bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance of antimicrobial resistant Shiga toxin-producing E. coli O157:H7 in England, 2016–2020
Authors: Greig David R , Do Nascimento Vivienne , Olonade Israel , Swift Craig , Nair Satheesh , Jenkins Claire 
Published: August 2023

Abstract

Objectives
Shiga toxin-producing Escherichia coli (STEC) O157:H7 are zoonotic pathogens and transmission to humans occurs via contaminated food or contact with infected animals. The aim of this study was to describe the frequency, and distribution across the phylogeny, of antimicrobial resistance (AMR) determinants in STEC O157:H7 isolated from human cases in England.

Methods
Short-read whole-genome sequencing data from 1473 isolates of STEC O157:H7 from all seven sub-lineages (Ia-Ic, IIa-IIc and I/II) were mapped to genes known to confer phenotypic resistance to 10 different classes of antibiotic. Long-read sequencing was used to determine the location and genomic architecture of the AMR determinants within phylogenetic clusters exhibiting multidrug resistance.

Results
Overall, 216/1473 (14.7%) isolates had at least one AMR determinant, although the proportion of isolates exhibiting AMR varied by sub-lineage. The highest proportion of AMR determinants were detected in sub-lineages Ib (28/64, 43.7%), I/II (18/51, 35.3%) and IIc (122/440, 27.7%). In all sub-lineages, the most commonly detected AMR determinants conferred resistance to the aminoglycosides, tetracyclines and sulphonamides, while AMR determinants conferring resistance to fluroquinolones, macrolides and third-generation cephalosporins were rarely detected. Long-read sequencing analysis showed that the AMR determinants were co-located on the chromosome in sub-lineages Ib and lineage I/II, whereas those associated with sub-lineage IIc were encoded on the chromosome and/or large plasmids.

Conclusions
AMR genes were unevenly distributed across the different sub-lineages of STEC O157:H7 and between different clades within the same sub-lineage. Long-read sequencing facilitates tracking the transmission of AMR at the pathogen and mobile genetic element level.
Decay kinetics of HIV-1-RNA in seminal plasma with dolutegravir/lamivudine versus dolutegravir plus emtricitabine/tenofovir alafenamide in treatment-naive people living with HIV
Authors: Saborido-Alconchel Abraham , Serna-Gallego Ana , Lopez-Cortes Luis E , Trujillo-Rodriguez María , Praena-Fernandez Juan Manuel , Dominguez-Macias Montserrat , Lozano Carmen , Muñoz-Muela Esperanza , Espinosa Nuria , Roca-Oporto Cristina , Sotomayor Cesar , Herrero Marta , Gutierrez-Valencia Alicia , Lopez-Cortes Luis F 
Published: August 2023

Abstract

Background
This was a substudy of a Phase IV, randomized clinical trial (ClinicalTrials.gov identifier: NCT04295460) aiming to compare the activity of dolutegravir/lamivudine versus dolutegravir plus tenofovir alafenamide/emtricitabine (DTG + TAF/FTC) in the male genital tract.

Methods
Participants were asymptomatic adults without sexually transmitted diseases, treatment-naive people living with HIV (PLWH), with CD4+ T cell counts &gt;200 cells/mm3 and plasma HIV-1-RNA levels &gt;5000 and &lt;500 000 copies/mL, randomized (1:1) to DTG + TAF/FTC or dolutegravir/lamivudine. Blood plasma (BP) and seminal plasma (SP) were collected at baseline and Weeks 4, 8, 12 and 24. HIV-1-RNA was measured in BP and SP using the Cobas 6800 system (Roche Diagnostics) with a lower detection limit of 20 copies/mL. The primary efficacy endpoint was the proportion of subjects with undetectable SP HIV-1-RNA at Week 12 by intention-to-treat analysis.

Results
Fifteen participants in the DTG + TAF/FTC and 16 in the dolutegravir/lamivudine arms were analysed, with basal SP viral load of 4.81 (4.30–5.43) and 4.76 (4.09–5.23), P = 0.469, respectively. At Week 12, only one participant in each treatment arm had a detectable SP HIV-1-RNA (DTG + TAF/FTC, 141 copies/mL; dolutegravir/lamivudine, 61 copies/mL). Based on the estimated means, there was no significant difference in the decay of HIV-1-RNA in both BP and SP over time between the two arms of treatment (F = 0.452, P = 0.662, and F = 1.147, P = 0.185, respectively).

Conclusions
After 12 weeks of treatment, there were no differences in the percentage of undetectable SP HIV-1-RNA in naive PLWH who started dolutegravir/lamivudine compared with DTG + TAF/FTC.
Fine-mesh exclusion netting reduces Drosophila suzukii (Diptera: Drosophilidae) infestation and improves organic fall-bearing raspberry yields
Authors: Kuesel Ryan , Avery Chelsea , Jones Sarah , Gauger Alexis , Scott Delia , Gonthier David 
Published: August 2023

Abstract
The economical production of small fruits has been significantly complicated by the spotted-wing drosophila, Drosophila suzukii Matsumura, throughout its invaded rage. Fall-bearing red raspberries are especially susceptible to D. suzukii, and significant efforts to mitigate their damage are undertaken by growers. Exclusion barriers made from fine-mesh netting has emerged as an organic compliant strategy to mitigate damage from D. suzukii. Identifying less susceptible raspberry cultivars may also alleviate D. suzukii damage. Key pollination complications arise from exclusion-based tactics, but properly timing exclusion establishment may provide a remedy. In a 2-yr-old fall-bearing raspberry planting containing 3 cultivars, exclusion barriers were erected at 2 phenological timings. Spinosad- and pyrethrin-based pesticides were also applied to separate rows throughout harvest and a fourth treatment group matured without management. A subsection of raspberries was harvested and examined for marketability or damage, and D. suzukii adult populations were sampled with baited traps. An exclusion barrier applied early in fruit development was the most effective pest management strategy of those we tested. Its use decreased D. suzukii captures by 75%, decreased D. suzukii-infested fruit weights by 48%, and increased marketable yield by 63% compared to the no management control; however, it also increased pollination deficient fruit weights. Exclusion netting applied later in fruit maturation also decreased D. suzukii captures, infested fruit weights, and the weight of fruits damaged by other arthropod pests but did not significantly increase marketable yield. Our results indicate that netting exclusions may hold promise for the economical production of fall-bearing raspberries.
Computing minimal unsatisfiable core for LTL over finite traces
Authors: Niu Tong , Xiao Shengping , Zhang Xiaoyu , Li Jianwen , Huang Yanhong , Shi Jianqi 
Published: August 2023

Abstract
In this paper, we consider the minimal unsatisfiable core (MUC) problem for linear temporal logic over finite traces (LTL$_{f}$), which nowadays is a popular formal-specification language for AI-related systems. Efficient algorithms to compute such MUCs can help locate the inconsistency rapidly in the written LTL$_{f}$ specification and are very useful for the system designers to amend the flawed requirement. As far as we know, there are no available tools off-the-shelf so far that provide MUC computation for LTL$_{f}$. We present here two generic approaches NaiveMUC and BinaryMUC to compute an MUC for LTL$_{f}$. Moreover, we introduce heuristics that are based on the Boolean unsatisfiable core (UC) technique to accelerate the two approaches, which are named NaiveMUC+UC and BinaryMUC+UC, respectively. In particular, for global LTL$_{f}$ formulas, we show that the MUC computation can be reduced to the pure Boolean MUC computation, which therefore conducts the GlobalMUC approach. Our experiments show that GlobalMUC performs the best to compute an MUC for global formulas, and BinaryMUC+UC is the best for an arbitrary unsatisfiable formula.
A parametrized axiomatization for a large number of restricted second-order logics
Authors: Badia Guillermo , Bell John L 
Published: August 2023

Abstract
By limiting the range of the predicate variables in a second-order language, one may obtain restricted versions of second-order logic such as weak second-order logic or definable subset logic. In this note, we provide an infinitary strongly complete axiomatization for several systems of this kind having the range of the predicate variables as a parameter. The completeness argument uses simple techniques from the theory of Boolean algebras.
This article is dedicated to our friend John N. Crossley on the occasion of his 86th birthday.
Long-term remission of VEXAS syndrome achieved by a single course of CHOP therapy: A case report
Authors: Miyoshi Yuji , Kise Takayasu , Morita Kaoru , Okada Haruka , Imadome Ken-Ichi , Tsuchida Naomi , Maeda Ayaka , Uchiyama Yuri , Kirino Yohei , Matsumoto Naomichi , Yokogawa Naoto 
Published: August 2023

ABSTRACT
We herein describe the case of a 52-year-old male patient who presented with fever, arthritis, and neutrophilic dermatosis in 2013 and subsequently experienced macrophage activation syndrome treated with high-dose glucocorticoid therapy. Due to the persistent symptoms refractory to several immunomodulatory and immunosuppressive (IS) drug therapies with dapsone, methotrexate, tacrolimus, infliximab (IFX), and tocilizumab (TCZ), he received prednisolone (PSL) ≥20 mg/day to suppress disease activity. In 2017, Epstein–Barr virus (EBV)–associated haemophagocytic lymphohistiocytosis (HLH) was diagnosed and initially treated with immunochemotherapy consisting of dexamethasone, cyclosporine (CyA), and etoposide (ET). Because of the suboptimal response to the initial therapy, cytoreduction therapy consisting of CHOP (combination chemotherapy consisting of cyclophosphamide, doxorubicin, vincristine, and PSL) was administered. This regimen improved the EBV-associated HLH. Later, the patient’s condition stabilised with methylprednisolone 1 mg/day and CyA 100 mg/day. In 2022, ubiquitylation-initiating E1 enzyme (UBA1) variant analysis using Sanger sequencing of peripheral blood leukocytes detected a previously reported somatic variant (NM_003334.3: c.118-1G&gt;C), confirming the diagnosis of vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome. The clinical course in the present case suggested the possibility that CHOP could be a potential treatment option for VEXAS syndrome, in the pathophysiology of which the expansion of clones with UBA1 variant seems to play a pivotal role.
Click display: a rapid and efficient in vitro protein display method for directed evolution
Authors: Zeng Yu , Woolley Michael , Chockalingam Karuppiah , Thomas Benjamin , Arora Srishtee , Hook Magnus , Chen Zhilei 
Published: August 2023

Abstract
We describe a novel method for in vitro protein display—click display—that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein–cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translation and reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker—ML—generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed &gt;600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.
Crystal structure of a cap-independent translation enhancer RNA
Authors: Lewicka Anna , Roman Christina , Jones Stacey , Disare Michael , Rice Phoebe A , Piccirilli Joseph A 
Published: August 2023

Abstract
In eukaryotic messenger RNAs, the 5′ cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5′ cap structure, some contain cap-independent translation elements (CITEs) in their 3′ untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV2) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV2 tertiary architecture is conserved among these homologs.
Baseline Tumor Size as Prognostic Index in Patients With Advanced Solid Tumors Receiving Experimental Targeted Agents
Authors: Nicolò Eleonora , Tarantino Paolo , D’Ecclesiis Oriana , Antonarelli Gabriele , Boscolo Bielo Luca , Marra Antonio , Gandini Sara , Crimini Edoardo , Giugliano Federica , Zagami Paola , Corti Chiara , Trapani Dario , Morganti Stefania , Criscitiello Carmen , Locatelli Marzia , Belli Carmen , Esposito Angela , Minchella Ida , Cristofanilli Massimo , Tolaney Sara M , Curigliano Giuseppe 
Published: August 2023

Abstract

Background
Baseline tumor size (BTS) has been associated with outcomes in patients with cancer treated with immunotherapy. However, the prognostic impact of BTS on patients receiving targeted therapies (TTs) remains undetermined.

Methods
We reviewed data of patients with advanced solid tumors consecutively treated within early-phase clinical trials at our institution from 01/2014 to 04/2021. Treatments were categorized as immunotherapy-based or TT-based (biomarker-matched or not). BTS was calculated as the sum of RECIST1.1 baseline target lesions.

Results
A total of 444 patients were eligible; the median BTS was 69 mm (IQR 40-100). OS was significantly longer for patients with BTS lower versus higher than the median (16.6 vs. 8.2 months, P &lt; .001), including among those receiving immunotherapy (12 vs. 7.5 months, P = .005). Among patients receiving TT, lower BTS was associated with longer PFS (4.7 vs. 3.1 months, P = .002) and OS (20.5 vs. 9.9 months, P &lt; .001) as compared to high BTS. However, such association was only significant among patients receiving biomarker-matched TT, with longer PFS (6.2 vs. 3.3 months, P &lt; .001) and OS (21.2 vs. 6.7 months, P &lt; .001) in the low-BTS subgroup, despite a similar ORR (28% vs. 22%, P = .57). BTS was not prognostic among patients receiving unmatched TT, with similar PFS (3.7 vs. 4.4 months, P = .30), OS (19.3 vs. 11.8 months, P = .20), and ORR (33% vs. 28%, P = .78) in the 2 BTS groups. Multivariate analysis confirmed that BTS was independently associated with PFS (P = .03) and OS (P &lt; .001) but not with ORR (P = .11).

Conclusions
Higher BTS is associated with worse survival outcomes among patients receiving biomarker-matched, but not biomarker-unmatched TT.
KAI2 Can Do: Karrikin Receptor Function in Plant Development and Response to Abiotic and Biotic Factors
Authors: Varshney Kartikye , Gutjahr Caroline 
Published: August 2023

Abstract
The α/β hydrolase KARRIKIN INSENSITIVE 2 (KAI2) functions as a receptor for a yet undiscovered phytohormone, provisionally termed KAI2 ligand (KL). In addition, it perceives karrikin, a butenolide compound found in the smoke of burnt plant material. KAI2-mediated signaling is involved in regulating seed germination and in shaping seedling and adult plant morphology, both above and below ground. It also governs responses to various abiotic stimuli and stresses and shapes biotic interactions. KAI2-mediated signaling is being linked to an elaborate cross-talk with other phytohormone pathways such as auxin, gibberellin, abscisic acid, ethylene and salicylic acid signaling, in addition to light and nutrient starvation signaling. Further connections will likely be revealed in the future. This article summarizes recent advances in unraveling the function of KAI2-mediated signaling and its interaction with other signaling pathways.
Membrane microdomains: Structural and signaling platforms for establishing membrane polarity
Authors: Li Ruili , Zhao Ran , Yang Mei , Zhang Xi , Lin Jinxing 
Published: August 2023

AbstractCell polarity results from the asymmetric distribution of cellular structures, molecules, and functions. Polarity is a fundamental cellular trait that can determine the orientation of cell division, the formation of particular cell shapes, and ultimately the development of a multicellular body. To maintain the distinct asymmetric distribution of proteins and lipids in cellular membranes, plant cells have developed complex trafficking and regulatory mechanisms. Major advances have been made in our understanding of how membrane microdomains influence the asymmetric distribution of proteins and lipids. In this review, we first give an overview of cell polarity. Next, we discuss current knowledge concerning membrane microdomains and their roles as structural and signaling platforms to establish and maintain membrane polarity, with a special focus on the asymmetric distribution of proteins and lipids, and advanced microscopy techniques to observe and characterize membrane microdomains. Finally, we review recent advances regarding membrane trafficking in cell polarity establishment and how the balance between exocytosis and endocytosis affects membrane polarity.
A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Authors: Martín-Hervás M Rosario , Carmona Leila , Jensen Kathe R , Krug Patrick J , Vitale Fabio , Cervera Juan Lucas 
Published: August 2023

Abstract
The genus Elysia comprises about one-third of the species richness in Sacoglossa. However, the species diversity in the genus remains poorly characterized in some areas like the north-eastern Atlantic and Mediterranean waters. To clarify the systematics of this genus and to characterize the species diversity in undersampled regions, we performed an integrative study based on a thorough literature review, molecular and morphological analyses, and species delimitation approaches. We conducted phylogenetic analyses of partial sequences of two mitochondrial genes (COI and 16S) and two nuclear genes (H3, 28S) using Bayesian inference and maximum likelihood methods, which confirmed the presence of five of the recognized European Elysia species: Elysia viridis, E. timida, E. flava, E. margaritae, and E. rubeni. Moreover, a new species (Elysia azorica sp. nov.) was identified in the Azores, and E. gordanae, currently considered a junior synonym of E. margaritae, was recovered as a distinct species. In addition, we consider E. hetta as a junior synonym of E. gordanae, and E. translucens as a taxon inquirendum. Finally, the tropical E. evelinae is recorded along European coasts for the first time. Our results demonstrate the value of integrative approaches in resolving taxonomic uncertainty surrounding polymorphism and unravelling potential cases of cryptic or pseudocryptic species complexes.
Duration and Timing of In Utero Opioid Exposure and Incidence of Neonatal Withdrawal Syndrome
Authors: Wang Yi , Berger Lawrence , Durrance Christine , Kirby Russell S. , Kuo Daphne , Pac Jessica , Ehrenthal Deborah B. 
Published: August 2023

OBJECTIVE:
To evaluate the association between prenatal prescription opioid analgesic exposure (duration, timing) and neonatal opioid withdrawal syndrome (NOWS).

METHODS:
We conducted a retrospective cohort study of Wisconsin Medicaid–covered singleton live births from 2011 to 2019. The primary outcome was a NOWS diagnosis in the first 30 days of life. Opioid exposure was identified with any claim for prescription opioid analgesic fills during pregnancy. We measured exposure duration cumulatively in days (1–6, 7–29, 30–89, and 90 or more) and identified timing as early (first two trimesters only) or late (third trimester, regardless of earlier pregnancy use). We used logistic regression modeling to assess NOWS incidence by exposure duration and timing, with and without propensity score matching.

RESULTS:
Overall, 31,456 (14.3%) of 220,570 neonates were exposed to prescription opioid analgesics prenatally. Among exposed neonates, 19,880 (63.2%) had 1–6 days of exposure, 7,694 (24.5%) had 7–29 days, 2,188 (7.0%) had 30–89 days, and 1,694 (5.4%) had 90 or more days of exposure; 15,032 (47.8%) had late exposure. Absolute NOWS incidence among neonates with 1–6 days of exposure was 7.29 per 1,000 neonates (95% CI 6.11–8.48), and incidence increased with longer exposure: 7–29 days (19.63, 95% CI 16.53–22.73); 30–89 days (58.96, 95% CI 49.08–68.84); and 90 or more days (177.10, 95% CI 158.90–195.29). Absolute NOWS incidence for early and late exposures were 11.26 per 1,000 neonates (95% CI 9.65–12.88) and 35.92 per 1,000 neonates (95% CI 32.95–38.90), respectively. When adjusting for confounders including timing of exposure, neonates exposed for 1–6 days had no increased odds of NOWS compared with unexposed neonates, whereas those exposed for 30 or more days had increased odds of NOWS (30–89 days: adjusted odds ratio [aOR] 2.15, 95% CI 1.22–3.79; 90 or more days: 2.80, 95% CI 1.36–5.76). Late exposure was associated with elevated odds of NOWS (aOR 1.57, 95% CI 1.25–1.96) when compared with unexposed after adjustment for exposure duration.

CONCLUSION:
More than 30 days of prenatal prescription opioid exposure was associated with NOWS regardless of exposure timing. Third-trimester opioid exposure, irrespective of exposure duration, was associated with NOWS.
Surgical management of uterine fibroids
Authors: Lazaridis Alexandros , Hirsch Martin , Pistofidis George , Odejinmi Funlayo 
Published: August 2023

Purpose of review
Fibroids are benign pelvic masses and constitute the most common gynaecological condition. They create a significant health and social burden to many women because of heavy menstrual bleeding and fibroid pressure symptoms. Many women will be faced with the dilemma of surgical management to improve their symptoms at some point of their reproductive age. The aim of this article is to identify current surgical management of fibroids describing the technical steps, advantages, disadvantages and risks of each method.

Recent findings
The surgical management of fibroids remains challenging, as the overall prevalence, the clinical experience and the patient awareness is increasing because of an upgrade in our sonographic and magnetic resonance diagnostic tools. Unfortunately not every patient is able to benefit from tailor-made surgery that holistically evaluates individual needs including fertility aspirations.

Summary
This article provides the most current synopsis of every available surgical modality for fibroid management. Large prospective multicentre cohort studies are needed to definitely determine the most suitable operation for any individual suffering with fibroids; and perhaps artificial intelligence may offer a valuable tool in the future data analysis.