bluuebunny/crossref_metadata_2025_split huggingface dataset:
HER2DX ERBB2 mRNA expression in advanced HER2-positive breast cancer treated with T-DM1
Authors: Brasó-Maristany Fara , Griguolo Gaia , Chic Nuria , Pascual Tomás , Paré Laia , Maues Julia , Galván Patricia , Dieci Maria Vittoria , Miglietta Federica , Giarratano Tommaso , Martínez-Sáez Olga , Marín-Aguilera Mercedes , Schettini Francesco , Conte Benedetta , Angelats Laura , Vidal Maria , Adamo Barbara , Muñoz Montserrat , Sanfeliu Esther , González Blanca , Vivancos Ana , Villagrasa Patricia , Parker Joel S , Perou Charles M , Conte PierFranco , Prat Aleix , Guarneri Valentina 
Published: December 2022

AbstractIn advanced HER2-positive (HER2+) breast cancer, the new antibody-drug conjugate trastuzumab deruxtecan is more effective compared with trastuzumab emtansine (T-DM1). However, trastuzumab deruxtecan can have considerable toxicities, and the right treatment sequence is unknown. Biomarkers to guide the use of anti-HER2 therapies beyond HER2 status are needed. Here, we evaluated if preestablished levels of ERBB2 mRNA expression according to the HER2DX standardized assay are associated with response and survival following T-DM1. In ERBB2 low, medium, and high groups, the overall response rate was 0%, 29%, and 56%, respectively (P &lt; .001). ERBB2 mRNA was statistically significantly associated with better progression-free survival (P = .002) and overall survival (OS; P = .02). These findings were independent of HER2 immunohistochemistry (IHC) levels, hormone receptor, age, brain metastasis, and line of therapy. The HER2DX risk score (P = .04) and immunoglobulin signature (P = .04) were statistically significantly associated with overall survival since diagnosis. HER2DX provides prognostic and predictive information following T-DM1 in advanced HER2+ breast cancer.
Cognitive change in breast cancer patients up to 2 years after diagnosis
Authors: Lange Marie , Lefevre Arbogast Sophie , Hardy-Léger Isabelle , Rigal Olivier , Le Fel Johan , Pistilli Barbara , Petrucci Jean , Lévy Christelle , Capel Aurélie , Coutant Charles , Médeau Laure , Lerebours Florence , Vanlemmens Laurence , Brion Marine , Bourbouloux Emmanuelle , Blain Maxime , Binarelli Giulia , Vaz-Luis Ines , Giffard Bénédicte , Querel Ophélie , Everhard Sibille , André Fabrice , Charles Cécile , Dauchy Sarah , Joly Florence 
Published: December 2022

AbstractBackgroundUsing the large nationwide French, national, multicenter, prospective cancer and toxicities (CANTO) cohort, we assessed cognitive functioning change after cancer treatments in a subgroup of breast cancer (BC) patients.MethodsWe included patients with newly diagnosed invasive stage I-III BC enrolled in the CANTO substudy focused on cognitive evaluation and healthy control women matched for age and education. Episodic and working memory, executive functions, processing speed, attention, self-report cognitive difficulties (SRCD), fatigue, anxiety and depression were assessed with neuropsychological tests and self-report questionnaires before treatment (baseline) and approximately 1 (year 1) and 2 years (year 2) after diagnosis. We used linear mixed models to study changes in cognition and tested the effect of adjuvant chemotherapy.ResultsWe studied 276 localized BC patients (62% chemotherapy) compared with 135 healthy controls (HC). After adjustment, patients had lower baseline working memory, processing speed, and attention scores than HC (P ≤ .001), and the difference remained statistically significant over follow-up for working memory and processing speed. Executive function scores were similar between groups at baseline but decreased at year 1 among patients compared with HC (Pchange = .006). This decrease in chemotherapy patients was statistically significant compared with HC scores (Pchange &lt; .001). After adjustment, SRCD were similar between BC patients and HC at baseline but increased in patients after treatment at year 1 (Pchange = .002).ConclusionsCognitive difficulties are an important concern in BC patients, starting at diagnosis. Cancer treatments induce executive function decline and SRCD, which decrease over follow-up.
Coin Diving, Tourism, and Colonialism in the Caribbean, 1890–1940
Authors: Fonseca Stanley 
Published: December 2022

Abstract
Between the late nineteenth and mid-twentieth century, the ongoing crises of the late-colonial Caribbean mingled with an emerging trend: white American and European tourists who flocked in growing numbers to the tropics in search of pleasure, leisure, and adventure. As these travelers arrived in port in the era before commercial flight, they encountered a ubiquitous scene: boys and young men in small rowboats, who would surround the incoming steamship and, nude or nearly nude, dive in the tropical surf for coins tossed overboard. Images and accounts of these coin divers circulated widely in travel media, and were instrumental in constructing a tourist-friendly vision of the Caribbean seaside as exotic, picturesque, erotic, and accessible. In colonial Caribbean sources, however, coin divers were viewed not as an alluring spectacle but as a criminal threat, somewhere between beggar, truant, and sex worker. The divers themselves were working-class youth inhabiting a harbor-world on the periphery of a stratified and shifting society. They experienced firsthand the transition from Caribbean colonialism to mass tourism, and used the harbor to enact a limited autonomy and demand recognition within a system that provided few meaningful alternatives. Analyzing the tensions between these contrasting modes of power—one that commodified and one that criminalized—we can better understand the complex dynamics in the transition from plantation colonialism to tourist neocolonialism in the Caribbean.
Genome-wide association study revealsWRKY42as a novel plant transcription factor that influences oviposition preference ofPierisbutterflies
Authors: Coolen Silvia , Van Dijen Marcel , Van Pelt Johan A , Van Loon Joop J A , Pieterse Corné M J , Van Wees Saskia C M 
Published: December 2022

AbstractInsect herbivores are amongst the most destructive plant pests, damaging both naturally occurring and domesticated plants. As sessile organisms, plants make use of structural and chemical barriers to counteract herbivores. However, over 75% of herbivorous insect species are well adapted to their host’s defenses and these specialists are generally difficult to ward off. By actively antagonizing the number of insect eggs deposited on plants, future damage by the herbivore’s offspring can be limited. Therefore, it is important to understand which plant traits influence attractiveness for oviposition, especially for specialist insects that are well adapted to their host plants. In this study, we investigated the oviposition preference of Pieris butterflies (Lepidoptera: Pieridae) by offering them the choice between 350 different naturally occurring Arabidopsis accessions. Using a genome-wide association study of the oviposition data and subsequent fine mapping with full genome sequences of 164 accessions, we identified WRKY42 and AOC1 as candidate genes that are associated with the oviposition preference observed for Pieris butterflies. Host plant choice assays with Arabidopsis genotypes impaired in WRKY42 or AOC1 function confirmed a clear role for WRKY42 in oviposition preference of female Pieris butterflies, while for AOC1 the effect was mild. In contrast, WRKY42-impaired plants, which were preferred for oviposition by butterflies, negatively impacted offspring performance. These findings exemplify that plant genotype can have opposite effects on oviposition preference and caterpillar performance. This knowledge can be used for breeding trap crops or crops that are unattractive for oviposition by pest insects.
Medicinal terpenoid UDP-glycosyltransferases in plants: recent advances and research strategies
Authors: Lu Xu , Huang Lijin , Scheller Henrik V , Keasling Jay D 
Published: December 2022

AbstractTerpenoid glycosides have significant curative effects on many kinds of diseases. Most of these compounds are derived from medicinal plants. Glycosylation is a key step in the biosynthesis of medicinal terpenoids. In plants, UDP-dependent glycosyltransferases comprise a large family of enzymes that catalyze the transfer of sugars from donor to acceptor to form various bioactive glycosides. In recent years, numerous terpenoid UDP-glycosyltransferases (UGTs) have been cloned and characterized in medicinal plants. We review the typical characteristics and evolution of terpenoid-related UGTs in plants and summarize the advances and research strategies of terpenoid UGTs in medicinal plants over the past 20 years. We provide a reference for the study of glycosylation of terpenoid skeletons and the biosynthetic pathways for medicinal terpenoids in plants.
Overexpression of maizeZmLOX6inArabidopsis thalianaenhances damage-induced pentyl leaf volatile emissions that affect plant growth and interaction with aphids
Authors: Tolley Jordan P , Gorman Zachary , Lei Jiaxin , Yeo In-Cheol , Nagashima Yukihiro , Joshi Vijay , Zhu-Salzman Keyan , Kolomiets Michael V , Koiwa Hisashi 
Published: December 2022

AbstractPentyl leafy volatiles (PLV) are C5 volatiles produced from polyunsaturated fatty acids by plant 13-lipoxygenases (13-LOX) in concert with other lipid metabolizing enzymes. Unlike related C6 volatiles (GLV, green leafy volatiles), little is known about the biosynthesis and physiological function of PLV in plants. Zea mays LOX6 (ZmLOX6) is an unusual plant LOX that lacks lipid oxygenation activity but acts as a hydroperoxide lyase hypothesized to be specifically involved in PLV synthesis. We overexpressed ZmLOX6 in Arabidopsis thaliana and established that it indeed produces PLVs. Overexpression of ZmLOX6 caused a mild chlorotic phenotype, and induced a similar phenotype in untransformed Col-0 plants grown in close proximity, suggesting that airborne signals, such as PLVs, are responsible for the phenotype. PLV production, dependency on the substrate from endogenous 13-LOX(s), and likely competition with endogenous 13-oxylipin pathway were consistent with the model that ZmLOX6 functions as a hydroperoxide lyase. The abundance of individual PLVs was differentially affected by ZmLOX6 overexpression, and the new profile indicated that ZmLOX6 had reaction products distinct from endogenous PLV-producing activities in the Arabidopsis host plants. ZmLOX6 overexpression also induced a new hormonal status, which is likely responsible for increased attraction and propagation of aphids, nonetheless improving host plant tolerance to aphid infestation.
Likelihood ratios for categorical count data with applications in digital forensics
Authors: Longjohn Rachel , Smyth Padhraic , Stern Hal S 
Published: December 2022

AbstractWe consider the forensic context in which the goal is to assess whether two sets of observed data came from the same source or from different sources. In particular, we focus on the situation in which the evidence consists of two sets of categorical count data: a set of event counts from an unknown source tied to a crime and a set of event counts generated by a known source. Using a same-source versus different-source hypothesis framework, we develop an approach to calculating a likelihood ratio. Under our proposed model, the likelihood ratio can be calculated in closed form, and we use this to theoretically analyse how the likelihood ratio is affected by how much data is observed, the number of event types being considered, and the prior used in the Bayesian model. Our work is motivated in particular by user-generated event data in digital forensics, a context in which relatively few statistical methodologies have yet been developed to support quantitative analysis of event data after it is extracted from a device. We evaluate our proposed method through experiments using three real-world event datasets, representing a variety of event types that may arise in digital forensics. The results of the theoretical analyses and experiments with real-world datasets demonstrate that while this model is a useful starting point for the statistical forensic analysis of user-generated event data, more work is needed before it can be applied for practical use.
Weak lensing the non-linear Lyα forest
Authors: Shaw Patrick , Croft Rupert A C , Metcalf R Benton 
Published: December 2022

ABSTRACT
We evaluate the performance of the Lyman α forest weak gravitational lensing estimator of Metcalf et al. on forest data from hydrodynamic simulations and ray-trace simulated lensing potentials. We compare the results to those obtained from the Gaussian random field simulated Lyα forest data and lensing potentials used in previous work. We find that the estimator is able to reconstruct the lensing potentials from the more realistic data and investigate dependence on spectrum signal to noise. The non-linearity and non-Gaussianity in this forest data arising from gravitational instability and hydrodynamics causes a reduction in signal to noise by a factor of ∼2.7 for noise free data and a factor of ∼1.5 for spectra with signal to noise of order unity (comparable to current observational data). Compared to Gaussian field lensing potentials, using ray-traced potentials from N-body simulations incurs a further signal-to-noise reduction of a factor of ∼1.3 at all noise levels. The non-linearity in the forest data is also observed to increase bias in the reconstructed potentials by $5-25{{\ \rm per\ cent}}$, and the ray-traced lensing potential further increases the bias by $20-30{{\ \rm per\ cent}}$. We demonstrate methods for mitigating these issues including Gaussianization and bias correction which could be used in real observations.
The optical spectral features of 27 Fermi blazars
Authors: Zhang Bing-Kai , Tang Wei-Feng , Wang Chun-Xiao , Wu Qi , Jin Min , Dai Ben-Zhong , Zhu Feng-Rong 
Published: December 2022

ABSTRACT
Spectral variation accompanied by flux variability is a commonly observed phenomenon for blazars. In order to investigate the optical spectral feature of blazars further, we collected the long-term optical V- and R-band data of 27 blazars (14 BL Lacaerte objects, BL Lacs, and 13 flat-spectrum radio quasars, FSRQs) and calculated their optical spectral indices. The results show that the spectral indices vary with respect to brightness for all of these blazars. In general, the optical spectrum progressively becomes flatter (or steeper), when the brightness increases. However the spectrum changes more and more slowly, until it tends to stability. In other words, the source becomes bluer (or redder) and then gradually stabilizes when it brightens, behaviours that are referred to as bluer-stable-when-brighter (BSWB) and redder-stable-when-brighter (RSWB), respectively. A total of 13 of the 14 BL Lacs show the BSWB behaviour, the exception being AO 0235+164. In contrast, most of the FSRQs (10 out of 13) exhibit the RSWB trend. It is confirmed that blazars follow the two universal optical spectral behaviours, namely BSWB and RSWB. The model of two constant-spectral-index components can explain the optical spectral features well both qualitatively and quantitatively. The results illustrate that the optical emission is composed mainly of two stable-colour components, namely less variable thermal emission and highly variable synchrotron radiation. Furthermore, in most cases, the thermal component of BL Lacs is redder than that of synchrotron radiation, whereas the opposite is true for FSRQs.
Population Genetic Considerations Regarding Evidence for Biased Mutation Rates inArabidopsis thaliana
Authors: Charlesworth Brian , Jensen Jeffrey D 
Published: December 2022

AbstractIt has recently been proposed that lower mutation rates in gene bodies compared with upstream and downstream sequences in Arabidopsis thaliana are the result of an “adaptive” modification of the rate of beneficial and deleterious mutations in these functional regions. This claim was based both on analyses of mutation accumulation lines and on population genomics data. Here, we show that several questionable assumptions were used in the population genomics analyses. In particular, we demonstrate that the difference between gene bodies and less selectively constrained sequences in the magnitude of Tajima's D can in principle be explained by the presence of sites subject to purifying selection and does not require lower mutation rates in regions experiencing selective constraints.
WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly
Authors: Liao Hong-qing , Guo Zi-yi , Huang Li-hua , Liu Gang , Lu Jin-feng , Zhang Yun-fei , Xing Xiao-wei 
Published: December 2022

AbstractSpermatogenesis is a complex process that includes spermatogonia self-renewal, spermatocyte meiosis and spermatozoa assembly. Recent studies have revealed that WD40-repeat domain-containing (WDR) proteins play important roles in spermatocyte division, spermatozoa flagella assembly and head shaping. In this study, we investigated the expression pattern of WDR87 and found that it was highly expressed in the testis of both humans and mice. Immunofluorescence staining revealed that mouse WDR87 was distributed in the perinuclear cytoplasm of primary spermatocytes, secondary spermatocytes and round spermatids. In the spermiogenesis stage, with extension of the nucleus, WDR87 migrated to the manchette and finally localized to the middle piece of the spermatozoa tail. Furthermore, we identified a cilia- and flagella-associated protein, CFAP47, which interacted with WDR87 in the flagellar midpiece of the spermatozoa, suggesting that WDR87 may be associated with multiple morphological abnormalities of the flagella (MMAF). Subsequently, we screened gene mutations in seven MMAF individuals and found two novel mutations in CFAP47 (c.706G&gt;A, Val236Met; c.1337C&gt;T, Thr446Met) in one case. Immunoblotting and immunofluorescence revealed that CFAP47 was dramatically reduced in spermatozoa from the CFAP47-mutated man. Meanwhile, the expression of WDR87 was also significantly decreased, and weak signals were detected adjacent to the spermatozoa nuclei, indicating that CFAP47 was necessary for WDR87 transportation during spermatozoa flagella biogenesis. These data indicate that WDR87 is located in the middle piece of the sperm tail and interacts with CFAP47 to form a complex which is involved in spermatozoa tail assembly.
Using Tumor-Informed Circulating Tumor DNA (ctDNA)-Based Testing for Patients with Anal Squamous Cell Carcinoma
Authors: Azzi Georges , Tavallai Mehrad , Aushev Vasily N , Koyen Malashevich Allyson , Botta Gregory P , Tejani Mohamedtaki A , Hanna Diana , Krinshpun Shifra , Malhotra Meenakshi , Jurdi Adham , Aleshin Alexey , Kasi Pashtoon M 
Published: December 2022

AbstractBackgroundAnal squamous cell carcinoma (SCCA) is an uncommon malignancy with a rising incidence that has a high cure rate in its early stages. There is an unmet need for a reliable method to monitor response to treatment and assist in surveillance. Circulating tumor DNA (ctDNA) testing has shown great promise in other solid tumors for monitoring disease progression and detecting relapse in real time. This study aimed to determine the feasibility and use of personalized and tumor-informed ctDNA testing in SCCA.Patients and MethodsWe analyzed real-world data from 251 patients (817 plasma samples) with stages I-IV SCCA, collected between 11/5/19 and 5/31/22. The tumor genomic landscape and feasibility of ctDNA testing was examined for all patients. The prognostic value of longitudinal ctDNA testing was assessed in patients with clinical follow-up (N = 37).ResultsWhole-exome sequencing analysis revealed PIK3CA as the most commonly mutated gene, and no associations between mutations and stage. Anytime ctDNA positivity and higher ctDNA levels (MTM/mL) were associated with metastatic disease (P = .004). For 37 patients with clinical follow-up, median follow-up time was 21.0 months (range: 4.1-67.3) post-diagnosis. For patients with stages I-III disease, anytime ctDNA-positivity after definitive treatment was associated with reduced DFS (HR: 28.0; P = .005).ConclusionsOur study demonstrates the feasibility of personalized and tumor-informed ctDNA testing as an adjunctive tool in patients with SCCA as well as potential use for detection of molecular/minuteimal residual disease, and relapse during surveillance. Prospective studies are needed to better evaluate the use of ctDNA testing in this indication.
Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture
Authors: Guan Jiahn-Chou , Li Changsheng , Flint-Garcia Sherry , Suzuki Masaharu , Wu Shan , Saunders Jonathan W , Dong Lemeng , Bouwmeester Harro J , McCarty Donald R , Koch Karen E 
Published: December 2022

Abstract
The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required profound developmental changes. However, the underlying mechanisms remain unclear and can only be partly attributed to the known domestication gene Teosinte glume architecture 1 (Tga1). Here we show that a more complete conversion involves strigolactones (SLs), and that these are prominent players not only in the Tga1 phenotype but also other domestication features of the ear and kernel. Genetic combinations of a teosinte tga1 allele with three SL-related mutants progressively enhanced ancestral morphologies. The SL mutants, in addition to modulating the tga1 phenotype, also reshaped kernel-bearing pedicels and cupules in a teosinte-like manner. Genetic and molecular evidence are consistent with SL regulation of TGA1, including direct interaction of TGA1 with components of the SL-signaling system shown here to mediate TGA1 availability by sequestration. Roles of the SL network extend to enhancing maize seed size and, importantly, coordinating increased kernel growth with remodeling of protective maternal tissues. Collectively, our data show that SLs have central roles in releasing kernels from restrictive maternal encasement and coordinating other factors that increase kernel size, physical support, and their exposure on the grain-bearing surface.
Relational Troubles Structuralist Worries for an Epistemology of Powers-Based Modality
Authors: Giannini Giacomo , Schoonen Tom 
Published: December 2022

AbstractDispositionalism is the theory of modality that grounds all modal truths in powers: all metaphysically possible and necessary truths are to be explained by pointing to some actual power, or absence thereof. One of the main reasons to endorse dispositionalism is that it promises to deliver an especially desirable epistemology of modality. However, so far this issue has not be fully investigated with the care it is due. The aim of this paper is to fill this gap. We will cast some doubts on whether the dispositionalist really is in a better position to explain our modal knowledge. In fact, we argue that there is a tension between some core tenets of a powers metaphysics and the very features that make dispositionalism the ideal backdrop for a desirable epistemology of modality. We conclude that this leaves dispositionalists who want to deliver the promised epistemology with a hard, currently unfulfilled, task.
Stratification and the comparison between homological and tensor triangular support
Authors: Barthel Tobias , Heard Drew , Sanders Beren 
Published: December 2022

Abstract
We compare the homological support and tensor triangular support for ‘big’ objects in a rigidly-compactly generated tensor triangulated category. We prove that the comparison map from the homological spectrum to the tensor triangular spectrum is a bijection and that the two notions of support coincide whenever the category is stratified, extending the work of Balmer. Moreover, we clarify the relations between salient properties of support functions and exhibit counter-examples highlighting the differences between homological and tensor triangular support.