bluuebunny/crossref_metadata_2025_split huggingface dataset:
A recombination-resistant genome for live attenuated and stable PEDV vaccines by engineering the transcriptional regulatory sequences
Authors: Niu Xiaoyu , Liu Mingde , Yang Shaomin , Xu Jiayu , Hou Yixuan J. , Liu Dongxiao , Tang Qiyi , Zhu Hua , Wang Qiuhong 
Published: November 2023

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) is a deadly coronavirus for neonatal piglets and no effective vaccines are available. Transcriptional regulatory sequences (TRSs) are critical in regulating coronavirus discontinuous transcription. Also, TRSs contribute to a high recombination rate of coronaviruses, leading to difficulty in developing safe live vaccines. We hypothesize that recoding the TRS core sequences (TRS-CSs) of PEDV can make the recombination impossible between the engineered vaccine virus and field strains or wild-type viruses. We used an infectious clone-derived reporter PEDV, dORF3-enhanced green fluorescent protein (EGFP), as the backbone to generate a remodeled TRS (RMT) mutant that carries the recoded leader and body TRS-CSs (except for the EGFP). The RMT and dORF3-EGFP showed comparable replication efficiency in Vero cells. However, the incompatibility between the rewired and wild-type TRS-CSs led to few EGFP in RMT-infected cells. Furthermore, RMT and dORF3-EGFP had a similar attenuated phenotype, replication efficiency, and protective immunogenicity in neonatal pigs. RNA sequencing analysis indicated that EGFP transcription directed by the heterogeneous TRS-CSs was significantly reduced to an extremely low level. Meanwhile, recombinant viruses were not detected in Vero cells and in pigs that were co-infected with RMT and a PEDV S-INDEL strain, Iowa106.
In vitro
and
in vivo
passaging of the RMT did not result in reversion mutations in the rewired TRS-CSs, introduced gaps, and disrupted wild-type TRSs. In summary, the RMT mutant was resistant to recombination and genetically stable and can be further optimized (e.g., deletion of the EGFP) to serve as a platform to develop safe PEDV live attenuated vaccines.

IMPORTANCE
Coronaviruses are important pathogens of humans and animals, and vaccine developments against them are imperative. Due to the ability to induce broad and prolonged protective immunity and the convenient administration routes, live attenuated vaccines (LAVs) are promising arms for controlling the deadly coronavirus infections. However, potential recombination events between vaccine and field strains raise a safety concern for LAVs. The porcine epidemic diarrhea virus (PEDV) remodeled TRS (RMT) mutant generated in this study replicated efficiently in both cell culture and in pigs and retained protective immunogenicity against PEDV challenge in pigs. Furthermore, the RMT PEDV was resistant to recombination and genetically stable. Therefore, RMT PEDV can be further optimized as a backbone for the development of safe LAVs.
Draft genome sequence of endolichenic fungus
Dothichiza
sp. strain YAFEF048, isolated from
Usnea longissima
on Haba Snow Mountain
Authors: Wei Jiansheng , Yuan Xiaolong , Geng Yunfen , Bi Wei , Wang Yi 
Published: November 2023

ABSTRACT

In this study, we report a draft genome sequence of the endolichenic fungus
Dothichiza
sp. strain YAFEF048, isolated from the lichen
Usnea longissim
a on Haba Snow Mountain. The genome resource will support future research into the endolichenic lifestyle and potential secondary metabolite diversity of this fungus.
A sensitive and simple RT-LAMP assay for sarbecovirus screening in bats
Authors: Chan Tony Tat-Yin , Chow Franklin Wang-Ngai , Fung Joshua , Cheng Flora Ka-Kei , Lo George Chi-Shing , Tsang Chi-Ching , Luk Hayes Kam-Hei , Wong Antonio Cheuk-Pui , He Zirong , Aw-Yong Kam Leng , Liu Xueyan , Yuen Kwok-Yung , Woo Patrick Chiu-Yat , Lau Susanna Kar-Pui 
Published: November 2023

ABSTRACT

The availability of simple, inexpensive assays for coronavirus (CoV) detection is critical for conducting animal surveillance studies to prevent new zoonotic epidemics. We have previously developed a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for diagnosing coronavirus disease 2019 (COVID-19) in humans using respiratory samples. In this study, we improved and extended the application of this assay to detect other sarbecoviruses in bats. Twenty-four and twenty-one out of 838 oral and alimentary samples collected during 2017–2019 were sarbecovirus-positive by quantitative reverse transcription PCR (qRT-PCR) and our colorimetric RT-LAMP assay, respectively. PCR and Sanger sequencing of the partial spike (S) gene in the S1 subunit region and RNA-dependent RNA polymerase gene of the 21 sarbecovirus-positive samples showed that they were all closely related to bat SARS-related coronavirus HKU3. A green fluorescent nucleic acid stain, SYTO9, was also added for real-time quantification and evaluated in the colorimetric RT-LAMP assay. We observed a positive correlation (Spearman’s rank correlation coefficient of 0.77,
P
< 0.0001) between the time to positivity in the colorimetric RT-LAMP assay and cycle threshold (Ct) values in qRT-PCR assay, suggesting that our assay allows quantitative analysis of viral load in samples. This easily performed, highly sensitive, and specific colorimetric RT-LAMP assay could facilitate mass screening for sarbecoviruses in bats and other animal populations. It will be particularly useful for field studies without sophisticated laboratory equipment and expertise.

IMPORTANCE
We report the application of a colorimetric and fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to facilitate mass screening for sarbecoviruses in bats. The assay was evaluated using a total of 838 oral and alimentary samples from bats and demonstrated comparable sensitivity and specificity to quantitative reverse transcription PCR (qRT-PCR), with a simple setup. The addition of SYTO9, a fluorescent nucleic acid stain, also allows for quantitative analysis. The scalability and simplicity of the assay are believed to contribute to improving preparedness for detecting emerging coronaviruses by applying it to field studies and surveillance.
A standardized nomenclature for resistance-modifying agents in the Comprehensive Antibiotic Resistance Database
Authors: Smith Keaton W. , Alcock Brian P. , French Shawn , Farha Maya A. , Raphenya Amogelang R. , Brown Eric D. , McArthur Andrew G. 
Published: November 2023

ABSTRACT
Resistance-modifying agents have been historically underrepresented in the Comprehensive Antibiotic Resistance Database (CARD). In the process of curating over 60 new molecules into CARD’s Antibiotic Resistance Ontology, the limitations of current classification and nomenclature for these molecules were addressed. We propose a new standardized nomenclature based on mechanism of action, including inhibitors of antibiotic resistance mechanisms, adjuvants enhancing antibiotic entry, adjuvants inhibiting antibiotic removal, adjuvants that alter cell physiology, and host-related antibiotic adjuvants.

IMPORTANCE
While increasing rates of antimicrobial resistance undermine our current arsenal of antibiotics, resistance-modifying agents (RMAs) hold promise to extend the lifetime of these important molecules. We here provide a standardized nomenclature for RMAs within the Comprehensive Antibiotic Resistance Database in aid of RMA discovery, data curation, and genome mining.
Symptom assessment in the dying: family members versus healthcare professionals
Authors: Martinsson Lisa , Brännström Margareta , Andersson Sofia 
Published: November 2023

Objectives
Symptom management and support of the family members (FMs) are considered essential aspects of palliative care. During end of life, patients are often not able to self-report symptoms. There is little knowledge in the literature of how healthcare professionals (HCPs) assess symptoms compared with FMs. The objective was to compare the assessment of symptoms and symptom relief during the final week of life between what was reported by FMs and what was reported by HCPs.

Methods
Data from the Swedish Register of Palliative Care from 2021 and 2022 were used to compare congruity of the assessments by the FMs and by HCPs regarding occurrence and relief of three symptoms (pain, anxiety and confusion), using Cohen’s kappa.

Results
A total of 1131 patients were included. The agreement between FMs and HCPs was poor for occurrence of pain and confusion (kappa 0.25 and 0.16), but fair for occurrence of anxiety (kappa 0.30). When agreeing on a symptom being present, agreement on relief of that symptom was poor (kappa 0.04 for pain, 0.10 for anxiety and 0.01 for confusion). The trend was that HCPs more often rated occurrence of pain and anxiety, less often occurrence of confusion and more often complete symptom relief compared with the FMs.

Conclusions
The views of FMs and HCPs of the patients’ symptoms differ in the end-of-life context, but both report important information and their symptom assessments should be considered both together and individually. More communication between HCPs and FMs could probably bridge some of these differences.
Taste changes in paediatric oncology: longitudinal evaluation
Authors: Mehrdadi Ida , Dhaliwal Neeraj , Chakkalackal Lauren , Green Gloria , Schechter Tal , Zupanec Sue , Dupuis L Lee , Sung Lillian 
Published: November 2023

ObjectivesChanges in taste is a common symptom in paediatric patients receiving cancer therapies. The primary objective was to describe the prevalence of taste changes longitudinally over a 6-month time frame among paediatric patients with newly diagnosed cancer. Secondary objective was to identify factors associated with taste changes over time.MethodsIn this longitudinal, single centre study, we included paediatric patients newly diagnosed with cancer within the previous 8 weeks who were 4–18 years of age. Interviews were conducted once monthly for 6 months. We asked participants about their experience with taste changes, whether potential interventions were successful and whether taste changes influenced eating. Risk factors were evaluated using generalised linear mixed-effects models.ResultsOverall, 60 participants were included. At baseline, 23 (38.3%) participants reported experiencing changes in taste, with the proportion significantly declining over time to 13 (21.7%) at 6 months. The most common specific taste changes were food tasting different, bad or bland. The most common helpful strategies were eating liked foods only, brushing teeth or using mouthwash, drinking more liquids and eating food with strong flavour. Taste change was commonly associated with eating less than usual and reduced enjoyment in eating. Nausea, dry mouth and recent vincristine were independent risk factors for taste changes.ConclusionsChanges in taste were common within 8 weeks of cancer diagnosis and declined significantly over time. Nausea, dry mouth and recent vincristine were independent risk factors. Future studies should develop and evaluate interventions for managing taste changes in paediatric patients with cancer.
Medical cannabis for refractory cancer-related pain in a specialised clinical service: a cross-sectional study
Authors: Sharon Haggai , Agbaria Yara , Brill Silviu , de Santiago Jesus , Hochberg Uri 
Published: November 2023

Background and objectivesCancer-related pain management in advanced stages presents a significant challenge that often requires a multidisciplinary approach. Although advancements in pharmacological and interventional therapies, a considerable number of patients still suffer from refractory pain, leading to unmet clinical needs. This study shares our experience with medical cannabis (MC) as a potential therapy for this specific population of patients with cancer-related refractory pain.MethodsIn a cross-sectional study, 252 consecutive refractory cancer-related pain patients (mean age=61.71, SD=14.02, 47.6% males) filled out detailed self-report questionnaires. Of these, 126 patients (55%) were treated with MC and 105 patients (45%) were not.ResultsMost patients received pain management from their oncologist, not a pain specialist. MC was mainly started for pain relief, sleep difficulties and anorexia. About 70% of patients reported subjective improvement from MC, with almost 40% reporting a significant improvement in coping with their illness. Side effects were generally mild, with fatigue and dizziness being the most common (21.78% and 23.46%, respectively). No patient required dedicated medical care for side effects. Of non-users, 65% had tried MC before and stopped due to lack of effectiveness or side effects (39.7% and 34.6%, respectively).ConclusionRefractory cancer pain necessitates innovative approaches. This registry highlights that MC can effectively improve symptoms in non-responsive patients, with favourable safety profiles for this vulnerable population.
Master integrals for four-loop massless form factors
Authors: Lee Roman N. , von Manteuffel Andreas , Schabinger Robert M. , Smirnov Alexander V. , Smirnov Vladimir A. , Steinhauser Matthias 
Published: November 2023

AbstractWe present analytical results for all master integrals for massless three-point functions, with one off-shell leg, at four loops. Our solutions were obtained using differential equations and direct integration techniques. We review the methods and provide additional details.
LEIA: Linguistic Embeddings for the Identification of Affect
Authors: Aroyehun Segun Taofeek , Malik Lukas , Metzler Hannah , Haimerl Nikolas , Di Natale Anna , Garcia David 
Published: November 2023

AbstractThe wealth of text data generated by social media has enabled new kinds of analysis of emotions with language models. These models are often trained on small and costly datasets of text annotations produced by readers who guess the emotions expressed by others in social media posts. This affects the quality of emotion identification methods due to training data size limitations and noise in the production of labels used in model development. We present LEIA, a model for emotion identification in text that has been trained on a dataset of more than 6 million posts with self-annotated emotion labels for happiness, affection, sadness, anger, and fear. LEIA is based on a word masking method that enhances the learning of emotion words during model pre-training. LEIA achieves macro-F1 values of approximately 73 on three in-domain test datasets, outperforming other supervised and unsupervised methods in a strong benchmark that shows that LEIA generalizes across posts, users, and time periods. We further perform an out-of-domain evaluation on five different datasets of social media and other sources, showing LEIA’s robust performance across media, data collection methods, and annotation schemes. Our results show that LEIA generalizes its classification of anger, happiness, and sadness beyond the domain it was trained on. LEIA can be applied in future research to provide better identification of emotions in text from the perspective of the writer.
Identification of a defected fuel rod in the TRIGA R.C.-1 facility of the ENEA Casaccia Research Center: radiation protection aspects
Authors: Sperandio Luciano , Lepore Luigi , Borra Enrico Maria , Ciciani Luca , Fabrizio Valentina , Falconi Luca , Formenton Davide , Iorio Maria Grazia , Puddu Valerio , Rizzo Alessandro , Roberti Andrea , Ruscitti Stefano , Scaramuzzo Luigi , Vilardi Ignazio 
Published: November 2023

AbstractThe nuclear facility TRIGA RC-1 is located at the ENEA Casaccia Research Center in Rome. It is a thermal spectrum research reactor with a thermal power of 1 MW and a Mark III containment. The failure of the fuel cladding of the General Atomic TRIGA is a well-known phenomenon in the literature and is normally expected during its lifetime. Depending on the severity of the cracking, this results in the transfer of radioactivity from inside the fuel rods to the demineralized moderation and cooling water of the primary circuit. This occurs especially when the fuel is heated, as the temperature rise leads to an increase in the internal pressure inside the rods, causing fission products, especially gaseous ones, to be released through the cracks. The sustained release of these fission products over time causes impurities with longer half-lives (e.g., Cs-137) to accumulate in the primary water purification system and, in particular, in the ion exchange resin tank. Therefore, the detection of Cs-137 in the ion exchange resins of the primary water purification system of the reactor is a sufficiently clear indication of the occurrence of such disturbances. Indeed, Cs-137 is not only a direct fission product of U-235, but is also produced by the decay of Xe-137 (one of the major fission noble gasses), which, because of its physical nature, readily escapes through the rod cladding. To ensure worker protection from ionizing radiation during the identification and replacement of defective fuel rods, a special program of physical, environmental, and personal radiation protection monitoring was conducted. In addition to a brief description of the work performed, this report presents the results of radiometric measurements and associated individual dose assessment performed before, during, and after the identification and replacement of the defected fuel elements.
A Multiscale Spatiotemporal Epidemiological Analysis of Neighborhood Correlates of Triple-Negative Breast Cancer
Authors: Goldfinger Erica , Stoler Justin , Goel Neha 
Published: November 2023

Abstract

Background:
Women living in disadvantaged neighborhoods present with increased prevalence rates of triple-negative breast cancer (TNBC). This study takes a spatiotemporal epidemiological approach to understand the impact of socioenvironmental contextual factors on TNBC prevalence rates.

Methods:
We analyzed 935 TNBC cases from a major cancer center registry, between 2005 and 2017, to explore spatial and space–time clusters of TNBC prevalence rates at the census tract and neighborhood scales. Spatial regression analysis was performed to examine relationships between nine socioenvironmental factors and TNBC prevalence rates at both ecological scales.

Results:
We observed spatial clustering of high TNBC prevalence rates along a north–south corridor of Miami-Dade County along Interstate 95, a region containing several majority non-Hispanic Black neighborhoods. Among the ecologic measures, the percent of a region designated as a brownfield was associated with TNBC prevalence rates at the tract-level (β = 4.27; SE = 1.08; P &lt; 0.001) and neighborhood-level (β = 8.61; SE = 2.20; P &lt; 0.001).

Conclusions:
Our spatiotemporal analysis identified robust patterns of hot spots of TNBC prevalence rates in a corridor of several disadvantaged neighborhoods in the northern half of the county. These patterns of TNBC align with the literature regarding at-risk groups and neighborhood-level effects on TNBC; however, remain to be validated in a population-based sample.

Impact:
Spatial epidemiological approaches can help public health officials and cancer care providers improve place-specific screening, patient care, and understanding of socioenvironmental factors that may shape breast cancer subtype through gene-environment and epigenetic interactions.
Foreignizing Translation and Chinese
Authors: Forster Michael N. 
Published: November 2023

Abstract
This article explains a new ‘foreignizing’ approach to translation that was invented in the late 18th and early 19th centuries, especially by Herder and Schleiermacher, and that has since become the predominant approach in translation theory. The article argues that despite the great virtues of this approach, it was based on an unduly narrow restriction to Indo-European languages, which leaves considerable room for further improvement. Greater attention to Hebrew has since made up this deficit to a certain extent. But Chinese holds the potential for even more important refinements of the original theory. The article explains the original theorists’ failure to exploit this case in terms of a certain prejudice against Chinese language and culture that had arisen at the time, and for which these theorists were themselves partly responsible. It then tries to show in some detail how deeply enriching for the theory a consideration of Chinese can be.
Translating Philosophy from and into Chinese in the Light of Humboldt’s Comparativism
Authors: Zhang Yijing 
Published: November 2023

Abstract
This article re-examines Humboldt’s comparative linguistics by analyzing two cases: the reception of Chinese philosophy in France and the translation of Greek philosophy in China. Humboldt’s legacy is treated in opposite ways which result in two translation methods. I argue that Humboldt’s statement about the inferiority of Chinese should not be taken in a literal sense. It highlights the grammatical differences between Greek and Chinese, and can lead to questioning some basic assumptions about the concept of being. Humboldtian comparativism, understood as the recognition of differences and the respect for the foreign, can shed light on transcultural understanding in general.
‘Transcendence’ in Being and Time and Its Chinese Translation
Authors: Wang Qingjie James 
Published: November 2023

Abstract
The problem of ‘transcendence’/‘transcendental’/ ‘transcendent’ runs throughout Heidegger’s Being and Time, and it is central to many of its core concerns. The confusion about the different meanings of using the same words in the history of philosophy from Kant to Heidegger causes not only problems in understanding but also problems in the translation of the philosophical classics, especially in a non-Indo-European language such as Chinese. Through examination of Kant’s conception of the ‘transcendental’ and a critical textual analysis of Heidegger’s reinterpretation of ‘transcendence’ as a temporal ecstatic Dasein’s existence, this essay attempts to show that the problem of transcendence, along with the debates over the Chinese translation of the relevant terms, is not merely a problem in a traditional theory of knowledge or epistemology. Rather, it belongs primarily and essentially to fundamental ontology and thus to Heidegger’s question of Being.
Pollution in the Bible and in Cognitive Science: A Review of Recent Works by Thomas Kazen and Yitzhaq Feder
Authors: Watts James W. 
Published: November 2023

Abstract
This essay constitutes a thematic review of two recent publications that utilize cognitive science to illuminate biblical concepts of pollution and purity. The review, adapted and expanded from James W. Watts, Leviticus 11–20 (HCOT; Leuven: Peeters, 2023), 31–34, sets these works in the broader context of each author’s work and juxtaposes their insights with other major publications on purity and pollution in the Bible.