bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remodeling the cellular stress response for enhanced genetic code expansion in mammalian cells
Authors: Sushkin Mikhail E. , Koehler Christine , Lemke Edward A. 
Published: October 2023

AbstractGenetic code expansion (GCE) reprograms the translational machinery to site-specifically incorporate noncanonical amino acids (ncAAs) into a selected protein. The efficiency of GCE in mammalian cells might be compromised by cellular stress responses, among which, the protein kinase R(PKR)-dependent eIF2α phosphorylation pathway can reduce translation rates. Here we test several strategies to engineer the eIF2α pathway and boost the rate of translation and show that such interventions increase GCE efficiency in mammalian cells. In particular, addition of the N-terminal PKR fragment (1–174) provides a substantial enhancement in cytoplasmic GCE and also in GCE realized by OTOs (orthogonally translating designer organelles), which built on the principle of 2D phase separation to enable mRNA-selective ncAA incorporation. Our study demonstrates an approach for improving the efficiency of GCE and provides a means by which the power of designer organelles can be further optimized to tune protein translation.
Nickel-catalyzed acylzincation of allenes with organozincs and CO
Authors: Wu Xianqing , Wang Chenglong , Liu Ning , Qu Jingping , Chen Yifeng 
Published: October 2023

AbstractTransition metal-catalyzed carbonylative reaction with CO gas are among the central task in organic synthesis, enabling the construction of highly valuable carbonyl compound. Here, we show an earth-abundant nickel-catalyzed three-component tandem acylzincation/cyclization sequence of allene and alkylzinc reagent with 1 atm of CO under mild conditions. This protocol is featured by broad functional group tolerance with high reaction selectivity, providing a rapid and convenient synthetic method for the construction of diverse fully substituted benzotropone derivatives. Mechanistic studies reveal that the installation of a cyano group tethered to allene moiety enables the high regio- and stereoselectivity of this acylzincation of allene, allowing the selective formation of three consecutive C-C bonds in a highly efficient manner.
An in situ dual-anchoring strategy for enhanced immobilization of PD-L1 to treat autoimmune diseases
Authors: Wang Shenqiang , Zhang Ying , Wang Yanfang , Yang Yinxian , Zhao Sheng , Sheng Tao , Zhang Yuqi , Gu Zhen , Wang Jinqiang , Yu Jicheng 
Published: October 2023

AbstractImmune checkpoints play key roles in maintaining self-tolerance. Targeted potentiation of the checkpoint molecule PD-L1 through in situ manipulation offers clinical promise for patients with autoimmune diseases. However, the therapeutic effects of these approaches are often compromised by limited specificity and inadequate expression. Here, we report a two-step dual-anchor coupling strategy for enhanced immobilization of PD-L1 on target endogenous cells by integrating bioorthogonal chemistry and physical insertion of the cell membrane. In both type 1 diabetes and rheumatoid arthritis mouse models, we demonstrate that this approach leads to elevated and sustained conjugation of PD-L1 on target cells, resulting in significant suppression of autoreactive immune cell activation, recruitment of regulatory T cells, and systematic reshaping of the immune environment. Furthermore, it restores glucose homeostasis in type 1 diabetic mice for over 100 days. This specific in situ bioengineering approach potentiates the functions of PD-L1 and represents its translational potential.
Prognosis of recurrence after complete resection in early-stage lung adenocarcinoma based on molecular alterations: a systematic review and meta-analysis
Authors: Zhou Chu , Jing Zhongying , Liu Wei , Ma Zihuan , Liu Siyao , Fang Yueyu 
Published: October 2023

AbstractMolecular biomarkers have the potential to predict the recurrence risk of early-stage lung adenocarcinoma (LUAD) after complete resection, but the study results are controversial. We aimed to clarify the association of molecular alterations with disease-free survival (DFS) and recurrence-free survival (RFS) in early-stage LUAD with R0 resection. Comprehensive searches were conducted in PubMed/MEDLINE, Web of Science, and Cochrane Library for this systematic review and meta-analysis with date restrictions from 2012 to 2022. In the 18 included studies, data from a total of 7417 participants in 11 studies and 4167 participants in 9 studies were collected for the EGFR and KRAS meta-analyses, respectively. Two studies were assessed as having a moderate risk of bias, and the others were all assessed as having a high individual risk of bias. The molecular alterations in KRAS rather than EGFR, were associated with a high risk of recurrence for early-stage LUAD patients suffering from R0 resection, especially for those in pStage I, the pooled hazard ratios (HRs) of KRAS were 2.71 (95% CI, 1.81–4.06; I2 = 22%; P < 0.00001) and 1.95 (95% CI, 1.25–3.20; I2 = 57%; P = 0.003) with small interstudy heterogeneity in univariate and multivariate analyses, respectively. This finding suggests that molecular alterations in KRAS that could be detected by polymerase chain reaction techniques would provide new insight into stratifying risk and personalizing patient postoperative follow-up.
GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data
Authors: Haseeb Muhammad , Saeed Fahad 
Published: October 2023

AbstractDatabase peptide search is the primary computational technique for identifying peptides from the mass spectrometry (MS) data. Graphical Processing Units (GPU) computing is now ubiquitous in the current-generation of high-performance computing (HPC) systems, yet its application in the database peptide search domain remains limited. Part of the reason is the use of sub-optimal algorithms in the existing GPU-accelerated methods resulting in significantly inefficient hardware utilization. In this paper, we design and implement a new-age CPU-GPU HPC framework, called GiCOPS, for efficient and complete GPU-acceleration of the modern database peptide search algorithms on supercomputers. Our experimentation shows that the GiCOPS exhibits between 1.2 to 5$$\times$$
×
speed improvement over its CPU-only predecessor, HiCOPS, and over 10$$\times$$
×
improvement over several existing GPU-based database search algorithms for sufficiently large experiment sizes. We further assess and optimize the performance of our framework using the Roofline Model and report near-optimal results for several metrics including computations per second, occupancy rate, memory workload, branch efficiency and shared memory performance. Finally, the CPU-GPU methods and optimizations proposed in our work for complex integer- and memory-bounded algorithmic pipelines can also be extended to accelerate the existing and future peptide identification algorithms. GiCOPS is now integrated with our umbrella HPC framework HiCOPS and is available at: https://github.com/pcdslab/gicops.
Pyrethroid insecticides susceptibility profiles and evaluation of L1014F kdr mutant alleles in Culex quinquefasciatus from lymphatic filariasis endemic communities
Authors: Okafor Martina Anurika , Ekpo Ndifreke Daniel , Opara Kenneth Nnamdi , Udoidung Nsima Ibanga , Ataya Farid S. , Yaro Clement Ameh , Batiha Gaber El-Saber , Alexiou Athanasios , Papadakis Marios 
Published: October 2023

AbstractThis study investigated the dynamics in pyrethriod resistance and the presence/frequencies of L1014F knockdown resistance mutant allelles in Culex quinquefasciatus vector populations from Uruan Local Government Area of AkwaIbom State, Southern Nigeria between the months of March and November, 2021. Uruan LGA is among the endemic LGAs for lymphatic filariasis in AkwaIbomState. Female Anopheles mosquitoes from Eman Uruan, Ituk Mbang and Idu Uruan were exposed to permethrin, deltamethrin and alphacypermethrin in CDC insecticide coated bottles for susceptibility bioassay following standard protocols. The mosquitoes were obtained as aquatic forms from the study sites and reared under laboratory conditions to adults. The adult mosquitoes were used for this study. All the mosquitoes used for the insecticide susceptibility bioassay were morphologically identified. Standard Polymerase chain reaction (PCR) was used for authenticating the Culex quinquefasciatus species. A portion of the vgsc (917 bp) gene spanning the entire intron and the exon containing the L1014F mutation associated with knockdown resistance (kdr) in the vectorswere amplified using Allele-SPECIFIC POLYMERASE CHAIN REACTION (AS-PCR) in order to detect target site insensitivity in the vectors from the study sites. Results obtained revealed that vectors from all the study sites were resistant to permethrin insecticide (mortality rate: 18–23%). Suspected resistance (mortality rate: 90–93%) to deltamethrin and low resistance (mortality rate: 82–85%) to alphacypermethrin insecticides were detected. knockdown was more rapid with deltamethrin and alphacypermethrin than with permethrin across the study sites considering their KDT50 and KDT95. The frequency of the resistant phenotypes ranged from 35.14 to 55.3% across the study sites with a net of 45.1% resistant phenotype recorded in this study. The 1014F allelic frequency calculated from Hardy–Weinberg principle for vector populations across the study sites ranged from 0.500 (50.00%) to 0.7763 (77.63%). All populations witnessed significant (p < 0.05) deviations from Hardy–Weinberg equilibrium in the distribution of these alleles. The findings of this study show that there is a tendency to record an entire population of resistant vectors in this study area over time due to natural selection. The public health implication of these findings is that the use of pyrethroid based aerosols, coils, sprays, LLITNs and others for the purpose of controlling vectors of lymphatic filariasis and other diseases may be effort in futility.
Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.)
Authors: Mishra Shefali , Chaudhary Reeti , Pandey Bharti , Singh Gyanendra , Sharma Pradeep 
Published: October 2023

AbstractThe GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.
Zero-shot learning of aerosol optical properties with graph neural networks
Authors: Lamb K. D. , Gentine P. 
Published: October 2023

AbstractBlack carbon (BC), a strongly absorbing aerosol sourced from combustion, is an important short-lived climate forcer. BC’s complex morphology contributes to uncertainty in its direct climate radiative effects, as current methods to accurately calculate the optical properties of these aerosols are too computationally expensive to be used online in models or for observational retrievals. Here we demonstrate that a Graph Neural Network (GNN) trained to predict the optical properties of numerically-generated BC fractal aggregates can accurately generalize to arbitrarily shaped particles, including much larger ($$10\times$$

10
×

) aggregates than in the training dataset. This zero-shot learning approach could be used to estimate single particle optical properties of realistically-shaped aerosol and cloud particles for inclusion in radiative transfer codes for atmospheric models and remote sensing inversions. In addition, GNN’s can be used to gain physical intuition on the relationship between small-scale interactions (here of the spheres’ positions and interactions) and large-scale properties (here of the radiative properties of aerosols).
Biogeography and evolutionary history of Puntius sensu lato (Teleostei: Cyprinidae) in Sri Lanka
Authors: Sudasinghe Hiranya , Ranasinghe Tharindu , Dahanukar Neelesh , Raghavan Rajeev , Rüber Lukas , Pethiyagoda Rohan , Meegaskumbura Madhava 
Published: October 2023

AbstractSri Lanka’s biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of—and diversification on—Sri Lanka by a group of four closely-related genera of cyprinid fishes (Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to discern phylogeographic patterns. The origin of Puntius s.l. is dated to ~ 20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an ‘Out of Sri Lanka’ scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island’s perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka’s montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.
Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis
Authors: Chen Xiaoli , Li Buyu , Zhang Xuemei 
Published: October 2023

AbstractThe identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
Assessment of in vitro anti-skin aging activities of Phyllanthus indofischeri Bennet extracts for dermatological and aesthetic applications
Authors: Boonpisuttinant Korawinwich , Taka Thanachai , Ruksiriwanich Warintorn , Chutoprapat Romchat , Udompong Sarinporn , Kansawang Rattiya , Sangsee Jinapa , Chompoo Wirinda , Samothai Kitrawi , Srisuttee Ratakorn 
Published: October 2023

AbstractGiant Indian Gooseberry (GIG) or Phyllanthus indofischeri Bennet are commercially cultivated and commonly used herbs in Traditional medicine, especially in Thailand. The aim of this study was to assess the potential of the GIG extracts in anti-aging activities to be a dermatological application. The juice, meat residues, and seeds of GIG collected from Sra Kaeo Province, Thailand, were extracted by the Boiling method (B) and the Maceration process (M) by using 95% ethanol as a solvent. The GIG extracts gave the total phenolic, total flavonoid contents and quercetin contents, as well as exhibited anti-oxidative activities. The GIG-R-B extract inhibited tyrosinase activity and had the highest anti-melanogenesis activity on B16F10 cells at 31.63 ± 0.70%. The GIG-S-B, GIG-S-M, and GIG-R-M extracts demonstrated the highest collagen biosynthesis, which was comparable to vitamin C (p < 0.05), whereas the GIG-R-B extracts gave the highest stimulation of anti-aging genes (SIRT1 and FOXO1). All extracts at the concentration of 0.1 mg/mL showed no cytotoxicity on human skin fibroblasts. Therefore, the GIG-S-B extract was discovered to be a promising natural anti-aging agent for dermatological health and aesthetic applications that can be further developed in cosmetic, functional food and food supplement industries.
Availability of iron ions impacts physicochemical properties and proteome of outer membrane vesicles released by Neisseria gonorrhoeae
Authors: Płaczkiewicz Jagoda , Gieczewska Katarzyna , Musiałowski Marcin , Adamczyk-Popławska Monika , Bącal Paweł , Kwiatek Agnieszka 
Published: October 2023

AbstractOuter membrane vesicles (OMVs) are bilayer structures released by bacteria for various purposes, e.g., response to environmental factors, bacterial communication, and interactions with host cells. One of the environmental variables bacteria need to react is the amount and availability of iron, a crucial element for bacteria biology. We have investigated the impact of the iron amount and availability on OMV secretion by pathogenic Neisseria gonorrhoeae, which, depending on the infection site, challenges different iron availability. N. gonorrhoeae releases OMVs in iron starvation and repletion growth environments. However, OMVs differed in physicochemical features and proteome according to iron amount and availability during the bacteria growth, as was analyzed by Liquid Chromatography-Tandem Mass Spectrometry, Infrared spectroscopy with a Fourier transform infrared spectrometer, and Atomic Force Microscopy. OMVs from iron starvation and repletion conditions had a higher variation in size, different flexibility, and different membrane protein and lipid components than OMVs isolated from control growth conditions. These OMVs also varied qualitatively and quantitatively in their total proteome composition and contained proteins unique for iron starvation and repletion conditions. Thus, the modulation of OMVs' properties seems to be a part of N. gonorrhoeae adaptation to surroundings and indicates a new direction of antigonococcal proceeding.
Mathematical modeling of BCG-based bladder cancer treatment using socio-demographics
Authors: Savchenko Elizaveta , Rosenfeld Ariel , Bunimovich-Mendrazitsky Svetlana 
Published: October 2023

AbstractCancer is one of the most widespread diseases around the world with millions of new patients each year. Bladder cancer is one of the most prevalent types of cancer affecting all individuals alike with no obvious “prototypical patient”. The current standard treatment for BC follows a routine weekly Bacillus Calmette-Guérin (BCG) immunotherapy-based therapy protocol which is applied to all patients alike. The clinical outcomes associated with BCG treatment vary significantly among patients due to the biological and clinical complexity of the interaction between the immune system, treatments, and cancer cells. In this study, we take advantage of the patient’s socio-demographics to offer a personalized mathematical model that describes the clinical dynamics associated with BCG-based treatment. To this end, we adopt a well-established BCG treatment model and integrate a machine learning component to temporally adjust and reconfigure key parameters within the model thus promoting its personalization. Using real clinical data, we show that our personalized model favorably compares with the original one in predicting the number of cancer cells at the end of the treatment, with$$14.8\%$$14.8%improvement, on average.
Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice
Authors: López-Pérez Ana , Remeseiro Silvia , Hörnblad Andreas 
Published: October 2023

AbstractSeveral preclinical models have been recently developed for metabolic associated fatty liver disease (MAFLD) and associated hepatocellular carcinoma (HCC) but comprehensive analysis of the regulatory and transcriptional landscapes underlying disease in these models are still missing. We investigated the regulatory and transcriptional landscape in fatty livers and liver tumours from DIAMOND mice that faithfully mimic human HCC development in the context of MAFLD. RNA-sequencing and ChIP-sequencing revealed rewiring of the Wnt/β-catenin regulatory network in DIAMOND tumours, as manifested by chromatin remodelling and associated switching in the expression of the canonical TCF/LEF downstream effectors. We identified splicing as a major mechanism leading to constitutive oncogenic activation of β-catenin in a large subset of DIAMOND tumours, a mechanism that is independent on somatic mutations in the locus and that has not been previously shown. Similar splicing events were found in a fraction of human HCC and hepatoblastoma samples.