bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strengthened impact of late autumn Arctic sea ice on Asian winter cold extremes after 1999/2000
Authors: Wang Cen , Su Hui , Zheng Jianqiu , Yu Shiwei , Jiang Linwei , Mo Huisi 
Published: June 2024

Abstract
Winter cold extremes (WCEs) frequently plague densely populated areas of Asia, leading to substantial economic losses and even fatalities. It has been found that the late autumn sea ice concentration (SIC) anomalies in the northern (SICN) and southern Arctic (SICS) are significantly positively and negatively correlated with the occurrence frequency of WCE in Asia, respectively (Wang and Su 2024). Our study demonstrates that the impacts of SICN and SICS have strengthened after 1999/2000. Specifically, before 1999/2000, the influences of SICN and SICS on the Asian WCE (AWCE) were relatively weak, possibly related to the weak intensity of SICS and the limited correlation between SICN and SICS. After 1999/2000, the interannual variability of SICS became larger and anti-correlated with that of SICN, resulting in a stronger teleconnection between the Arctic SIC and AWCE. It is revealed that after 1999/2000, the greater loss of SICS modified atmospheric stability through changes in surface heat fluxes and surface upward longwave radiation fluxes. This alteration weakened the magnitudes of westerly winds and increased the frequency of blocking events over the northern Eurasian continent, leading directly to a higher occurrence of cold extremes in Asia. These interdecadal differences in the influence of Arctic SIC on AWCE may be associated with long-term climate change.
Reducing hardware requirements for entanglement distribution via joint hardware-protocol optimization
Authors: Labay Mora Adrià , Ferreira da Silva Francisco , Wehner Stephanie 
Published: June 2024

Abstract
We conduct a numerical investigation of fiber-based entanglement distribution over distances of up to 1600 km using a chain of processing-node quantum repeaters. We determine minimal hardware requirements while simultaneously optimizing over protocols for entanglement generation and entanglement purification, as well as over strategies for entanglement swapping. Notably, we discover that through an adequate choice of protocols the hardware improvement cost scales linearly with the distance covered. Our results highlight the crucial role of good protocol choices in significantly reducing hardware requirements, such as employing purification to meet high-fidelity targets and adopting a swap as soon as possible policy for faster rates. To carry out this analysis, we employ an extensive simulation framework implemented with NetSquid, a discrete-event-based quantum-network simulator, and a genetic-algorithm-based optimization methodology to determine minimal hardware requirements.
Engineering intelligent motion control protocol for dual-resolution linear actuator with unified coupled drive system
Authors: Agrawal Gagan , Patel Naimesh , Mathur Neeraj , Joshi Shaunak R , S Shri Hari 
Published: June 2024

Abstract
Actuators with high resolution and high range are always in demand for critical applications such as space applications, machining, and medical equipment. A dual-resolution actuator that has a coarse motion segment and a fine motion segment in itself that runs through a common drive system was designed. A coupling mechanism is employed to engage and disengage with the coarse motion of the actuator, enabling the use of coarse motion only when required. The actuator can achieve the target in any of three methods: (1) directly through fine motion, (2) utilizing a combination of fine and coarse motion without the need to overshoot the target value, and (3) employing both fine and coarse motion with a need for overshoot of the target value. An intelligent algorithm employing multiple techniques to address sensor-induced delays and enhance runtime efficiency was developed and tested on the realized actuator. This paper describes the techniques adopted and the sequence of conditions used to enable the actuator to reach the target in the shortest time and minimum possible steps.
GaAs-on-insulator ridge waveguide nanobeam cavities with integrated InAs quantum dots
Authors: Zhou Yueguang , Yang Yuhui , Wang Yujing , Koulas-Simos Aris , C Palekar Chirag , Limame Imad , Li Shulun , Liu Hanqing , Ni Haiqiao , Niu Zhichuan , Yvind Kresten , Gregersen Niels , Pu Minhao , Reitzenstein Stephan 
Published: June 2024

Abstract
This study investigates nanobeam cavities on a GaAs-on-insulator (GaAsOI) chip with InAs quantum dots (QDs), including design, fabrication, and experimental characterization. The nanobeam cavities are optimized for high photon coupling efficiency and pronounced light-matter interaction. Numerical studies yield Q factors up to about 1400, a coupling efficiency of nearly 70

%

and a maximum Purcell factor of approximately 100. Experimentally, these devices have a Q factor of about 1300, and comparing the lifetime of QDs in on-resonance and off-resonance conditions, a Purcell factor of

10.46
±
0.14

is obtained. Moreover, in the single-emitter regime, we observe strong multiphoton suppression with

g

(
2
)

(
0
)
=
0.297

. Our results demonstrate the high potential of nanobeam cavities on a GaAsOI platform for quantum photonic applications.
Late Acceleration
Authors: Chatterjee Elizabeth 
Published: June 2024

Abstract
The energy crisis of the early 1970s briefly opened up a radically new horizon of energetic possibilities that played out differently around the world. For India, that energy crisis did not begin with the famous Arab oil embargo of 1973. Instead, like many poor oil-importing nations, it experienced the first oil shock as merely one component of a broader climate-food-energy emergency that reverberated throughout the political system. This crisis brought a twinned set of fateful changes. By June 1975, Prime Minister Indira Gandhi had resorted to imposing a constitutional dictatorship—the Emergency—for the first and only time in independent India’s existence, one among a series of coups and authoritarian takeovers that swept the Global South. Less noticed was a second transformation with planetary ramifications. Rising popular expectations collided with the energy crisis to impel a state-led embrace of coal, despite elite reservations about the environmental damage that would follow. Analyzing these dynamics is crucial to understanding India’s intensifying coal dependence, and its rapidly rising carbon emissions, in the decades that followed. Only when we accurately recognize the forces that created and hold carbon-intensive energy regimes in place can we begin to see how they might be dislodged.
A Prospective, Randomized, Double-Blind, Split-Face, Comparative Study to Evaluate the Efficacy and Safety of DKL23 and Juvéderm Volift for Correcting Moderate-to-Severe Nasolabial Folds
Authors: Alimohammadi Mohammad , Furman-Assaf Sharon , Nilsson Johan 
Published: June 2024

Abstract

Background
Hyaluronic acid dermal fillers are used for multiple indications, including wrinkle correction and restoration of volume/fullness.

Objectives
The aim of this study was to compare the efficacy and safety of 2 hyaluronic acid products for correcting moderate to severe nasolabial folds (NLFs).

Methods
A prospective, randomized, double-blind, split-face study was undertaken. The subjects’ left and right NLFs were randomly allocated for treatment with DKL23 or Juvéderm Volift. Follow-up was conducted at 1, 3, 6, and 9 months. The changes from baseline on the Wrinkle Severity Rating Scale and the Global Aesthetics Improvement Scale were evaluated. Posttreatment adverse events (AEs) were recorded.

Results
Forty-eight women (median age, 57.0 years) with Type I to VI skin were enrolled. Both treatments showed statistically significant improvement (P &lt; .0001) in NLFs according to the Wrinkle Severity Rating Scale score from baseline to each of the time points assessed. The improvement in NLFs was maintained until the end of the study (9 months). Furthermore, the change from baseline to each of the time points assessed was similar between DKL23 and Juvéderm Volift. Investigator- and subject-rated Global Aesthetics Improvement Scale scores showed similar rates of improvement (indicated by the sum of responses of improved, much improved, or very much improved) between the 2 products. The AEs reported in the study were in line with previous and expected experience after injection of hyaluronic acid dermal fillers. The types of AEs, their rates, intensity, and duration were comparable between the 2 products.

Conclusions
DKL23 improved NLF severity from baseline and for up to 9 months, and the results were comparable to the improvement shown by Juvéderm Volift. Treatment was safe and well tolerated.

Level of Evidence: 2
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer
Authors: Xu Xiaopeng , Xu Chencheng , He Wenjia , Wei Lesong , Li Haoyang , Zhou Juexiao , Zhang Ruochi , Wang Yu , Xiong Yuanpeng , Gao Xin 
Published: June 2024

Abstract

Motivation
Macrocyclic peptides hold great promise as therapeutics targeting intracellular proteins. This stems from their remarkable ability to bind flat protein surfaces with high affinity and specificity while potentially traversing the cell membrane. Research has already explored their use in developing inhibitors for intracellular proteins, such as KRAS, a well-known driver in various cancers. However, computational approaches for de novo macrocyclic peptide design remain largely unexplored.

Results
Here, we introduce HELM-GPT, a novel method that combines the strength of the hierarchical editing language for macromolecules (HELM) representation and generative pre-trained transformer (GPT) for de novo macrocyclic peptide design. Through reinforcement learning (RL), our experiments demonstrate that HELM-GPT has the ability to generate valid macrocyclic peptides and optimize their properties. Furthermore, we introduce a contrastive preference loss during the RL process, further enhanced the optimization performance. Finally, to co-optimize peptide permeability and KRAS binding affinity, we propose a step-by-step optimization strategy, demonstrating its effectiveness in generating molecules fulfilling both criteria. In conclusion, the HELM-GPT method can be used to identify novel macrocyclic peptides to target intracellular proteins.

Availability and implementation
The code and data of HELM-GPT are freely available on GitHub (https://github.com/charlesxu90/helm-gpt).
Ragas: integration and enhanced visualization for single cell subcluster analysis
Authors: Balaji Uthra , Rodríguez-Alcázar Juan , Balasubramanian Preetha , Smitherman Cynthia , Baisch Jeanine , Pascual Virginia , Gu Jinghua 
Published: June 2024

Abstract

Summary
Subcluster analysis is a powerful means to improve clustering and characterization of single cell RNA-Seq data. However, there are no existing tools to systematically integrate results from multiple subclusters, which creates hurdles for accurate data quantification, visualization, and interpretation in downstream analysis. To address this issue, we developed Ragas, an R package that integrates multi-level subclustering objects for streamlined analysis and visualization. A new data structure was implemented to seamlessly connect and assemble miscellaneous single cell analyses from different levels of subclustering, along with several new or enhanced visualization functions. Moreover, a re-projection algorithm was developed to integrate nearest-neighbor graphs from multiple subclusters in order to maximize their separability on the combined cell embeddings, which significantly improved the presentation of rare and homogeneous subpopulations.

Availability and implementation
The Ragas package and its documentation can be accessed through https://github.com/jig4003/Ragas and its source code is also available at https://zenodo.org/records/11244921.
Integrative profiling of untreated primary membranous nephropathy at the single-cell transcriptome level
Authors: Gu Qiuhua , Wen Yuchen , Cheng Xi , Qi Yan , Cao Xin , Gao Xiqian , Mao Xiaoming , Shang Wenya , Wei Li , Jia Junya , Yan Tiekun , Cai Zhigang 
Published: June 2024

ABSTRACT

Background
Primary membranous nephropathy (PMN) is an autoimmune kidney disease. Despite the identification of certain autoantigens, the etiology and pathophysiology of PMN are still largely unknown.

Methods
Five patients with biopsy-proven PMN were enrolled in this study. Their blood, kidney and urine samples were collected respectively to profile cellular, molecular and immunological alterations by using single-cell RNA sequencing (scRNA-seq). Experimental verifications were also implemented in kidney tissue.

Results
In the peripheral blood mononuclear cell (PBMC) samples, portions of B cells and plasma cells were increased in PMN patients. Cell–cell communication analysis suggests that APRIL (a proliferation-inducing ligand from B cells) might be a potential molecule that regulates the activity of plasma cells. In the kidney samples, scRNA-seq analysis showed that the infiltration of T cells, as well as the myeloid cells, appears abundant compared with healthy controls, suggesting that immune cells are actively recruited to kidney. Furthermore, we observed an enhanced interaction between inflammatory cells and podocytes, which might contribute to kidney injury. Accordingly, scRNA-seq analysis of urinary samples is partially reminiscent of the kidney cell landscape, especially T cells and myeloid cells, suggesting monitoring urinary samples is a promising method to monitor PMN development. Additionally, integrative analysis across the blood, kidney and urine identified LTB, HERP1, ANXA1, IL1RN and ICAM1 as common regulators of PMN. Finally, immune repertoire in PBMC also showed an elevated diversity of clonal type, implying the existence of autoreactive T-cell receptor/B-cell receptor.

Conclusion
Our study comprehensively profiled the transcriptomic landscapes of blood, kidney and urine in patients with PMN using scRNA-seq. We depicted the alterations including cell compositions and cell–cell communication in PMN. These results offer important clues with regard to the diagnosis and pathogenesis of PMN and potential intervention of PMN progression.
Cold mountain stream chironomids (Diptera) of the genus Diamesa indicate both historical and recent climate change
Authors: Dočkalová Kateřina , Stuchlík Evžen , Hamerlík Ladislav , Bitušík Peter , Turek Jan , Svitok Marek , Novikmec Milan , Lackner Reinhard , Dvorak Martin , Kopáček Jiří , Tátosová Jolana , Camarero Lluís , Füreder Leopold , Vondrák Daniel 
Published: June 2024

Abstract
Chironomids of the genus Diamesa (Meigen, 1835, Diptera: Chironomidae) inhabit cold, oxygen-rich running waters. We have investigated the presence of Diamesa and other freshwater macroinvertebrates at 22 stream sampling sites in 3 European high mountain regions (the Central Pyrenees, the Ötztal Alps, and the Tatra Mountains) to establish suitable temperature conditions for Diamesa dominance. It has been generally accepted that their high abundance was linked to the presence of glaciers; however, we have shown that in the Tatra Mountains, where there are no glaciers, the conditions for the dominance of Diamesa species are created due to permanent snowfields, the geographical orientation of the valley and shading by the surrounding high peaks. The historical connection of Diamesa to glaciers was investigated from the paleolimnological records of subfossil chironomid assemblages from the Bohemian Forest, where glaciers disappeared before or during the Late Glacial period.
As expected, water temperature seems to be the main driver of Diamesa distribution, and we determined that the relative abundance of Diamesa species was significantly higher at the sites with a mean July water temperature below 6.5 °C. The Diamesa-dominated stream communities seems to be endangered due to ongoing climate warming and this assumption is supported by our paleolimnological results from the Bohemian Forest lakes, where Diamesa has disappeared due to warming of lake inflows at the beginning of the Holocene. These findings strengthen the former suggestions that some Diamesa species could be used as an indicator for tracking recent environmental changes in vulnerable ecosystems of cold mountain streams.
PAX3 haploinsufficiency in Maine Coon cats with dominant blue eyes and hearing loss resembling the human Waardenburg syndrome
Authors: Rudd Garces Gabriela , Farke Daniela , Schmidt Martin J , Letko Anna , Schirl Katja , Abitbol Marie , Leeb Tosso , Lyons Leslie A , Lühken Gesine 
Published: June 2024

Abstract
This study investigated the dominant blue eyes (DBE) trait linked to hearing impairment and variable white spotting in Maine Coon cats. Fifty-eight animals descending from 2 different DBE lineages, the Dutch and the Topaz lines, were sampled. They comprised 48 cats from the Dutch bloodline, including 9 green-eyed and 31 blue-eyed cats, with some individuals exhibiting signs of deafness, and 8 stillborn kittens. Samples from the Topaz lineage included 10 blue-eyed animals. A brainstem auditory evoked response test revealed a reduced to absent response to auditory stimuli and absent physiological waveforms in all of the 8 examined DBE animals. We sequenced the genome of 2 affected cats from the Dutch line and searched for variants in 19 candidate genes for the human Waardenburg syndrome and pigmentary disorders. This search yielded 9 private protein-changing candidate variants in the genes PAX3, EDN3, KIT, OCA2, SLC24A5, HERC2, and TYRP1. The genotype–phenotype cosegregation was observed for the PAX3 variant within all animals from the Dutch lineage. The mutant allele was absent from 461 control genomes and 241 additionally genotyped green-eyed Maine Coons. We considered the PAX3 variant as the most plausible candidate—a heterozygous nonsense single base pair substitution in exon 6 of PAX3 (NC_051841.1:g.205,787,310G&gt;A, XM_019838731.3:c.937C&gt;T, XP_019694290.1:p.Gln313*), predicted to result in a premature stop codon. PAX3 variants cause auditory–pigmentary syndrome in humans, horses, and mice. Together with the comparative data from other species, our findings strongly suggest PAX3:c.937C&gt;T (OMIA:001688-9685) as the most likely candidate variant for the DBE, deafness, and minimal white spotting in the Maine Coon Dutch line. Finally, we propose the designation of DBERE (Rociri Elvis Dominant Blue Eyes) allele in the domestic cat.
Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases
Authors: Raubenolt Bryan , Blankenberg Daniel 
Published: June 2024

Abstract
Viral helicases are promising targets for the development of antiviral therapies. Given their vital function of unwinding double-stranded nucleic acids, inhibiting them blocks the viral replication cycle. Previous studies have elucidated key structural details of these helicases, including the location of substrate binding sites, flexible domains, and the discovery of potential inhibitors. Here we present a series of new Galaxy tools and workflows for performing and analyzing molecular dynamics simulations of viral helicases. We first validate them by demonstrating recapitulation of data from previous simulations of Zika (NS3) and SARS-CoV-2 (NSP13) helicases in apo and complex with inhibitors. We further demonstrate the utility and generalizability of these Galaxy workflows by applying them to new cases, proving their usefulness as a widely accessible method for exploring antiviral activity.
The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis
Authors: Wang Hengchao , Xu Dong , Jiang Fan , Wang Sen , Wang Anqi , Liu Hangwei , Lei Lihong , Qian Wanqiang , Fan Wei 
Published: June 2024

Abstract

Background
The Coreopsideae tribe, a subset of the Asteraceae family, encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely employed in medicine, horticulture, ecology, and food applications. Nevertheless, the lack of reference genomes hinders evolutionary and biological investigations in this tribe.

Results
Here, we present 3 haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including 2 popular flowering plants (Dahlia pinnata and Cosmos bipinnatus) and 1 invasive weed plant (Bidens alba), with assembled genome sizes 3.93 G, 1.02 G, and 1.87 G, respectively. We found that Gypsy transposable elements contribute mostly to the larger genome size of D. pinnata, and multiple chromosome rearrangements have occurred in tribe Coreopsideae. Besides the shared whole-genome duplication (WGD-2) in the Heliantheae alliance, our analyses showed that D. pinnata and B. alba each underwent an independent recent WGD-3 event: in D. pinnata, it is more likely to be a self-WGD, while in B. alba, it is from the hybridization of 2 ancestor species. Further, we identified key genes in the inulin metabolic pathway and found that the pseudogenization of 1-FEH1 and 1-FEH2 genes in D. pinnata and the deletion of 3 key residues of 1-FFT proteins in C. bipinnatus and B. alba may probably explain why D. pinnata produces much more inulin than the other 2 plants.

Conclusions
Collectively, the genomic resources for the Coreopsideae tribe will promote phylogenomics in Asteraceae plants, facilitate ornamental molecular breeding improvements and inulin production, and help prevent invasive weeds.
Diagnosis-based design of electric power steering system considering multiple degradations: role of designable generative adversarial network anomaly detection
Authors: Kim Jeongbin , Yang Dabin , Lee Jongsoo 
Published: June 2024

Abstract
Recently, interest in functional safety has surged because vehicle technology increasingly relies on electronics and automation. Failure of certain system components can endanger driver safety and is costly to address. The detection of abnormal data is crucial for enhancing the reliability, safety, and efficiency. This study introduces a novel anomaly-detection method of designable generative adversarial network anomaly detection (DGANomaly). DGANomaly combines the data augmentation method of a designable generative adversarial network (DGAN) with a generative adversarial network anomaly-detection data classification technique. DGANomaly not only generates virtual data that are challenging to obtain or simulate but also produces a range of statistical design variables for normal and abnormal data. This approach enables the specific identification of normal and abnormal design variables. To demonstrate its effectiveness, the DGANomaly method was applied to an electric power steering (EPS) model when multiple degradations of gear stiffness, gear friction, and rack displacement were considered. An EPS model was constructed and validated using simulation programs such as Prescan, Amesim, and Simulink. Consequently, DGANomaly exhibited a higher classification accuracy than the other methods, allowing for more accurate detection of abnormal data. Additionally, a clearer range of statistical designs can be obtained for normal data. These results indicate that the statistical design variables that are less likely to fail can be obtained using minimal data.