bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models
Authors: Brockman Qierra R. , Scherer Amanda , McGivney Gavin R. , Gutierrez Wade R. , Rytlewski Jeffrey , Sheehan Alexa , Warrier Akshaya , Laverty Emily A. , Roughton Grace , Carnevale Nina C. , Knepper-Adrian Vickie , Dodd Rebecca D. 
Published: September 2023

AbstractCRISPR/Cas9 gene editing has evolved from a simple laboratory tool to a powerful method of in vivo genomic engineering. As the applications of CRISPR/Cas9 technology have grown, the need to characterize the breadth and depth of indels generated by editing has expanded. Traditionally, investigators use one of several publicly-available platforms to determine CRISPR/Cas9-induced indels in an edited sample. However, to our knowledge, there has not been a cross-platform comparison of available indel analysis software in samples generated from somatic in vivo mouse models. Our group has pioneered using CRISPR/Cas9 to generate somatic primary mouse models of malignant peripheral nerve sheath tumors (MPNSTs) through genetic editing of Nf1. Here, we used sequencing data from the in vivo editing of the Nf1 gene in our CRISPR/Cas9 tumorigenesis model to directly compare results across four different software platforms. By analyzing the same genetic target across a wide panel of cell lines with the same sequence file, we are able to draw systematic conclusions about the differences in these software programs for analysis of in vivo-generated indels. Surprisingly, we report high variability in the reported number, size, and frequency of indels across each software platform. These data highlight the importance of selecting indel analysis platforms specific to the context that the gene editing approach is being applied. Taken together, this analysis shows that different software platforms can report widely divergent indel data from the same sample, particularly if larger indels are present, which are common in somatic, in vivo CRISPR/Cas9 tumor models.
Predictors of lower exercise capacity in patients with cancer
Authors: Evertz Ruben , Diehl Christine , Gödde Katharina , Valentova Miroslava , Garfias-Veitl Tania , Overbeck Tobias R. , Braulke Friederike , Lena Alessia , Hadzibegovic Sara , Bleckmann Annalen , Keller Ulrich , Landmesser Ulf , König Alexander O. , Hasenfuss Gerd , Schuster Andreas , Anker Markus S. , von Haehling Stephan 
Published: September 2023

AbstractMaintaining cancer patients’ exercise capacity and therefore patients’ ability to live a self-determined life is of huge importance, but little is known about major determinants. We sought to identify determinants of exercise capacity in patients with a broad spectrum of cancer types, who were already receiving cancer treatment or about to commence such therapy. Exercise capacity was assessed in 253 consecutive patients mostly suffering from advanced cancer using the 6-min walk test (6-MWT). All patients underwent echocardiography, physical examination, resting electrocardiogram, hand grip strength (HGS) measurement, and laboratory assessments. Patients were divided into two groups according to the median distance in the 6-MWT (459 m). Patients with lower exercise capacity were older, had significantly lower HGS and haemoglobin and higher values of high sensitive (hs) Troponin T and NT-proBNP (all p < 0.05). Whilst the co-morbidity burden was significantly higher in this group, no differences were detected for sex, body mass index, tumor type, or cachexia (all p > 0.2). Using multivariable logistic regression, we found that the presence of anaemia (odds ratio (OR) 6.172, 95% confidence interval (CI) 1.401–27.201, p = 0.016) as well as an increase in hs Troponin T (OR 3.077, 95% CI 1.202–5.301, p = 0.019) remained independent predictors of impaired exercise capacity. Increasing HGS was associated with a reduced risk of a lower exercise capacity (OR 0.896, 95% CI 0.813–0.987, p = 0.026). Screening patients for elevated hs troponin levels as well as reduced HGS may help to identify patients at risk of lower exercise capacity during cancer treatment.
Numerical treatment and global error estimation for thermal electro-osmosis effect on non-Newtonian nanofluid flow with time periodic variations
Authors: Ahmed O. S. , Eldabe N. T. , Abou-zeid M. Y. , El-kalaawy O. H. , Moawad S. M. 
Published: September 2023

AbstractThe essential purpose of this study is to discuss the impact of time-periodic variations on mixed convection heat transfer for MHD Eyring-Powell nanofluid. The fluid flows through a non-Darcy porous medium over an infinite vertical plate. The effects of viscous dissipation, Ohmic dissipation, electro-osmosis force, heat source, thermal radiation, Dufour feature, and chemical reaction are presumed. The system of partial differential equations which governs the problem is transformed into a system of non-linear algebraic equations and then an explicit finite difference approach is espoused to solve these nonlinear algebraic equations. The numerical results for the velocity, temperature, and nanoparticles concentration distributions are computed and displayed through a set of graphs. Also, the skin friction coefficient, reduced Nusselt number, and Sherwood number are computed numerically for various values of the physical parameters. It is found that the velocity becomes greater with an elevation in the value of the Helmholtz–Smoluchowski velocity. Meanwhile, it enlarges with rising in the value of the electro-osmotic parameter. The rise in the value of the thermal radiation parameter causes a dwindling influence on both temperature and nanoparticles concentration. Investigations of these effects together are very useful due to their important vital applications in various scientific fields, especially in medicine and medical industries, such as endoscopes, respirators, and diverse medical implementations, as nanoparticles can be utilized in the remedy of cancer tumors. Additionally, electroosmotic flow is important due to its ability to control fluid movement and enhance mass transport, making it valuable in various application such as sample separation, drug delivery, and DNA analysis, offering enhanced efficiency and sensitivity.
Bubble-enhanced basanite–tephrite mixing in the early stages of the Cumbre Vieja 2021 eruption, La Palma, Canary Islands
Authors: González-García Diego , Boulesteix Thomas , Klügel Andreas , Holtz François 
Published: September 2023

AbstractSyneruptive magma mixing is widespread in volcanic eruptions, affecting explosivity and composition of products, but its evidence in basaltic systems is usually cryptic. Here we report direct evidence of mixing between basanitic and tephritic magmas in the first days of the 2021 Tajogaite eruption of Cumbre Vieja, La Palma. Groundmass glass in tephritic tephra from the fifth day of the eruption is locally inhomogeneous, showing micron-scale filamentary structures of Si-poor and Fe-, Mg-rich melt, forming complex filaments attached to bubbles. Their compositional distribution attests the presence of primitive basanitic magma, with compositions similar to late-erupted melts, interacting with an evolved tephritic melt during the first week of the event. From filament morphology, we suggest their generation by dragging and folding of basanitic melt during bubble migration through melt interfaces. Semi-quantitative diffusion modelling indicates that the filamentary structures are short-lived, dissipating in timescales of tens of seconds. In combination with thermobarometric constraints, we suggest a mixing onset by sub-Moho remobilization of a tephritic reservoir by basanite input, followed by turbulent ascent of a mingled magma. In the shallow conduit or lava fountain, bubble nucleation and migration triggered further mingling of the distinct melt-phases. This phenomenon might have enhanced the explosive behaviour of the eruption in such period, where violent strombolian explosions were common.
Optical phase retrieving of a projected object by employing a differentiation of a single pattern of two-beam interference
Authors: Ramadan W. A. , El-Tawargy A. S. , Wahba H. H. 
Published: September 2023

AbstractIn this work, we present a new approach to retrieve the optical phase map of an object which is projected by a single differentiated two-beam interference pattern. This approach is based on the differentiation of the intensity equation of the two-beam interference with respect to the carrier’s phase angle. Therefore, two interference patterns which are shifted by a very small phase angle can be obtained. Then, these two patterns are projected on the object. By exploiting the definition of the mathematical differentiation, the optical phase object’s variations are retrieved from the recorded intensity distributions of both projected patterns. According to this method, the extracted optical phase angles are raised as an inverse “sin” function. This means that the unwrapping process of this function limits the recovered phase angles between − π/2 and π/2. So, the unwrapping process of these unusual wrapped phase angles is explained. The proposed method is applied on (a) two objects which are simulated by combinations of multiple Gaussian functions and (b) a 3D real object. It is found that the inclination of the projected interference pattern on the object redistributes the intensity distribution due to the Lamber’s “cos” aw of illumination. This effect is considered in the retrieving process of the object’s phase map. The limitations of the presented method are discussed and the obtained results are found promising.
Nanomaterial accumulation in boiling brines enhances epithermal bonanzas
Authors: Cano Néstor , González-Jiménez José M. , Camprubí Antoni , Domínguez-Carretero Diego , González-Partida Eduardo , Proenza Joaquín A. 
Published: September 2023

AbstractEpithermal bonanza-type ores, characterized by weight-percent contents of e.g., gold and silver in a few mm to cm, are generated by mixtures of magmatic-derived hydrothermal brines and external fluids (e.g., meteoric) that transport a variety of metals to the site of deposition. However, the low solubilities of precious metals in hydrothermal fluids cannot justify the high concentrations necessary to produce such type of hyper-enriched metal ore. Here we show that boiling metal-bearing brines can produce, aggregate, and accumulate metal nanomaterials, ultimately leading to focused gold + silver ± copper over-enrichments. We found direct nano-scale evidence of nanoparticulate gold- and/or silver-bearing ores formed via nonclassical growth (i.e., nanomaterial attachment) during boiling in an intermediate-sulfidation epithermal bonanza. The documented processes may explain the generation of bonanzas in metal-rich brines from a range of mineral deposit types.
Efficient symptomatic treatment and viral load reduction for children with influenza virus infection by nasal-spraying Bacillus spore probiotics
Authors: Tran Tu Thanh , Phung Thuy Thi Bich , Tran Dien Minh , Bui Huyen Thi , Nguyen Phuc Thanh Thi , Vu Tam Thi , Ngo Nga Thi Phuong , Nguyen Mai Thi , Nguyen Anh Hoa , Nguyen Anh Thi Van 
Published: September 2023

AbstractInfluenza virus is a main cause of acute respiratory tract infections (ARTIs) in children. This is the first double-blind, randomized, and controlled clinical trial examining the efficacy of nasal-spraying probiotic LiveSpo Navax, which contains 5 billion of Bacillus subtilis and B. clausii spores in 5 mL, in supporting treatment of influenza viral infection in pediatric patients. We found that the nasal-spraying Bacillus spores significantly shortened the recovery period and overall treatment by 2 days and increased treatment effectiveness by 58% in resolving all ARTIs’ symptoms. At day 2, the concentrations of influenza virus and co-infected bacteria were reduced by 417 and 1152 folds. Additionally, the levels of pro-inflammatory cytokines IL-8, TNF-α, and IL-6 in nasopharyngeal samples were reduced by 1.1, 3.7, and 53.9 folds, respectively. Compared to the standard control group, treatment regimen with LiveSpo Navax demonstrated significantly greater effectiveness, resulting in 26-fold reduction in viral load, 65-fold reduction in bacterial concentration, and 1.1–9.5-fold decrease in cytokine levels. Overall, nasal-spraying Bacillus spores can support the symptomatic treatment of influenza virus-induced ARTIs quickly, efficiently and could be used as a cost-effective supportive treatment for respiratory viral infection in general.Clinical trial registration no: NCT05378022 on 17/05/2022.
Clinical characteristics and cytokine profiles of adult obese asthma with type2 inflammation
Authors: To Masako , Arimoto Yoshihito , Honda Natsue , Kurosawa Yusuke , Haruki Kosuke , To Yasuo 
Published: September 2023

AbstractObesity-related non-eosinophilic asthma has been identified as a phenotype of asthma. However, mepolizumab and omalizumab improve asthma control in severe asthma with obesity, implying that type-2 cytokines may be involved in the deterioration of control in obese asthma. Despite this, the clinical details of obese asthma with positive type-2 inflammation markers have not yet been reported. The objective of this study was to investigate the clinical characteristics of patients with obese asthma with positive type-2 inflammation markers. Adult obese asthmatic patients were enrolled and were classified into two groups: obese asthma with positive type-2 inflammation markers (T2) and obese asthma with negative type-2 inflammation markers (NT2), then data were compared. In total, 434 patients were enrolled (85% of patients were at GINA therapy step 4–5). The T2 group had a higher proportion of patients with persistent asthma since childhood and with allergic rhinitis. A higher percentage of patients used high-dose inhaled corticosteroids (ICS) and experienced acute exacerbations (annual exacerbation ratio ≥ 1) in the T2 group. Multivariate logistic regression analysis showed that the T2 group was independently associated with younger age, comorbidity of allergic rhinitis, persistent asthma since childhood, use of high-dose ICS, and acute exacerbation rate ≥ 1. Adipocytokine levels were similar between the groups. Collectively, obese asthma with positive type-2 inflammation markers is characterised by a higher percentage of persistent asthma since childhood and more severe asthma.
Learning hyperparameter predictors for similarity-based multidisciplinary topology optimization
Authors: Bujny Mariusz , Yousaf Muhammad Salman , Zurbrugg Nathan , Detwiler Duane , Menzel Stefan , Ramnath Satchit , Rios Thiago , Duddeck Fabian 
Published: September 2023

AbstractTopology optimization (TO) plays a significant role in industry by providing engineers with optimal material distributions based exclusively on the information about the design space and loading conditions. Such approaches are especially important for current multidisciplinary design tasks in industry, where the conflicting criteria often lead to very unintuitive solutions. Despite the progress in integrating manufacturing constraints into TO, one of the main factors restricting the use of TO in practice is the users’ limited control of the final material distribution. To address this problem, recently, a universal methodology for enforcing similarity to reference structures in various TO methods by applying scaling of elemental energies was proposed. The method, however, requires an expensive hyperparameter sampling, which involves running multiple TO processes to find the design of a given similarity to a reference structure. In this article, we propose a novel end-to-end approach for similarity-based TO, which integrates a machine learning model to predict the hyperparameters of the method, and provide the engineer, at minimal computational cost, with a design satisfying multidisciplinary criteria expressed by the similarity to a reference. The training set for the model is generated based on an academic linear elastic problem, but the model generalizes well to both nonlinear dynamic crash and industrial-scale TO problems. We show the latter by applying the proposed methodology to a real-world multidisciplinary TO problem of a car hood frame, which demonstrates the usefulness of the approach in industrial settings.
Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn’s disease
Authors: Yeo Soyoung , Park Hyunjoon , Kim Heebal , Ryu Chang Beom , Huh Chul Sung 
Published: September 2023

AbstractThe human gut microbiota is a complex ecology comprising approximately 10 to 100 trillion microbial cells. Most of the bacteria detected by 16s rRNA sequencing have yet to be cultured, but intensive attempts to isolate the novel bacteria have improved our knowledge of the gut microbiome composition and its roles within human host. In our culturomics study, a novel gram-negative, motile, obligately anaerobic, rod-shaped bacteria, designated as strain ICN-92133T, was isolated from a fecal sample of a 26-year-old patient with Crohn’s disease. Based on the 16s rRNA sequence of strain ICN-92133T, the phylogeny analysis placed the strain into the family Selenomonadaceae, showing 93.91% similarity with the closely related Massilibacillus massiliensis strain DSM 102838T. Strain ICN-92133T exhibited a genome size of 2,679,003 bp with a GC content of 35.5% which was predicted to contain 26 potential virulence factors and five antimicrobial resistance genes. In comparative genomic analysis, strain ICN-92133T showed digital DNA–DNA Hybridization and OrthoANI values lower than 21.9% and 71.9% with the closest type strains, respectively. In addition, comparing phenotypic, biochemical, and cellular fatty acids with those of closely related strains revealed the distinctiveness of strain ICN-92133T. Based on the taxonogenomic results, strain ICN-92133T is proposed as a novel species belonging to a new genus. Therefore, we suggest the name of the new genus Selenobaculum gen. nov. within the family Selenomonadaceae and strain ICN-92133T (= KCTC 25622T = JCM 36070T) as a type strain of new species Selenobaculum gbiensis sp. nov.
CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions
Authors: Suzuki Maya , Sakai Satoshi , Ota Kosuke , Bando Yuki , Uchida Chiharu , Niida Hiroyuki , Kitagawa Masatoshi , Ohhata Tatsuya 
Published: September 2023

AbstractPairs of sense and antisense transcriptions that are adjacent at their 5′ and 3′ regions are called divergent and convergent transcription, respectively. However, the structural properties of divergent/convergent transcription in different species or RNA biotypes are poorly characterized. Here, we developed CCIVR2, a program that facilitates identification of both overlapping and non-overlapping antisense transcripts produced from divergent/convergent transcription whose transcription start sites (TSS) or transcript end sites (TES) are located within a specified region. We used CCIVR2 to analyze antisense transcripts starting around the sense TSS (from divergent transcription) or ending around the sense TES (from convergent transcription) in 11 different species and found species- and RNA biotype-specific features of divergent/convergent transcription. Furthermore, we confirmed that CCIVR2 enables the identification of multiple sense/antisense transcript pairs from divergent transcription, including those with known functions in processes such as embryonic stem cell differentiation and TGFβ stimulation. CCIVR2 is therefore a valuable bioinformatics tool that facilitates the characterization of divergent/convergent transcription in different species and aids the identification of functional sense/antisense transcript pairs from divergent transcription in specified biological processes.
Computationally-efficient statistical design and yield optimization of resonator-based notch filters using feature-based surrogates
Authors: Koziel Slawomir , Haq Tanveerul 
Published: September 2023

AbstractModern microwave devices are designed to fulfill stringent requirements pertaining to electrical performance, which requires, among others, a meticulous tuning of their geometry parameters. When moving up in frequency, physical dimensions of passive microwave circuits become smaller, making the system performance increasingly susceptible to manufacturing tolerances. In particular, inherent inaccuracy of fabrication processes affect the fundamental operating parameters, such as center frequency or bandwidth, which is especially troublesome for narrow-band structures, including notch filters. The ability to quantify the effects of tolerances, and—even more—to account for these in the design process, are instrumental in making the designs more reliable, and to increase the likelihood that adequate operation is ensured despite manufacturing errors. This paper proposes a simple yet computationally efficient and reliable procedure for statistical analysis and yield optimization of resonator-based notch filters. Our methodology involves feature-based surrogate models that can be established using a handful of training data points, and employed for rapid evaluation of the circuit fabrication yield. Furthermore, a yield optimization procedure is developed, which iteratively sets up a sequence of feature-based models, constructed within local domains relocated along the optimization path, and uses them as predictors to find a robust (maximum yield) design at a low computational cost. The presented approach has been demonstrated using two complementary split ring resonator (CSRR)-based notch filters. The cost of statistical design is about a hundred of EM simulations of the respective filter, with yield evaluation reliability corroborated through EM-based Monte Carlo analysis.
Predictors of galcanezumab response in a real-world study of Korean patients with migraine
Authors: Kim Seung Ae , Jang Hyemin , Lee Mi Ji 
Published: September 2023

AbstractTo assess factors associated with galcanezumab response in a real-world study of Korean patients with migraine. Predictors of the efficacy of monoclonal antibodies targeting calcitonin gene-related peptide (CGRP) or its receptor (anti-CGRP(-R) mAb) have been rarely investigated in Asians. We prospectively recruited and followed up patients with migraine who received monthly galcanezumab treatment in a single university hospital from June 2020 to October 2021. We defined the treatment response with ≥ 50% reduction in moderate/severe headache days in the 3rd month of treatment compared to baseline. Responders and non-responders were compared in terms of demographics, disease characteristics and severity, and previous response to migraine prophylactic treatments. Potential predictors of anti-CGRP(-R) mAb response were tested by using the univariable and multivariable logistic regression analyses. Among 104 patients (81.7% female; mean age 42.0 ± 13.02; 76.9% chronic migraine; and 45.5% medication overuse headache) included, 58 (55.7%) were responders. Non-responders had more chronic migraine, medication overuse headache, monthly headache days, days with acute medication, and daily headaches (i.e. chronic migraine persisting everyday without remission). The multivariable logistic analysis showed chronic migraine (OR 0.05 [95% CI 0.00–0.82], p = 0.036) and the number of previously failed preventive medication classes (OR 0.55 [95% CI 0.33–0.92], p = 0.024] were independently associated with treatment response. Chronic migraine and multiple failures from preventive medication are associated with poor galcanezumab response. Further studies are needed to investigate if earlier treatment before disease chronification or multiple failures may lead to a greater therapeutic gain from anti-CGRP(-R) mAb treatment.