bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parents’ expectations, preferences, and recall of germline findings in a childhood cancer precision medicine trial
Authors: McGill Brittany C. , Wakefield Claire E. , Tucker Katherine M. , Daly Rebecca A. , Donoghoe Mark W. , Vetsch Janine , Warby Meera , Fuentes‐Bolanos Noemi A. , Barlow‐Stewart Kristine , Kirk Judy , Courtney Eliza , O’Brien Tracey A. , Marshall Glenn M. , Pinese Mark , Cowley Mark J. , Tyrrell Vanessa , Deyell Rebecca J. , Ziegler David S. , Hetherington Kate 
Published: June 2023

AbstractBackgroundGermline genome sequencing in childhood cancer precision medicine trials may reveal pathogenic or likely pathogenic variants in cancer predisposition genes in more than 10% of children. These findings can have implications for diagnosis, treatment, and the child’s and family’s future cancer risk. Understanding parents’ perspectives of germline genome sequencing is critical to successful clinical implementation.MethodsA total of 182 parents of 144 children (<18 years of age) with poor‐prognosis cancers enrolled in the Precision Medicine for Children with Cancer trial completed a questionnaire at enrollment and after the return of their child’s results, including clinically relevant germline findings (received by 13% of parents). Parents’ expectations of germline genome sequencing, return of results preferences, and recall of results received were assessed. Forty‐five parents (of 43 children) were interviewed in depth.ResultsAt trial enrollment, most parents (63%) believed it was at least “somewhat likely” that their child would receive a clinically relevant germline finding. Almost all expressed a preference to receive a broad range of germline genomic findings, including variants of uncertain significance (88%). Some (29%) inaccurately recalled receiving a clinically relevant germline finding. Qualitatively, parents expressed confusion and uncertainty after the return of their child’s genome sequencing results by their child’s clinician.ConclusionsMany parents of children with poor‐prognosis childhood cancer enrolled in a precision medicine trial expect their child may have an underlying cancer predisposition syndrome. They wish to receive a wide scope of information from germline genome sequencing but may feel confused by the reporting of trial results.
Determinants of overall survival in patients with metastatic uveal melanoma
Authors: Demkowicz Patrick , Pointdujour‐Lim Renelle , Miguez Sofia , Lee Yesung , Jones Bailey S. C. L. , Barker Christopher A. , Bosenberg Marcus , Abramson David H. , Shoushtari Alexander N. , Kluger Harriet , Francis Jasmine H. , Sznol Mario , Bakhoum Mathieu F. 
Published: June 2023

AbstractBackgroundDespite improvements in the treatment of primary uveal melanoma (UM), patients with metastatic disease continue to exhibit poor survival.MethodsA retrospective review of metastatic UM patients at Yale (initial cohort) and Memorial Sloan Kettering (validation cohort) was conducted. Cox proportional hazards regression was used to determine baseline factors that are associated with overall survival, including sex, Eastern Cooperative Oncology Group (ECOG) Performance Status Scale, laboratory measurements, metastasis location, and use of anti‐CTLA‐4 and anti‐PD‐1 therapies. Differences in overall survival were analyzed using Kaplan–Meier analysis.ResultsA total of 89 patients with metastatic UM were identified; 71 and 18, in the initial and validation cohorts, respectively. In the initial cohort, median follow‐up was 19.8 months (range, 2–127 months) and median overall survival was 21.8 months (95% CI, 16.6–31.3). Female sex, anti–CTLA‐4, and anti–PD‐1 therapy were associated with better survival outcomes with adjusted death hazard ratios (HRs) of 0.40 (95% CI, 0.20–0.78), 0.44 (0.20–0.97), and 0.42 (0.22–0.84), respectively, whereas development of hepatic metastases and ECOG score ≥1 (per 1 U/L) were associated with worse survival outcomes with HRs of 2.86 (1.28–7.13) and 2.84 (1.29–6.09), respectively. In both the initial and validation cohorts, use of immune checkpoint inhibitors was associated with improved overall survival after adjusting for sex and ECOG score, with death HRs of 0.22 (0.08–0.56) and 0.04 (0.002–0.26), respectively.ConclusionsDevelopment of extrahepatic‐only metastases, ECOG of 0, immune checkpoint therapy, and female sex were each associated with more than 2‐fold reductions in risk of death.Plain Language SummaryMetastatic uveal melanoma patients face limited treatment options and poor survival rates.Results from this retrospective analysis indicate that immune checkpoint inhibitors, such as anti–CTLA‐4 and anti–PD‐1 therapies, were associated with improved survival outcomes. Factors such as extrahepatic‐only metastases, better baseline performance status, and female sex contributed to a more than 2‐fold reduction in death risk.These findings highlight the potential of immunotherapy in treating metastatic uveal melanoma.
Prevalence, trends, and characteristics of trials investigating local therapy in contemporary phase 3 clinical cancer research
Authors: Sherry Alexander D. , Corrigan Kelsey L. , Kouzy Ramez , Jaoude Joseph Abi , Yang Yumeng , Patel Roshal R. , Totten Douglas J. , Newman Neil B. , Das Prajnan , Taniguchi Cullen , Minsky Bruce , Snyder Rebecca A. , Fuller C. David , Ludmir Ethan 
Published: June 2023

AbstractBackgroundAlthough most patients with cancer are treated with local therapy (LT), the proportion of late‐phase clinical trials investigating local therapeutic interventions is unknown. The purpose of this study was to determine the proportion, characteristics, and trends of phase 3 cancer clinical trials assessing the therapeutic value of LT over time.MethodsThis was a cross‐sectional analysis of interventional randomized controlled trials in oncology published from 2002 through 2020 and registered on ClinicalTrials.gov. Trends and characteristics of LT trials were compared to all other trials.ResultsOf 1877 trials screened, 794 trials enrolling 584,347 patients met inclusion criteria. A total of 27 trials (3%) included a primary randomization assessing LT compared with 767 trials (97%) investigating systemic therapy or supportive care. Annual increase in the number of LT trials (slope [m] = 0.28; 95% confidence interval [CI], 0.15–0.39; p < .001) was outpaced by the increase of trials testing systemic therapy or supportive care (m = 7.57; 95% CI, 6.03–9.11; p < .001). LT trials were more often sponsored by cooperative groups (22 of 27 [81%] vs. 211 of 767 [28%]; p < .001) and less often sponsored by industry (5 of 27 [19%] vs. 609 of 767 [79%]; p < .001). LT trials were more likely to use overall survival as primary end point compared to other trials (13 of 27 [48%] vs. 199 of 767 [26%]; p = .01).ConclusionsIn contemporary late‐phase oncology research, LT trials are increasingly under‐represented, under‐funded, and evaluate more challenging end points compared to other modalities. These findings strongly argue for greater resource allocation and funding mechanisms for LT clinical trials.Plain language summary

Most people who have cancer receive treatments directed at the site of their cancer, such as surgery or radiation.
We do not know, however, how many trials test surgery or radiation compared to drug treatments (that go all over the body).
We reviewed trials testing the most researched strategies (phase 3) completed between 2002 and 2020.
Only 27 trials tested local treatments like surgery or radiation compared to 767 trials testing other treatments.
Our study has important implications for funding research and understanding cancer research priorities.
Fast Depolymerization of PET Bottle Mediated by Microwave Pre‐Treatment and An Engineered PETase**
Authors: Guo Boyang , Lopez‐Lorenzo Ximena , Fang Yuan , Bäckström Eva , Capezza Antonio Jose , Vanga Sudarsan Reddy , Furó István , Hakkarainen Minna , Syrén Per‐Olof 
Published: June 2023

AbstractRecycling plastics is the key to reaching a sustainable materials economy. Biocatalytic degradation of plastics shows great promise by allowing selective depolymerization of man‐made materials into constituent building blocks under mild aqueous conditions. However, insoluble plastics have polymer chains that can reside in different conformations and show compact secondary structures that offer low accessibility for initiating the depolymerization reaction by enzymes. In this work, we overcome these shortcomings by microwave irradiation as a pre‐treatment process to deliver powders of polyethylene terephthalate (PET) particles suitable for subsequent biotechnology‐assisted plastic degradation by previously generated engineered enzymes. An optimized microwave step resulted in 1400 times higher integral of released terephthalic acid (TPA) from high‐performance liquid chromatography (HPLC), compared to original untreated PET bottle. Biocatalytic plastic hydrolysis of substrates originating from PET bottles responded to 78 % yield conversion from 2 h microwave pretreatment and 1 h enzymatic reaction at 30 °C. The increase in activity stems from enhanced substrate accessibility from the microwave step, followed by the administration of designer enzymes capable of accommodating oligomers and shorter chains released in a productive conformation.
Implementation of AI/DEEP learning disruption predictor into a plasma control system
Authors: Tang William , Dong Ge , Barr Jayson , Erickson Keith , Conlin Rory , Boyer Dan , Kates‐Harbeck Julian , Felker Kyle , Rea Cristina , Logan Nikolas , Svyatkovskiy Alexey , Feibush Eliot , Abbatte Joseph , Clement Mitchell , Grierson Brian , Nazikian Raffi , Lin Zhihong , Eldon David , Moser Auna , Maslov Mikhail 
Published: June 2023

AbstractThis paper reports on advances in the state‐of‐the‐art deep learning disruption prediction models based on the Fusion Recurrent Neural Network (FRNN) originally introduced in a 2019 NATURE publication [https://doi.org/10.1038/s41586‐019‐1116‐4]. In particular, the predictor now features not only the “disruption score,” as an indicator of the probability of an imminent disruption, but also a “sensitivity score” in real time to indicate the underlying reasons for the imminent disruption. This adds valuable physics interpretability for the deep learning model and can provide helpful guidance for control actuators now implemented into a modern plasma control system (PCS). The advance is a significant step forward in moving from modern deep learning disruption prediction to real‐time control and brings novel AI‐enabled capabilities relevant for application to the future burning plasma ITER system. Our analyses use large amounts of data from JET and DIII‐D vetted in the earlier NATURE publication. In addition to “when” a shot is predicted to disrupt, this paper addresses reasons “why” by carrying out sensitivity studies. FRNN is accordingly extended to use more channels of information, including measured DIII‐D signals such as (i) the “n1rms” signal that is correlated with the n = 1 modes with finite frequency, including neoclassical tearing mode and sawtooth dynamics; (ii) the bolometer data indicative of plasma impurity control; and (iii) “q‐min”—the minimum value of the safety factor relevant to the key physics of kink modes. The additional channels and interpretability features expand the ability of the deep learning FRNN software to provide information about disruption subcategories as well as more precise and direct guidance for the actuators in a PCS.
UHPLC–MS/MS method for the quantification of ultra‐traces of irinotecan and its metabolites in red blood cells and plasma to detect caregivers' contamination
Authors: Rodier Simon , Saint‐Lorant Guillaume , Since Marc , Lagadu Stéphanie , Benoist Hubert , Palix Agnès , Guilloit Jean‐Marc , Faveyrial Audrey , Divanon Fabienne , Delépée Raphaël 
Published: June 2023

AbstractThe occupational exposure of caregivers to antineoplastic agents has been demonstrated since 1979. Since the early 1990s, numerous studies from several countries have demonstrated the contamination of care facilities by antineoplastic drugs. As it is easier to sample, most contamination measurements in workers are carried out in urine sample. The distribution and elimination half‐lives of irinotecan suggest that blood can be considered as better than urine for the biomonitoring of a potential contamination of healthcare workers. We describe here the development and the validation of a UHPLC–MS/MS method to simultaneously quantify irinotecan, and two of its main metabolites, APC and SN‐38, at ultra‐trace levels in plasma and red blood cells (RBC). This method has been applied to blood samples collected from several healthcare services in a French comprehensive cancer center. The results demonstrate that the method is sensitive enough to identify a contamination of healthcare workers by irinotecan and SN‐38 at very low concentrations. Moreover, the results show that analysis of RBC is of great interest and complementary to that of serum.
Population structure and distribution of geladas (Theropithicus gelada, Ruppell 1835) in Kotu forest, Northern Ethiopia
Authors: Abate Degu , Girma Zerihun 
Published: June 2023

AbstractEndemic gelada populations outside protected areas are less investigated, and population census data are not available. As a result, a study was conducted to investigate the population size, structure, and distribution of geladas in Kotu forest and associated grasslands, in northern Ethiopia. The study area was stratified into five dominant habitat types namely, grassland, wooded grassland, plantation forest, natural forest, and bushland based on dominant vegetation type. Each habitat type was further divided into blocks, and a total counting technique was used to count the individuals of gelada. The total mean population size of gelada in Kotu forest was 229 ± 6.11. The mean ratio of male to female was 1:1.178. The gelada age composition comprised is as follows: 113 (49.34%) adults, 77 (33.62%) sub‐adults, and 39 (17.03%) juveniles. The mean number of group one‐male unit ranged from 1.5 ± 0.2 in the plantation forest to 4.5 ± 0.7 in the grassland habitat. On the other hand, all‐male unit social system group was recorded only from grassland (1.5) and plantation forest (1) habitats. The average band size (number of individuals per band) was 45.0 ± 2.53. The largest number of geladas was recorded from grassland habitat 68 (29.87%), and the lowest was recorded from plantation forest habitat 34 (14.74%). Even though, the sex ratio was female biased, the proportion of juveniles to other age classes was very low compared with geladas in relatively well‐protected areas, indicating negative consequences for the future viability of the gelada populations in the area. Geladas were widely distributed over open grassland habitat. Therefore, for sustainable conservation of the geladas in the area, there is a need for integrated management of the area with special attention on the conservation of the grassland habitat.
The clustering of spatially associated species unravels patterns in tropical tree species distributions
Authors: Pang Sean E. H. , Slik J. W. Ferry , Zurell Damaris , Webb Edward L. 
Published: June 2023

AbstractComplex distribution data can be summarized by grouping species with similar or overlapping distributions to unravel spatial patterns and separate trends (e.g., of habitat loss) among spatially unique groups. However, such classifications are often heuristic, lacking the transparency, objectivity, and data‐driven rigor of quantitative methods, which limits their interpretability and utility. Here, we develop and illustrate the clustering of spatially associated species, a methodological framework aimed at statistically classifying species using explicit measures of interspecific spatial association. We investigate several association indices and clustering algorithms and show how these methodological choices drive substantial variations in clustering outcomes and performance. To facilitate robust decision‐making, we provide guidance on choosing methods appropriate to one's study objective(s). As a case study, we apply our framework to modeled tree distributions in Borneo and subsequently evaluate the impact of land‐cover change on separate species groupings. Based on the modeled distribution of 390 tree species prior to anthropogenic land‐cover changes, we identified 11 distinct clusters that unraveled ecologically meaningful patterns in Bornean tree distributions. These clusters then enabled us to quantify trends of habitat loss tied to each of those specific clusters, allowing us to discern particularly vulnerable species clusters and their distributions. This study demonstrates the advantages of adopting quantitatively derived clusters of spatially associated species and elucidates the potential of resultant clusters as a spatially explicit framework for investigating distribution‐related questions in ecology, biogeography, and conservation. By adopting our methodological framework and publicly available codes, practitioners can leverage the ever‐growing abundance of distribution data to better understand complex spatial patterns among species distributions and the disparate effects of global changes on biodiversity.
Sterically Demanding Novel Triazole Based Tertiary Phosphines: Synthesis, Transition Metal Chemistry and Catalytic Applications
Authors: Kote Basvaraj S. , Mohite Manali A. , Mondal Dipanjan , Pandey Madhusudan K. , Balakrishna Maravanji S. 
Published: June 2023

AbstractSterically demanding 2,6‐dibenzhydryl‐4‐methylphenyl and 1,2,3‐triazole based tertiary phosphines, [Ar*{1,2,3‐N3C(Ph)C(PR2)}] (R=Ph, 3; R=iPr, 4) were obtained by the temperature‐controlled lithiation of 1‐(2,6‐dibenzydryl‐4‐methyl)‐5‐iodo‐4‐phenyl‐1H‐1,2,3‐triazole (2) followed by the reaction with R2PCl (R=Ph, iPr). Treatment of 3 with H2O2, elemental sulfur and selenium yielded chalcogenides [Ar*{1,2,3‐N3C(Ph)C(P(E)Ph2)}] (E=O, 5; E=S, 6; E=Se, 7). The reaction of 3 with [Pd(COD)Cl2] in 1 : 1 molar ratio, afforded dimeric complex [Pd(μ2‐Cl)Cl{Ar*{1,2,3‐N3C(Ph)C(PPh2)}‐κ1‐P}]2 (8), whereas the reactions of 3 and 4 with [Pd(η3‐C3H5)Cl]2 in 2 : 1 molar ratios produced complexes [Pd(η3‐C3H5)Cl{Ar*{1,2,3‐N3C(Ph)C(PR2)}‐κ1‐P}] (R=Ph, 9; R=iPr, 10). Treatment of 3 with [Pd(OAc)2] in 1 : 1 molar ratio afforded a rare trinuclear complex [{Pd3(OAc)4}{Ar*{1,2,3‐N3C(C6H4)C(PPh2)}‐κ2‐C,P}2] (11). Treatment of 3 and 4 with [AuCl(SMe2)] resulted in [AuCl{Ar*{1,2,3‐N3C(Ph)C(PR2)}‐κ1‐P}] (R=Ph, 12; R=iPr, 13). Bulky phosphine 4 was very effective in Suzuki‐Miyaura coupling and amination reactions with very low catalyst loading. Molecular structures of 3–5, and 8–13 were confirmed by single‐crystal X‐ray diffraction studies.
Anionic Boraza‐Crown Ethers
Authors: Lenz Tabea , Hepp Alexander , Layh Marcus , Hebenbrock Marian 
Published: June 2023

AbstractMaking one out of two: Dimeric boraza‐crown ethers bridge the gap between metallacrowns and aza‐crown ethers with a strikingly simple synthesis. Dioxazaborocanes react with alkoxides to form the corresponding anionic boronates, which combine to form dimers upon ring‐opening reactions. The presence of the dimers was proven in the solid state and in solution by X‐ray crystallography and NMR spectroscopy, respectively. The influence of the sodium and potassium ions on the stability of boraza‐crown ethers was examined using DFT calculations. The dissociation of the dimers to the monomeric species was found to be endothermic, independently of the counterion. Finally, their ability to engage in cross‐coupling reactions was validated for two different compounds.
Acid Catalyzed Multicomponent Reaction to Access Functionalized N‐Benzhydryl Amides: A Tandem Ritter Reaction
Authors: Karu Sudheer Kumar , Malapaka Chandrasekharam 
Published: June 2023

AbstractAcid catalyzed multicomponent reaction (MCR) for the synthesis of N‐benzhydryl amide derivatives from aldehydes, N,N‐disubstituted arylamines and nitriles is reported. The reaction is compatible with electronically differentiating aryl/heteroaryl aldehydes/acetals, different nucleophiles (cyclic and acyclic N,N‐disubstituted arylamines,β‐naphthols, 1,3 dicarbonyl, 1,3,5‐trimethoxy benzene), alkyl nitriles, aryl/heteroaryl nitriles in catalytic TFA/TfOH through tandem Ritter reaction. The one‐pot MCR with broad substrate scope generated a wide variety of sterically hindered N‐substituted amides and is successfully applied for the synthesis of isoindolinone.
Building the Campus as a Lab (CaaL) platform
Authors: Popoviciu Ciprian , Sawyer Colby 
Published: June 2023

AbstractInternet of Things (IoT) related and IoT enabled education and research are becoming more prevalent in today's academic environment. One of the challenges faced by educators and researchers is the availability of resources to support lab based, hands on learning and research projects. Existing resources are often highly customized, balkanized, and difficult to manage. For new technology areas such as IoT, these environments rarely provide opportunities for resource sharing and interdisciplinary collaboration. In this paper, we describe the development of a multi‐tenant, IoT centric platform, the Environmental Sensing Data Network (ESDN) meant to support plug and play sensor deployment and the tools necessary for data management. The platform turns the University campus into an open platform that can be used to easily set up IoT based labs for education, research, campus infrastructure management and community applications innovation. The paper covers the development of a sensor augmentation module facilitating easy deployment and management. The operational tools and services integration are also described. We believe the platform is an important step in facilitating distance and in person education and research. ESDN is rapidly expanding beyond the multi‐site University campus supporting a growing number of research and community projects.
Study on mechanical properties and fracture modes of sandstone with cracks under triaxial compression
Authors: Liu Yongsheng , Liu Wang , Wang Cui 
Published: June 2023

AbstractThis study examines the mechanical properties and fracture modes of sandstone with single and double cracks under varying confining pressures through triaxial compression tests. The stress–strain curves, mechanical parameters, and fracture modes of both intact and cracked sandstone are analyzed based on experimental results. The study finds that the presence of cracks has a significant impact on the mechanical properties of sandstone, with greater damage observed with an increase in the number of cracks. The peak strength and strain of a cracked rock sample increase with the increase in crack angle. The fracture mode of sandstone is influenced by both crack angle and confining pressure. When the crack angle is small, the fracture mode is a combination of shear and tensile failure, while a large crack angle results in shear failure. Moreover, as the confining pressure increases, the degree of damage to the sandstone also increases.