bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneity in the immune microenvironment of bone metastasis in driver‐positive non‐small cell lung cancer
Authors: Yang Xiao‐Rong , Pi Can , Zhang Yi‐Chen , Chen Zhi‐Hong , Zhang Xu‐Chao , Zhu Dong‐Qin , Yang Ling‐Ling , Yin Jiani C. , Deng Jia‐Yi , Yang Ming‐Yi , Luo Wei‐Chi , Wu Yi‐Long , Zhou Qing 
Published: April 2023

AbstractMutations in epidermal growth factor receptor and anaplastic lymphoma kinase are common driver events in non‐small cell lung cancer (NSCLC), which are associated with a high frequency of bone metastases (BMs). While the bone marrow represents a specialized immune microenvironment, the immune repertoire of BMs remains unknown. Considering the higher incidence of BMs in driver gene‐positive NSCLCs, and the unique biology of the bone, herein, we assessed the infiltrating immune cells and T cell receptor (TCR) profile of BMs in driver‐positive NSCLCs. Immune profile of BMs in driver gene‐positive NSCLC were assessed in 10 patients, where 6 had driver gene‐positive mutation. TCR and bulk RNA sequencing were performed on malignant bone samples. The diversity and clonality of the TCR repertoire were analyzed. The cellular components were inferred from bulk gene expression profiles computationally by CIBERSORT. Although BMs were generally regarded as immune‐cold tumors, immune cell composition analyses showed co‐existence of cytotoxic and suppressor immune cells in driver‐positive BM samples, as compared to primary lung. Analysis of the TCR repertoire indicated a trend of higher diversity and similar clonality in the driver‐positive compared with the driver‐negative subsets. In addition, we identified two cases that showed the opposite response to immune checkpoint blockade. A comparison of these two patients' BM samples showed more highly amplified clones, fewer M2 macrophages and more activated natural killer cells in the responder. In summary, BMs in NSCLC are heterogeneous in their immune microenvironment, which might be related to differential clinical outcomes to immune checkpoint blockade.
Transcriptomic identification of differentially expressed genes in Levonorgestrel resistant endometrial cancer cell lines
Authors: Dore Molly , Faya Ngonidzashe , Filoche Sara , Henry Claire 
Published: April 2023

AbstractEndometrial cancer (EC) is the most common gynecologic malignancy in the world and incidence is steadily increasing. The Levonorgestrel Intrauterine System (LNG‐IUS) is an alternative conservative treatment for early‐stage EC, however, Levonorgestrel (LNG) resistance occurs for 1 in 3 people. This study aimed to present potential LNG resistance mechanisms and identify differentially expressed genes (DEGs) in EC cell lines. Two LNG resistant cell lines were developed through long term culture in LNG (MFE296R and MFE319R). Whole transcriptome sequencing was carried out on triplicate RNA samples. EdgeR v3.32.1 was used to identify differentially DEGs. Blast2go V6.0 (BioBam software) was used for functional annotation and analysis of genomic datasets. Protein interactions were investigated using the STRING database, including the identification of genes with high levels of interaction (HUB genes). Select DEGs and HUB genes were validated by quantitative real‐time polymerase chain reaction (qRT‐PCR) and Western blot. Fifteen DEGs were identified according to FDR < 0.05 and logFC < 2. Protein analysis identified six HUB genes with a degree of connectivity > 10. Relative mRNA expression of MAOA, MAOB, THRSP, CD80, NDP, LINC01474, DUSP2 and CXCL8 was significantly upregulated in both LNGR cell lines. Relative protein expression of GNAO1 and MAOA were significantly upregulated in both LNGR cell lines. This research identified novel markers of resistance in LNGR cell lines. We discussed potential mechanisms of LNG resistance including dedifferentiation and immunostimulation. The next step for this research is to validate these findings further in both translational and clinical settings.
A systems biology‐based approach to screen key splicing factors in hepatocellular carcinoma
Authors: Zhu Rui , Wang Xue , Yu Qi , Guo Wenna , Zhu Liucun 
Published: April 2023

AbstractA splicing factor is as an important upstream regulator of the alternative splicing process. Hence, it is considered to be a therapeutic target for hepatocellular carcinoma (HCC) tissues. In this study, a systems biology‐based methodology was used to screen the essential splicing factors precisely and efficiently. A more comprehensive set of alternative splicing events, which were linked to patient survival, was constructed by performing the bivariate Cox regression and receiver operating characteristic (ROC) analyses. Then, the expression data was obtained from The Cancer Genome Altas (TCGA) data set and the three Gene Expression Omnibus (GEO) datasets. It was used to obtain the survival‐related splicing factors, which showed a significantly differential expression in the tumor and normal tissues. Using the topological properties of the bipartite graph association network of the alternative splicing events and the splicing factors, we identified the five key splicing factors. Among them, four factors were found to play a prominent role in the development of HCC. The remaining factor was Survival Motor Neuron Domain Containing 1(SMNDC1), which showed a positive correlation with the immune cell infiltration, the biomarkers of immune cells, and the immune checkpoint genes. By performing quantitative real‐time polymerase chain reaction analyses, we proved that SMNDC1 was overexpressed in tumor cells. Following the knockdown of its expression, the proliferation and the migration of HCC cells could be suppressed. These results confirmed that the screening method of this study was reliable and accurate. It provided new insights into the mechanism through which splicing factors elicit tumor development.
An elliptical‐shaped rectangular slot antenna at 2.48 GHz for hyperthermia application
Authors: Khan Azharuddin , Dubey Satya Kesh , Singh Amit K. 
Published: April 2023

AbstractIn this paper, a novel integrated elliptical ringtone antenna has been proposed. The proposed antenna operates in the industrial, scientific and medical band and the overall size of the antenna is 128 × 128 × 1.58 mm3. The antenna provides a valid specific absorption rate input profile and displays better performance at 2.48 GHz. Simulation of the proposed structure was done on FEM‐based high frequency structure simulator 2020R1 software and validated by measured results.
Second‐line treatment of pediatric patients with relapsed rhabdomyosarcoma adapted to initial risk stratification: Data of the European Soft Tissue Sarcoma Registry (SoTiSaR)
Authors: Heinz Amadeus T. , Ebinger Martin , Schönstein Anton , Fuchs Jörg , Timmermann Beate , Seitz Guido , Vokuhl Christian , Münter Marc W. , Pajtler Kristian W. , Stegmaier Sabine , von Kalle Thekla , Kratz Christian P. , Rößler Jochen , Ljungman Gustaf , Klingebiel Thomas , Koscielniak Ewa , Sparber‐Sauer Monika ,   the Cooperative Weichteilsarkom Studiengruppe (CWS)
Published: April 2023

AbstractBackgroundOutcome of relapsed disease of localized rhabdomyosarcoma remains poor. An individual treatment approach considering the initial systemic treatment and risk group was included in the Cooperative Weichteilsarkom Studiengruppe (CWS) Guidance.MethodsSecond‐line chemotherapy (sCHT) ACCTTIVE based on anthracyclines (adriamycin, carboplatin, cyclophosphamide, topotecan, vincristine, etoposide) was recommended for patients with initial low‐ (LR), standard‐ (SR), and high‐risk (HR) group after initial treatment without anthracyclines. TECC (topotecan, etoposide, carboplatin, cyclophosphamide) was recommended after initial anthracycline‐based regimen in the very high‐risk (VHR) group. Data of patients with relapse (n = 68) registered in the European Soft Tissue Sarcoma Registry SoTiSaR (2009–2018) were retrospectively analyzed.ResultsPatients of initial LR (n = 2), SR (n = 16), HR (n = 41), and VHR (n = 9) group relapsed. sCHT consisted of ACCTTIVE (n = 36), TECC (n = 12), or other (n = 15). Resection was performed in 40/68 (59%) patients and/or radiotherapy in 47/68 (69%). Initial risk stratification, pattern/time to relapse, and achievement of second complete remission were significant prognostic factors. Microscopically incomplete resection with additional radiotherapy was not inferior to microscopically complete resection (p = .17). The 5‐year event‐free survival (EFS) and overall survival (OS) were 26% (±12%) and 31% (±14%). The 5‐year OS of patients with relapse of SR, HR, and VHR groups was 80% (±21%), 20% (±16%), and 13% (±23%, p = .008), respectively.ConclusionAdapted systemic treatment of relapsed disease considering the initial risk group and initial treatment is reasonable. New treatment options are needed for patients of initial HR and VHR groups.
Distribution of gestational age at birth by maternal and infant characteristics in U.S. birth certificate data: Informing gestational age assumptions when clinical estimates are not available
Authors: Margulis Andrea V. , Calingaert Brian , Kawai Alison T. , Rivero‐Ferrer Elena , Anthony Mary S. 
Published: April 2023

AbstractPurposeWe aimed to describe the distribution of gestational age at birth (GAB) to inform the estimation of GAB when clinical or obstetric estimates are not available for perinatal pharmacoepidemiology studies.MethodsWe estimated GAB (median, mode, mean, and standard deviation) and percentage born at each gestational week in groups based on plurality and other variables for live births in CDC's U.S. birth data.ResultsIn 2020, 3 617 213 newborns had birth certificates with nonmissing GAB. Among singletons (3 501 693), median and mode GAB were both 39 weeks. Births with lower median GAB were from women with eclampsia (37 weeks) or receiving intensive care (37 weeks); newborns receiving intensive care (37 weeks); newborns with birth weight <2500 g (35 weeks), <1500 g (28 weeks), or <1000 g (25 weeks); and newborns not discharged alive (23 weeks). Among twins (112 633), median GAB was 36 weeks (mode, 37 weeks). Additional noteworthy groups were women with 0–6 prenatal visits (median, 34 weeks) or 7–8 prenatal visits (median, 35 weeks) or aged 15–19 years (median, 35 weeks).ConclusionsSome maternal and infant groups had distinct GAB distributions in the United States. This information can be useful in estimating GAB when individual‐level clinical estimates are not available, such as in database studies of medication use during pregnancy.
Use of CFTR modulators in special populations, part 3: Solid organ transplant
Authors: Kadouh Nour K. , Elijah Joseph , Fitzgerald Linda J. , Phan Hanna 
Published: April 2023

AbstractBackgroundSolid organ transplant (SOT) recipients with cystic fibrosis (CF) may benefit from the pulmonary and extrapulmonary benefits associated with CF transmembrane conductance regulator modulators. Nevertheless, evolution of modulator safety and efficacy data prompts consideration.MethodsThe search terms “transplant” AND “ivacaftor"(IVA) OR "lumacaftor"(LUM) OR "tezacaftor" (TEZ) OR "elexacaftor" (ELX) were utilized to conduct a scoping review of English articles from the period of January 1, 2012 to December 31, 2022. Search results from PubMed and Embase databases were reviewed by title and abstract for relevance. Included studies reported efficacy and safety outcomes of modulators in SOT recipients.ResultsOne hundred thirty‐six patients from one cohort study (90 lung transplant recipients) and eight case reports and series (29 lung transplant recipients, 16 liver transplant recipients and one lung/liver transplant patient) were included. Post‐modulator initiation, 33 patients did not necessitate tacrolimus dose adjustments, 10 required dose uptitration, and 43 required dose reductions. Moreover, LUM/IVA use with azole antifungals may lead to subtherapeutic levels but opposing effects sustained tacrolimus levels. Liver transplant recipients were more likely to experience elevations in transaminases requiring pharmacologic or medical interventions. Majority of patients experienced improvements in pulmonary function, fasting blood glucose, hemoglobin, body mass index, and rhinosinusitis symptoms. However, intolerance or lack of benefit prompted discontinuation of ELX/TEZ/IVA in over 40% of lung‐transplant recipients in one study.ConclusionModulator therapy has been reported to produce pulmonary and extra‐pulmonary benefits in the CF population with SOT. Considerations for modulator therapy initiation ought to include modulator pharmacokinetics, concomitant medications, and transplant type due to the complex nature of SOT recipients.
Spirometry and respiratory oscillometry: Feasibility and concordance in schoolchildren with asthma
Authors: Domínguez‐Martín Clara , Cano Alfredo , Díez‐Monge Nuria , Alonso‐Rubio Ana María , Pérez‐García Isabel , Arroyo‐Romo María Teresa , Casares‐Alonso Irene , Barbero‐Rodríguez Ana María , Grande‐Alvarez Reyes , Martínez‐Rivera María Teresa , Sanz‐Fernández Mónica 
Published: April 2023

AbstractObjectiveThe purpose of this study was to describe the feasibility of respiratory oscillometry (RO) in schoolchildren with asthma, and the concordance of its results with those of spirometry, to determine its clinical usefulness.MethodsRO and spirometry were performed in 154 children (6 to 14‐year‐old) with asthma, following strict quality criteria for the tests. Their feasibility (probability of valid test, time of execution, number of maneuvers needed to achieve a valid test, and perceived difficulty) was compared. The factors that influence feasibility were analyzed with multivariate methods. FEV1, FEV1/FVC, FVC and FEF25‐75 for spirometry, and R5, AX and R5‐19 for RO, were converted into z‐scores and their concordance was investigated through intraclass correlation coefficients (ICC) and kappa indices for normal/abnormal values.ResultsThere were no differences in the probability of obtaining a valid RO or spirometry (83.1% vs. 81.8%, p = 0.868). RO required a lower number of maneuvers [mean (SD) 4.2 (1.8) versus 6.0 (1.6), p < 0.001] and less execution time [5.1 (2.7) versus 7.6 (2.4) minutes, p < 0.001], and patients considered it less difficult. Age increased the probability of obtaining valid RO and spirometry. The concordance of results between RO and spirometry was low, and only between zFEV1 and zAX could it be considered moderate (ICC = 0.412, kappa = 0.427).ConclusionRO and spirometry are feasible in children with asthma. RO has some practical advantages, but the concordance of its results with spirometry is low.
Distributed Quantum Computing with Photons and Atomic Memories
Authors: Oh Eun , Lai Xuanying , Wen Jianming , Du Shengwang 
Published: April 2023

AbstractThe promise of universal quantum computing requires scalable single‐ and inter‐qubit control interactions. Currently, three of the leading candidate platforms for quantum computing are based on superconducting circuits, trapped ions, and neutral atom arrays. However, these systems have strong interaction with environmental and control noises that introduce decoherence of qubit states and gate operations. Alternatively, photons are well decoupled from the environment and have advantages of speed and timing for quantum computing. Photonic systems have already demonstrated capability for solving specific intractable problems like Boson sampling, but face challenges for practically scalable universal quantum computing solutions because it is extremely difficult for a single photon to “talk” to another deterministically. Here, a universal distributed quantum computing scheme based on photons and atomic‐ensemble‐based quantum memories is proposed. Taking the established photonic advantages, two‐qubit nonlinear interaction is mediated by converting photonic qubits into quantum memory states and employing Rydberg blockade for the controlled gate operation. Spatial and temporal scalability of this scheme is demonstrated further. These results show photon‐atom network hybrid approach can be a potential solution to universal distributed quantum computing.
Sex affects immune response capacity against COVID‐19 infection
Authors: Zovi Andrea , Ferrara Francesco , Langella Roberto , Cavallaro Fabiola , Vitiello Antonio 
Published: April 2023

AbstractThe genetic variability of each individual may lead to the identification of completely different genetic polymorphisms which are associated with a different sensitivity to infectious diseases in humans. Such genetic variability allows the immune system to respond differently to viral agents, therefore only a fraction of humans develop severe symptoms, as happened with SARS‐CoV‐2. Such knowledge is critical to enable the development of appropriate pharmacological solutions to prevent the consequences of insufficient immunity in dealing with serious viral diseases such as SARS‐CoV‐2. For instance, global epidemiological data show that male sex is a risk factor for the severe evolution of SARS‐CoV‐2 disease. Men, due to higher production of Testosterone (TLT), are more vulnerable than females. Women, due to greater expression of the TLR7 gene found on the X chromosome, a key innate immunity gene that encodes Toll‐like proteins, are able to synthesise more antiviral proteins and interferons in dendritic cells, resulting in a more robust immune system capable of preventing severe SARS‐CoV‐2 viral disease. This manuscript highlights how human genetic variability can lead to severe infectious symptoms in some individuals who must take appropriate prophylactic actions, such as vaccination, to prevent this.
Landscape features control river's confluences water quality and tributary fish composition
Authors: Bowes Rachel E. , Bergman Eva , Donadi Serena , Greenberg Larry , Sandin Leonard , Lind Lovisa 
Published: April 2023

AbstractRivers networks represent hierarchical dendritic habitats within terrestrial landscapes and differences in connectivity and land use influence dispersal, and consequently biodiversity patterns. We, therefore, measured variation in water chemistry and fish abundance and related these to a number of landscape characteristics (e.g., wetland, urban, wooded, and agricultural) in the River Klarälven and its 30 permanently flowing tributaries. We hypothesized that these environmental attributes would differ between tributary and main stem habitat and that these differences would be driven by landscape attributes including land use. We found considerable intertributary variation in temperature and nutrient levels, and between the tributaries and the main stem. Generally, water temperature was lower in the tributaries, whereas nutrient levels were higher in the tributaries. The lower water temperature has implications for coldwater fishes, and we found two fishes, burbot and lamprey, associated with coldwater tributaries. We also found an inverse relationship between water quality and anthropogenic land use. Protecting tributaries with low anthropogenic impact will likely become increasingly important with ongoing global warming as they can function as thermal refugia for coldwater fishes. Hence, this study underscores the need to evaluate water courses at regional scales to identify spatial refuges and ensure connectivity.
Different Dimensionalities, Morphological Advancements and Engineering of g‐C3N4‐Based Nanomaterials for Energy Conversion and Storage
Authors: Hayat Asif , Sohail Muhammad , El Jery Atef , Al‐Zaydi Khadijah M. , Alshammari Khaled F , Khan Javid , Ali Hamid , Ajmal Zeeshan , Taha T. A. , Ud Din Israf , Altamimi Rashid , Hussein Mahmoud Ali , Al‐Hadeethi Yas , Orooji Yasin , Ansari Mohd Zahid 
Published: April 2023

AbstractGraphitic carbon nitride (g‐C3N4) has gained tremendous interest in the sector of power transformation and retention, because of its distinctive stacked composition, adjustable electronic structure, metal‐free feature, superior thermodynamic durability, and simple availability. Furthermore, the restricted illumination and extensive recombination of photoexcitation electrons have inhibited the photocatalytic performance of pure g‐C3N4. The dimensions of g‐C3N4 may impact the field of electronics confinement; as a consequence, g‐C3N4 with varying dimensions shows unique features, making it appropriate for a number of fascinating uses. Even if there are several evaluations emphasizing on the fabrication methods and deployments of g‐C3N4, there is certainly an insufficiency of a full overview, that exhaustively depicts the synthesis and composition of diverse aspects of g‐C3N4. Consequently, from the standpoint of numerical simulations and experimentation, several legitimate methodologies were employed to deliberately develop the photocatalyst and improve the optimal result, including elements loading, defects designing, morphological adjustment, and semiconductors interfacing. Herein, this evaluation initially discusses different dimensions, the physicochemical features, modifications and interfaces design development of g‐C3N4. Emphasis is given to the practical design and development of g‐C3N4 for the various power transformation and inventory applications, such as photocatalytic H2 evolution, photoreduction of CO2 source, electrocatalytic H2 evolution, O2 evolution, O2 reduction, alkali‐metal battery cells, lithium‐ion batteries, lithium–sulfur batteries, and metal‐air batteries. Ultimately, the current challenges and potential of g‐C3N4 for fuel transformation and retention activities are explored.
“Simple Tidy GeneCoEx”: A gene co‐expression analysis workflow powered by tidyverse and graph‐based clustering in R
Authors: Li Chenxin , Deans Natalie C. , Buell C. Robin 
Published: April 2023

AbstractGene co‐expression analysis is an effective method to detect groups (or modules) of co‐expressed genes that display similar expression patterns, which may function in the same biological processes. Here, we present “Simple Tidy GeneCoEx”, a gene co‐expression analysis workflow written in the R programming language. The workflow is highly customizable across multiple stages of the pipeline including gene selection, edge selection, clustering resolution, and data visualization. Powered by the tidyverse package ecosystem and network analysis functions provided by the igraph package, the workflow detects gene co‐expression modules whose members are highly interconnected. Step‐by‐step instructions with two use case examples as well as source code are available athttps://github.com/cxli233/SimpleTidy_GeneCoEx.
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding
Authors: Song Lin , Endelman Jeffrey B. 
Published: April 2023

AbstractAt present, the potato (Solanum tuberosum L.) of international commerce is autotetraploid, and the complexity of this genetic system creates limitations for breeding. Diploid potato breeding has long been used for population improvement, and because of an improved understanding of the genetics of gametophytic self‐incompatibility, there is now sustained interest in the development of uniform F1 hybrid varieties based on inbred parents. We report here on the use of haplotype and quantitative trait locus (QTL) analysis in a modified backcrossing (BC) scheme, using primary dihaploids of S. tuberosum as the recurrent parental background. In Cycle 1, we selected XD3‐36, a self‐fertile F2 individual homozygous for the self‐compatibility gene Sli (S‐locus inhibitor). Signatures of gametic and zygotic selection were observed at multiple loci in the F2 generation, including Sli. In the BC1 cycle, an F1 population derived from XD3‐36 showed a bimodal response for vine maturity, which led to the identification of late versus early alleles in XD3‐36 for the gene CDF1 (Cycling DOF Factor 1). Greenhouse phenotypes and haplotype analysis were used to select a vigorous and self‐fertile F2 individual with 43% homozygosity, including for Sli and the early‐maturing allele CDF1.3. Partially inbred lines from the BC1 and BC2 cycles have been used to initiate new cycles of selection, with the goal of reaching higher homozygosity while maintaining plant vigor, fertility, and yield.