bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adding Visual Effects
Authors: Panchekha Pavel , Harrelson Chris 
Published: December 2024

Abstract
Right now our browser can only draw colored rectangles and text—pretty boring! Real browsers support all kinds of visual effects that change how pixels and colors blend together. To implement those effects, and also make our browser faster, we’ll need control over surfaces, the key low-level feature behind fast scrolling, visual effects, animations, and many other browser features. To get that control, we’ll also switch to using the Skia graphics library and even take a peek under its hood.
Reusing Previous Computations
Authors: Panchekha Pavel , Harrelson Chris 
Published: December 2024

Abstract
Compositing (see Chapter 13) makes animations smoother, but it doesn’t help with interactions that affect layout, like text editing or DOM modifications. Luckily, we can avoid redundant layout work by treating the layout tree as a kind of cache, and only recomputing the parts that change. This invalidation technique is traditionally complex and bug-prone, but we’ll use a principled approach and simple abstractions to make it manageable.
MiRNA-323 Alleviates Myocardial Ischemia-Reperfusion Injury by Modulating the Prostate Apoptosis Response-4/Cleaved Caspase-3 Pathway
Authors: Song Ji , Huang Bizhen , Sun Changqing , Liu Zuheng , Zheng Wuyang 
Published: December 2024

Abstract

OBJECTIVE
To investigate the impact of microRNA-323 (miR-323) on cardiomyocyte injury induced by ischemia-reperfusion.

METHODS
The H9C2 cell models for hypoxia/reoxygenation (HO) injury and mice models for ischemia/reperfusion were established. Cell viability was assessed through methyl thiazolyl tetrazolium colorimetry, while cardiomyocyte injury was determined using lactate dehydrogenase (LDH) release assays. Cardiac function was evaluated via ultrasound and the myocardial infarction area was measured through 2,3,5-triphenyl-2H-tetrazolium chloride-evans blue double staining. The protein levels of prostate apoptosis response-4 (PAR4) and cleaved caspase-3 were assessed via Western blot in H9C2 cell models both pre- and post-HO.

RESULTS
In the cellular experiment, after HO, the HO-miR-323 group demonstrated a substantially reduced LDH content (t = 13.65, P &lt; 0.01) compared to the control group, concurrently leading to a noteworthy amelioration in cell viability (t = 8.50, P &lt; 0.01). In contrast, the HO-miR-323-inhibitor group manifested a notable increase in LDH content (t = 22.75, P &lt; 0.01) and a significant reduction in cell viability (t = 8.46, P &lt; 0.01). In the animal experiment, miR-323-agomiR significantly improved cardiac function compared to the negative control group [left ventricular ejection fraction (LVEF): (39.9 ± 4.4)% vs. (32.0 ± 3.2)%, t = 3.54, P &lt; 0.01; left ventricular fractional shortening (LVFS): (19.2 ± 2.0)% vs. (15.4 ± 2.1)%, t = 3.17, P = 0.01]. But miR-323-antagomiR reversed this improvement [LVEF: (29.2 ± 3.7)% vs. (34.0 ± 4.1)%, t = 2.20, P = 0.04; LVFS: (11.9 ± 1.7)% vs. (14.9 ± 1.9)%, t = 2.74, P = 0.01]. Furthermore, compared to the control group, the miR-323-agomiR group exhibited a significant reduction in the infarct size percentage [(57.7 ± 5.9)% vs. (47.2 ± 9.1)%, t = 2.38, P = 0.04] and relative risk area [(44.9 ± 6.4)% vs. (30.2 ± 4.2)%, t = 4.70, P &lt; 0.01]. Conversely, the miR-323-antagomiR group demonstrated an opposite pattern, with an increase in infarction area [(53.2 ± 6.7)% vs. (65.1 ± 7.8)%, t = 2.84, P = 0.02] and the relative area at risk [(44.3 ± 7.5)% vs. (53.5 ± 4.5)%, t = 2.59, P = 0.03]. Transfection of miR-323 inhibited the protein expression of PAR4 and cleaved caspase-3 simultaneously in H9C2 cell models.

CONCLUSION
MiR-323 can ameliorate cardiomyocyte injury caused by ischemia/reperfusion and improve cardiac dysfunction by targeting PAR4 to regulate cleaved caspase-3.
De novo variants disrupt an LDB1-regulated transcriptional network in congenital ventriculomegaly
Authors: Allington Garrett , Mehta Neel H , Dennis Evan , Mekbib Kedous Y , Reeves Benjamin , Kiziltug Emre , Chen Shuang , Zhao Shujuan , Duy Phan Q , Saleh Maha , Ang Lee C , Fan Baojian , Nelson-Williams Carol , Moreno-de-Luca Andrés , Haider Shozeb , Lifton Richard P , Alper Seth L , McGee Stephen , Jin Sheng Chih , Kahle Kristopher T 
Published: December 2024

Abstract
Congenital hydrocephalus (CH), characterized by cerebral ventriculomegaly (CV), is among the most common and least understood pediatric neurosurgical disorders. We have identified in the largest-assembled CV cohort (&gt;2,697 parent-proband trios) an exome-wide significant enrichment of protein-altering de novo variants (DNVs) in LDB1 (p = 1.11 x 10-15). Eight unrelated patients with ventriculomegaly, developmental delay, and dysmorphic features harbored loss-of-function DNVs that truncate LDB1’s carboxy-terminal LIM interaction domain, which regulates assembly of LIM homeodomain-containing transcriptional modulators. Integrative multiomic analyses suggest LDB1 is a key transcriptional regulator in ventricular neuroprogenitors through it’s binding to LIM-homeodomain proteins, including SMARCC1 and ARID1B. Indeed, LIM-homeodomain-containing genes carry a disproportionate burden of protein-damaging DNVs in our cohort, with SMARCC1 (p = 5.83 x 10-9) and ARID1B (p = 1.80 x 10-17) surpassing exome-wide significance thresholds. These data identify LBD1 as a novel neurodevelopmental disorder gene and suggest an LDB1-regulated transcriptional program is essential for human brain morphogenesis.
The MaEIL4-MaMADS36-MaACS7 module transcriptionally regulates ethylene biosynthesis during banana fruit ripening
Authors: Fu Maoni , Zheng Yunke , Zhang Jing , Deng Chengju , Zhang Jianbin , Jia Caihong , Miao HongXia , Wang Jingyi , Zheng Sijun , Jin Zhiqiang , Li Xinguo , Xie Jianghui , Liu Juhua 
Published: December 2024

Abstract
The present research examined the regulatory function of MaEIL4 in the ripening process of banana. The findings demonstrated that MaEIL4 is a transcription factor with activity in the nucleus. The transient modulation of MaEIL4 expression in banana fruit slices has been found to exert a significant impact on maturation, either enhancing or inhibiting its progression, as shown by phenotype and endogenous gene expression. MaEIL4, MaMADS36, and MaACS7 were co-expressed in bananas. MaEIL4 interacted with both the MaMADS36 protein and the TGAA box of the MaMADS36 promoter to activate its expression. Moreover, MaMADS36 bound to the C(A/T)rG box of the MaACS7 promoter to regulate fruit ripening. The results have characterized the mechanism of MaMADS36’s response to upstream ethylene signals and established a new module, MaEIL4-MaMADS36-MaACS7, that transcriptionally regulates banana fruit ripening. This research has enhanced our comprehension of the pivotal function of MaMADS36 in controlling fruit maturation and thus suggests new strategies for fruit shelf-life improvement and post-harvest loss reduction.
Key genes in a “Galloylation-Degalloylation cycle” controlling the synthesis of hydrolyzable tannins in strawberry plants
Authors: Zhang Lingjie , Li Rui , Wang Maohao , Zhao Qiaomei , Chen Yifan , Huang Yipeng , Liu Yajun , Jiang Xiaolan , Wang Nana , Xia Tao , Gao Liping 
Published: December 2024

Abstract
Strawberry fruits, known for their excellent taste and potential health benefits, are particularly valued for their rich content of hydrolyzable tannins (HTs). These compounds play key roles in regulating growth and development. However, the molecular mechanisms underlying HT synthesis in plants remains poorly elucidated. In this study, based on a correlation analysis between the transcriptome and metabolome of HTs, galloyl glucosyltransferase (UGT84A22), serine carboxypeptidase-like acyltransferases (SCPL-ATs), and carboxylesterases (CXEs) were screened. Furthermore, in vitro enzymatic assays confirmed that FaSCPL3–1 acted as a hydrolyzable tannins synthase (HTS), catalyzing the continuous galloylation of glucose to form simple gallotannins (GTs). Additionally, FaCXE1/FaCXE3/FaCXE7 catalyzed the degalloylation of simple GTs and ellagitannins (ETs), and FaUGT84A22 catalyzed the glycosylation of gallic acid (GA) to produce 1-O-β-glucogallin (βG), a galloyl donor. Moreover, in FvSCPL3–1-RNAi transgenic strawberry plants, the contents of simple GT and some ET compounds were reduced, whereas, in FaCXE7 overexpressing strawberry plants, these compounds were increased. These enzymes constituted a biosynthetic pathway of galloyl derivatives, termed the “galloylation-degalloylation cycle” (G-DG cycle). Notably, the overexpression of FaCXE7 in strawberry plants not only promoted HT synthesis but also interfered with plant growth and development by reducing lignin biosynthesis. These findings offer new insights into the mechanisms of HT accumulation in plants, contributing to improving the quality of berry fruits quality and enhancing plant resistance.
Unwanted or negative treatment reactions in digital psychological interventions for adolescents with chronic pain
Authors: de la Vega Rocío , Yokoyama Kaylee , Daniels Kristen , Palermo Tonya M 
Published: December 2024

Abstract

Objective
Reports of pain clinical trials evaluating psychological treatments often lack sufficient details on the potential and actual harm resulting from intervention. We aimed to understand how frequent and intense treatment reactions, conceptualized as unwanted symptoms, were in three clinical trials of digital Cognitive Behavioral Therapy (CBT) for adolescents with: (1) chronic primary pain, (2) sickle cell disease, and (3) chronic pancreatitis. We also aimed to understand any differences by demographic and clinical variables.

Method
Analyses were conducted with 246 youths (12–18 years old) experiencing chronic pain and one of their caregivers. 66% of the total sample was female. The number, intensity, and type of treatment reactions experienced were assessed post treatment. T-tests and Chi-squared tests were conducted to explore whether certain treatment reactions were more frequent as a function of baseline or clinical characteristics.

Results
9% of participants experienced some negative treatment reaction. The average intensity of those events was very low on a 0–3 scale (M = 0.1, SD = 0.4). There were no differences in the prevalence or intensity as a function of participant’s sex, age, race, or baseline pain intensity. However, baseline anxiety [t = −2.4 (244); p &lt; .05] and baseline pain interference [t = −2.2 (223); p &lt; .05] were significantly higher in those who experienced negative treatment reactions.

Conclusions
A small number of participants reported experiencing negative treatment reactions, with a low intensity level. Those experiencing negative treatment reactions showed higher baseline anxiety and pain interference. Future research may build from our example to standardize collection of harms data in trials of psychological interventions.
Exploring the molecular mechanism of Taohong Siwu decoction in the treatment of non-small-cell lung cancer based on network pharmacology and molecular docking
Authors: Qin Yuan , Lian Jia-Ning , Chen Xin , Huang Feng-Yu , Chen Hai-Wen , Dong Tai-Wei , Jin Zuo-Lin 
Published: December 2024

Abstract

Objective
This study aimed to explore the mechanism of Taohong Siwu decoction (THSWD) in the treatment of non-small-cell lung cancer (NSCLC) by using comprehensive analysis.

Methods
The active components and relevant targets of THSWD were analyzed by network analysis to construct the active component-target-disease network diagram. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted on the core targets by the Metascape database. Molecular docking verification was used for molecular visualization.

Key findings
A total of 69 active compounds and 114 targets were filtered in lung cancer treatment with THSWD. KEGG analysis suggested that tumor necrosis factor (TNF) signaling pathway, and apoptosis pathway played critical roles. The results of molecular docking showed that populoside_qt with IL-6, baicalein with epidermal growth factor receptor (EGFR), and luteolin with MAPK8 had the strongest binding ability. Moreover, experiment validation revealed that THSWD regulated the expression of IL-6, AKT, Cyclin D1, E-cadherin, and LC3A/B, thereby inhibiting the proliferation and migration ability, promoting apoptosis, and blocking the cell cycle of NSCLC cells.

Conclusions
The potential targets and molecular mechanisms of THSWD in the treatment of NSCLC were preliminarily revealed by a comprehensive analysis in this study, which will provide new ideas and methods for the study of the mechanism of traditional Chinese medicine in treating lung cancer.
Use of optical techniques to evaluate the ionizing radiation effects on biological specimens
Authors: Fujita Hideaki , Watanabe Tomonobu M 
Published: December 2024

Abstract
Radiation induces various changes in biological specimens; however, the evaluation of these changes is usually complicated and can be achieved only through investment in time and labor. Optical methods reduce the cost of such evaluations as they require less pretreatment of the sample, are adaptable to high-throughput screening and are easy to automate. Optical methods are also advantageous, owing to their real-time and onsite evaluation capabilities. Here, we discuss three optical technologies to evaluate the effects of radiation on biological samples: single-molecule tracking microscopy to evaluate the changes in the physical properties of DNA, Raman spectral microscopy for dosimetry using human hair and second-harmonic generation microscopy to evaluate the effect of radiation on the differentiation of stem cells. These technologies can also be combined for more detailed information and are applicable to other biological samples. Although optical methods are not commonly used to evaluate the effects of radiation, advances in this technology may facilitate the easy and rapid assessment of radiation effects on biological samples.
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Authors: De Simone Marco , Hoover Jonathan , Lau Julia , Bennett Hayley M , Wu Bing , Chen Cynthia , Menon Hari , Au-Yeung Amelia , Lear Sean , Vaidya Samir , Shi Minyi , Lund Jessica M , Xavier-Magalhães Ana , Liang Yuxin , Kurdoglu Ahmet , O’Gorman William E , Modrusan Zora , Le Daniel , Darmanis Spyros 
Published: December 2024

Abstract
This study examined nine prominent commercially available single-cell RNA sequencing (scRNA-seq) kits across four technology groups. Each kit was characterized using peripheral blood mononuclear cells (PBMCs) from a single donor, which enabled consistent assessment of factors such as analytical performance, protocol duration and cost. The Chromium Fixed RNA Profiling kit from 10× Genomics, with its probe-based RNA detection method, demonstrated the best overall performance. The Rhapsody WTA kit from Becton Dickinson exhibited a balance between performance and cost. Importantly, we introduce the read utilization metric, which differentiates scRNA-seq kits based on the efficiency of converting sequencing reads into usable counts. Thus, read utilization is an important feature that substantially impacts sensitivity and cost. With data from 169, 262 cells, our work provides a comprehensive comparison of commercial scRNA-seq technologies to facilitate the effective implementation of single-cell studies.
Kinetoplast DNA: a polymer physicist’s topological Olympic dream
Authors: Michieletto Davide 
Published: December 2024

Abstract
All life forms are miraculous, but some are more inexplicable than others. Trypanosomes are by far one of the most puzzling organisms on Earth: their mitochondrial genome, also called kinetoplast DNA (kDNA) forms an Olympic-ring-like network of interlinked DNA circles, challenging conventional paradigms in both biology and physics. In this review, I will discuss kDNA from the astonished perspective of a polymer physicist and tell a story of how a single sub-cellular structure from a blood-dwelling parasite is inspiring generations of polymer chemists and physicists to create new catenated materials.
Weight and Metabolic Changes With Long-Acting Cabotegravir and Rilpivirine or Bictegravir/Emtricitabine/Tenofovir Alafenamide
Authors: Tan Darrell H. S. , Antinori Andrea , Eu Beng , Galindo Puerto María José , Kinder Clifford , Sweet Donna , Van Dam Cornelius N. , Sutton Kenneth , Sutherland-Phillips Denise , Berni Alessandro , Zhang Feifan , Urbaityte Rimgaile , Baugh Bryan , Spreen William , van Wyk Jean , Garges Harmony P. , Patel Parul , Batterham Rachel , D'Amico Ronald 
Published: December 2024

Background:
Modest weight and lipid changes have been observed in cabotegravir plus rilpivirine long-acting (CAB + RPV LA) phase 3/3b studies. The SOLAR study included standardized evaluations of weight and metabolic changes in people living with HIV switching to CAB + RPV LA dosed every 2 months (Q2M) vs. continuing bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF).

Setting:
Phase 3b, randomized, open-label study conducted in 118 centers across 14 countries.

Methods:
Participants (n = 687) were randomized 2:1; 454 switched to CAB + RPV LA Q2M and 227 continued BIC/FTC/TAF. Participants who started lipid-modifying agents or underwent cosmetic procedures were excluded. We analyzed changes in body weight, body mass index (BMI), waist circumference (WC), hip circumference (HC), waist-to-height ratio (WHtR), waist-to-hip ratio (WHR), muscle mass, body fat, and proportion with insulin resistance or metabolic syndrome at 1 year.

Results:
Median (interquartile range) change in body weight from baseline was −0.40 kg (−2.95 to +2.10) and +0.05 kg (−2.30 to +1.95) in the LA and BIC/FTC/TAF arm, respectively. Median (interquartile range) changes in WC and HC were +0.06 cm (−4.50 to 4.00) and +0.00 cm (−4.00 to 3.97) in the LA arm, and +1.14 cm (−3.00 to 5.09) and +0.13 cm (−3.10 to 4.00) in the BIC/FTC/TAF arm. There were no clinically relevant changes in WHtR, WHR, or the proportion with metabolic syndrome or insulin resistance in either arm.

Conclusions:
Standardized changes in weight, BMI, and body composition were minor and similar between participant switching to CAB + RPV LA Q2M or continuing BIC/FTC/TAF, with no clinically relevant changes in metabolic syndrome or insulin resistance.
Development and Validation of the Predictive and Prognostic ChemoResist Signature in Resected Pancreatic Ductal Adenocarcinoma
Authors: Huang Lei , Han Quanli , Zhao Liangchao , Wang Zhikuan , Dai Guanghai , Shi Yan 
Published: December 2024

Objective:
To develop and validate a signature to precisely predict prognosis in pancreatic ductal adenocarcinoma (PDAC) undergoing resection and adjuvant chemotherapy.

Summary Background Data:
PDAC is largely heterogeneous, and responds discrepantly to treatment.

Methods:
551 consecutive patients with PDAC from 3 tertiary centers were initially enrolled. Genetic events of the four most commonly mutated genes in PDAC and expressions of 12 PI3K/AKT/mTOR pathway markers were examined. A 9-feature signature for prediction of chemotherapy benefits was constructed in the training cohort using the LASSO Cox regression model, and validated in 2 independent cohorts.

Results:
Utilizing the LASSO model, a predictive and prognostic signature, named ChemoResist, was established based on KRAS SNV, PTEN and mTOR expressions, and six clinicopathologic features. Significant differences in survival were observed between high- and low-ChemoResist patients receiving chemotherapy in both the training (median OS, 17 vs. 42 months, P<0.001; median DFS, 10 vs. 23 months, P<0.001) and validation cohorts (median OS, 18 vs. 35 months, P=0.034; median DFS, 11 vs. 20 months, P=0.028). The ChemoResist classifier also significantly differentiated patient survival in the whole patients regardless of chemotherapy. Multivariable-adjusted analysis substantiated the ChemoResist signature as an independent predictive and prognostic factor. For predicting 2-year OS, the ChemoResist classifier had significantly higher AUC than TNM stage (0.788 vs. 0.636, P<0.001), other clinicopathologic characteristics (0.505-0.668), and single molecular markers (0.507-0.591) in the training cohort. Furthermore, patients with low ChemoResist score exhibited a more favorable response to adjuvant chemotherapy compared to those with high ChemoResist score (HR for OS: training, 0.22 vs. 0.57; validation, 0.26 vs. 0.50; HR for DFS: training, 0.35 vs. 0.54; validation, 0.18 vs. 0.59). The ChemoResist signature was further validated in the total cohort undergoing R0 resection.

Conclusions:
The ChemoResist signature could precisely predict survival in PDAC undergoing resection and chemotherapy, and its predictive value surpassed TNM stage and other clinicopathologic factors. Moreover, the ChemoResist classifier could assist with identifying patients who would more likely benefit from adjuvant chemotherapy.
Tunable counterpropagating twin photon source
Authors: Peralta Amores Albert , Swillo Marcin 
Published: December 2024

We present an optical configuration for the generation of degenerate counterpropagating photon pairs via spontaneous-parametric down-conversion in subwavelength thin waveguides with 4¯3m symmetry. The generated photon pairs exhibit orthogonal polarizations and excite TE- and TM-like modes. Compensation of the momentum mismatch between the excited modes by pump tilting enables tunable degenerate emission across the S, C, and L bands (1400 to 1600 nm). Experimental verification confirms an efficiency of ≈10−5 photon pairs per pump photon with an expected linewidth of 0.3 nm in 2-mm-long Ga0.51In0.49P waveguides.

Published by the American Physical Society
2024
Tackling food waste: unveiling causes, implications and solutions in Oman's fresh and short food supply chain
Authors: Mohammed Ahmed , Al Balushi Mohammed , Zubairu Nasiru 
Published: December 2024

PurposeThis study investigates food waste within the food supply chain (FSC), for the case of fresh and short FSC (FS-FSC), aiming to (1) reveal the major causes of waste across FSC (2) identify the food waste mitigation strategies, (3) measure food waste impacts at each supply stream, and (4) propose practical initiatives to support decision/policymakers in strategic food waste management, especially in the case country.Design/methodology/approachThis study adopts a mixed-method approach to investigating food waste, examining existing literature using template analysis. The focus is on three key elements: factors enabling food waste, its final destinations, and strategies to reduce it. The study then gathers information from a prominent regional retailer and consumers through interviews and surveys. The empirical data collected is then analysed using template analysis and descriptive statistics.FindingsThis research highlights key waste enablers across the food supply chain networks, including procurement and storage, processing, operation strategy, people, and consumers. The enablers differed in the amount of food waste produced, and the research outcome demonstrates that the end consumers were the largest contributors to the food waste generated. The changes in people's habits and tastes significantly affect the FS-FSC. Interestingly, results demonstrated that 40% of consumers utilise food leftovers as pet food.Practical implicationsThe proposed food waste management initiatives can help companies minimise and mitigate food waste at each supply chain stage. Practitioners can use the identified causes and mitigation strategies to implement mitigation efforts and translate them into actionable plans.Originality/valueThe article outlines a practical approach for addressing food waste in an FS-FSC case throughout the entire chain, encompassing supply, distribution, catering, delivery, and consumption. The study not only sheds light on the primary reasons for food wastage but also provides insights into potential solutions that are not only effective but also feasible in real-world scenarios.