bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytologic analysis of metaplastic breast carcinoma: Review of 66 cases diagnosed at the Institut Curie
Authors: Kowalewski Adam , Klijanienko Jerzy 
Published: November 2023

Abstract

Objectives
Cytology reports of metaplastic breast carcinoma (MBC) are rare and limited to short series and simple case reports. To adapt cytology diagnostic criteria to the most recent fifth edition of the World Health Organization Classification of Breast Tumours from 2019, we have reviewed our series from the files of the Institut Curie.

Methods
A cohort of 66 female patients investigated by cytology with corresponding histologic diagnosis of MBC was identified. Eight cytologic characteristics were analyzed: cellularity, adenocarcinoma cells, squamous cells, spindle cells, giant cells, cytonuclear atypia, necrosis, and osseous/chondroid matrix and compared with histology.

Results
Cytologic diagnoses were malignant in 58 (88%) cases (of which 29 cases were typed cytologically as MBC), suspicious in 6 (9%) cases, and nondiagnostic in 2 (3%) cases. None of the cytologic examinations was a benign diagnosis. Low-grade adenosquamous carcinoma and fibromatosis-like metaplastic carcinoma exhibited a low degree of cellular atypia. Fibromatosis-like metaplastic carcinoma and spindle cell carcinoma (SpCC) presented spindle cells, while SpCC also demonstrated varying degrees of atypia, the presence of giant cells, and necrosis. Squamous cell carcinoma was characterized by the presence of squamous cells, and metaplastic carcinoma with osseous/chondroid differentiation displayed an osseous/chondroid matrix.

Conclusions
Fine-needle aspiration holds considerable potential as a valid, independent, and complementary approach to histologic examination of MBC.
From bench to bedside: potential of translational research in COVID-19 and beyond
Authors: Shukla Nityendra , Shamim Uzma , Agarwal Preeti , Pandey Rajesh , Narayan Jitendra 
Published: November 2023

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) have been around for more than 3 years now. However, due to constant viral evolution, novel variants are emerging, leaving old treatment protocols redundant. As treatment options dwindle, infection rates continue to rise and seasonal infection surges become progressively common across the world, rapid solutions are required. With genomic and proteomic methods generating enormous amounts of data to expand our understanding of SARS-CoV-2 biology, there is an urgent requirement for the development of novel therapeutic methods that can allow translational research to flourish. In this review, we highlight the current state of COVID-19 in the world and the effects of post-infection sequelae. We present the contribution of translational research in COVID-19, with various current and novel therapeutic approaches, including antivirals, monoclonal antibodies and vaccines, as well as alternate treatment methods such as immunomodulators, currently being studied and reiterate the importance of translational research in the development of various strategies to contain COVID-19.
In search of genetic modifiers that explain the phenotypic variability in SMAD3-related aortopathy
Authors: Velchev J , Richer J , Meester J , Verstraeten A , Alaerts M , Loeys B 
Published: November 2023

Abstract

Introduction
Loeys-Dietz Syndrome (LDS) is an autosomal dominant connective tissue disorder presenting with thoracic aortic aneurysm and dissection (TAAD). Remarkably, some LDS patients remain cardiovascularly unaffected throughout life, while others carrying the exact same genetic variant die early because of an aortic dissection. We hypothesize that genetic modifiers are the basis of this observation.

Objectives
Identify genetic modifiers that explain the variability in LDS-related aortopathy.
Generate a patient-specific iPSC-vascular smooth muscle cell (VSMC) model to allow functional validation of genetic modifiers.

Material and Methods
We have access to a large LDS family segregating a pathogenic SMAD3 (p.Arg287Gln) variant. Identification of candidate modifiers in this family encompasses genome-wide SNP-based linkage analysis (n=19, available mutation carriers) and WGS (3 affected (AMC) and 4 unaffected mutation carriers (UMC)). Subsequent functional validation involves CRISPR/Cas-based modifier correction in iPSC-VSMCs of an affected variant carrier, which are created using the CytoTune iPS 2.0 Kit and the Granata et al. VSMC differentiation protocols.

Results
Linkage analysis suggests the presence of an aggravating modifier at chr2 (LOD: 2.68). The region of 6 Mb contains 19 protein coding genes of which the TNFAIP6 gene was ToppGene prioritized. There were no exonic variants in any of the genes that segregate with affection status at MAF 0.01%. However, we are currently adapting the the filtering strategy and will look into more common variants, MAF 10% for exonic and MAF 5% for intronic variants.
iPSCs of an AMC and its isogenic control were created. They express core pluripotency markers and possess trilineage differentiation potential in the absence of the Sendai vectors. SNP array confirmed the genomic stability and identity of the cells.

Conclusion and Future Work
The obtained data suggest the presence of an aggravating modifier at chr2. Further analyses are ongoing to pinpoint the exact modifier variant explaining the linkage signal. Subsequently, the identified modifier(s) will be modelled in an in-vitro created iPSC-VSMC model.
Linear accelerator–based stereotactic arrhythmia radioablation for paroxysmal atrial fibrillation in elderly: a prospective phase II trial
Authors: Di Monaco Antonio , Gregucci Fabiana , Bonaparte Ilaria , Romanazzi Imma , Troisi Federica , Surgo Alessia , Vitulano Nicola , Quadrini Federico , Valenti Noemi , Carbonara Roberta , Di Guglielmo Fiorella Cristina , Ludovico Elena , Calbi Roberto , Guida Pietro , Ciliberti Maria Paola , Fiorentino Alba , Grimaldi Massimo 
Published: November 2023

Abstract

Aims
Stereotactic arrhythmia radioablation (STAR) is a novel therapeutic approach for cardiac arrhythmias. The aim of this trial is to investigate the feasibility of STAR for the treatment of paroxysmal atrial fibrillation (AF) in elderly patients.

Methods and results
Inclusion criteria were age &gt;70 years, symptomatic AF, antiarrhythmic drugs failure, or intolerance. All patients underwent to 4D cardiac computed tomography simulation. The clinical target volume was identified in the area around pulmonary veins (PV). Stereotactic arrhythmia radioablation was performed with a total dose of 25 Gy (single fraction) delivered in 3 min. Twenty patients were enrolled and 18 underwent STAR. One patient withdrew informed consent before treatment and one patient was excluded due to unfavourable oesophagus position. With a median follow-up (FU) of 16 months (range 12–23), no acute toxicity more than Grade 3 was reported. Five patients had a Grade 1 oesophagitis 24 h after STAR; eight patients had an asymptomatic Grade 1 pericardial effusion, and one patient had a torsade de pointes treated effectively by electrical cardioversion and subsequent cardiac implantable cardioverter-defibrillator implantation. Most patients had a significant reduction in AF episodes. Five patients, due to arrhythmias recurrences after STAR, performed electrophysiological study documenting successful PV isolation. Finally, a significant improvement of quality of life was documented (48 ± 15 at enrolment vs. 75 ± 15 at 12 months FU; P &lt; 0.001).

Conclusion
The present phase II trial demonstrated the feasibility of STAR in paroxysmal AF elderly patients and its potential role in increasing the quality of life. Surely, more robust data are needed about safety and efficacy.

Trial registration
ClinicalTrials.gov: NCT04575662
Getting ready for reduced donor dependency: the co-financing of family planning commodities
Authors: Jha Ayan , Kolesar Robert John , Comas Sophia , Gribble Jay , Ugaz Jorge , Gonzalez-Pier Eduardo 
Published: November 2023

Abstract
Family planning (FP) programmes in low and lower-middle income countries are confronting the dual impact of reduced external donor commitments and stagnant or reduced domestic financing, worsened by economic consequences of the COVID-19 pandemic. Co-financing—a donor-government agreement to jointly fund aspects of a programme, with transition towards the government assuming increasing responsibility for total cost—can be a powerful tool to help build national ownership, fiscal sustainability and programme visibility. Using Gavi’s successful co-financing model as reference, the current paper draws out a set of key considerations for developing policies on co-financing of FP commodities in resource-poor settings. Macroeconomic and contextual sensitivities must be incorporated while classifying countries and determining co-financing obligations—using the actual GNI per capita on a scale or sovereign credit ratings, in conjunction with programmatic indicators, may be preferred. It is also important for policies to allow sufficiently long time for countries to transition—dependent on the country context, may be up to 10 years as allowed under the US Agency for International Development FP graduation policy and flexibility to revisit the terms following externalities that can influence the fiscal space for health. Incentivizing new domestic financing to pay for co-financing dues is critical, so as not to displace government funding from related health or social sector programs. Pragmatic ways to ensure country compliance can include engaging both the ministries of health and finance as co-signatories to identify and address known administrative and fiscal challenges; establishing dedicated co-financing account with the finance ministry; and instituting a mutual monitoring mechanism. Lastly, the overall process of policymaking can benefit from an alignment of goals and interests of the key development partners.
Variation in antibiotic consumption in very preterm infants—a 10 year population-based study
Authors: Huncikova Zuzana , Stensvold Hans Jørgen , Øymar Knut Asbjørn Alexander , Vatne Anlaug , Lang Astri Maria , Støen Ragnhild , Brigtsen Anne Karin , Moster Dag , Eriksen Beate Horsberg , Selberg Terje , Rønnestad Arild , Klingenberg Claus 
Published: November 2023

Abstract

Objectives
Wide variations in antibiotic use in very preterm infants have been reported across centres despite similar rates of infection. We describe 10 year trends in use of antibiotics and regional variations among very preterm infants in Norway.

Patients and Methods
All live-born very preterm infants (&lt;32 weeks gestation) admitted to any neonatal unit in Norway during 2009–18 were included. Main outcomes were antibiotic consumption expressed as days of antibiotic therapy (DOT) per 1000 patient days (PD), regional variations in use across four health regions, rates of sepsis and sepsis-attributable mortality and trends of antibiotic use during the study period.

Results
We included 5296 infants: 3646 (69%) were born at 28–31 weeks and 1650 (31%) were born before 28 weeks gestation with similar background characteristics across the four health regions. Overall, 80% of the very preterm infants received antibiotic therapy. The most commonly prescribed antibiotics were the combination of narrow-spectrum β-lactams and aminoglycosides, but between 2009 and 2018 we observed a marked reduction in their use from 100 to 40 DOT per 1000 PD (P &lt; 0.001). In contrast, consumption of broad-spectrum β-lactams remained unchanged (P = 0.308). There were large variations in consumption of vancomycin, broad-spectrum β-lactams and first-generation cephalosporins, but no differences in sepsis-attributable mortality across regions.

Conclusions
The overall antibiotic consumption was reduced during the study period. Marked regional variations remained in consumption of broad-spectrum β-lactams and vancomycin, without association to sepsis-attributable mortality. Our results highlight the need for antibiotic stewardship strategies to reduce consumption of antibiotics that may enhance antibiotic resistance development.
A chromosome-level genome assembly for the smoky rubyspot damselfly (Hetaerina titia)
Authors: Patterson Christophe W , Bonillas-Monge Erandi , Brennan Adrian , Grether Gregory F , Mendoza-Cuenca Luis , Tucker Rachel , Vega-Sánchez Yesenia M , Drury Jonathan 
Published: November 2023

Abstract
Smoky rubyspot damselflies (Hetaerina titia Drury, 1773) are one of the most commonly encountered odonates along streams and rivers on both slopes of Central America and the Atlantic drainages in the United States and southern Canada. Owing to their highly variable wing pigmentation, they have become a model system for studying sexual selection and interspecific behavioral interference. Here, we sequence and assemble the genome of a female smoky rubyspot. Of the primary assembly (i.e. the principle pseudohaplotype), 98.8% is made up of 12 chromosomal pseudomolecules (2N = 22A + X). There are 75 scaffolds in total, an N50 of 120 Mb, a contig-N50 of 0.64 Mb, and a high arthropod BUSCO score [C: 97.6% (S: 97.3%, D: 0.3%), F: 0.8%, M: 1.6%]. We then compare our assembly to that of the blue-tailed damselfly genome (Ischnura elegans), the most complete damselfly assembly to date, and a recently published assembly for an American rubyspot damselfly (Hetaerina americana). Collectively, these resources make Hetaerina a genome-enabled genus for further studies of the ecological and evolutionary forces shaping biological diversity.
The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
Authors: Wolf Magnus , Greve Carola , Schell Tilman , Janke Axel , Schmitt Thomas , Pauls Steffen U , Aspöck Horst , Aspöck Ulrike 
Published: November 2023

Abstract
Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.
Toward quantitative super-resolution microscopy: molecular maps with statistical guarantees
Authors: Proksch Katharina , Werner Frank , Keller–Findeisen Jan , Ta Haisen , Munk Axel 
Published: November 2023

Abstract
Quantifying the number of molecules from fluorescence microscopy measurements is an important topic in cell biology and medical research. In this work, we present a consecutive algorithm for super-resolution (stimulated emission depletion (STED)) scanning microscopy that provides molecule counts in automatically generated image segments and offers statistical guarantees in form of asymptotic confidence intervals. To this end, we first apply a multiscale scanning procedure on STED microscopy measurements of the sample to obtain a system of significant regions, each of which contains at least one molecule with prescribed uniform probability. This system of regions will typically be highly redundant and consists of rectangular building blocks. To choose an informative but non-redundant subset of more naturally shaped regions, we hybridize our system with the result of a generic segmentation algorithm. The diameter of the segments can be of the order of the resolution of the microscope. Using multiple photon coincidence measurements of the same sample in confocal mode, we are then able to estimate the brightness and number of molecules and give uniform confidence intervals on the molecule counts for each previously constructed segment. In other words, we establish a so-called molecular map with uniform error control. The performance of the algorithm is investigated on simulated and real data.
Solving the puzzle of climacteric fruit ripening: EMB1444-like and its regulatory function
Authors: Bellinazzo Francesca 
Published: November 2023

This article comments on:Zhao W, Wang S, Li W, Shan X, Naeem M, Zhang L, Zhao L. 2023. The transcription factor EMB1444-like affects tomato fruit ripening by regulating YELLOW-FRUITED TOMATO 1, a core component of ethylene signaling transduction. Journal of Experimental Botany 74, 6563–6574.
Bristling with potential: evaluating the effects of awns on yield under heat stress
Authors: Adamski Nikolai M 
Published: November 2023

This article comments on:DeWitt N, Lyerly J, Guedira M, Holland JB, Murphy JP, Ward BP, Boyles RE, Mergoum M, Babar MA, Shakiba E, Sutton R, Ibrahim A, Tiwari V, Santantonio N, Van Sanford DA, Howell K, Smith JH, Harrison SA, Brown-Guedira G. 2023. Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States. Journal of Experimental Botany 74, 6749–6759.
Auxin/cytokinin antagonism in shoot development: from moss to seed plants
Authors: Kotov Andrey A , Kotova Liudmila M 
Published: November 2023

This article comments on:
Cammarata J, Roeder AHK, Scanlon MJ. 2023. The ratio of auxin to cytokinin controls leaf development and meristem initiation in Physcomitrium patens. Journal of Experimental Botany 74, 6541–6550.
Arabidopsis G-protein β subunit AGB1 represses abscisic acid signaling via attenuation of the MPK3–VIP1 phosphorylation cascade
Authors: Xu Dongbei , Tang Wensi , Ma Yanan , Wang Xia , Yang Yanzhi , Wang Xiaoting , Xie Lina , Huang Suo , Qin Tengfei , Tang Weilin , Xu Zhaoshi , Li Lei , Tang Yimiao , Chen Ming , Ma Youzhi 
Published: November 2023

Abstract
Heterotrimeric G proteins play key roles in cellular processes. Although phenotypic analyses of Arabidopsis Gβ (AGB1) mutants have implicated G proteins in abscisic acid (ABA) signaling, the AGB1-mediated modules involved in ABA responses remain unclear. We found that a partial AGB1 protein was localized to the nucleus where it interacted with ABA-activated VirE2-interacting protein 1 (VIP1) and mitogen-activated protein kinase 3 (MPK3). AGB1 acts as an upstream negative regulator of VIP1 activity by initiating responses to ABA and drought stress, and VIP1 regulates the ABA signaling pathway in an MPK3-dependent manner in Arabidopsis. AGB1 outcompeted VIP1 for interaction with the C-terminus of MPK3, and prevented phosphorylation of VIP1 by MPK3. Importantly, ABA treatment reduced AGB1 expression in the wild type, but increased in vip1 and mpk3 mutants. VIP1 associates with ABA response elements present in the AGB1 promoter, forming a negative feedback regulatory loop. Thus, our study defines a new mechanism for fine-tuning ABA signaling through the interplay between AGB1 and MPK3–VIP1. Furthermore, it suggests a common G protein mechanism to receive and transduce signals from the external environment.
Single versus dual inoculation with indigenous Saccharomyces cerevisiae strains in winemaking
Authors: Chalvantzi Ioanna , Mallouchos Athanasios , Banilas Georgios , Nisiotou Aspasia 
Published: November 2023

Abstract
Indigenous Saccharomyces cerevisiae strains and their combinations may be used to diversify wines and add complexity to sensory profiles. Here, two S. cerevisiae strains that represent regional genetic and phenotypic specificities for two major winegrowing areas of Greece were used in single- and mixed-culture fermentations. The kinetics and metabolic activities of the strains were analyzed to evaluate the influence of each strain individually or in combination on wine quality. The two strains differentially affected the kinetics and the outcome of fermentation. They showed significant differences in the production of important metabolites that strongly affect the organoleptic profile of wines, such as volatile acidity, acetaldehyde, certain esters, and terpenes. Furthermore, the chemical and sensory profiles of wines produced by single cultures were different from those fermented by mixed-culture inoculum. The concentration of certain metabolites was enhanced (e.g. isoamyl acetate, 1-heptanol), while others were suppressed (e.g. hexyl acetate, octyl acetate). Results highlight the potential worth of indigenous S. cerevisiae strains to differentiate local wines. The mixed-culture S. cerevisiae inoculum was shown to generate novel wine characteristics, as compared to single cultures, thus offering alternatives to further diversify wines and increase their complexity.
Period variability in the pulsating Extreme Helium stars V652 Her and BX Cir
Authors: Kilkenny D , Worters H L , Baran A S 
Published: November 2023

ABSTRACT
Eighteen new timings of maxima of the radially pulsating Extreme Helium star, V652 Her, obtained during 2010–2023 are reported, together with 26 new timings of the very similar star, BX Cir, during 2014–2023. New ephemerides are derived from baselines which are now substantially longer than previously published. Both ephemerides are thus refined and, in the case of BX Cir, we find for the first time evidence of a cubic term (the period change rate is decreasing). BX Cir data from the Transiting Exoplanet Survey Satellite (TESS) reveals a previously unreported frequency near 65 μHz (period ∼ 0.179 d) with amplitude ∼0.002 mag.