warming goal in the Paris Agreement requires transparent, robust and timely metrics. Linearity between increases in atmospheric CO2 and temperature offers a framework that appears to satisfy these criteria, producing human-induced warming estimates that are at least 30% more certain than alternative methods. Here, for 2023, we estimate humans have caused a global increase of 1.49 ± 0.11 °C relative to a pre-1700 baseline.
TRBC1-CAR T cell therapy in peripheral T cell lymphoma: a phase 1/2 trial
Authors: Cwynarski Kate , Iacoboni Gloria , Tholouli Eleni , Menne Tobias , Irvine David A. , Balasubramaniam Nivetha , Wood Leigh , Shang Justin , Xue Eric , Zhang Yiyun , Basilico Silvia , Neves Margarida , Raymond Meera , Scott Ian , El-Kholy Mohamed , Jha Ram , Dainton-Smith Heather , Hussain Rehan , Day William , Ferrari Mathieu , Thomas Simon , Lilova Koki , Brugger Wolfram , Marafioti Teresa , Lao-Sirieix Pierre , Maciocia Paul , Pule Martin 
Published: November 2024

Abstract
Relapsed/refractory peripheral T cell lymphomas (PTCLs) are aggressive tumors with a poor prognosis. Unlike B cell lymphomas, treatment of PTCL has not benefited from advances in immunotherapy. This is largely due to a lack of suitable target antigens that discriminate malignant from normal T cells, thus avoiding severe immunosuppression consequent to depletion of the entire T cell compartment. We recently described a targeting strategy based on the mutually exclusive expression of T cell antigen receptor beta-chain constant domain (TRBC) 1 and 2. Selective targeting of the T cell antigen receptor beta-chain expressed by the (clonal) malignancy spares normal T cells expressing the other chain. The LibraT1 study is an ongoing, multicenter, international, single-arm phase 1/2 study of TRBC1-directed autologous chimeric antigen receptor (CAR) T cells (AUTO4) in relapsed/refractory TRBC1-positive PTCL. Primary objectives were assessment of safety and tolerability of AUTO4 infusion. Key secondary endpoints included efficacy, CAR T cell expansion and persistence. Here we describe the findings from dose escalation in LibraT1 in the first ten patients, in a non-prespecified interim analysis. AUTO4 resulted in low frequency of severe immunotoxicity, with one of ten patients developing grade 3 cytokine release syndrome. Complete metabolic response was observed in four of ten evaluable patients, with remissions being durable beyond 1 year in two patients. While an absence of circulating CAR T cells was observed, CAR T cells were readily detected in lymph node biopsy samples from sites of original disease suggesting homing to tumor sites. These results support the continuing exploration of TRBC1 targeting in PTCL. ClinicalTrials.gov registration: NCT03590574.
Salbutamol attenuates arrhythmogenic effect of aminophylline in a hPSC-derived cardiac model
Authors: Kabanov Daniil , Vrana Klimovic Simon , Beckerová Deborah , Molcan Martin , Scurek Martin , Brat Kristian , Bebarova Marketa , Rotrekl Vladimir , Pribyl Jan , Pesl Martin 
Published: November 2024

AbstractThe combination of aminophylline and salbutamol is frequently used in clinical practice in the treatment of obstructive lung diseases. While the side effects (including arrhythmias) of the individual bronchodilator drugs were well described previously, the side effects of combined treatment are almost unknown. We aimed to study the arrhythmogenic potential of combined aminophylline and salbutamol treatment in vitro. For this purpose, we used the established atomic force microscopy (AFM) model coupled with cardiac organoids derived from human pluripotent stem cells (hPSC-CMs). We focused on the chronotropic, inotropic, and arrhythmogenic effects of salbutamol alone and aminophylline and salbutamol combined treatment. We used a method based on heart rate/beat rate variability (HRV/BRV) analysis to detect arrhythmic events in the hPSC-CM based AFM recordings. Salbutamol and aminophylline had a synergistic chronotropic and inotropic effect compared to the effects of monotherapy. Our main finding was that salbutamol reduced the arrhythmogenic effect of aminophylline, most likely mediated by endothelial nitric oxide synthase activated by beta-2 adrenergic receptors. These findings were replicated and confirmed using hPSC-CM derived from two cell lines (CCTL4 and CCTL12). Data suggest that salbutamol as an add-on therapy may not only deliver a bronchodilator effect but also increase the cardiovascular safety of aminophylline, as salbutamol reduces its arrhythmogenic potential.
Aggregate morphing of self-aligning soft active disks in semi-confined geometry
Authors: Chugh Anshika , Karmakar Soumen De , Ganesh Rajaraman 
Published: November 2024

AbstractWe study the dependence of alignment and confinement on the aggregate morphology of self-aligning soft disks(particles) in a planer box (two dimensional) geometry confined along y direction using Langevin dynamics simulations. We show that when the box width decreases, the aggregate wall accumulation becomes non-uniform and displays non-monotonic behaviour in terms of phase behavior and height of these aggregates with an increase in alignment strength. Additionally, we identify two distinct categories of wall aggregates: layered and non-layered structures each exhibiting distinct local structural properties. For non-layered structures, local speed of the particles stay nearly constant as we move away from the boundary, while for layered structures, it increases with distance from the boundary. Our analysis shows that active pressure difference is a useful indicator for different aggregate morphologies and the peaks in the pressure curve are indicative of the average and minimum height of the structure.
Mitigating coherent loss in superconducting circuits using molecular self-assembled monolayers
Authors: Alghadeer Mohammed , Banerjee Archan , Lee Kyunghoon , Hussein Hussein , Fariborzi Hossein , Rao Saleem 
Published: November 2024

AbstractIn planar superconducting circuits, decoherence due to materials imperfections, especially two-level-system (TLS) defects at different interfaces, is a primary hurdle for advancing quantum computing and sensing applications. Traditional methods for mitigating TLS loss, such as etching oxide layers at metal and substrate interfaces, have proven to be inadequate due to the persistent challenge of oxide regrowth. In this work, we introduce a novel approach that employs molecular self-assembled monolayers (SAMs) to chemically bind at different interfaces of superconducting circuits. This technique is specifically tested here on coplanar waveguide (CPW) resonators, in which this method not only impedes oxide regrowth after surface etching but can also tailors the dielectric properties at different resonators interfaces. The deployment of SAMs results in a consistent improvement in the measured quality factors across multiple resonators, surpassing those with only oxide-etched resonators. The efficiency of our approach is supported by microwave measurements of multiple devices conducted at millikelvin temperatures and correlated with detailed X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) characterizations of SAM-passivated resonators. The compatibility of SAMs materials with the established fabrication techniques offers a promising route to improve the performance of superconducting quantum devices.
Strength and timing of austral winter Angolan coastal upwelling
Authors: Körner Mareike , Brandt Peter , Dengler Marcus 
Published: November 2024

AbstractThe tropical Angolan upwelling system (tAUS) is a highly productive ecosystem of great socio-economic importance. Productivity peaks in austral winter and is linked to the passage of remotely forced upwelling coastal trapped waves (CTWs), where the strength of the productivity peak is associated with the amplitude of the upwelling CTW. Here, we analyze the year-to-year variability in the timing and amplitude of the austral winter upwelling CTW by examining sea surface temperature, sea level anomaly, and wind fields. Our results show that the timing of the CTW is influenced by variability in the equatorial region and along the southern African coast. Weaker equatorial easterlies from April to July delay the generation of the upwelling Kelvin wave, leading to a later arrival of the upwelling CTW. In contrast, the amplitude of the CTW is primarily influenced by variability in the eastern equatorial Atlantic and the central South Atlantic, where the South Atlantic Anticyclone is located. A cooling in the eastern equatorial Atlantic three to four months before the arrival of the CTW causes stronger zonal winds, ultimately leading to a stronger austral winter upwelling CTW. Our results suggest that the timing and amplitude of the upwelling CTW in the tAUS during austral winter are predictable on seasonal time scales.
Instrumentation prospects for rocky exoplanet atmospheres studies with high resolution spectroscopy
Authors: Rukdee Surangkhana 
Published: November 2024

AbstractStudying the atmospheres of exoplanets is one of the most promising ways to learn about distant worlds beyond our solar system. The composition of an exoplanet’s atmosphere can provide critical insights into its geology and potential habitability. For instance, the presence of certain molecules such as water vapor, oxygen, or methane have been proposed to indicate the possibility of life. From an observation point of view, over the past fifteen years, significant progress has been made in characterizing exoplanetary atmospheres. This work reviews recent developments in ground-based high-resolution spectroscopic instruments that make it possible to analyze distant atmospheres in great detail. High-resolution transmission spectroscopy, one of the most effective methods used, has examined the atmospheres of Jupiter-like and is pushing towards the smaller, sub-Neptunian exoplanets. Numerous molecules have been detected using this technique, including $$\mathrm {CO, H_2O, TiO, HCN, CH_4, NH_3, C_2H_2, OH}$$

CO
,

H
2

O
,
TiO
,
HCN
,

CH
4

,

NH
3

,

C
2

H
2

,
OH

. We explore the intriguing possibilities that lie ahead for future ground-based instrumentation, particularly in the context of detecting biologically relevant molecules within Earth-analog exoplanetary atmospheres including molecular oxygen ($$\mathrm {O_2}$$

O
2

). With detailed exposure time calculations for detecting $$\mathrm {O_2}$$

O
2

we find that at the same exposure time spectral resolution of 300,000 reaches higher significance compared to 100,000. The exposure time and therefore the needed number of transits is reduced by a factor of 4 in challenging haze and cloud scenarios.
Effect of dietary Anabaena supplementation on nutrient utilization, metabolism and oxidative stress response in Catla catla fingerlings
Authors: Mule S. R. , Singh Dilip Kumar , Prakash Patekar , Narsale Swapnil Ananda , Aklakur M. D. , Sardar Parimal , Biswas Gouranga , Sahoo Sujata , Jayant Manish , Mishra Samikshya 
Published: November 2024

AbstractA 60-day feeding trial was conducted to evaluate the effects of dietary Anabaena blue-green algae (ABGA) meal on the growth performance, digestibility, and physio-metabolic responses of Catla catla fingerlings (initial average weight 9.45 ± 0.15 g). Six iso-nitrogenous (30% crude protein) and iso-caloric (378.09 Kcal. digestible energy/100 g) diets were formulated: a control diet (A0, 0% ABGA) and five experimental diets with varying ABGA inclusion levels (A3: 3%, A6: 6%, A9: 9%, A12: 12%, A15: 15%). The results demonstrated that there were no significant differences (P > 0.05) in percentage weight gain (PWG), specific growth rate (SGR), protein efficiency ratio (PER), and feed conversion ratio (FCR) among the experimental groups. Additionally, dietary ABGA did not significantly affect (P > 0.05) body carcass composition among different groups. However, amylase activity significantly decreased (P < 0.05) in the A12 and A15 fed groups, whereas lipase and protease activities remained insignificant (P > 0.05) across all groups. Notably, oxidative stress responses (SOD; superoxide dismutase and CAT; catalase), carbohydrate metabolic enzymes (LDH; lactate dehydrogenase and MDH; malate dehydrogenase), and serum glucose levels increased significantly (P < 0.05) with higher ABGA inclusion. Conversely, serum albumin content significantly decreased (P < 0.05) in the ABGA-fed groups. There were no significant differences (P > 0.05) observed in serum total protein, albumin/globulin (A/G) ratio, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) activities among the experimental groups. Hematological parameters revealed that RBC (red blood cell) count, hemoglobin (Hb) concentration, and packed cell volume (PCV) significantly decreased (P < 0.05), while WBC (white blood cell) count significantly (P < 0.05) increased with higher dietary ABGA inclusion. In conclusion, the inclusion of dietary ABGA up to 15% did not impair nutrient utilization and supported normal growth performance in C. catla fingerlings. However, higher inclusion levels may have a detrimental effect on their growth, nutrient utilization, and physio-metabolic responses.
Dealing with adverse drug reactions in the context of polypharmacy using regression models
Authors: Sommer Jakob , Viviani Roberto , Wozniak Justyna , Stingl Julia C. , Just Katja S. 
Published: November 2024

AbstractPolypharmacy in older adults increases the risk of adverse drug reactions (ADRs), but studying this relationship is complex. In real-world data, the high number of medications, coupled with rare drug combinations, results in high-dimensional datasets that are difficult to analyze using conventional statistical methods. This study applies horseshoe and lasso regression for analyzing rare events in polypharmacy contexts, focusing on severe ADRs such as falls and bleedings. These regression models are executed on a multi-center dataset compiling 7175 cases from the ADRED project to detect potential ADR-associated drugs among 100 most common drugs in emergency department admissions. Positive predictors are classified by using 50% and 90% credibility intervals. This study demonstrates that regression models with horseshoe or lasso priors are effective for analyzing ADRs, providing a comprehensive consideration of multiple factors in large, sparse datasets and improving signal detection in polypharmacy, addressing a significant challenge in pharmacovigilance. Both priors yielded consistent and clinically meaningful results. The horseshoe regression resulted in fewer potential positive predictors overall, which could make it suitable as a diagnostic tool. While these regressions generate valuable information, there are still challenges in setting appropriate thresholds for determining and interpreting the positive results.
Educational boundaries explain strength and variation in global fertility convergence
Authors: Wu Hanbo , Pesando Luca Maria 
Published: November 2024

AbstractThis paper shows that the level and timing of fertility are converging strongly over different measures of educational attainment using 65 years of data from 146 countries. Global convergence patterns are primarily driven by high-income societies, while sub-Saharan Africa is the world region that is converging most slowly, if not converging at all. Most importantly, levels of education matter heavily for explaining strength and variation in global fertility convergence, with two intersecting educational gradients suggesting: (i) stronger convergence over tertiary education followed, in turn, by secondary and primary; (ii) stronger convergence over education completed relative to education attended. Our findings provide important insights for addressing key challenges in global development and demography, and for informing policymakers as they evaluate the suitability of specific educational policies aimed at further narrowing inequalities between societies—such as supporting higher education as well as the successful completion of targeted educational cycles.
Nonlinear time series analysis of state-wise COVID-19 in Malaysia using wavelet and persistent homology
Authors: Phang Piau , Ling Carey Yu-Fan , Liew Siaw-Hong , Razak Fatimah Abdul , Wiwatanapataphee Benchawan 
Published: November 2024

AbstractThe nonlinear progression of COVID-19 positive cases, their fluctuations, the correlations in amplitudes and phases across different regions, along with seasonality or periodicity, pose challenges to thoroughly examining the data for revealing similarities or detecting anomalous trajectories. To address this, we conducted a nonlinear time series analysis combining wavelet and persistent homology to detect the qualitative properties underlying COVID-19 daily infection numbers at the state level from the pandemic’s onset to June 2024 in Malaysia. The first phase involved investigating the evolution of daily confirmed cases by state in the time-frequency domain using wavelets. Subsequently, a topological feature-based time series clustering is performed by reconstructing a higher-dimensional phase space through a delay embedding method. Our findings reveal a prominent 7-day periodicity in case numbers from mid-2021 to the end of 2022. The state-wise daily cases are moderately correlated in both amplitudes and phases during the Delta and Omicron waves. Biweekly averaged data significantly enhances the detection of topological loops associated with these waves. Selangor demonstrates unique case trajectories, while Pahang shows the highest similarity with other states. This methodological framework provides a more detailed understanding of epidemiological time series data, offering valuable insights for preparing for future public health crises.
Bacteriophage-related epigenetic natural and non-natural pyrimidine nucleotides and their influence on transcription with T7 RNA polymerase
Authors: Gracias Filip , Pohl Radek , Sýkorová Veronika , Hocek Michal 
Published: November 2024

AbstractDNA modifications on pyrimidine nucleobases play diverse roles in biology such as protection of bacteriophage DNA from enzymatic cleavage, however, their role in the regulation of transcription is underexplored. We have designed and synthesized a series of uracil 2ʹ-deoxyribonucleosides and 5ʹ-O-triphosphates (dNTPs) bearing diverse modifications at position 5 of nucleobase, including natural nucleotides occurring in bacteriophages, α-putrescinylthymine, α-glutaminylthymine, 5-dihydroxypentyluracil, and methylated or non-methylated 5-aminomethyluracil, and non-natural 5-sulfanylmethyl- and 5-cyanomethyluracil. The dNTPs bearing basic substituents were moderate to poor substrates for DNA polymerases, but still useful in primer extension synthesis of modified DNA. Together with previously reported epigenetic pyrimidine nucleotides, they were used for the synthesis of diverse DNA templates containing a T7 promoter modified in the sense, antisense or in both strands. A systematic study of the in vitro transcription with T7 RNA polymerase showed a moderate positive effect of most of the uracil modifications in the non-template strand and some either positive or negative influence of modifications in the template strand. The most interesting modification was the non-natural 5-cyanomethyluracil which showed significant positive effect in transcription.
MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling
Authors: Raouraoua Nessim , Mirabello Claudio , Véry Thibaut , Blanchet Christophe , Wallner Björn , Lensink Marc F. , Brysbaert Guillaume 
Published: November 2024

AbstractMassive sampling in AlphaFold enables access to increased structural diversity. In combination with its efficient confidence ranking, this unlocks elevated modeling capabilities for monomeric structures and foremost for protein assemblies. However, the approach struggles with GPU cost and data storage. Here we introduce MassiveFold, an optimized and customizable version of AlphaFold that runs predictions in parallel, reducing the computing time from several months to hours. MassiveFold is scalable and able to run on anything from a single computer to a large GPU infrastructure, where it can fully benefit from all the computing nodes.
Experience-driven development of decision-related representations in the auditory cortex
Authors: Kazanovich Itay , Itzhak Shir , Resnik Jennifer 
Published: November 2024

AbstractAssociating sensory stimuli with behavioral significance induces substantial changes in stimulus representations. Recent studies suggest that primary sensory cortices not only adjust representations of task-relevant stimuli, but actively participate in encoding features of the decision-making process. We sought to determine whether this trait is innate in sensory cortices or if choice representation develops with time and experience. To trace choice representation development, we perform chronic two-photon calcium imaging in the primary auditory cortex of head-fixed mice while they gain experience in a tone detection task with a delayed decision window. Our results reveal a progressive increase in choice-dependent activity within a specific subpopulation of neurons, aligning with growing task familiarity and adapting to changing task rules. Furthermore, task experience correlates with heightened synchronized activity in these populations and the ability to differentiate between different types of behavioral decisions. Notably, the activity of this subpopulation accurately decodes the same action at different task phases. Our findings establish a dynamic restructuring of population activity in the auditory cortex to encode features of the decision-making process that develop over time and refines with experience.
Palmitoylation by ZDHHC4 inhibits TRPV1-mediated nociception
Authors: Zhang Youjing , Zhang Mengyu , Tang Cheng , Hu Junyan , Cheng Xufeng , Li Yang , Chen Zefeng , Yin Yuan , Xie Chang , Li Dongdong , Yao Jing 
Published: November 2024

AbstractTransient receptor potential vanilloid 1 (TRPV1) is a capsaicin-sensitive ion channel implicated in pain sensation. While TRPV1 potentiation in hyperalgesia development has been extensively investigated, its functional decline during pain relief remains largely unexplored. Here, by molecular, electrophysiological and in vivo evidence, we reveal that S-palmitoylation fine-tunes TRPV1 function by promoting its degradation via the lysosome pathway thereby facilitating inflammatory pain relief. The palmitoyl acyltransferase ZDHHC4 is identified to physically interact with TRPV1 and to catalyze S-palmitoylation at the cysteine residues C157, C362, C390, and C715 of the channel. Furthermore, we show that TRPV1 palmitoylation is counterbalanced by the depalmitoylase acyl-protein thioesterase 1 (APT1), thereby reinstating pain sensation. These findings provide important mechanistic insights into the relief phase of inflammatory pain.
Implementing Transparency in Learning and Teaching in Higher Ed in Speech Science Coursework: A Tutorial
Authors: Mandulak Kerry Callahan 
Published: November 2024

Purpose:
Transparent Instruction in Learning and Teaching in Higher Ed (TILT Higher Ed) is an evidence-based teaching method that can be used in Speech Science teaching to facilitate success of all learners. In addition, TILT Higher Ed has been found to provide an inclusive learning environment and promote belonging in the classroom context.

Conclusions:
The goal of this tutorial is to provide background information, a rationale, and a guide for implementation of the core principles of TILT Higher Ed into Speech Science coursework, which includes Transparent Assessment Design and Transparent Teaching Methods. A case will also be made for an overall shift of increased use of inclusive teaching methods within undergraduate communication sciences and disorders courses.