bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endovascular Thrombectomy Versus Intravenous Alteplase For Distal Medium Vessel Occlusions: A Propensity Score‐Matched Analysis
Authors: Yoshie Tomohide , Ueda Toshihiro , Hasegawa Yasuhiro , Takeuchi Masataka , Morimoto Masafumi , Tsuboi Yoshifumi , Yamamoto Ryoo , Kaku Shogo , Ayabe Junichi , Akiyama Takekazu , Yamamoto Daisuke , Mori Kentaro , Kagami Hiroshi , Ito Hidemichi , Onodera Hidetaka , Kaga Yasuyuki , Ohtsubo Haruki , Tatsuno Kentaro , Usuki Noriko , Takaishi Satoshi , Yamano Yoshihisa ,   the K‐NET Registry Investigators
Published: July 2024

Background
The benefits of endovascular thrombectomy (EVT) for distal medium vessel occlusions (DMVOs) are not well established. This study aimed to determine the superiority of EVT over intravenous tissue‐type plasminogen activator (IV tPA) in the treatment of DMVOs.

Methods
This study analyzed data from the Kanagawa Intravenous and Endovascular Treatment of Acute Ischemic Stroke Registry, a prospective, multicenter, observational registry of acute ischemic stroke patients treated with EVT or IV tPA. The study evaluated patients with acute DMVOs who were treated with EVT and/or IV tPA. DMVOs was defined as occlusions in M2–M3 segment of the middle cerebral artery, anterior cerebral artery, or posterior cerebral artery. The analysis included primary DMVOs and excluded secondary DMVOs, such as distal embolism after recanalization of proximal vessel occlusion. Propensity score‐matched analysis was conducted to compare the outcomes between EVT and IV tPA alone. A good outcome was defined as a modified Rankin Scale score 0–2 or no worsening at 90 days. An excellent outcome was defined as an modified Rankin Scale score 0–1.

Results

The study included 1148 patients with DMVOs, of whom 816 were treated with EVT and 332 were IV tPA alone. Before propensity score matching, the incidence of good and excellent outcomes was significantly lower in EVT group (good outcomes: EVT 50.3% versus IV tPA 68.0%;
P
< 0.01; excellent outcomes: 39.8% versus 59.8%;
P
< 0.001). After propensity score matching, there were no significant differences between EVT and IV tPA groups in good outcomes (EVT 57.8% versus IV tPA 61.3%;
P
= 0.51), excellent outcomes (46.6% versus 55.0%;
P
= 0.17), all cerebral hemorrhage (11.6% versus 12.7%;
P
= 0.74), and symptomatic hemorrhage (2.9% versus 0.6%;
P
= 0.13). Subarachnoid hemorrhage was more frequent in EVT group (14.5% versus IV tPA 0%).

Conclusion
The benefits of EVT for acute DMVOs were similar to IV tPA alone. Randomized multicenter trials are warranted to establish the superiority of EVT over IV tPA alone for DMVOs.
Multilayer meta-matching: Translating phenotypic prediction models from multiple datasets to small data
Authors: Chen Pansheng , An Lijun , Wulan Naren , Zhang Chen , Zhang Shaoshi , Ooi Leon Qi Rong , Kong Ru , Chen Jianzhong , Wu Jianxiao , Chopra Sidhant , Bzdok Danilo , Eickhoff Simon B. , Holmes Avram J. , Yeo B.T. Thomas 
Published: July 2024

Abstract
Resting-state functional connectivity (RSFC) is widely used to predict phenotypic traits in individuals. Large sample sizes can significantly improve prediction accuracies. However, for studies of certain clinical populations or focused neuroscience inquiries, small-scale datasets often remain a necessity. We have previously proposed a “meta-matching” approach to translate prediction models from large datasets to predict new phenotypes in small datasets. We demonstrated a large improvement over classical kernel ridge regression (KRR) when translating models from a single source dataset (UK Biobank) to the Human Connectome Project Young Adults (HCP-YA) dataset. In the current study, we propose two meta-matching variants (“meta-matching with dataset stacking” and “multilayer meta-matching”) to translate models from multiple source datasets across disparate sample sizes to predict new phenotypes in small target datasets. We evaluate both approaches by translating models trained from five source datasets (with sample sizes ranging from 862 participants to 36,834 participants) to predict phenotypes in the HCP-YA and HCP-Aging datasets. We find that multilayer meta-matching modestly outperforms meta-matching with dataset stacking. Both meta-matching variants perform better than the original “meta-matching with stacking” approach trained only on the UK Biobank. All meta-matching variants outperform classical KRR and transfer learning by a large margin. In fact, KRR is better than classical transfer learning when less than 50 participants are available for finetuning, suggesting the difficulty of classical transfer learning in the very small sample regime. The multilayer meta-matching model is publicly available at https://github.com/ThomasYeoLab/Meta_matching_models/tree/main/rs-fMRI/v2.0.
A Continuity in Logical Development: Domain-General Disjunctive Inference by Toddlers
Authors: Cesana-Arlotti Nicolò , Halberda Justin 
Published: July 2024

Abstract
Children grow up surrounded by opportunities to learn (the language of their community, the movements of their body, other people's preferences and mental lives, games, social norms, etc.). Here, we find that toddlers (N = 36; age range 2.3–3.2 years) rely on a logical reasoning strategy, Disjunctive Inference (i.e., A OR B, A is ruled out, THEREFORE, B), across a variety of situations, all before they have any formal education or extensive experience with words for expressing logical meanings. In learning new words, learning new facts about a person, and finding the winner of a race, toddlers systematically consider and reject competitors before deciding who must be the winner. This suggests that toddlers may have a general-purpose logical reasoning tool that they can use in any situation.
Low-intensity transcranial focused ultrasound suppresses pain by modulating pain-processing brain circuits
Authors: Kim Min Gon , Yu Kai , Yeh Chih-Yu , Fouda Raghda , Argueta Donovan , Kiven Stacy , Ni Yunruo , Niu Xiaodan , Chen Qiyang , Kim Kang , Gupta Kalpna , He Bin 
Published: July 2024

Abstract
There is an urgent and unmet clinical need to develop nonpharmacological interventions for chronic pain management because of the critical side effects of opioids. Low-intensity transcranial focused ultrasound (tFUS) is an emerging noninvasive neuromodulation technology with high spatial specificity and deep brain penetration. Here, we developed a tightly focused 128-element ultrasound transducer to specifically target small mouse brains using dynamic focus steering. We demonstrate that tFUS stimulation at pain-processing brain circuits can significantly alter pain-associated behaviors in mouse models in vivo. Our findings indicate that a single-session focused ultrasound stimulation to the primary somatosensory cortex (S1) significantly attenuates heat pain sensitivity in wild-type mice and modulates heat and mechanical hyperalgesia in a humanized mouse model of chronic pain in sickle cell disease. Results further revealed a sustained behavioral change associated with heat hypersensitivity by targeting deeper cortical structures (eg, insula) and multisession focused ultrasound stimulation to S1 and insula. Analyses of brain electrical rhythms through electroencephalography demonstrated a significant change in noxious heat hypersensitivity-related and chronic hyperalgesia–associated neural signals after focused ultrasound treatment. Validation of efficacy was carried out through control experiments, tuning ultrasound parameters, adjusting interexperiment intervals, and investigating effects on age, sex, and genotype in a head-fixed awake model. Importantly, tFUS was found to be safe, causing no adverse effects on motor function or the brain’s neuropathology. In conclusion, the validated proof-of-principle experimental evidence demonstrates the translational potential of novel focused ultrasound neuromodulation for next-generation pain treatment without adverse effects.
Evaluation on Configuration Stiffness of Overconstrained 2R1T Parallel Mechanisms
Authors: Ma Xuejian , Xu Zhenghe , Xu Yundou , Wang Yu , Yao Jiantao , Zhao Yongsheng 
Published: July 2024

AbstractCurrently, two rotations and one translation (2R1T) three-degree-of-freedom (DOF) parallel mechanisms (PMs) are widely applied in five-DOF hybrid machining robots. However, there is a lack of an effective method to evaluate the configuration stiffness of mechanisms during the mechanism design stage. It is a challenge to select appropriate 2R1T PMs with excellent stiffness performance during the design stage. Considering the operational status of 2R1T PMs, the bending and torsional stiffness are considered as indices to evaluate PMs' configuration stiffness. Subsequently, a specific method is proposed to calculate these stiffness indices. Initially, the various types of structural and driving stiffness for each branch are assessed and their specific values defined. Subsequently, a rigid-flexible coupled force model for the over-constrained 2R1T PM is established, and the proposed evaluation method is used to analyze the configuration stiffness of the five 2R1T PMs in the entire workspace. Finally, the driving force and constraint force of each branch in the whole working space are calculated to further elucidate the stiffness evaluating results by using the proposed method above. The obtained results demonstrate that the bending and torsional stiffness of the 2RPU/UPR/RPR mechanism along the x and y-directions are larger than the other four mechanisms.
Identification, validation and candidate gene analysis of major QTL for Supernumerary spikelets in wheat
Authors: Wang Zhiqiang , Li Haojie , Zhou Xinjian , Mou Yuzhou , Zhang Ying , Yu Lang , Chen Xudong , Wu Fangkun , Zhou Hong , Lin Yu , Li Caixia , Liu Yaxi 
Published: July 2024

Abstract
Background
The number of spikelets per spike is a key trait that affects the yield of bread wheat (Triticum aestivum L.). Identification of the QTL for spikelets per spike and its genetic effects that could be used in molecular assistant breeding in the future.

Results
In this study, four recombinant inbred line (RIL) populations were generated and used, having YuPi branching wheat (YP), with Supernumerary Spikelets (SS) phenotype, as a common parent. QTL (QSS.sicau-2 A and QSS.sicau-2D) related to SS trait were mapped on chromosomes 2 A and 2D through bulked segregant exome sequencing (BSE-Seq). Fourteen molecular markers were further developed within the localization interval, and QSS.sicau-2 A was narrowed to 3.0 cM covering 7.6 Mb physical region of the reference genome, explaining 13.7 − 15.9% the phenotypic variance. Similarly, the QSS.sicau-2D was narrowed to 1.8 cM covering 2.4 Mb physical region of the reference genome, and it explained 27.4 − 32.9% the phenotypic variance. These two QTL were validated in three different genetic backgrounds using the linked markers. QSS.sicau-2 A was identified as WFZP-A, and QSS.sicau-2D was identified a novel locus, different to the previously identified WFZP-D. Based on the gene expression patterns, gene annotation and sequence analysis, TraesCS2D03G0260700 was predicted to be a potential candidate gene for QSS.sicau-2D.

Conclusion
Two significant QTL for SS, namely QSS.sicau-2 A and QSS.sicau-2D were identified in multiple environments were identified and their effect in diverse genetic populations was assessed. QSS.sicau-2D is a novel QTL associated with the SS trait, with TraesCS2D03G0260700 predicted as its candidate gene.
Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates
Authors: Luan Tu , Commichaux Seth , Hoffmann Maria , Jayeola Victor , Jang Jae Hee , Pop Mihai , Rand Hugh , Luo Yan 
Published: July 2024

AbstractBackgroundOxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed to correct these errors, but it is uncertain if they obtain the accuracy needed for the high-resolution source tracking of foodborne illness outbreaks.ResultsWe tested 132 combinations of assembly and short- and long-read polishing tools to assess their accuracy for reconstructing the genome sequences of 15 highly similarSalmonella entericaserovar Newport isolates from a 2020 onion outbreak. While long-read polishing alone improved accuracy, near perfect accuracy (99.9999% accuracy or ~ 5 nucleotide errors across the 4.8 Mbp genome, excluding low confidence regions) was only obtained by pipelines that combined both long- and short-read polishing tools. Notably, medaka was a more accurate and efficient long-read polisher than Racon. Among short-read polishers, NextPolish showed the highest accuracy, but Pilon, Polypolish, and POLCA performed similarly. Among the 5 best performing pipelines, polishing with medaka followed by NextPolish was the most common combination. Importantly, the order of polishing tools mattered i.e., using less accurate tools after more accurate ones introduced errors. Indels in homopolymers and repetitive regions, where the short reads could not be uniquely mapped, remained the most challenging errors to correct.ConclusionsShort reads are still needed to correct errors in nanopore sequenced assemblies to obtain the accuracy required for source tracking investigations. Our granular assessment of the performance of the polishing pipelines allowed us to suggest best practices for tool users and areas for improvement for tool developers.
Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors
Authors: McQuarrie David W. J. , Alizada Azad , Nicholson Benjamin Czech , Soller Matthias 
Published: July 2024

Abstract
Background
The piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila, this pathway relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine and Piwi) that associate with 23–28 nucleotide piRNAs, directing the silencing of transposon-derived transcripts. Transposons constitute a primary driver of genome evolution, yet the evolution of piRNA pathway factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact piRNA processing, exhibit regions of rapid evolution in their promoters. Consequently, the question arises whether such a mode of evolution is a general feature of transposon silencing pathways.

Results
By employing genomic analysis of coding and promoter regions within genes that function in transposon silencing in Drosophila, we demonstrate that the promoters of germ cell-specific piRNA factors are undergoing rapid evolution. Our findings indicate that rapid promoter evolution is a common trait among piRNA factors engaged in germline silencing across insect species, potentially contributing to gene expression divergence in closely related taxa. Furthermore, we observe that the promoters of genes exclusively expressed in germ cells generally exhibit rapid evolution, with some divergence in gene expression.

Conclusion
Our results suggest that increased germline promoter evolution, in partnership with other factors, could contribute to transposon silencing and evolution of species through differential expression of genes driven by invading transposons.
Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination
Authors: Hao Zhigang , Zhang Zhiping , Jiang Juan , Pan Lei , Zhang Jinan , Cui Xiufen , Li Yingbin , Li Jianqiang , Luo Laixin 
Published: July 2024

AbstractMelia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.
A gibberellin-assisted study of the transcriptional and hormonal changes occurring at floral transition in peach buds (Prunus persica L. Batsch)
Authors: Girardi Francesco , Canton Monica , Populin Francesca , Tijero Verónica , Bettio Giorgia , Munné-Bosch Sergi , Rasori Angela , Cardillo Valerio , Costa Guglielmo , Botton Alessandro 
Published: July 2024

Abstract
Background
Flower load in peach is an important determinant of final fruit quality and is subjected to cost-effective agronomical practices, such as the thinning, to finely balance the sink-source relationships within the tree and drive the optimal amount of assimilates to the fruits. Floral transition in peach buds occurs as a result of the integration of specific environmental signals, such as light and temperature, into the endogenous pathways that induce the meristem to pass from vegetative to reproductive growth. The cross talk and integration of the different players, such as the genes and the hormones, are still partially unknown. In the present research, transcriptomics and hormone profiling were applied on bud samples at different developmental stages. A gibberellin treatment was used as a tool to identify the different phases of floral transition and characterize the bud sensitivity to gibberellins in terms of inhibition of floral transition.

Results
Treatments with gibberellins showed different efficacies and pointed out a timeframe of maximum inhibition of floral transition in peach buds. Contextually, APETALA1 gene expression was shown to be a reliable marker of gibberellin efficacy in controlling this process. RNA-Seq transcriptomic analyses allowed to identify specific genes dealing with ROS, cell cycle, T6P, floral induction control and other processes, which are correlated with the bud sensitivity to gibberellins and possibly involved in bud development during its transition to the reproductive stage. Transcriptomic data integrated with the quantification of the main bioactive hormones in the bud allowed to identify the main hormonal regulators of floral transition in peach, with a pivotal role played by endogenous gibberellins and cytokinins.

Conclusions
The peach bud undergoes different levels of receptivity to gibberellin inhibition. The stage with maximum responsiveness corresponded to a transcriptional and hormonal crossroad, involving both flowering inhibitors and inductors. Endogenous gibberellin levels increased only at the latest developmental stage, when floral transition was already partially achieved, and the bud was less sensitive to exogenous treatments. A physiological model summarizes the main findings and suggests new research ideas to improve our knowledge about floral transition in peach.
Association between preoperative persistent hyperglycemia and postoperative delirium in geriatric hip fracture patients
Authors: Wang Wei , Zhang Yingqi , Yao Wei , Tang Wanyun , Li Yuhao , Sun Hongbo , Ding Wenbo 
Published: July 2024

Abstract
Background
The management of preoperative blood glucose levels in reducing the incidence of postoperative delirium (POD) remains controversial. This study aims to investigate the impact of preoperative persistent hyperglycemia on POD in geriatric patients with hip fractures.

Methods
This retrospective cohort study analyzed medical records of patients who underwent hip fracture surgery at a tertiary medical institution between January 2013 and November 2023. Patients were categorized based on preoperative hyperglycemia (hyperglycemia defined as ≥ 6.1mmol/L), clinical classification of hyperglycemia, and percentile thresholds. Multivariate logistic regression and propensity score matching analysis (PSM) were employed to assess the association between different levels of preoperative glucose and POD. Subgroup analysis was conducted to explore potential interactions.

Results
A total of 1440 patients were included in this study, with an incidence rate of POD at 19.1% (275/1440). Utilizing multiple logistic analysis, we found that patients with hyperglycemia had a 1.65-fold increased risk of experiencing POD compared to those with normal preoperative glucose levels (95% CI: 1.17–2.32). Moreover, a significant upward trend was discerned in both the strength of association and the predicted probability of POD with higher preoperative glucose levels. PSM did not alter this trend, even after meticulous adjustments for potential confounding factors. Additionally, when treating preoperative glucose levels as a continuous variable, we observed a 6% increase in the risk of POD (95% CI: 1-12%) with each 1mmol/L elevation in preoperative glucose levels.

Conclusions
There exists a clear linear dose-response relationship between preoperative blood glucose levels and the risk of POD. Higher preoperative hyperglycemia was associated with a greater risk of POD.

Clinical trial number
NCT06473324.