bluuebunny/crossref_metadata_2025_split huggingface dataset:
The King's aquatic desires: 16th‐century fish and crayfish introductions into Spain
Authors: Clavero Miguel 
Published: June 2022

AbstractHumans have introduced species out of their native areas for millennia, and characterising these historical introductions can provide insights into the long‐term progress of invasion processes. Here, archival sources and other historical documents are used to describe the motivations, negotiations and actions leading to fish and crayfish introductions into Spain in the second half of the 16th century. King Philip II of Spain brought to the Iberian Peninsula several gardening customs from central Europe, including the construction of fish ponds and their stocking with different aquatic species, many of which were naturally absent from Iberia. These interests led to the introduction of pike (Esox Lucius, Esocidae), common carp (Cyprinus carpio, Cyprinidae), tench (Tinca tinca, Cyprinidae) and Italian crayfish (Austropotamobius italicus, Astacidae). Historical documents allowed describing introduction events, their early management and their outcomes with high temporal, spatial and taxonomic precision. These results introduce a centuries‐long view on the history of the presence of these introduced species in the Iberian Peninsula, where they have all been successful invaders in different historical periods. This work exemplifies the large potential of archival documents to inform about long‐term human–nature relationships, with implications for present‐day environmental management (e.g. setting conservation targets). However, this potential has been only sparsely explored, arguably due to the lack of interactions between humanities and natural sciences. Interdisciplinary historical ecology research should be promoted in order to build robust and applicable knowledge on the long‐term variability of ecosystems and their biota.
Befovacimab, an anti‐tissue factor pathway inhibitor antibody: Early termination of the multiple‐dose, dose‐escalating Phase 2 study due to thrombosis
Authors: Mancuso Maria Elisa , Ingham Sheila J. M. , Kunze Marc 
Published: June 2022

AbstractIntroductionBefovacimab (formerly BAY 1093884) is a fully human monoclonal antibody able to bind to tissue factor pathway inhibitor (TFPI) and developed as a non‐replacement therapy for individuals with haemophilia A/B, with or without inhibitors.AimTo assess the safety of multiple escalating doses of befovacimab in individuals with severe haemophilia A/B with or without inhibitors.MethodsIn this non‐randomised, open‐label Phase 2 study (NCT03597022), adult males with <1% factor VIII or <2% factor IX and ≥4 bleeds in the previous six months were enrolled in three dose cohorts (100/225/400 mg). Participants received befovacimab subcutaneously once weekly. The primary endpoint was safety; secondary endpoints included annualised bleeding rate (ABR) and pharmacokinetics/pharmacodynamics (PK/PD) of befovacimab.ResultsA total of 24 participants (n = 8 in each dose cohort) were treated for 2–47 weeks. Patients treated with 100 mg and 225 mg doses of befovacimab demonstrated improved bleeding control compared with pre‐study bleeding rates, with a dose‐dependent effect. Dosing was suspended and the study prematurely terminated following three drug‐related thrombotic serious adverse events (SAEs): two at the 225 mg dose and one at the 400 mg dose. These occurred in the absence of bleeding episodes or concomitant use of replacement/bypass therapies. No laboratory abnormalities were observed, and PK/PD data did not show correlation between SAE occurrence and levels of circulating befovacimab or free TFPI.ConclusionDespite favourable initial results from preclinical and clinical studies, a positive safety profile of befovacimab was not confirmed. The lack of SAE‐related laboratory abnormalities or differentiating PK/PD characteristics in participants experiencing SAEs raises concerns about the predictability of thrombosis following befovacimab treatment and emphasises the need for further investigation into the therapeutic window of anti‐TFPI treatment.
Correlates of protection against SARS‐CoV‐2 infection and COVID‐19 disease
Authors: Goldblatt David , Alter Galit , Crotty Shane , Plotkin Stanley A. 
Published: June 2022

AbstractAntibodies against epitopes in S1 give the most accurate CoP against infection by the SARS‐CoV‐2 coronavirus. Measurement of those antibodies by neutralization or binding assays both have predictive value, with binding antibody titers giving the highest statistical correlation. However, the protective functions of antibodies are multiple. Antibodies with multiple functions other than neutralization influence efficacy. The role of cellular responses can be discerned with respect to CD4+ T cells and their augmentation of antibodies, and with respect to CD8+ cells with regard to control of viral replication, particularly in the presence of insufficient antibody. More information is needed on mucosal responses.
Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient
Authors: Cyle K. Taylor , Klein Annaleise R. , Aristilde Ludmilla , Martínez Carmen Enid 
Published: June 2022

Abstract

Aim
Low-molecular-weight organic substances (LMWOSs) are at the nexus between micro-organisms, plant roots, detritus, and the soil mineral matrix. The nominal oxidation state of carbon (NOSC) has been suggested as a potential parameter for modelling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass.

Methods and Results
In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil micro-organisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046–0.316 h−1) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p &lt; 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 &lt; 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16 to 0.99 and there was no observed relationship between NOSC and SUE.

Conclusion
Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution.

Significance and Impact of the Study
Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
Antibiofilm mechanism of a novel milk-derived antimicrobial peptide against Staphylococcus aureus by downregulating agr quorum sensing system
Authors: Li Yufang , Li Shijun , Yang Kun , Guo Rongxiang , Zhu Xin , Shi Yanan , Huang Aixiang 
Published: June 2022

Abstract

Aims
Staphylococcus aureus has emerged as a serious threat to food safety owing to biofilm formation. The study aimed to examine the antibiofilm mechanism of a novel milk-derived antimicrobial peptide BCp12 against it.

Methods and results
Antibiofilm activity of BCp12 was studied by crystal violet staining, MTT assay, motility, SEM and CLSM. TMT proteome, real-time PCR and molecular docking in silico were conducted to evaluate the mechanism of BCp12 against S. aureus biofilm. The results showed that BCp12 had significant antibiofilm activity at 1 × MIC and sub-MIC. BCp12 induced the dispersion of structure of S. aureus biofilm BCp12 inhibited the movement of S. aureus. A total of 703 proteins were downregulated and 334 proteins were upregulated after BCp12 treatment. The proteins (agrA, agrB, agrC and psmβ) of the QS systems were downregulated. Additionally, the expression of the agr-related genes, agrA, agrB, agrC and psmβ, was downregulated. BCp12 was bound to the receptor proteins agrA and agrC through hydrogen bonds and π–π bonds.

Conclusions
The results showed the antibiofilm activity of BCp12 and it inhibits the biofilm formation by interfering agr QS system.

Significance and Impact of Study
BCp12 has the potential to be a novel antibiofilm agent against S. aureus biofilm and used in the food industry.
Multistage semisupervised active learning framework for crack identification, segmentation, and measurement of bridges
Authors: Zheng Yue , Gao Yuqing , Lu Shiyuan , Mosalam Khalid M. 
Published: June 2022

AbstractIn bridge health monitoring (BHM), crack identification and width measurement are two of the most important indices for evaluating the functionality of bridges. In order to reduce the labor cost in field detection, researchers have proposed a variety of deep learning (DL)‐based detection techniques for crack recognition. However, some problems still exist in extending these techniques to practical applications, such as data annotation difficulty, limited model generalization ability, and inaccuracy of the DL identification of the actual crack width measurement. In this paper, an application‐oriented multistage crack recognition framework is proposed, namely, Convolutional Active Learning Identification‐Segmentation‐Measurement (CAL‐ISM). It includes four steps: (1) pretraining of the benchmark classification model, (2) retraining of the semisupervised active learning model, (3) pixel‐level crack segmentation, and (4) crack width measurement. Beyond numerical experiments, the performance of the CAL‐ISM is validated for practical applications: (i) bridge column test specimen and (ii) field BHM projects. In conclusion, the obtained results from these applications shed light on the high potential of CAL‐ISM for BHM applications, which is recommended in future deployments for BHM.
Exploring epigenomic mechanisms of neural tube defects using multi‐omics methods and data
Authors: Huang Wanqi , Yuan Zhengwei , Gu Hui 
Published: June 2022

AbstractNeural tube defects (NTDs) are a heterogeneous set of malformations attributed to disruption in normal neural tube closure during early embryogenesis. An in‐depth understanding of NTD etiology and mechanisms remains elusive, however. Among the proposed mechanisms, epigenetic changes are thought to play an important role in the formation of NTDs. Epigenomics covers a wide spectrum of genomic DNA sequence modifications that can be investigated via high‐throughput techniques. Recent advances in epigenomic technologies have enabled epigenetic studies of congenital malformations and facilitated the integration of big data into the understanding of NTDs. Herein, we review clinical epigenomic data that focuses on DNA methylation, histone modification, and miRNA alterations in human neural tissues, placental tissues, and leukocytes to explore potential mechanisms by which candidate genes affect human NTD pathogenesis. We discuss the links between epigenomics and gene regulatory mechanisms, and the effects of epigenetic alterations in human tissues on neural tube closure.
Human duodenal organoid‐derived monolayers serve as a suitable barrier model for duodenal tissue
Authors: Weiß Franziska , Holthaus David , Kraft Martin , Klotz Christian , Schneemann Martina , Schulzke Jörg D. , Krug Susanne M. 
Published: June 2022

AbstractUsually, duodenal barriers are investigated using intestinal cell lines like Caco‐2, which in contrast to native tissue are limited in cell‐type representation. Organoids can consist of all intestinal cell types and are supposed to better reflect the in vivo situation. Growing three‐dimensionally, with the apical side facing the lumen, application of typical physiological techniques to analyze the barrier is difficult. Organoid‐derived monolayers (ODMs) were developed to overcome this. After optimizing culturing conditions, ODMs were characterized and compared to Caco‐2 and duodenal tissue. Tight junction composition and appearance were analyzed, and electrophysiological barrier properties, like paracellular and transcellular barrier function and macromolecule permeability, were evaluated. Furthermore, transcriptomic data were analyzed. ODMs had tight junction protein expression and paracellular barrier properties much more resembling the originating tissue than Caco‐2. Transcellular barrier was similar between ODMs and native tissue but was increased in Caco‐2. Transcriptomic data showed that Caco‐2 expressed fewer solute carriers than ODMs and native tissue. In conclusion, while Caco‐2 cells differ mostly in transcellular properties, ODMs reflect trans‐ and paracellular properties of the originating tissue. If cultured under optimized conditions, ODMs possess reproducible functionality, and the variety of different cell types makes them a suitable model for human tissue‐specific investigations.
Parliamentary Hansard records and epicentral influence in Australia, New Zealand and Papua New Guinea
Authors: Smith Adam , Korhonen Minna 
Published: June 2022

AbstractThis paper investigates the possibility of epicentral influence from two endonormative varieties of English – Australian English (AusE) and New Zealand English (NZE) – on a norm‐developing variety, Papua New Guinean English (PNGE). Through a keyword analysis of recent parliamentary Hansard data, we are able to identify some structural language features that distinguish the Pacific varieties from British English (BrE) – the use of got, going (to) and choice of pronoun case. While each of these features showed the Pacific varieties to have shared usage patterns that distinguished them from BrE, a diachronic analysis of them for AusE and NZE did not produce clear patterns from which a source of epicentral influence could be identified. Further study, with more detailed diachronic data, could well prove useful in explaining current trends and identifying whether AusE or NZE act as epicentres within the Pacific region.
Continuous cardiac monitoring in a patient with terminal pulmonary hypertension and eventual bilateral lung transplantation
Authors: Andersen Mads Ørbæk , Diederichsen Søren Zöga , Svendsen Jesper Hastrup , Carlsen Jørn 
Published: June 2022

As pulmonary arterial hypertension (PAH) progress, arrhythmias are becoming an increasingly prominent phenomenon. Supraventricular tachycardias have been shown to have an incidence of up to 35% in pulmonary hypertension.Continuous cardiac monitoring was deployed in a patient with severe PAH 100 days before bilateral lung transplantation (BLTX). Despite being graded as WHO functional class IV, no arrhythmias were observed before BLTX. Furthermore, the case describes clinical improvement, along with a significant increase in heart rate variability (HRV) and decrease in night-time heart rate in the post-transplantation period.No arrhythmias were observed preoperatively during continuous monitoring in a 100-day period despite the patient’s intrinsically high risk for arrhythmias. Increasing HRV and lower resting heart rate were observed after BLTX. Since these parameters correlate with the clinical condition, they might be valuable in risk assessment in patients with pulmonary hypertension.
Protocol for Rhapsody: a longitudinal observational study examining the feasibility of speech phenotyping for remote assessment of neurodegenerative and psychiatric disorders
Authors: Hampsey Elliot , Meszaros Marton , Skirrow Caroline , Strawbridge Rebecca , Taylor Rosie H , Chok Lazarus , Aarsland Dag , Al-Chalabi Ammar , Chaudhuri Ray , Weston Jack , Fristed Emil , Podlewska Aleksandra , Awogbemila Olabisi , Young Allan H 
Published: June 2022

IntroductionNeurodegenerative and psychiatric disorders (NPDs) confer a huge health burden, which is set to increase as populations age. New, remotely delivered diagnostic assessments that can detect early stage NPDs by profiling speech could enable earlier intervention and fewer missed diagnoses. The feasibility of collecting speech data remotely in those with NPDs should be established.Methods and analysisThe present study will assess the feasibility of obtaining speech data, collected remotely using a smartphone app, from individuals across three NPD cohorts: neurodegenerative cognitive diseases (n=50), other neurodegenerative diseases (n=50) and affective disorders (n=50), in addition to matched controls (n=75). Participants will complete audio-recorded speech tasks and both general and cohort-specific symptom scales. The battery of speech tasks will serve several purposes, such as measuring various elements of executive control (eg, attention and short-term memory), as well as measures of voice quality. Participants will then remotely self-administer speech tasks and follow-up symptom scales over a 4-week period. The primary objective is to assess the feasibility of remote collection of continuous narrative speech across a wide range of NPDs using self-administered speech tasks. Additionally, the study evaluates if acoustic and linguistic patterns can predict diagnostic group, as measured by the sensitivity, specificity, Cohen’s kappa and area under the receiver operating characteristic curve of the binary classifiers distinguishing each diagnostic group from each other. Acoustic features analysed include mel-frequency cepstrum coefficients, formant frequencies, intensity and loudness, whereas text-based features such as number of words, noun and pronoun rate and idea density will also be used.Ethics and disseminationThe study received ethical approval from the Health Research Authority and Health and Care Research Wales (REC reference: 21/PR/0070). Results will be disseminated through open access publication in academic journals, relevant conferences and other publicly accessible channels. Results will be made available to participants on request.Trial registration numberNCT04939818.
Nuclear data evaluation for decay heat analysis of spent nuclear fuel over 1–100 k year timescale
Authors: Doran Hannah R. , Cresswell Alan J. , Sanderson David C. W. , Falcone Gioia 
Published: June 2022

AbstractAccurate nuclear data are essential in the evaluation of decay heat from spent nuclear fuel (SNF). The accuracy of such data was assessed using an approach that compares values reported in different evaluated libraries and determines whether discrepancies reflect inaccuracies in primary data. A short list of 43 isotopes which are most significant to SNF decay heat calculations over 1–100 k years was produced by combining generic reactor inventory code with decay heat analysis for undifferentiated SNF. Decay properties (half-lives and decay energies) and neutron interactions (cross section and fission yields) were compared from 6 evaluated libraries. Fission product (FP) discrepancies identified are 90Sr half-life, where inclusion of a single measurement significantly reduces the evaluated value; 95mNb beta energy, where DDEP evaluation omits the decay to the 95Mo ground state; 99Tc beta energy, where evaluations differ by approximately 10% with a variety of shape factors used; 126Sb/126mSb beta (JEF2.2/3.1.1/3.3) and electron energies (JEFF3.1.1), where intensity differences are reported; and 137Cs beta energy, where ENDF/B-VIII.0 and JEF3.3 evaluations use incorrect shape factors. For actinides, the major discrepancies identified were 237Np alpha energy (JEF2.2/3.1.1) and 225Ac electron energies (ENDF/B-VIII.0) but overall show less discrepancies during long-term disposal (0.1–100 ky) compared to FP’s during interim storage (1–100 years). Further assessments of the 90Sr half-life and the best shape factor for the 99Tc beta decay are needed to improve future decay heat analyses, which are important for designing future stores and evaluating schemes for possible heat recovery.
Saliva and Lung Microbiome Associations with Electronic Cigarette Use and Smoking
Authors: Ying Kevin L. , Brasky Theodore M. , Freudenheim Jo L. , McElroy Joseph P. , Nickerson Quentin A. , Song Min-Ae , Weng Daniel Y. , Wewers Mark D. , Whiteman Noah B. , Mathe Ewy A. , Shields Peter G. 
Published: June 2022

AbstractThe microbiome has increasingly been linked to cancer. Little is known about the lung and oral cavity microbiomes in smokers, and even less for electronic cigarette (EC) users, compared with never-smokers. In a cross-sectional study (n = 28) of smokers, EC users, and never-smokers, bronchoalveolar lavage and saliva samples underwent metatranscriptome profiling to examine associations with lung and oral microbiomes. Pairwise comparisons assessed differentially abundant bacteria species. Total bacterial load was similar between groups, with no differences in bacterial diversity across lung microbiomes. In lungs, 44 bacteria species differed significantly (FDR &lt; 0.1) between smokers/never-smokers, with most decreased in smokers. Twelve species differed between smokers/EC users, all decreased in smokers of which Neisseria sp. KEM232 and Curvibacter sp. AEP1-3 were observed. Among the top five decreased species in both comparisons, Neisseria elongata, Neisseria sicca, and Haemophilus parainfluenzae were observed. In the oral microbiome, 152 species were differentially abundant for smokers/never-smokers, and 17 between smokers/electronic cigarette users, but only 21 species were differentially abundant in both the lung and oral cavity. EC use is not associated with changes in the lung microbiome compared with never-smokers, indicating EC toxicity does not affect microbiota. Statistically different bacteria in smokers compared with EC users and never-smokers were almost all decreased, potentially due to toxic effects of cigarette smoke. The low numbers of overlapping oral and lung microbes suggest that the oral microbiome is not a surrogate for analyzing smoking-related effects in the lung.Prevention Relevance:The microbiome affects cancer and other disease risk. The effects of e-cig usage on the lung microbiome are essentially unknown. Given the importance of lung microbiome dysbiosis populated by oral species which have been observed to drive lung cancer progression, it is important to study effects of e-cig use on microbiome.
Nudging COVID-19 Vaccine Uptake by Changing the Default: A Randomized Controlled Trial
Authors: Tentori Katya , Pighin Stefania , Giovanazzi Giulia , Grignolio Andrea , Timberlake Benjamin , Ferro Antonio 
Published: June 2022

Background Although vaccination against SARS-CoV-2 is considered the central strategy against the pandemic, uptake lags behind target rates. Method To explore whether this rate could be enhanced by a nudging strategy that exploits the status quo bias, we conducted a randomized controlled trial in northern Italy comparing vaccination acceptance among 2000 adults, ages 50 to 59 years, who were either invited to set an appointment (opt-in group) or assigned an individual appointment (opt-out group). Results Results indicate a difference of 3.2 percentage points, which represents a 32% relative increase in the vaccination rate for the opt-out group compared with the opt-in group. Conclusions A significant portion of those who remain unvaccinated may not hold strong beliefs against vaccination but rather tend to inaction and may therefore be nudged toward vaccination with a reduction of action required. Highlights Reluctant adults (50-59 years), who had not yet received vaccines against COVID-19, were sent letters announcing appointment availability In an RCT, the status quo option in the notices influenced the rate of vaccine acceptance Nudging via pre-scheduled appointments encouraged vaccine uptake more than invitations to schedule did Switching the default option yielded a 32% relative increase (13.1% vs. 9.9%) in vaccination