bluuebunny/crossref_metadata_2025_split huggingface dataset:
Properties of interconnected negative imaginary systems and extension to formation‐containment control of networked multi‐UAV systems with experimental validation results
Authors: Su Yu‐Hsiang , Bhowmick Parijat , Lanzon Alexander 
Published: December 2023

AbstractThis paper extends the properties of a positive feedback interconnection of two negative imaginary (NI) systems to multi‐agent NI systems and proposes a new formation‐containment control methodology relying on the characteristic loci technique. Inspired by recent applications of NI and passivity‐based control techniques in the multi‐agent systems (MAS) domain, a new formation‐tracking and containment control scheme is developed for a class of networked multi‐UAV systems. The proposed scheme offers a two‐stage and two‐loop control configuration where the inner loop uses a cascaded PID controller to ensure stable hovering of the UAVs, and the outer loop deploys a distributed “mixed” SNI and strictly passive controller to achieve the formation‐containment objectives. This scheme works with a dynamic output feedback control strategy; hence, it offers advantages when the full‐state measurement is not possible. In contrast to the well‐known Lyapunov theory‐based cooperative control schemes, the present one exploits the characteristic loci technique to prove the formation‐tracking and containment phenomena theoretically. The paper also provides experimental validation results on a fleet of Crazyflie 2.1 nano quadcopters.
The energy landscape of the ribosome
Authors: Byju Sandra , Hassan Asem , Whitford Paul C. 
Published: December 2023

AbstractThe ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large‐scale (10–100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
The genomic and immune landscapes of gastric cancer and their correlations with HER2 amplification and PD‐L1 expression
Authors: Jing Xiaoqian , Luo Zhiping , Wu Jiayan , Ye Feng , Li Jianfang , Song Zijia , Zhang Yaqi , Shi Minmin , Sun Huaibo , Fang Yi , Jiang Yimei , Ji Xiaopin 
Published: December 2023

AbstractBackgroundAnti‐PD1/PD‐L1 antibody plus human epidermal growth factor receptor 2 (HER2) antibody and chemotherapy have become the new first‐line therapy for HER2 overexpression‐positive advanced gastric cancers (GC), suggesting that HER2 and PD‐L1 play a vital role in guiding systemic treatment for patients with GC. This study aimed to depict the genomic and immune landscapes of Chinese patients with GC and investigate their correlations with HER2 amplification and PD‐L1 expression.Patients and MethodsNext‐generation targeted sequencing and PD‐L1 immunohistochemistry were performed on tumor samples from 735 patients with pathologically diagnosed GC. The genomic and immune landscapes and their correlations with HER2 amplification and PD‐L1 expression were analyzed.ResultsThe most commonly mutated genes in Chinese GC were TP53 (64%), CDH1 (20%), ARID1A (18%), HMCN1 (15%), KMT2D (11%), and PIK3CA (11%). Seventy‐six (10%) patients were HER2 amplification, and 291 (40%) had positive PD‐L1 expression. Classifying the total population based on HER2 amplification and PD‐L1 expression level, 735 patients were divided into four subgroups: HER2+/PD‐L1+ (4.5%), HER2+/PD‐L1− (5.9%), HER2−/PD‐L1+ (35.1%), and HER2−/PD‐L1− (54.5%). The HER2+/PD‐L1− and HER2+/PD‐L1+ subgroups exhibited dramatically higher rate of TP53 mutations, CCNE1 and VEGF amplifications. The HER2+/PD‐L1− subgroup also had a markedly higher rate of MYC amplification and KRAS mutations. The HER2−/PD‐L1+ subgroup had significantly higher rate of PIK3CA mutations. HER2+/PD‐L1− subgroup had the highest TMB level and HER2−/PD‐L1+ subgroup had the highest proportion of patients with microsatellite instability‐high than other subgroups. Furthermore, we observed that different HER2 amplification levels had distinct impacts on the correlations between PD‐L1 expression and therapeutic genomic alterations, but no impact on the prognosis.ConclusionThe combination of HER2 amplification and PD‐L1 expression in Chinese patients with GC could stratify the total populations into several subgroups with distinctive genomic and immune landscapes, which should be considered when making personalized treatment decisions.
Vesicovaginal fistula associated with massive bladder calculi: An urogynecological case report
Authors: Sharma Muna , Karn Mitesh , Adhikari Hritika , Basnet Binita , Bhattarai Ishuvi , Chapagain Sachita , Pandit Chandika 
Published: December 2023

Key Clinical MessageIn developing countries, VVF mainly occurs due to obstructed labor unlike developed countries where common causes are radiotherapy and malignancy. Due to social taboos, patients do not seek medical attention for problems like urinary incontinence and dysuria, thus presenting very late.
Navigating through Complexity: Optimizing Cathodes for Organic Electrohydrogenation through Coherent Workflows
Authors: Kräenbring Mena‐Alexander , Wickert Leon , Hansen Meinert , Sanden Sebastian , Pellumbi Kevinjeorjios , Wolf Jonas , Siegmund Daniel , Özcan Fatih , Apfel Ulf‐Peter , Segets Doris 
Published: December 2023

AbstractElectrochemical hydrogenation reactions offer a green and sustainable production pathway for both bulk and fine chemicals employed in the modern chemical industry. However, optimizing such systems can be tremendously challenging due to the number of variables that potentially influence the overall performance. The tailored and scalable electrode fabrication via catalytic inks can be especially difficult due to the complex interplay of material and process variables during the formulation of the inks and their deposition on suitable substrates. As a result, the significance of each variable must be systematically investigated to reveal the high‐impact and low‐impact variables, enabling rapid progression towards finding optimal conditions and parameters. In this work, we present an adaptable, coherent workflow to proficiently optimize electrode fabrication for electrochemical hydrogenation reactions with well‐adjustable experimental effort. Using the hydrogenation of phenylacetylene as a model reaction in a scalable zero‐gap reactor, we demonstrate the influence of deposition techniques, substrates, and catalyst loadings as well as the interactions of binders and additives on the electrochemical performance. Future works can greatly benefit from this coherent workflow as it enables direct comparability between datasets and functional, multidimensional optimization, hastening the rate at which new material systems are understood, reach maturity, and become industrially relevant.
Conformations and Rearrangements of Collinolactone – Experiments and Theory on a Dynamic Cyclodecatriene
Authors: Decker Rhena L. , Schray David , Pfeffer Heiko I. , Grond Stephanie , Wagner J. Philipp 
Published: December 2023

AbstractCollinolactone A is a microbial specialized metabolite with a unique 6‐10‐7 tricyclic bislactone skeleton which was isolated from Streptomyces bacteria. The unusual cyclodecatriene motif features dynamic interconversions of two rotamers. Given the biological profiling of collinolactone A as neuroprotective agent, semisynthetic modifications represent an invaluable strategy to enhance its efficacy. Since understanding conformations and reactions of bioactive substances is crucial for rational structure‐based design and synthesis of derivatives, we conducted computational studies on conformational behavior as well as experiments on thermal and acid induced rearrangements of the cyclodecatriene. Experimental conformer ratios of collinolactone A and its biosynthetic ketolactone precursor are well reproduced by computations at the PW6B95‐D3/def2‐QZVPP//r2SCAN‐3c level. Upon heating collinolactone A in anhydrous dioxane at 100 °C, three collinolactone B stereoisomers exhibiting enollactone structures form via Cope rearrangements. Our computations predict the energetic preference for a boat‐like transition state in agreement with the stereochemical outcome of the main reaction pathway. Constriction of the ten‐membered ring forms collinolactone C with four annulated rings and an exocyclic double bond. Computations and semisynthetic experiments demonstrate strong preference for an acid‐catalyzed reaction pathway over an alternative Alder‐ene route to collinolactone C with a prohibitive reaction barrier, again in line with stereochemical observations.
Efficacy of Cobas HPV testing for predicting grade 2+ cervical intraepithelial neoplasia in a cancer prevention center and a gynecologic oncology clinic: A single‐institution experience
Authors: Davaro Elizabeth , Tinnirello Agata A. , Bevers Therese B. , Milbourne Andrea , Bassett Roland , Stewart John , Guo Ming 
Published: December 2023

AbstractBackgroundTo evaluate the efficacy of Cobas human papillomavirus (HPV) testing to predict cervical intraepithelial neoplasia of grade 2 or higher (CIN2+), Cobas HPV testing results were correlated with follow‐up biopsy in patients from Cancer Prevention Center (CPC) and Gynecologic Oncology Clinic (GOC) of The University of Texas MD Anderson Cancer Center.MethodsInstitutional data for patients who underwent Cobas HPV and Papanicolaou (Pap) cytology cotesting from 2019 to 2020 were retrospectively reviewed. Surgical follow‐up results were compared with Cobas HPV testing results in two populations.ResultsA total of 2226 patients, including 921 women (mean age, 55.2 years) seen at the CPC and 1305 women (mean age, 49.3 years) seen at the GOC, were included. Specimens from GOC patients had a significantly higher HPV positivity rate than did those from CPC patients (22.9% vs. 10.1%; p < .001). Cobas HPV testing was positive in all seven CPC patients with surgical follow‐up results showing CIN2+. Among 36 GOC patients with CIN2+ lesions, five patients had HPV−/Pap+ testing results. Although only seven CPC patients had CIN2+, Cobas HPV testing showed 100% sensitivity for predicting CIN2+ in this group. Sensitivity for CIN2+ was 86.5% in the GOC group, whereas 13.9% of GOC patients with CIN2+ had negative HPV testing results.ConclusionsCobas HPV testing was highly efficacious for predicting CIN2+ lesions in the low‐risk CPC population, which supports HPV primary screening for cervical cancer in low‐risk populations. For high‐risk patients, especially those with a history of CIN2+/cervical cancer, HPV/Pap cotesting may still be necessary to maintain a high clinical sensitivity for CIN2+.
Enabling the execution of HPC applications on public clouds with HPC@Cloud toolkit
Authors: Munhoz Vanderlei , Castro Márcio 
Published: December 2023

AbstractThe advent of cloud computing has made access to computing infrastructure available to millions of users that face resource constraints. In the context of high performance computing (HPC), public cloud resources have emerged as a cost‐effective alternative to expensive on‐premises clusters. However, there are several challenges and limitations in adopting this approach. This paper proposes HPC@Cloud , a provider‐agnostic open‐source software toolkit that facilitates the migration, testing, and execution of HPC applications in public clouds. The toolkit takes advantage of various fault tolerance technologies to enable the use of inexpensive transient cloud infrastructure, commonly known as “spot” instances. Also, it features integration with singularity containers, allowing users to run complex applications on virtual HPC clusters in a portable and reproducible way. Finally, it provides a data‐based empirical approach to estimating cloud infrastructure costs for HPC workloads. The results obtained on two public cloud providers (AWS and Vultr) show that: (i) HPC@Cloud can efficiently build virtual HPC clusters on the cloud; (ii) the new adaptive fault tolerance strategy outperforms other existing strategies based on blocking restoration; (iii) the integration of singularity containers into HPC@Cloud improves the portability of HPC applications to public clouds with negligible performance penalty to the applications; (iv) the proposed cost prediction approach can estimate the cost of running the applications on AWS and Vultr with up to 93% accuracy on average.
Understanding and improving resistance to Hessian fly (Mayetiola destructor) in US wheat using genetic mapping and molecular techniques
Authors: Melson Ellen E. , Ibrahim Amir M. H. , Drake David R. 
Published: December 2023

AbstractHessian fly (Mayetiola destructor) is a worldwide pest of wheat (Triticum spp.) causing significant yield losses. Utilizing resistant varieties of wheat is the most effective method of control, particularly in mild climates. The effectiveness of resistance genes is lost over time due to genetic diversity within fly populations, and most cultivars have only one resistance gene making them vulnerable to this loss of resistance. Thirty‐seven resistance genes have been mapped along with four Hessian fly response genes and 11 novel quantitative trait loci (QTL). The majority of these exhibit antibiotic resistance, but new research suggests two or more novel QTL are associated with a valuable tolerant response. Studies suggest that fitness costs associated with resistance can be overcome after the initial infestation, but this may not hold true with repeated fly attacks and should be considered when pyramiding genes. Several of these genes do show temperature sensitivity, which should also be considered during breeding. Resistance mechanisms include increased levels of salicylic acid, upregulation of oxo‐phytodienoic acid reductase genes and genes responsible for lipid and protein mobilization, and increased synthesis of polyphenols, among others. These mechanisms are part of an effector‐triggered response. Resistant genes and QTL with KASP markers for use in creating gene pyramids include QHf.hwwg‐6BS, Qhara.icd‐6B, h4, H7, H32, H33, H34, H35, and H36. GWAS has been used to screen large numbers of elite breeding lines for resistance to Hessian fly. Marker trait associations discovered through GWAS can potentially be used in creating gene pyramids with multiple pest and pathogen resistance genes.
Borohydride Ionic Liquids as Reductants of CO2 in the Selective N‐formylation of Amines
Authors: Pąchalska Paulina , Skarżyńska Anna , Matias Ines A. S. , Trzeciak Anna M. 
Published: December 2023

AbstractBorohydride imidazolium ionic liquids, [IL]BH4, used for the first time as reductants in the N‐formylation of various amines with CO2, provided an excellent yield of formamides. Under the same conditions, 5 bar CO2 and 80 °C, NaBH4 produced a mixture of N‐formylated and N‐methylated products in a ratio of 1 : 2. An alternative approach, based on the addition of halide imidazolium salts ([IL]Cl or [IL]Br) to the reactions of amine with NaBH4 and CO2, resulted in a significant increase of selectivity to formamide. However, no effect was noted for [IL]BF4 and [IL]PF6. Monitoring the reaction course in time using 1H NMR brought about new insight into the role of BH3 in the reduction of CO2 and the functionalization of amines. The formation of N‐methylaniline – borane intermediate was evidenced.
A workflow for the enrichment, the identification, and the isolation of non‐apoptotic single circulating tumor cells for RNA sequencing analysis
Authors: Abramova Anna , Rivandi Mahdi , Yang Liwen , Stamm Nadia , Cieslik Jan‐Philipp , Honisch Ellen , Niederacher Dieter , Fehm Tanja , Neubauer Hans , Franken André 
Published: December 2023

AbstractCirculating tumor cells (CTCs) are constantly shed by tumor tissue and can serve as a valuable analyte for a gene expression analysis from a liquid biopsy. However, a high proportion of CTCs can be apoptotic leading to rapid mRNA decay and challenging the analysis of their transcriptome. We established a workflow to enrich, to identify, and to isolate single CTCs including the discrimination of apoptotic and non‐apoptotic CTCs for further single CTC transcriptome analysis. Viable tumor cells—we first used cells from breast cancer cell lines followed by CTCs from metastatic breast cancer patients—were enriched with the CellSearch system from diagnostic leukapheresis products, identified by immunofluorescence analysis for neoplastic markers, and isolated by micromanipulation. Then, their cDNA was generated, amplified, and sequenced. In order to exclude early apoptotic tumor cells, staining with Annexin V coupled to a fluorescent dye was used. Annexin V staining intensity was associated with decreased RNA integrity as well as lower numbers of total reads, exon reads, and detected genes in cell line cells and CTCs. A comparative RNA analysis of single cells from MDA‐MB‐231 and MCF7 cell lines revealed the expected differential transcriptome profiles. Enrichment and staining procedures of cell line cells that were spiked into blood had only little effect on the obtained RNA sequencing data compared to processing of naïve cells. Further, the detection of transcripts of housekeeping genes such as GAPDH was associated with a significantly higher quality of expression data from CTCs. This workflow enables the enrichment, detection, and isolation of single CTCs for individual transcriptome analyses. The discrimination of apoptotic and non‐apoptotic cells allows to focus on CTCs with a high RNA integrity to ensure a successful transcriptome analysis.
Clinical phenotypes of cardiogenic shock survivors: insights into late host responses and long‐term outcomes
Authors: Soussi Sabri , Ahmadiankalati Mojtaba , Jentzer Jacob C. , Marshall John C. , Lawler Patrick R. , Herridge Margaret , Mebazaa Alexandre , Gayat Etienne , Lu Zihang , dos Santos Claudia C. ,   the French and European Outcome Registry in Intensive Care Units (FROG‐ICU) and CCCTBG trans‐trial group study for InFACT – the International Forum for Acute Care Trialists
Published: December 2023

AbstractAimsAn elevated risk of adverse events persists for years in cardiogenic shock (CS) survivors with high mortality rate and physical/mental disability. This study aims to link clinical CS‐survivor phenotypes with distinct late host‐response patterns at intensive care unit (ICU) discharge and long‐term outcomes using model‐based clustering.Methods and resultsIn the original prospective, observational, international French and European Outcome Registry in Intensive Care Units (FROG‐ICU) study, ICU patients with CS on admission were identified (N = 228). Among them, 173 were discharged alive from the ICU and included in the current study. Latent class analysis was applied to identify distinct CS‐survivor phenotypes at ICU discharge using 15 readily available clinical and laboratory variables. The primary endpoint was 1 year of mortality after ICU discharge. Secondary endpoints were readmission and physical/mental disability [short form‐36 questionnaire (SF‐36) score] within 1 year after ICU discharge. Two distinct phenotypes at ICU discharge were identified (A and B). Patients in Phenotype B (38%) were more anaemic and had higher circulating levels of lactate, sustained kidney injury, and persistent elevation in plasma markers of inflammation, myocardial fibrosis, and endothelial dysfunction compared with Phenotype A. They had also a higher rate of non‐ischaemic origin of CS and right ventricular dysfunction on admission. CS survivors in Phenotype B had higher 1 year of mortality compared with Phenotype A (P = 0.045, Kaplan–Meier analysis). When adjusted for traditional risk factors (i.e. age, severity of illness, and duration of ICU stay), Phenotype B was independently associated with 1 year of mortality [adjusted hazard ratio = 2.83 (95% confidence interval 1.21–6.60); P = 0.016]. There was a significantly lower physical quality of life in Phenotype B patients at 3 months (i.e. SF‐36 physical component score).ConclusionsA phenotype with sustained inflammation, myocardial fibrosis, and endothelial dysfunction at ICU discharge was identified from readily available data and was independently associated with poor long‐term outcomes in CS survivors.
Gallate and Indate Salts with Unsaturated Electron Withdrawing Groups
Authors: Porath Sven , Neumann Beate , Stammler Hans‐Georg , Hoge Berthold 
Published: December 2023

AbstractThe introduction of a number of unsaturated fluorinated and chlorinated substituents onto gallium and indium was investigated. Gallate, [GaR4]−, and indate, [InR4]−, anions with trifluorovinyl (CF=CF2), 1‐chloro‐2,2‐difluorovinyl (CCl=CF2), (E)‐pentafluoropropen‐1‐yl (E‐CF=CFCF3), 3,3,3‐trifluoropropynyl (C≡C−CF3) and dichloromethyl (CHCl2) substituents were synthesized and isolated as the respective tetraphenylphosphonium salts. The respective gallate and indate salts were characterized by various methods, including NMR spectroscopy, mass spectrometry and X‐ray diffraction analysis. The generation of the respective organyllithium reagents, required for the syntheses of the gallate and indates, was performed starting from commercially available materials. This series of novel gallate and indate salts extends the chemistry of electron withdrawing groups to gallium and indium compounds.
Exploiting the synergistic effects of combined carbon‐based materials for rape drug diazepam electrochemical sensing: Application to simulated casework matrices
Authors: de Oliveira Borges Isabelle , Goularte Rayane Bueno , Vanoni Caio Raphael , Silva Lima Adriano Rogerio , Scheide Marcos Roberto , Zambelli Mezalira Daniela , Vitali Luciano , Stulzer Hellen Karine , Jost Cristiane Luisa 
Published: December 2023

AbstractDiazepam (DZP), a long‐lasting benzodiazepine and controlled substance, is prevalent on the illegal market, notably as a date rape drug. This study presents a novel electrochemical sensor (CPE/GCPE/MWCNTs) for DZP determination in lab routines. Characterized through LSV, EIS, and SEM, the sensor revealed a pH‐dependent, irreversible reduction process at approximately −0.70 V (vs. Ag/AgCl(sat)). Optimization with SWV and 0.1 mol L−1 B–R solution (pH 1.0) produced a calibration curve spanning 1.49 to 21.5 μmol L−1. LOD and LOQ were 0.33 and 1.10 μmol L−1, respectively. Quantification in spiked samples exhibited no significant differences compared to HPLC‐DAD, endorsing the sensor for monitoring date rape drugs in forensic analysis.