bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective oil palm (Elaeis sp) materials for high tocotrienol content
Authors: Setiowati R D , Ernayunita  , Panjaitan F R , Mardiana C , Lubis M I
Published: March 2024

Crude palm oil (CPO) contains various forms of vitamin E, including tocopherol, tocotrienol and a small amount of tocomonoenol, collectively known as tocols. Among these, tocotrienol is dominant in CPO, constituting approximately 70% of the total tocols; unlike tocopherol, which is known for its anti-ageing properties, tocotrienol exhibits potent antioxidant activities, 60 times stronger than tocopherol. Tocotrienol is recognized for its diverse health benefits as a neuroprotective, nephroprotective, anti-cancer, anti-cholesterol, anti-diabetic, and anti-inflammatory agent. Consequently, tocotrienol holds immense potential for pharmaceutical and nutraceutical applications. The exploration of oil palm materials planted in Kebun Adolina PTPN IV, North Sumatera, has been conducted since 2020, encompassing diverse genetic backgrounds, including commercial palm DxP varieties, an interspecific hybrid of Elaeis oleifera x Elaeis guineensis, wild-type palm materials originated from Angola and Cameroon, and palm clones of commercial DxP varieties. The analysis revealed a wide range of total vitamin E (tocol) content, ranging from 310.78 ppm to 1681.45 ppm. Among the genotypes studied, AD14S311 and AD14S2220 emerged as promising candidates for ortets to develop oil palm varieties with high content, especially tocotrienol. These genotypes demonstrated a high oil extraction rate (OER) and a total vitamin E level above 1000 ppm. These findings remade the potential genotypes as genetic resources for breeding programs in developing oil palm varieties enriched with tocotrienol and fulfilled the commercial value.
Estimation of oil palm’s leaf area index (LAI) using Unmanned Aerial Vehicle (UAV) images
Authors: Pradiko I , Wati D , Wiratmoko D , Darlan N H
Published: March 2024

Leaf Area Index (LAI) is a parameter commonly used to indicate oil palm growth and production. The destructive method is the standard method to estimate LAI. However, this method requires much effort and cost and can only be done at a specific period. Unmanned Aerial Vehicles (UAVs), which have been widely used for mapping and calculating trees in oil palm plantations, have the potential to estimate LAI values quickly, efficiently, and without disturbing the oil palm tree. This research was conducted to develop the model for predicting LAI based on UAV images. Data was collected from six plots of 12-year-old oil palm trees at Adolina Estate, Serdang Bedagai, North Sumatra, Indonesia. The research was conducted on six varieties released by IOPRI, consisting of DxP Yangambi, DxP Langkat, DxP Simalungun, DyP Dumpy, DxP LaMe, and DxP PPKS 540. The estimated canopy cover from the UAV images was employed as an independent factor (x) compared to the calculated LAI from the destructive method, which was used as a dependent factor (y). The results showed that the LAI estimation using UAV imagery followed a linear model with R-squared values ranging from 0.3874-0.9556. In conclusion, despite requiring further research, UAV images could be used as rapid tools to estimate oil palm LAI.
Implementation of environmental policies by six oil palm plantation companies in South Sumatra
Authors: Komarudin N A , Siregar H H
Published: March 2024

South Sumatra Province, situated in Indonesia, ranks as the sixth-largest palm oil producer in the country, boasting an extensive plantation area of 1.2 million hectares. Unfortunately, the province has faced significant environmental challenges in recent times due to inadequate environmental management and recurring forest fires. These issues have resulted in adverse effects on the local ecosystem. Consequently, it becomes crucial to conduct a gap analysis of the existing environmental policies and their implementation by oil palm plantation companies operating in South Sumatra Province. The objective of this research is to assess the environmental management practices of companies operating in the oil palm industry in South Sumatra Province, specifically focusing on their adherence to the Indonesia Sustainable Oil Palm (ISPO) criteria. The study aims to evaluate how effectively these companies have implemented environmental policies and identify any disparities or gaps that may exist between the policies and their actual implementation. To achieve this, the research employs a regulatory gap analysis method. The oil palm plantation company in South Sumatra Province has met 105 out of the 126 environmental indicators specified in the ISPO criteria. In general, the implementation of environmental policies on these plantations has achieved an 85% score, indicating a successful fulfillment of the policies outlined by Indonesia Sustainable Palm Oil (ISPO). The relatively low gap value of 0.15 further confirms this success, signifying that the environmental policies have been effectively and adequately implemented in accordance with ISPO’s guideline..
Fixation method of a single muscle fiber by magnetic force for stretching, transportation, and evaluation of mechanical properties
Authors: Wang Zhaoyu , Masuda Taisuke , Arai Fumihito
Published: March 2024

Engineered muscle fibers are attracting interest in bio-actuator research as they can contribute to the fabrication of actuators with a high power/size ratio for micro-robots. These fibers require to be stretched during culture for functional regulation as actuators and require a fixation on a rigid substrate for stretching in culture and evaluation of mechanical properties, such as Young’s modulus and contraction force. However, the conventional fixation methods for muscle fibers have many restrictions as they are not repeatable and the connection between fixation part and the muscle fibers detaches during culture; therefore, the fixation becomes weak during culture, and direct measurement of the muscle fibers’ mechanical properties by a force sensor is difficult. Therefore, we propose a facile and repeatable fixation method for muscle fibers by mixing magnetite nanoparticles at both ends of the muscle fibers to fabricate magnetic ends. The fiber can be easily attached and detached repeatedly by manipulating a magnet that applies a magnetic force larger than 3 mN to the magnetic ends. Thus, the muscle fiber can be stretched fiber during culture for functional regulation, transported between the culture dish and measurement system, and directly connected to the force sensor for measurement with magnetic ends. The muscle fiber connected with magnetic ends have a long lifetime (∼4 weeks) and the cells inside had the morphology of a skeletal muscle. Moreover, the muscle fiber showed a contraction (specific force of 1.02 mN mm−2) synchronized with electrical stimulation, confirming the muscle fiber fabricated and cultured using our method had similar morphology and function as bio-actuators in previous research. This research demonstrates the advantages of the fixation method using muscle fibers with magnetic ends; the fibers are stretched during culture, and the transportation and force measurement of weak and tiny muscle fibers could be finished in 1 min.
A COMSOL novel micromirror matrix model for digital image display
Authors: Karaoui Fares , Benblidia Nadjia , Bougherira Hamida
Published: March 2024

Digital micromirror devices (DMD) have gained significant attention in various scientific and industrial domains due to their potential for spatial light and laser modulation. However existing micromirrors designs often face limitations in terms of rotation angles, voltage consumption, and stability time for some type of applications. In this paper, we address these issues by exploring micromirror structure materials, more precisely, the materials for the torsion bar. To achieve this, we have used COMSOL Multiphysics knowing to provide accurate predictive simulation results, to design a micromirror model incorporating three inclination modes: unidirectional, bidirectional, and a user-defined free mode. Through extensive simulations, we have compared different materials for the torsion bar of the micromirror and have evaluated their performance in terms of voltage consumption, stability time, rotation angles and electric energy consumption. Aluminum 3008-H18 emerged as the optimal choice, exhibiting a stability time of 40 μs and achieving a maximum tilt of 12.75 degrees. The micromirror system has demonstrated stable position within the voltage range (from 0 volts to 27 volts) and maximum electric energy consumption of 7.72 × 10−8
μJ. Our micromirror design features a 10 × 10 μm reflective element capable of achieving a maximum inclination of ±12.75 degrees. To enhance the capabilities of the micromirror, an 8 × 8 micromirror matrix has been developed, enabling collective and coordinated movements of individual micromirrors. Also, a process for translating digital images into micromirror states has been devised, enabling accurate image display on the matrix. Simulation results demonstrate the effectiveness of the micromirror matrix design and the image processing script, images displayed on the micromirror matrix exhibit high accuracy, faithfully reproducing desired patterns in the primary images. Overall, our proposed micromirror model and micromirror matrix model offer enhanced performance, versatility, and accuracy, enabling a diverse array of simulations across scientific research and industrial domains.
Systems level analysis of time and stimuli specific signaling through PKA
Authors: Plank Michael , Carmiol Nicole , Mitri Bassam , Lipinski Austin A. , Langlais Paul R. , Capaldi Andrew P.
Published: March 2024

It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
Loss of Grp170 results in catastrophic disruption of endoplasmic reticulum function
Authors: Mann Melissa J. , Melendez-Suchi Chris , Vorndran Hannah E. , Sukhoplyasova Maria , Flory Ashley R. , Irvine Mary Carson , Iyer Anuradha R. , Guerriero Christopher J. , Brodsky Jeffrey L. , Hendershot Linda M. , Buck Teresa M.
Published: March 2024

GRP170 ( Hyou1) is required for mouse embryonic development, and its ablation in kidney nephrons leads to renal failure. Unlike most chaperones, GRP170 is the lone member of its chaperone family in the ER lumen. However, the cellular requirement for GRP170, which both binds nonnative proteins and acts as nucleotide exchange factor for BiP, is poorly understood. Here, we report on the isolation of mouse embryonic fibroblasts obtained from mice in which LoxP sites were engineered in the Hyou1 loci ( Hyou1LoxP/LoxP). A doxycycline-regulated Cre recombinase was stably introduced into these cells. Induction of Cre resulted in depletion of Grp170 protein which culminated in cell death. As Grp170 levels fell we observed a portion of BiP fractionating with insoluble material, increased binding of BiP to a client with a concomitant reduction in its turnover, and reduced solubility of an aggregation-prone BiP substrate. Consistent with disrupted BiP functions, we observed reactivation of BiP and induction of the unfolded protein response (UPR) in futile attempts to provide compensatory increases in ER chaperones and folding enzymes. Together, these results provide insights into the cellular consequences of controlled Grp170 loss and provide hypotheses as to why mutations in the Hyou1 locus are linked to human disease.
Civic Virtue and State Power
Authors: Bascom Ben
Published: March 2024

This chapter focuses on how race—specifically Blackness—was understood as a barrier to civic belonging and participation. By focusing on Jeffrey Brace’s memoir The Blind African Slave (1810)—a neglected anti-slavery narrative about a Black Revolutionary War veteran—this chapter shows how this narrative challenges white republican narratives of belonging. Brace’s narrative offers an important precursor for nineteenth-century abolitionists for how he challenges the conventions that led to his being pressed to leave the Vermont town he called home. This chapter argues that Brace actively queers the norms of propertied whiteness that exclude him even as he reclaims them for himself.
Eliot’s Statements
Authors: Blanton C D
Published: March 2024

The appearance of T. S. Eliot’s Complete Prose makes available a critical object that was always there in scattered form but remained elusive for a century. It now concentrates the poet’s thought, his statements, in a single edition. It also, I argue, makes visible the deeper tendency of that thought, toward a philosophical system glimpsed in incipient but programmatically coherent form. With this collection, Eliot’s theories of logical reference and of truth are (again) not only formulated but also relentlessly enacted. Critically, those theories bear too on the definition of poetic language, taken to consist not in pseudostatements but in logical judgments.
Integrating network pharmacology and in silico analysis deciphers Withaferin-A’s anti-breast cancer potential via hedgehog pathway and target network interplay
Authors: Srinivasan Mythili , Gangurde Apeksha , Chandane Ashwini Y , Tagalpallewar Amol , Pawar Anil , Baheti Akshay M
Published: March 2024

This study examines the remarkable effectiveness of Withaferin-A (WA), a withanolide obtained from Withania somnifera (Ashwagandha), in encountering the mortiferous breast malignancy, a global peril. The predominant objective is to investigate WA’s intrinsic target proteins and hedgehog (Hh) pathway proteins in breast cancer targeting through the application of in silico computational techniques and network pharmacology predictions. The databases and webtools like Swiss target prediction, GeneCards, DisGeNet and Online Mendelian Inheritance in Man were exploited to identify the common target proteins. The culmination of the WA network and protein–protein interaction network were devised using Stitch and String web tools, through which the drug–target network of 30 common proteins was constructed employing Cytoscape-version 3.9. Enrichment analysis was performed by incorporating Gprofiler, Metascape and Cytoscape plugins. David compounded the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, and enrichment was computed through bioinformatics tools. The 20 pivotal proteins were docked harnessing Glide, Schrodinger Suite 2023-2. The investigation was governed by docking scores and affinity. The shared target proteins underscored the precise Hh and WA network roles with the affirmation enrichment P-value of <0.025. The implications for hedgehog and cancer pathways were profound with enrichment (P < 0.01). Further, the ADMET and drug-likeness assessments assisted the claim. Robust interactions were noticed with docking studies, authenticated through molecular dynamics, molecular mechanics generalized born surface area scores and bonds. The computational investigation emphasized WA’s credible anti-breast activity, specifically with Hh proteins, implying stem-cell-level checkpoint restraints. Rigorous testament is imperative through in vitro and in vivo studies.
New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics
Authors: Mokhtari Majid , Khoshbakht Samane , Ziyaei Kobra , Akbari Mohammad Esmaeil , Moravveji Sayyed Sajjad
Published: March 2024

Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data. Quantum mechanics has recently emerged as a promising tool for the analysis of biological systems, leading to the development of quantum bioinformatics. This new field employs the principles of quantum mechanics, quantum algorithms, and quantum computing to solve complex problems in molecular biology, drug design, and protein folding. However, the intersection of bioinformatics, biology, and quantum mechanics presents unique challenges. One significant challenge is the possibility of confusion among scientists between quantum bioinformatics and quantum biology, which have similar goals and concepts. Additionally, the diverse calculations in each field make it difficult to establish boundaries and identify purely quantum effects from other factors that may affect biological processes. This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics. We examine the challenges and unique features of this field and propose a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress. By unlocking the full potential of quantum bioinformatics, this review aims to contribute to our understanding of quantum mechanics in biological systems.
Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization
Authors: Wang Rui , Wang Tao , Zhuo Linlin , Wei Jinhang , Fu Xiangzheng , Zou Quan , Yao Xiaojun
Published: March 2024

Antimicrobial peptides (AMPs), short peptides with diverse functions, effectively target and combat various organisms. The widespread misuse of chemical antibiotics has led to increasing microbial resistance. Due to their low drug resistance and toxicity, AMPs are considered promising substitutes for traditional antibiotics. While existing deep learning technology enhances AMP generation, it also presents certain challenges. Firstly, AMP generation overlooks the complex interdependencies among amino acids. Secondly, current models fail to integrate crucial tasks like screening, attribute prediction and iterative optimization. Consequently, we develop a integrated deep learning framework, Diff-AMP, that automates AMP generation, identification, attribute prediction and iterative optimization. We innovatively integrate kinetic diffusion and attention mechanisms into the reinforcement learning framework for efficient AMP generation. Additionally, our prediction module incorporates pre-training and transfer learning strategies for precise AMP identification and screening. We employ a convolutional neural network for multi-attribute prediction and a reinforcement learning-based iterative optimization strategy to produce diverse AMPs. This framework automates molecule generation, screening, attribute prediction and optimization, thereby advancing AMP research. We have also deployed Diff-AMP on a web server, with code, data and server details available in the Data Availability section.
Prediction of protein–ligand binding affinity via deep learning models
Authors: Wang Huiwen
Published: March 2024

Accurately predicting the binding affinity between proteins and ligands is crucial in drug screening and optimization, but it is still a challenge in computer-aided drug design. The recent success of AlphaFold2 in predicting protein structures has brought new hope for deep learning (DL) models to accurately predict protein–ligand binding affinity. However, the current DL models still face limitations due to the low-quality database, inaccurate input representation and inappropriate model architecture. In this work, we review the computational methods, specifically DL-based models, used to predict protein–ligand binding affinity. We start with a brief introduction to protein–ligand binding affinity and the traditional computational methods used to calculate them. We then introduce the basic principles of DL models for predicting protein–ligand binding affinity. Next, we review the commonly used databases, input representations and DL models in this field. Finally, we discuss the potential challenges and future work in accurately predicting protein–ligand binding affinity via DL models.
KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction
Authors: Xue Haoliang , Gallopin Mélina , Marchet Camille , Nguyen Ha N , Wang Yunfeng , Lainé Antoine , Bessiere Chloé , Gautheret Daniel
Published: March 2024

Motivation

KaMRaT is designed for processing large k-mer count tables derived from multi-sample, RNA-seq data. Its primary objective is to identify condition-specific or differentially expressed sequences, regardless of gene or transcript annotation.

Results

KaMRaT is implemented in C++. Major functions include scoring k-mers based on count statistics, merging overlapping k-mers into contigs and selecting k-mers based on their occurrence across specific samples.

Availability and implementation

Source code and documentation are available via https://github.com/Transipedia/KaMRaT.
SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments
Authors: Mohanty Chitrasen , Prasad Aman , Cheng Lingxin , Arkin Lisa M , Shields Bridget E , Drolet Beth , Kendziorski Christina
Published: March 2024

Motivation

Spatial transcriptomics (ST) experiments provide spatially localized measurements of genome-wide gene expression allowing for an unprecedented opportunity to investigate cellular heterogeneity and organization within a tissue. Statistical and computational frameworks exist that implement robust methods for pre-processing and analyzing data in ST experiments. However, the lack of an interactive suite of tools for visualizing ST data and results currently limits the full potential of ST experiments.

Results

To fill the gap, we developed SpatialView, an open-source web browser-based interactive application for visualizing data and results from multiple 10× Genomics Visium ST experiments. We anticipate SpatialView will be useful to a broad array of clinical and basic science investigators utilizing ST to study disease.

Availability and implementation

SpatialView is available at https://github.com/kendziorski-lab/SpatialView (and https://doi.org/10.5281/zenodo.10223907); a demo application is available at https://www.biostat.wisc.edu/˜kendzior/spatialviewdemo/
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data
Authors: Linderman Michael D , Wallace Jacob , van der Heyde Alderik , Wieman Eliza , Brey Daniel , Shi Yiran , Hansen Peter , Shamsi Zahra , Liu Jeremiah , Gelb Bruce D , Bashir Ali
Published: March 2024

Motivation

Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, particularly for the many SVs first detected with long-read sequencing, will improve our understanding of genetic variation.

Results

NPSV-deep is a deep learning-based approach for genotyping previously reported insertion and deletion SVs that recasts this task as an image similarity problem. NPSV-deep predicts the SV genotype based on the similarity between pileup images generated from the actual SRS data and matching SRS simulations. We show that NPSV-deep consistently matches or improves upon the state-of-the-art for SV genotyping accuracy across different SV call sets, samples and variant types, including a 25% reduction in genotyping errors for the Genome-in-a-Bottle (GIAB) high-confidence SVs. NPSV-deep is not limited to the SVs as described; it improves deletion genotyping concordance a further 1.5 percentage points for GIAB SVs (92%) by automatically correcting imprecise/incorrectly described SVs.

Availability and implementation

Python/C++ source code and pre-trained models freely available at https://github.com/mlinderm/npsv2.
Shu: visualization of high-dimensional biological pathways
Authors: Carrasco Muriel Jorge , Cowie Nicholas , Taylor Parkins Shannara , Mansouvar Marjan , Groves Teddy , Nielsen Lars Keld
Published: March 2024

Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing volume of multi-omics data, leveraging the metabolic maps developed by the metabolic modeling community. In addition, shu offers a streamlined python API, based on the Grammar of Graphics, for easy integration with data pipelines.

Availability and implementation

Freely available at https://github.com/biosustain/shu under MIT/Apache 2.0 license. Binaries are available in the release page of the repository and the web application is deployed at https://biosustain.github.io/shu.
AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides
Authors: Zhang Shengli , Zhao Ya , Liang Yunyun
Published: March 2024

Motivation

Anticancer peptides (ACPs) have natural cationic properties and can act on the anionic cell membrane of cancer cells to kill cancer cells. Therefore, ACPs have become a potential anticancer drug with good research value and prospect.

Results

In this article, we propose AACFlow, an end-to-end model for identification of ACPs based on deep learning. End-to-end models have more room to automatically adjust according to the data, making the overall fit better and reducing error propagation. The combination of attention augmented convolutional neural network (AAConv) and multi-layer convolutional neural network (CNN) forms a deep representation learning module, which is used to obtain global and local information on the sequence. Based on the concept of flow network, multi-head flow-attention mechanism is introduced to mine the deep features of the sequence to improve the efficiency of the model. On the independent test dataset, the ACC, Sn, Sp, and AUC values of AACFlow are 83.9%, 83.0%, 84.8%, and 0.892, respectively, which are 4.9%, 1.5%, 8.0%, and 0.016 higher than those of the baseline model. The MCC value is 67.85%. In addition, we visualize the features extracted by each module to enhance the interpretability of the model. Various experiments show that our model is more competitive in predicting ACPs.
Surgical stress response in robot-assisted versus laparoscopic surgery for colon cancer (SIRIRALS): randomized clinical trial
Authors: Cuk Pedja , Tiskus Mindaugas , Möller Sören , Lambertsen Kate Lykke , Backer Mogensen Christian , Festersen Nielsen Michael , Helligsø Per , Gögenur Ismail , Bremholm Ellebæk Mark
Published: March 2024

Background

Evidence for the routine use of robotic technology and its impact on short-term outcomes in colon cancer surgery is lacking. The aim of this study was to compare the surgically induced systemic stress response and clinical and patient-reported outcomes for patients undergoing robot-assisted or laparoscopic colon cancer surgery.

Methods

In this double-blinded superiority RCT completed between August 2021 and March 2023, patients with stage 1–3 colon cancer were randomized in a 1 : 1 ratio to undergo either robot-assisted or laparoscopic colon cancer surgery. The primary outcome was changes in the systemic stress response, characterized by C-reactive protein expression in the first three postoperative days. Secondary outcomes were intraoperative and postoperative complications and patient-reported outcomes. The latter included quality of recovery-15 and pain intensity using a visual analogue scale.

Results

In total, 128 patients were screened for potential inclusion in this study; 50 patients (25 in the robot-assisted group and 25 in the laparoscopic group) were included in the final follow-up and analysis. The postoperative C-reactive protein response was higher on the first postoperative day in the laparoscopic group (mean difference = 19.88 mg/l, 95% c.i. 3.89–35.86; P = 0.045). No statistically significant differences were noted for C-reactive protein expression on the second and third postoperative days.

Conclusion

Adopting robot-assisted surgery for stage 1–3 colon cancer is associated with a reduction in the surgical stress response.

Registration number

NCT04687384 (http://www.clinicaltrials.gov).
Middle Pleistocene climate change influenced northward divergence and cold adaptation in an Asian lady’s slipper orchid, Cypripedium macranthos Sw. (Orchidaceae)
Authors: Chang Jui-Tse , Zhang Yu , Andronova Elena , Averyanov Leonid V , Filippov Evgeniy G , Kawahara Takayuki , Shefferson Richard , Kim Joo-Hwan , Hsu Rebecca C-C , Cho Yu-Hsiu , Luo Min-Xin , Liao Pei-Chun , Lee Yung-I
Published: March 2024

The Pleistocene was characterized by climate fluctuations with rapid transitions between glacial and interglacial periods. East Asia’s land bridge dynamics and monsoon system during the Middle Pleistocene transition (MPT) further constrained species distributions and dispersals, which promoted local adaptation and species diversification, making East Asia an excellent location to study species biogeography. Cypripedium macranthos Sw., a terrestrial orchid, diverged in the Pleistocene and became widespread in Russia, China, Korea, and Japan. Many populations are now at risk due to illegal harvesting or habitat loss. With comprehensive sampling including 171 individuals among 22 populations across the entire distribution range, together with plastid DNA sequencing, we have explored the origin and impact of palaeoclimate on its spatial genetic structure and historical biogeography. Regression-based analyses commonly used in landscape genetics were also applied to investigate the effects of precipitation, temperature, and wind on gene flow. The results revealed northeastern China as the probable cradle of C. macranthos, with northeastward divergence and range expansion during the MPT, aided by monsoon shifts and wind-driven seed dispersal. Isolation by environment was detected with winter temperature as a driver for north–south divergence controlling for an effect of isolation by distance, revealing cold adaptation of the northern populations or temperature-driven genetic differentiation. We also emphasize the founder speciation of an unique variety on Rebun Island of Japan. The widespread but genetically and ecologically divergent C. macranthos populations highlight the need for more conservation attention on northern populations under global warming.
Synaptopathy: presynaptic convergence in frontotemporal dementia and amyotrophic lateral sclerosis
Authors: Clayton Emma L , Huggon Laura , Cousin Michael A , Mizielinska Sarah
Published: March 2024

Frontotemporal dementia and amyotrophic lateral sclerosis are common forms of neurodegenerative disease that share overlapping genetics and pathologies. Crucially, no significantly disease-modifying treatments are available for either disease. Identifying the earliest changes that initiate neuronal dysfunction is important for designing effective intervention therapeutics. The genes mutated in genetic forms of frontotemporal dementia and amyotrophic lateral sclerosis have diverse cellular functions, and multiple disease mechanisms have been proposed for both. Identification of a convergent disease mechanism in frontotemporal dementia and amyotrophic lateral sclerosis would focus research for a targetable pathway, which could potentially effectively treat all forms of frontotemporal dementia and amyotrophic lateral sclerosis (both familial and sporadic).

Synaptopathies are diseases resulting from physiological dysfunction of synapses, and define the earliest stages in multiple neuronal diseases, with synapse loss a key feature in dementia. At the presynapse, the process of synaptic vesicle recruitment, fusion and recycling is necessary for activity-dependent neurotransmitter release. The unique distal location of the presynaptic terminal means the tight spatio-temporal control of presynaptic homeostasis is dependent on efficient local protein translation and degradation.

Recently, numerous publications have shown that mutations associated with frontotemporal dementia and amyotrophic lateral sclerosis present with synaptopathy characterized by presynaptic dysfunction. This review will describe the complex local signalling and membrane trafficking events that occur at the presynapse to facilitate neurotransmission and will summarize recent publications linking frontotemporal dementia/amyotrophic lateral sclerosis genetic mutations to presynaptic function. This evidence indicates that presynaptic synaptopathy is an early and convergent event in frontotemporal dementia and amyotrophic lateral sclerosis and illustrates the need for further research in this area, to identify potential therapeutic targets with the ability to impact this convergent pathomechanism.
LncRNAs act as modulators of macrophages within the tumor microenvironment
Authors: Li Kangning , Xie Tao , Li Yong , Huang Xuan
Published: March 2024

Long non-coding RNAs (lncRNAs) have been established as pivotal players in various cellular processes, encompassing the regulation of transcription, translation and post-translational modulation of proteins, thereby influencing cellular functions. Notably, lncRNAs exert a regulatory influence on diverse biological processes, particularly in the context of tumor development. Tumor-associated macrophages (TAMs) exhibit the M2 phenotype, exerting significant impact on crucial processes such as tumor initiation, angiogenesis, metastasis and immune evasion. Elevated infiltration of TAMs into the tumor microenvironment (TME) is closely associated with a poor prognosis in various cancers. LncRNAs within TAMs play a direct role in regulating cellular processes. Functioning as integral components of tumor-derived exosomes, lncRNAs prompt the M2-like polarization of macrophages. Concurrently, reports indicate that lncRNAs in tumor cells contribute to the expression and release of molecules that modulate TAMs within the TME. These actions of lncRNAs induce the recruitment, infiltration and M2 polarization of TAMs, thereby providing critical support for tumor development. In this review, we survey recent studies elucidating the impact of lncRNAs on macrophage recruitment, polarization and function across different types of cancers.
Association between diabetic status and risk of all-cause and cause-specific mortality on dialysis following first kidney allograft loss
Authors: Samarasinghe Amali , Wong Germaine , Teixeira-Pinto Armando , Johnson David W , Hawley Carmel , Pilmore Helen , Mulley William R , Roberts Matthew A , Polkinghorne Kevan R , Boudville Neil , Davies Christopher E , Viecelli Andrea K , Ooi Esther , Larkins Nicholas G , Lok Charmaine , Lim Wai H
Published: March 2024

Background

Diabetes mellitus (DM) is associated with a greater risk of mortality in kidney transplant patients, primarily driven by a greater risk of cardiovascular disease (CVD)-related mortality. However, the associations between diabetes status at time of first allograft loss and mortality on dialysis remain unknown.

Methods

All patients with failed first kidney allografts transplanted in Australia and New Zealand between 2000 and 2020 were included. The associations between diabetes status at first allograft loss, all-cause and cause-specific mortality were examined using competing risk analyses, separating patients with diabetes into those with pre-transplant DM or post-transplant diabetes mellitus (PTDM).

Results

Of 3782 patients with a median (IQR) follow-up duration of 2.7 (1.1–5.4) years, 539 (14%) and 390 (10%) patients had pre-transplant DM or developed PTDM, respectively. In the follow-up period, 1336 (35%) patients died, with 424 (32%), 264 (20%) and 199 (15%) deaths attributed to CVD, dialysis withdrawal and infection, respectively. Compared to patients without DM, the adjusted subdistribution HRs (95% CI) for pre-transplant DM and PTDM for all-cause mortality on dialysis were 1.47 (1.17–1.84) and 1.47 (1.23–1.76), respectively; for CVD-related mortality were 0.81 (0.51–1.29) and 1.02 (0.70–1.47), respectively; for infection-related mortality were 1.84 (1.02–3.35) and 2.70 (1.73–4.20), respectively; and for dialysis withdrawal-related mortality were 1.71 (1.05–2.77) and 1.51 (1.02–2.22), respectively.

Conclusions

Patients with diabetes at the time of kidney allograft loss have a significant survival disadvantage, with the excess mortality risk attributed to infection and dialysis withdrawal.
Disease Acceptance, but not Perceived Control, is Uniquely Associated with Inflammatory Bowel Disease-related Disability
Authors: Teugels Anouk , van den Eijnden Ilse , Keersmaekers Bep , Verstockt Bram , Sabino João , Vermeire Séverine , Guadagnoli Livia , Van Diest Ilse , Ferrante Marc
Published: March 2024

Background and Aims

Disability, an important aspect of disease burden in patients with inflammatory bowel disease [IBD], has been suggested as a valuable clinical endpoint. We aimed to investigate how disease acceptance and perceived control, two psychological predictors of subjective health, are associated with IBD-related disability.

Methods

In this cross-sectional study, adult IBD patients from the University Hospitals Leuven received a survey with questions about clinical and demographic characteristics, disease acceptance and perceived control [Subjective Health Experience model questionnaire], and IBD-related disability [IBD Disk]. Multiple linear regressions assessed predictors of IBD-related disability in the total sample and in the subgroups of patients in clinical remission or with active disease.

Results

In the total sample (N = 1250, 54.2% female, median [interquartile range: IQR] age 51 [39–61] years, 61.3% Crohn’s disease, 34.9% active disease), adding the psychological predictors to the model resulted in an increased explained variance in IBD-related disability of 19% compared with a model with only demographic and clinical characteristics [R2adj 38% vs 19%, p <0.001]. The increase in explained variance was higher for patients in clinical remission [ΔR2adj 20%, p <0.001] compared with patients with active disease [ΔR2adj 10%, p <0.001]. Of these predictors, disease acceptance was most strongly associated with disability in the total sample [β = -0.44, p <0.001], as well as in both subgroups [β = -0.47, p <0.001 and β = -0.31, p <0.001 respectively]. Perceived control was not significantly associated with disability when accounting for all other predictors.

Conclusions

Disease acceptance is strongly associated with IBD-related disability, supporting further research into disease acceptance as a treatment target.
Host plant preference of Lygus hesperus (Hemiptera: Miridae) in 4 field crops: potato, alfalfa, carrot, and pea
Authors: Shrestha Govinda , Rondon Silvia I
Published: March 2024

The western tarnished plant bug, Lygus hesperus (Knight), has emerged as a pest of potatoes (Solanum tuberosum L.) in the Lower Columbia Basin of Oregon and Washington. This species is generally found infesting several other field-grown crops in the region; however, their host preference is poorly understood. Thus, greenhouse cage experiments were conducted to evaluate L. hesperus host preference by simultaneously presenting adults with 4 host plants: potato, alfalfa, Medicago sativa L., carrot, Daucus carota L., and pea, Pisum sativum L. In addition, an oviposition test was conducted. The results indicated that L. hesperus actively chose as a host and as an oviposition substrate among the 4 host plants. We found a significantly higher number of adults on alfalfa and potato plants over carrot or pea plants at 6 h, 24 h, and 48 h after adults were released into the cage. However, 96 h after release, more L. hesperus were found in alfalfa. In addition, female L. hesperus strongly preferred potato and alfalfa plants as an oviposition substrate over carrot and pea plants at 96 h after release.
Impact of cardiac size on diagnostic performance of single-photon emission computed tomography myocardial perfusion imaging: insights from the REgistry of Fast Myocardial Perfusion Imaging with NExt generation single-photon emission computed tomography
Authors: Randazzo Michael J , Elias Pierre , Poterucha Timothy J , Sharir Tali , Fish Matthews B , Ruddy Terrence D , Kaufmann Philipp A , Sinusas Albert J , Miller Edward J , Bateman Timothy , Dorbala Sharmila , Di Carli Marcelo , Castillo Michelle , Liang Joanna X , Miller Robert J H , Dey Damini , Berman Daniel S , Slomka Piotr J , Einstein Andrew J
Published: March 2024

Aims

Variation in diagnostic performance of single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) has been observed, yet the impact of cardiac size has not been well characterized. We assessed whether low left ventricular volume influences SPECT MPI’s ability to detect obstructive coronary artery disease (CAD) and its interaction with age and sex.

Methods and results

A total of 2066 patients without known CAD (67% male, 64.7 ± 11.2 years) across nine institutions underwent SPECT MPI with solid-state scanners followed by coronary angiography as part of the REgistry of Fast Myocardial Perfusion Imaging with NExt Generation SPECT. Area under receiver-operating characteristic curve (AUC) analyses evaluated the performance of quantitative and visual assessments according to cardiac size [end-diastolic volume (EDV); <20th vs. ≥20th population or sex-specific percentiles], age (<75 vs. ≥75 years), and sex. Significantly decreased performance was observed in patients with low EDV compared with those without (AUC: population 0.72 vs. 0.78, P = 0.03; sex-specific 0.72 vs. 0.79, P = 0.01) and elderly patients compared with younger patients (AUC 0.72 vs. 0.78, P = 0.03), whereas males and females demonstrated similar AUC (0.77 vs. 0.76, P = 0.67). The reduction in accuracy attributed to lower volumes was primarily observed in males (sex-specific threshold: EDV 0.69 vs. 0.79, P = 0.01). Accordingly, a significant decrease in AUC, sensitivity, specificity, and negative predictive value for quantitative and visual assessments was noted in patients with at least two characteristics of low EDV, elderly age, or male sex.

Conclusion

Detection of CAD with SPECT MPI is negatively impacted by small cardiac size, most notably in elderly and male patients.
Plasma lipidomics and coronary plaque changes: a substudy of the SMARTool clinical trial
Authors: Smit Jeff M , Rocchiccioli Silvia , Signore Giovanni , Michelucci Elena , Di Giorgi Nicoletta , van Rosendael Alexander R , El Mahdiui Mohammed , Neglia Danilo , Knuuti Juhani , Saraste Antti , Buechel Ronny R , Teresinska Anna , Pizzi Maria N , Roque Albert , Poddighe Rosa , Mertens Bart J , Caselli Chiara , Parodi Oberdan , Pelosi Gualtiero , Scholte Arthur J
Published: March 2024

Aims

To date, no studies have investigated the association between lipid species and coronary plaque changes over time, quantitatively assessed by serial imaging. We aimed to prospectively determine the association between lipid species quantified by a plasma lipidomic analysis and coronary plaque changes according to composition assessed by a quantitative serial analysis of coronary computed tomography angiography (CTA).

Methods and results

Patients with suspected coronary artery disease (CAD) undergoing baseline coronary CTA were prospectively enrolled by seven EU centres in the SMARTool study and submitted to clinical, molecular, and coronary CTA re-evaluation at follow-up (an inter-scan period of 6.39 ± 1.17 years). Out of 202 patients who were analysed in the SMARTool main clinical study, a lipidomic analysis was performed in 154 patients before the baseline coronary CTA, and this group was included in the present study. A quantitative CTA analysis was performed by using a separate core laboratory blinded from clinical data. In the univariable analysis, it was found that no lipid species were significantly associated with annual total and calcified plaque changes. After adjusting for clinical variables at baseline and statin use, it was found that three lipid species were significantly associated with non-calcified plaque progression. In detail, cholesteryl ester(20:3), sphingomyelin (SM)(40:3), and SM(41:1) were found to be positively related to non-calcified plaque progression (Bonferroni-adjusted P-values = 0.005, 0.016, and 0.004, respectively).

Conclusion

The current study showed an independent relationship between specific lipid species determined by a plasma lipidomic analysis and non-calcified coronary plaque progression assessed by a serial, quantitative coronary CTA analysis.
A rare case report of type 1 congenital disorders of glycosylation with acute decompensated heart failure and the incidental discovery of congenital disorders of glycosylation associated dilated cardiomyopathy and acute myocarditis
Authors: Yang Woo Sze , Grover Suchi , Smith Emma , Selvanayagam Joseph B
Published: March 2024

Background

Congenital disorders of glycosylation (CDG) are rare genetically inherited defects leading to enzyme deficiency or malfunction in the glycosylation pathway. Normal glycosylation is essential to the development of normal cardiac anatomy and function. Congenital disorders of glycosylation–related cardiomyopathy are often the first manifestation detected in early life and may lead to sudden cardiac death. Approximately one-fifth of CDG types are related to cardiac diseases that include cardiomyopathy, rhythm disturbances, pericardial effusions, and structural heart disease.

Case summary

We report a rare case of a 26-year-old lady with CDG-1 who presented with acute-onset dyspnoea. She had respiratory tract symptoms for the past 2 weeks. With the relevant clinical and biochemical findings, including supportive findings on echocardiogram and cardiac magnetic resonance imaging, we have managed to arrive at a diagnosis of severe pneumonia leading to acute decompensated heart failure, as well as the discovery of an underlying CDG-associated dilated cardiomyopathy (DCM) and acute myocarditis. Anti-failure medications and i.v. methylprednisolone were commenced, and she showed gradual clinical improvement with an increase of her left ventricular function. She was discharged home well with anti-failure therapy, prednisolone, and a follow-up echocardiogram with further review in the heart failure clinic.

Discussion

In conclusion, this case report highlights the need for accurate diagnosis and prompt management of CDG-associated DCM, leading to a successful recovery and discharge from hospital care. With this, we hope to add to the increasing number of reported cases of CDG-related cardiac disease in the medical literature to emphasize the importance of screening and follow-up for any underlying cardiac diseases in patients with CDG.