bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the impact of different factors on changes in carbon intensity of the world economies
Authors: Provornaya Irina V. , Filimonova Irina V. , Krutilina Arina D. 
Published: May 2024

Relevance. With the restructuring of the economy in the carbon-neutral side, the negative anthropogenic impact can be weakened. It is very likely that there will be a comprehensive analysis of the impact of various climatic accidents in the country and its action to eliminate the risk of carbon dioxide. Moreover, studies in the experience of the peoples of the states make it possible to use their achievements in the field of climate policy in Russia, improve and modernize their advantages from the characteristics of the national economy. Aim. To assess the degree of influence of environmental, climatic and macroeconomic factors on the change in the carbon intensity of the economies of the world. Objects. The parameters of the climate policy of the countries of the world in the field of regulation of carbon dioxide emissions, the subject of the study is the relationship of environmental, climatic and macroeconomic factors with the carbon intensity of the economies of the world. Methods. Econometric method of panel data analysis. Scientific novelty. The paper confirms the hypothesis of the negative impact of one of the main climate policy instruments of the countries of the world (carbon prices) on the carbon intensity of the economy using the construction of the original panel data model. Results. The authors have substantiated a set of factors that affect the carbon intensity of the countries of the world, supplemented by such an indicator as the carbon price, which is one of the main indicators of climate policy development in the country. All factors were divided into two groups (macroeconomic and ecological-climatic) and a database was formed for 24 countries. Using the panel data method, the authors constructed the equation of the dependence of the carbon intensity of the economies of countries on macroeconomic and ecological and climatic factors. The authors tested the hypothesis of the carbon price negative impact on the carbon intensity of the economies of countries. Evaluation of various model specifications allowed us to confirm this hypothesis, which indicates the importance of the climate policy development within each country and the feasibility of introducing new tools to regulate carbon dioxide emissions. It was also determined that GDP, as a general indicator of the development of the entire economy, has the greatest impact on reducing carbon intensity. At the same time, in order to reduce the ratio of carbon dioxide emissions to gross domestic product, it is necessary to pursue a policy of replacing fossil fuels with low-carbon energy sources, but only taking into account the country raw material capabilities and the industry specifics of the economy.
Preexposure Prophylaxis (PrEP) for HIV Prevention at Outpatient Substance Use Treatment Facilities, United States, 2021
Authors: Bunting Samuel R. , Vidyasagar Nitin , Wilson Allison P. , Hazra Aniruddha 
Published: May 2024

Objectives. To determine the percentage of US outpatient substance use treatment facilities that offer HIV preexposure prophylaxis (PrEP). Methods. We used a retrospective cross-sectional design with data from the National Substance Use and Mental Health Services Survey, which was administered to directors of US outpatient substance use treatment facilities in 2021. We evaluated the percentage of outpatient substance use treatment facilities offering PrEP and factors associated with the likelihood of offering PrEP. Results. We included 12 182 outpatient substance use treatment facilities. Of these, 637 (5.2%) offered PrEP. Offering HIV treatment (adjusted odds ratio [AOR] = 45.3; 95% confidence interval [CI] = 36.0, 56.9) and offering programs for LGBTQ (lesbian, gay, bisexual, transgender, and queer or questioning) people (AOR = 1.3; 95% CI = 1.0, 1.6) were associated with higher likelihoods of offering PrEP. Conclusions. PrEP is highly effective and recommended for patients at risk for HIV from injection drug use. Nearly 95% of US outpatient substance use treatment facilities did not offer PrEP—a missed opportunity for harm reduction through primary HIV prevention. Public Health Implications. Diversification of the array of available HIV PrEP options and the ongoing HIV and opioid use epidemics require outpatient substance use treatment facilities to expand PrEP availability. ( Am J Public Health. 2024;114(8):833–837. https://doi.org/10.2105/AJPH.2024.307699 )
On the Graph-Based Extension of the Set Based Model: A New Approach on Graph Representation and Model Ensemble
Authors: Kalogeropoulos Nikitas Rigas , Skamnelos Nikolaos , Makris Christos 
Published: May 2024

Abstract

The purpose of this paper is to present a set of algorithmic improvements upon an extension of the Set-Based Model (Kalogeropoulos et al (2020)) that focuses on the dependence among document terms employing graph representations. A graph-based approach to document representation can positively affect the information retrieval process due to the ability of graphs to capture the syntactic notion and, in some cases, the semantic relationship among document terms. The aforementioned model generates complete graphs; thus, each document term will be interdependent with the rest. Consequently, an interdependent segment or multiple parts of a document called a window is defined, in which the graph creation algorithms are applied. The proposed methods aim to approximate the window size by exploiting the document length. Moreover, an attempt to create multiple windows is made, considering the relationship between a sentence and a paragraph, which is reflected in the semantic importance of nodes and edges. An attempt to tackle the stop-word detection problem on bridge nodes is made by implementing algorithmic schemes that use core decomposition (Seid-man (1983a)) to identify the importance of such nodes in a sample of the corpus collection. Finally, a simple reranking scheme and an ensemble voting technique are implemented to enhance model performance on queries where the proposed approach lacks performance. The experimental analysis made on multiple document collections exhibits performance improvements and in some queries, our 1 approach outperforms even state-of-the-art models such as BM25 (Robertson et al (2004)) and ColBERT (Khattab and Zaharia (2020)).
Multiplexed Detection of Respiratory Virus RNA Using Optical pH Sensors and Injection Molded Centrifugal Microfluidics
Authors: Nagl Stefan , Suarez Gianmarco , Tang Yuki , Bayer Steevanson , Cheung Peter 
Published: May 2024

Abstract

Infectious pathogens, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are a threat to global health and prosperity, with the coronavirus disease 2019 (COVID-19) pandemic causing deaths and negative economic impacts worldwide. Pathogens continuously mutate, evading vaccines and treatments; monitoring is therefore crucial to preventing future outbreaks. But there are still many shortcomings in available diagnostic technologies, and scalable and convenient point-of-care technologies are highly demanded. In this work, we demonstrate the application of injection molded centrifugal microfluidic chips with integrated optical pH sensors for multiplexed detection of SARS-CoV-2, influenza A, and influenza B RNA. The optical pH sensors generated sensitive fluorescent readouts from diagnostic reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions; limits of detection for influenzas A and B, and SARS-CoV-2 of 89, 245, and 38 RNA copies per reaction, respectively, were attained. Results were obtainable within 44 minutes for SARS-CoV-2 and influenza A, and 48 minutes for influenza B. We implemented a data processing strategy that allowed for reliable, quantitative thresholds for deciding reaction outcomes based on numerical derivatives of the fluorescence curves, enabling 100% specificity. This work demonstrates the utility of optical pH sensors and injection molded centrifugal microfluidics for multiplexed infectious disease diagnostics with point-of-care applications.
Midkine is a Potential Novel Biomarker for Acro-osteolysis in Systemic Sclerosis
Authors: Gogulamudi Venkateswara R , Adeogun Ganiat , Donato Anthony J. , Petrey Aaron , Wood Sarah , Zent Roy , Frech Tracy M. 
Published: May 2024

Abstract

Background: Digital acro-osteolysis can result from ischemia and is a complication of systemic sclerosis (SSc). Midkine (MK) is an angiogenic growth factor that plays a key role in bone remodeling. The objective of this study was to examine serum MK level as a biomarker of acro-osteolysis in SSc.
Methods: The study population consisted of patients who consented to undergo ethics approval at two institutions and had Raynaud's phenomenon (RP), abnormal capillaroscopy, and hand radiographs. Age- and sex-matched healthy controls without hypertension, Raynaud phenomenon, or digital lesions were included. Serum MK concentration was measured using an enzyme-linked immunosorbent assay. An analysis of variance test assessed the differences in MK concentrations among SSc patients with acro-osteolysis, SSc patients without acro-osteolysis, and age-and sex-matched healthy controls.
Results: A total of 54 SSc registry patients and 20 age-sex matched healthy controls were included in the cross-sectional analysis of MK levels. Except for digital ulcers, there were no sociodemographic or clinical features that were statistically significantly associated with the presence of acro-osteolysis. There were significantly higher MK levels between SSc without acro-osteolysis than in acro-osteolysis (p=0.0001), as well as in SSc without acro-osteolysis and in healthy controls (p=0.01). There were no significant differences between SSc patients with acro-osteolysis and healthy controls (p=0.31).
Conclusions: Our study suggests that MK may maintain an intact digital tip in SSc patients. A reduction in serum MK level is associated with progressive digital vasculopathy,defined by the presence of acro-osteolysis.
Author Contributions: TMF, VG, GA, AJD, SW, RZ contributed to the design and implementation of the research analysis of the results and to the writing of the manuscript. TMF conceived the original and supervised the project.
EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma
Authors: Shen Shensi , Peng Haoning , Wang Zhile , Wang Mengyao , Tang Xinpu , Li Kaixiu , Yu Xuejiao , Song Siyang , Wang Yuqing , Lu Tianjian , Dong Bo , Wang Youyu , Chen Minqi , Ceng Dongjian , Deng Yulan , Xia Liang , Guo Chenglin , Pu Qiang , Li Lu , Cerezo Michael , Wang Weiya , Liu Lunxu 
Published: May 2024

Abstract

Drug-tolerant persister cells withstand treatments by adapting their identity through lineage-dependent plasticity during systemic anti-cancer therapies. This phenomenon is evident in small-cell lung carcinoma (SCLC), a lethal neuroendocrine cancer initially responsive (60-80%) to platinum-based chemotherapy but succumbing to resistance within 6 months in advanced stages. This resistance associates with the transdifferentiation of residual tumour cells into a non-neuroendocrine state, a process intricately tied to SCLC's chemotolerance, yet molecular mechanisms governing this lineage conversion remain completed understood. Here we report that first-line chemotherapy induces translation initiation factor eIF6 in drug-tolerant persister-like cells in SCLC, associating with the non-neuroendocrine state in both SCLC genetically engineered mouse model and patient samples. Intervening eIF6 inhibits non-neuroendocrine transdifferentiation, thus enhancing SCLC responsiveness to chemotherapy. Mechanistically, therapy-induced eIF6 dissociates from ribosomes whereas interacts with the extracellular matrix complex CD104/FAK, leading to the activation of MAPK pathway and a global translational remodelling in SCLC drug-tolerant persister-like cells. This prompts us to develop an eIF6-CD104/FAK proximity ligation assay applicable to clinical samples, showing its prognostic value for SCLC clinical outcomes. This study of eIF6’s moonlight function sheds light on its potential therapeutic interventions to mitigate treatment resistance in SCLC.
Plant hormones determine the differentiation of callus tissue during tissue culture of mature and immature Brachypodium distachyon embryos
Authors: Ouyang Dandan , Wei Jiagu , Ran Liping , Liu Peiyao , Xiong Fei , Yu Xurun 
Published: May 2024

Abstract

Brachypodium distachyon has emerged as a new model for the structural and functional genomics of temperate grasses. Somatic embryo culture serves as an effective method for the genetic transformation of B. distachyon. However, the role of regulatory genes in inducing somatic embryogenesis through endogenous hormone modulation in B. distachyon remains unexplored. This study investigated the endogenous hormone levels and transcriptome data of embryogenic calli (EC) derived from both mature and immature B. distachyon embryos. Our findings indicate that higher levels of IAA and GAs promote the formation of mature embryo-produced compact embryogenic calli (MEC), whereas higher tZR and lower ABA levels promote the development of immature embryo-produced compact embryogenic calli (IEC). The differential expression of genes involved in the biosynthesis and signal transduction of auxin (YUCCA,ALDH, AUX/IAA), trans-zeatin riboside (CKX), gibberellin (KAO, GA3ox), and abscisic acid (AAO3, SnRK2) influences the endogenous hormone concentrations in MEC and IEC of B. distachyon. Specifically, increased expression of AUX/IAA is linked to MEC formation. Thus, the differential expression of genes associated with the AUX, CK, GA, and ABA biosynthesis and signal transduction pathways may modulate endogenous hormone levels, steering the differentiation of MEC and IEC in B. distachyon.
Keywords Brachypodium distachyon·embryogenic calli· differentially expressed genes·endogenous hormone
Adaptive Hyperparameter Selection in Kernel-based Partition of Unity Methods by Global Optimization Techniques
Authors: Cavoretto Roberto , De Rossi Alessandra , Haider Adeeba , Sergeyev Yaroslav D. 
Published: May 2024

Abstract

In this article, we present a new numerical algorithm to detect the kernel shape parameter and the subdomain radius size within a partition of unity method for scattered data interpolation. Since an adaptive search of such hyperparameters is quite expensive from the computational point of view, we propose the use of a leave-one-out cross validation technique combined with univariate global optimization tools from the class of Lipschitz derivative-free method. Particularly, we consider efficient global optimization strategies characterized by optimistic and pessimistic improvements. The resulting algorithm allows us to improve the performance of the standard approach in terms of both accuracy and efficiency. Numerical results deriving from the study of some test cases and an application to real-world data support our analysis.
MSC Classification: 65D05 , 65D15 , 90C26 , 65K05
Temporal Interactions between Neural Proxies for Memory Recall, Negative Affect, and Emotion Regulation in Major Depression
Authors: Michel Christina , Schmidt Mike , Mann J. John , Herzog Sarah , Ochsner Kevin , Davachi Lila , Schneck Noam 
Published: May 2024

Abstract

Dysfunction in emotion regulation (ER) and autobiographical memory are components of major depressive disorder (MDD). However, little is known about how they mechanistically interact with mood disturbances in real time. Using machine learning-based neural signatures, we can quantify negative affect (NA), ER, and memory continuously to evaluate how these processes dynamically interact in MDD. Unmedicated individuals with MDD (N=45) and healthy volunteers (HV; N=38) completed a negative autobiographical memory functional magnetic resonance imaging task wherein they recalled, distanced from (an ER strategy), and immersed into memories. We used a negative affect signature (PINES) and an emotion regulation signature (ERS) to quantify moment-to-moment NA and ER. We then examined whether memory engagement, indexed by hippocampal activity, predicted subsequent change in PINES and ERS over time. During memory recall and immersion, greater hippocampal activity predicted increased PINES across groups. During distancing, greater hippocampal activity in HVs predicted increased ERS but not PINES. In MDD, greater hippocampal activity predicted increased PINES but not ERS. Findings suggest abnormalities in the real-time relationship between memory, NA, and ER in MDD. During distancing, as predicted, HVs showed an attenuation of the linkage between memory engagement and NA, and they had subsequent increases in ER following memory reactivation. In contrast, MDD was characterized by continued linkage between memory engagement and NA, without subsequent increases in ER. Deficits in engagement of ER and ineffective modulation of NA following negative memory recall may contribute to the mood disturbances in MDD and are potential targets for clinical intervention.
INAEME: Integral Neoantigen Analysis with Entirety of Mutational Events
Authors: Kovacevic Vladimir , Milicevic Ognjen , Raicevic Nevena Ilic , Kojicic Milica , Lazic Ana Mijalkovic , Skundric Nikola , DiGiovanna Jack 
Published: May 2024

Abstract

Neoantigens are peptides on the surface of cancer cells presented to the immune system. Multiple novel therapeutic approaches involve the administration of neoantigens to trigger immunity-induced tumor regression. Identification of neoantigens includes a personalized approach consisting of detailed analyses of the sequenced tumor tissue and its comparison with wild type to identify somatic mutations. Alternated peptides are translated from nucleotides around somatic mutations and their binding affinity and immunogenicity need to be further evaluated. Still, the entire bioinformatics analysis is very complex, and accurate prediction of the neoantigen candidates represents a true challenge. Here, we present the novel, integral bioinformatic analysis workflow for neoantigen discovery, denoted INAEME (Integral Neoantigen Analysis with Entirety of Mutational Events). The workflow performs integral processing of an individual's DNA tumor-normal and RNA tumor raw reads to output prioritized neoantigen candidates. Our evaluation analysis includes a wide scope of mutational events so far not considered in the existing solutions, including phasing of variants, influence of both somatic and germline variants, positions of all transcripts, neighboring variants, and frameshifts. The influence of each mutational event on the accuracy of predicted neoantigen candidates is tested across 300 TCGA samples from multiple cancer types. The obtained results have demonstrated the significance of considering the entirety of mutational events to obtain an accurate set of strong neoantigen candidates for cancer immunotherapy targets or vaccines. The adaption of the described methods in the bioinformatics analysis minimizes the existence of false positives which are only later discovered in a laboratory environment using expensive methods such as mass spectrometry or microscopy.
MRPL27 as a new prognostic biomarker involved in immune cell infiltration and hepatocellular carcinoma progression
Authors: Yang JiaYing , Lin Qinghua , Liu Xiayan , Chen Ke , Chen Xinyi , Han Junyong , Liao Zhijun 
Published: May 2024

Abstract

Mitochondrial ribosomal protein L27 (MRPL27) is a member of mitochondrial ribosomal proteins (MRPs). However, the biological function of MRPL27 in hepatocellular carcinoma (LIHC) is still unclear. Use UALCAN, TIMER, TISIDB, Kaplan Meier, and GEPIA database systems to analyze the expression, prognostic value, and relationship between MRPL27 and immune infiltration in LIHC. The expression and clinical significance of MRPL27 in LIHC patients were validated using tissue microarray. Conduct cell function experiments to detect the effects of overexpression and knockdown of MRPL27 on the proliferation, migration, and invasion of Huh7 cells. The tissue microarray results confirmed that MRPL27 expression is upregulated in LIHC, and high MRPL27 expression is associated with poorer prognosis. The expression of MRPL27 is significantly correlated with the infiltration levels of immune modulators, chemokines, and various immune cells. In addition, MRPL27 affects the proliferation, migration, and invasion of LIHC cells. These data indicate that MRPL27 is a new prognostic biomarker for LIHC and is associated with immune infiltration in LIHC.
PET Imaging of Sphingosine-1-Phosphate Receptor 1 with [18F]TZ4877 in Nonhuman Primates
Authors: Gu Jiwei , Zheng Ming-Qiang , Holden Daniel , Fowles Krista , Qiu Lin , Felchner Zachary , Zhang Li , Ropchan Jim , Gropler Robert J , Carson Richard E , Tu Zhude , Huang Yiyun , Hillmer Ansel T 
Published: May 2024

Abstract

Purpose
The sphingosine-1-phosphate receptor-1 (S1PR1) is involved in regulating responses to neuroimmune stimuli. There is a need for S1PR1-specific radioligands with clinically suitable brain pharmcokinetic properties to complement existing radiotracers. This work evaluated a promising S1PR1 radiotracer, [18F]TZ4877, in nonhuman primates.
Procedures:
[18F]TZ4877 was produced via nucleophilic substitution of tosylate precursor with K[18F]/F− followed by deprotection. Brain PET imaging data were acquired with a Focus220 scanner in two Macaca mulatta (6, 13 years old) for 120–180 min following bolus injection of 118–163 MBq [18F]TZ4877, with arterial blood sampling and metabolite analysis to measure the parent input function and plasma free fraction (fP). Each animal was scanned at baseline, 15–18 min after 0.047–0.063 mg/kg of the S1PR1 inhibitor ponesimod, 33 min after 0.4–0.8 mg/kg of the S1PR1-specific compound TZ82112, and 167–195 min after 1 ng/kg of the immune stimulus endotoxin. Kinetic analysis with metabolite-corrected input function was performed to estimate the free fraction corrected total distribution volume (VT/fP). Whole-body dosimetry scans were acquired in 2 animals (1M, 1F) with a Biograph Vision PET/CT System, and absorbed radiation dose estimates were calculated with OLINDA.
Results
[18F]TZ4877 exhibited fast kinetics that were described by the reversible 2-tissue compartment model. Baseline [18F]TZ4877 fP was low (< 1%), and [18F]TZ4877 VT/fP values were 233–866 mL/cm3. TZ82112 dose-dependently reduced [18F]TZ4877 VT/fP, while ponesimod and endotoxin exhibited negligible effects on VT/fP, possibly due to scan timing relative to dosing. Dosimetry studies identified the critical organs of gallbladder (0.42 (M) and 0.31 (F) mSv/MBq) for anesthetized nonhuman primate.
Conclusions
[18F]TZ4877 exhibits reversible kinetic properties, but the low fP value limits quantification with this radiotracer. S1PR1 is a compelling PET imaging target, and these data support pursuing alternative F-18 labeled radiotracers for potential future human studies.