bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonorchis sinensis Reinfection Rate and Reinfection Determinants: A Prospective Cohort Study in Hengxian County, Guangxi, China
Authors: Li Zhongjie , Xin Hualei , Qian Men-Bao , Sun Junling , Yang Yichao , Chen Yingdan , Yu Jianxing , Chen Yu , Huang Zhuoxin , Hay Simon I , Jiang Zhihua , Li Shi-Zhu 
Published: August 2021

Abstract

Background
To understand Clonorchis sinensis reinfection and the determinants of reinfection in endemic areas is important in establishment of control measures.

Methods
A prospective cohort study was implemented in Hengxian County, Guangxi, China. Individuals with C. sinensis infection were completely treated, and those cured were enrolled as study subjects and followed up for 3, 6, and 12 months. The reinfection frequency and incidence were calculated, and a multivariable Cox proportional hazard model was constructed to capture reinfection determinants.

Results
Among 635 enrolled subjects, 436 (68.7%) completed follow-up. Of these, 177 (40.6%) were reinfected; 133 (75.1%) were reinfected once, 41 (23.2%) twice, and 3 (1.7%) three times. The incidence of reinfection was 64.0 per 100 person-years. Men (adjusted hazard ratio [aHR], 1.67; 95% confidence interval [CI], 1.14–2.44), those with underlying diseases (aHR, 1.41; 95% CI, 1.02–1.95), and those with moderate- or heavy-intensity infections (aHR, 1.45; 95% CI, 1.14–1.85) had increasing reinfection probabilities.

Conclusions
C. sinensis reinfection is high in endemic areas. Men and high-intensity infection are important determinants of reinfection. Repeated chemotherapy is necessary to control reinfection and its associated morbidities, especially in high-risk individuals. In addition, behavioral education is advised to decrease overall reinfection in endemic areas.
Consumer Timework
Authors: Robinson Thomas Derek , Veresiu Ela , Babić Rosario Ana 
Published: August 2021

AbstractThis article unpacks time as a cultural consumption resource and introduces the concept of consumer timework. Consumer timework refers to marketplace stakeholders’ negotiation of competing interpretations of how the past and the future relate using a wide range of consumption objects and activities. Building on the theory of temporalization, we argue that social tensions, conflicts, and breaks drive the past and the future apart in multiple incompatible ways that individuals and societies must contend. We theorize four fundamental dynamics of consumer timework in which market stakeholders engage: integrative, disintegrative, subjugatory, and emancipatory. Integrative and disintegrative consumer timework respectively harmonize and rupture the multiple temporal orientations (past, present, and future) to create shared communities or counter-communities of time through consumption. Subjugatory and emancipatory consumer timework respectively enforce and disrupt temporal hierarchies of power through consumption. We delineate these temporal dynamics using examples from extant consumer research. We conclude by establishing a future research agenda on consumer timework.
Long-term immunity after a single yellow fever vaccination in travelers vaccinated at 60 years or older: A 10-year follow-up study
Authors: Rosenstein Mareen D , de Visser Adriëtte W , Visser Leo G , Roukens Anna H E 
Published: August 2021

Abstract

Background
In 2013, the World Health Organization (WHO) revised their position on yellow fever vaccination, in which revaccination every 10 years was no longer required, and that a single-dose provided life-long protection. However, research data on the immunogenicity of YF vaccine in people aged 60 years and over are scarce. Indeed, immunosenescence may result in lower virus neutralizing antibody titers after primary vaccination and a more rapid waning immunity. Therefore, we tested the hypothesis that older travelers, vaccinated at 60 years or older are more likely to become seronegative in comparison to young adults 10 years after primary YF vaccination.

Methods
This is a 10-year follow-up study of an earlier prospective controlled cohort study. In the original trial, the neutralizing antibody response was measured in older travelers (aged 60–81 years, N = 28) and young adults (aged 18–28 years, N = 30) up to 28 days after a primary yellow fever vaccination. Ten years later, we collected serum samples of 22/28 (78%) elderly (71–85 years) and 14/30 (47%) controls (29–40 years), and determined their neutralizing antibody titers by plaque reduction neutralization test (PRNT80). Seropositivity was defined as plaque formation reduction of 80% at a serum dilution of 10 or more (PRNT80 ≥ 10).

Results
All participants (36/36) were still seropositive 10 years after primary vaccination. The geometric mean concentrations were not statistically different between the older and younger participants (6.7 IU/mL vs. 8.6 IU/mL, P = 0.5).

Conclusions
All older travelers were seropositive, 10 years after a primary YF vaccination at the age of ≥60 years. These data suggest that in older travelers a single vaccination is sufficient to convey long-lasting immunity for at least 10 years, and is in support the position of the WHO on a single-dose yellow fever vaccination.
Molecular Monitoring of BCR-ABL Fusion Transcripts in Patients with Chronic Myeloid Leukemia During Treatment Using the Endpoint Fluorescence Method
Authors: Amin Huma , Ahmed Suhaib 
Published: August 2021

Abstract

Objective
The purpose of the study was to compare results and evaluate the agreement between the endpoint fluorescence (EPF) method and quantitative real-time polymerase chain reaction (QPCR) during molecular monitoring of patients with chronic myeloid leukemia (CML) receiving treatment.

Materials and Methods
The study was conducted at Molecular Lab of Riphah International University, Islamabad, Pakistan, from January 2017 to December 2018. A total of 150 blood specimens from 30 patients with CML were analyzed at regular intervals during therapy. The detection/quantification of transcript mRNA was done simultaneously using QPCR and the EPF method.

Results
Out of a total of 150 RNA specimens analyzed, 117 (78%) specimens were positive, whereas 33 (22%) were negative for the transcript using both methods at various stages of treatment. Strong linear negative correlations between the cycle threshold and relative fluorescence unit values were observed with P &lt;.0001 at 0, 3, 6, 9, and 12 months of treatment. No significant difference (P &gt;.05) between the means of the BCR-ABL percentage was observed in either method at all stages of treatment. The bias between the 2 methods was calculated as 0.069 ± 3.50, and 95% limits of agreement were 6.92% to –6.79%.

Conclusion
We found that EPF is s simple method to detect/quantify BCR-ABL mRNA expression during treatment with comparable results to QPCR.
Modelling supra-classical logic in a Boltzmann neural network: I representation
Authors: Blanchette Glenn , Robins Anthony , Labuschagne Willem 
Published: August 2021

AbstractThis paper looks at the representation of supra-classical, non-monotonic (SCNM) logic by an artificial neural network. It identifies the features of defeasiblity in this logic related to inference in the context of common-sense reasoning. It considers the machine characteristics that make a representation possible, with reference to previous literature. We describe a theoretical environment for investigating the representation and provide experimental evidence confirming that a Boltzmann machine is a suitable network representation. A Boltzmann machine can learn an input distribution corresponding to a preference relation and explicitly retrieve appropriate model states, constituting one-to-many mappings, entailed by the uncertain information contained in a premiss. The place of the Boltzmann machine in knowledge representation is discussed. In future papers, this neural network model of SCNM logic will serve as an experimental gateway for exploration of typicality and belief revision.
Steps Towards a Minimalist Account of Numbers
Authors: Schindler Thomas 
Published: August 2021

AbstractThis paper outlines an account of numbers based on the numerical equivalence schema (NES), which consists of all sentences of the form ‘#x.Fx=n if and only if ∃nx Fx’, where # is the number-of operator and ∃n is defined in standard Russellian fashion. In the first part of the paper, I point out some analogies between the NES and the T-schema for truth. In light of these analogies, I formulate a minimalist account of numbers, based on the NES, which strongly parallels the minimalist (deflationary) account of truth. One may be tempted to develop the minimalist account in a fictionalist direction, according to which arithmetic is useful but untrue, if taken at face value. In the second part, I argue that this suggestion is not as attractive as it may first appear. The NES suffers from a similar problem to the T-schema: it is deductively weak and does not enable the derivation of any non-trivial generalizations. In the third part of the paper, I explore some strategies to deal with the generalization problem, again drawing inspiration from the literature on truth. In closing this paper, I briefly compare the minimalist to some other accounts of numbers.
Synthetic evolution tracks of giant planets
Authors: Müller Simon , Helled Ravit 
Published: August 2021

ABSTRACT
Giant planet evolution models play a crucial role in interpreting observations and constraining formation pathways. However, the simulations can be slow or prohibitively difficult. To address this issue, we calculate a large suite of giant planet evolution models using a state-of-the-art planetary evolution code. Using these data, we create the python program planetsynth that generates synthetic cooling tracks by interpolation. Given the planetary mass, bulk and atmospheric metallicity, and incident stellar irradiation, the program calculates how the planetary radius, luminosity, effective temperature, and surface gravity evolve with time. We demonstrate the capabilities of our models by inferring time-dependent mass–radius diagrams, estimating the metallicities from mass–radius measurements, and by showing how atmospheric measurements can further constrain the planetary bulk composition. We also estimate the mass and metallicity of the young giant planet 51 Eri b from its observed luminosity. Synthetic evolution tracks have many applications, and we suggest that they are valuable for both theoretical and observational investigations into the nature of giant planets.
A Bayesian inference and model selection algorithm with an optimization scheme to infer the model noise power
Authors: López-Santiago J , Martino L , Vázquez M A , Miguez J 
Published: August 2021

ABSTRACT
Model fitting is possibly the most extended problem in science. Classical approaches include the use of least-squares fitting procedures and maximum likelihood methods to estimate the value of the parameters in the model. However, in recent years, Bayesian inference tools have gained traction. Usually, Markov chain Monte Carlo (MCMC) methods are applied to inference problems, but they present some disadvantages, particularly when comparing different models fitted to the same data set. Other Bayesian methods can deal with this issue in a natural and effective way. We have implemented an importance sampling (IS) algorithm adapted to Bayesian inference problems in which the power of the noise in the observations is not known a priori. The main advantage of IS is that the model evidence can be derived directly from the so-called importance weights – while MCMC methods demand considerable postprocessing. The use of our adaptive target adaptive importance sampling (ATAIS) method is shown by inferring, on the one hand, the parameters of a simulated flaring event that includes a damped oscillation and, on the other hand, real data from the Kepler mission. ATAIS includes a novel automatic adaptation of the target distribution. It automatically estimates the variance of the noise in the model. ATAIS admits parallelization, which decreases the computational run-times notably. We compare our method against a nested sampling method within a model selection problem.
Expanding the chemical functionality of DNA nanomaterials generated by rolling circle amplification
Authors: Baker Ysobel R , Yuan Liyiwen , Chen Jinfeng , Belle Roman , Carlisle Robert , El-Sagheer Afaf H , Brown Tom 
Published: August 2021

Abstract
Rolling circle amplification (RCA) is a powerful tool for the construction of DNA nanomaterials such as hydrogels, high-performance scaffolds and DNA nanoflowers (DNFs), hybrid materials formed of DNA and magnesium pyrophosphate. Such DNA nanomaterials have great potential in therapeutics, imaging, protein immobilisation, and drug delivery, yet limited chemistry is available to expand their functionality. Here, we present orthogonal strategies to produce densely modified RCA products and DNFs. We provide methods to selectively modify the DNA component and/or the protein cargo of these materials, thereby greatly expanding the range of chemical functionalities available to these systems. We have used our methodology to construct DNFs bearing multiple surface aptamers and peptides capable of binding to cancer cells that overexpress the HER2 oncobiomarker, demonstrating their potential for diagnostic and therapeutic applications.
Problematic substance use: an assessment of workplace implications in midwifery
Authors: Pezaro S , Maher K , Bailey E , Pearce G 
Published: August 2021

Abstract

Background
Problematic substance use (PSU) poses occupational, personal and professional risks. As an occupational group, midwives have been under-represented in research on PSU.

Aims
The aim of this study was to assess self-reported occurrences of PSU, help-seeking behaviours and barriers, and perceptions of impairment in UK-based midwives.

Methods
Self-selecting registered midwives were anonymously surveyed using the Tobacco, Alcohol, Prescription Medications, and Substance Use/Misuse (TAPS) tool, the Perceptions of Nursing Impairment Inventory (PNII) and open-ended/closed questions. Quantitative data were used to explore PSU, help-seeking and attitudes to impairment. Qualitative responses were used to provide richer understandings.

Results
From 623 completed surveys, 28% (n = 176) self-reported PSU in response to work-related stress and anxiety, bullying, traumatic clinical incidents and maintenance of overall functioning. PSU was related to alcohol and a range of restricted drugs. While 11% of those affected indicated they had sought help, 27% felt they should seek help but did not. Reported barriers to help-seeking included fear of repercussions, shame, stigma, practicalities and a perceived lack of support either available or required. Perceptions of impairment were predominantly compassionate with a minority of stigmatizing attitudes displayed.

Conclusions
Overall, 10% of the sample reported they had attended work under the influence of alcohol, and 6% under the influence of drugs other than tobacco or those as prescribed to them. Furthermore, 37% indicated concern about a colleague’s substance use. As stigmatizing attitudes and punitive actions can dissuade help-seeking, changed perceptions and policies which favour alternatives to discipline are suggested to reduce the risk overall.
The Case for the Irreducibility of Geometry to Algebra
Authors: Pambuccian Victor , Schacht Celia 
Published: August 2021

ABSTRACTThis paper provides a definitive answer, based on considerations derived from first-order logic, to the question regarding the status of elementary geometry, whether elementary geometry can be reduced to algebra. The answer we arrive at is negative, and is based on a series of structural questions that can be asked only inside the geometric formal theory, as well as the consideration of reverse geometry, which is the art of finding minimal axiom systems strong enough to prove certain geometrical theorems, given that there are no algebraic structures that one could associate with those minimal axiom systems.
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes
Authors: Charon Justine , Murray Shauna , Holmes Edward C 
Published: August 2021

Abstract
Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
Melatonin induces Nrf2‐HO‐1 reprogramming and corrections in hepatic core clock oscillations in Non‐alcoholic fatty liver disease
Authors: Joshi Apeksha , Upadhyay Kapil K. , Vohra Aliasgar , Shirsath Kavita , Devkar Ranjitsinh 
Published: August 2021

AbstractMelatonin pleiotropically regulates physiological events and has a putative regulatory role in the circadian clock desynchrony‐mediated Non‐alcoholic fatty liver disease (NAFLD). In this study, we investigated perturbations in the hepatic circadian clock gene, and Nrf2‐HO‐1 oscillations in conditions of high‐fat high fructose (HFHF) diet and/or jet lag (JL)‐mediated NAFLD. Melatonin treatment (100 µM) to HepG2 cells led to an improvement in oscillatory pattern of clock genes (Clock, Bmal1, and Per) in oleic acid (OA)‐induced circadian desynchrony, while Cry, Nrf2, and HO‐1 remain oblivious of melatonin treatment that was also validated by circwave analysis. C57BL/6J mice subjected to HFHF and/or JL, and treated with melatonin showed an improvement in the profile of lipid regulatory genes (CPT‐1, PPARa, and SREBP‐1c), liver function (AST and ALT) and histomorphology of fatty liver. A detailed scrutiny revealed that hepatic mRNA and protein profiles of Bmal1 (at ZT6) and Clock (at ZT12) underwent corrective changes in oscillations, but moderate corrections were recorded in other components of clock genes (Per1, Per2, and Cry2). Melatonin induced changes in oscillations of anti‐oxidant genes (Nrf2, HO‐1, and Keap1) subtly contributed in the overall improvement in NAFLD recorded herein. Taken together, melatonin induced reprograming of hepatic core clock and Nrf2‐HO‐1 genes leads to an improvement in HFHF/JL‐induced NAFLD.
Spike protein of SARS‐CoV‐2 activates macrophages and contributes to induction of acute lung inflammation in male mice
Authors: Cao Xiaoling , Tian Yan , Nguyen Vi , Zhang Yuping , Gao Chao , Yin Rong , Carver Wayne , Fan Daping , Albrecht Helmut , Cui Taixing , Tan Wenbin 
Published: August 2021

AbstractThe spike protein of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) plays a crucial role in mediating viral entry into host cells. However, whether it contributes to pulmonary hyperinflammation in patients with coronavirus disease 2019 is not well known. In this study, we developed a spike protein–pseudotyped (Spp) lentivirus with the proper tropism of the SARS‐CoV‐2 spike protein on the surface and determined the distribution of the Spp lentivirus in wild‐type C57BL/6J male mice that received an intravenous injection of the virus. Lentiviruses with vesicular stomatitis virus glycoprotein (VSV‐G) or with a deletion of the receptor‐binding domain (RBD) in the spike protein [Spp (∆RBD)] were used as controls. Two hours postinfection (hpi), there were 27‐75 times more viral burden from Spp lentivirus in the lungs than in other organs; there were also about 3‐5 times more viral burden from Spp lentivirus than from VSV‐G lentivirus in the lungs, liver, kidney, and spleen. Deletion of RBD diminished viral loads in the lungs but not in the heart. Acute pneumonia was observed in animals 24 hpi. Spp lentivirus was mainly found in SPC+ and LDLR+ pneumocytes and macrophages in the lungs. IL6, IL10, CD80, and PPAR‐γ were quickly upregulated in response to infection in the lungs as well as in macrophage‐like RAW264.7 cells. Furthermore, forced expression of the spike protein in RAW264.7 cells significantly increased the mRNA levels of the same panel of inflammatory factors. Our results demonstrated that the spike protein of SARS‐CoV‐2 confers the main point of viral entry into the lungs and can induce cellular pathology. Our data also indicate that an alternative ACE2‐independent viral entry pathway may be recruited in the heart and aorta.
CITED2 inhibits STAT1‐IRF1 signaling and atherogenesis
Authors: Zafar Atif , Pong Ng Hang , Diamond‐Zaluski Rachel , Kim Gun‐Dong , Ricky Chan Ernest , Dunwoodie Sally L. , Smith Jonathan D. , Mahabeleshwar Ganapati H. 
Published: August 2021

AbstractMacrophages are the principal component of the innate immune system. They play very crucial and multifaceted roles in the pathogenesis of inflammatory vascular diseases. There is an increasing recognition that transcriptionally dynamic macrophages are the key players in the pathogenesis of inflammatory vascular diseases. In this context, the accumulation and aberrant activation of macrophages in the subendothelial layers govern atherosclerotic plaque development. Macrophage‐mediated inflammation is an explicitly robust biological response that involves broad alterations in inflammatory gene expression. Thus, cell‐intrinsic negative regulatory mechanisms must exist which can restrain inflammatory response in a spatiotemporal manner. In this study, we identified CBP/p300‐interacting transactivator with glutamic acid/aspartic acid‐rich carboxyl‐terminal domain 2 (CITED2) as one such cell‐intrinsic negative regulator of inflammation. Our in vivo studies show that myeloid‐CITED2‐deficient mice on the Apoe−/− background have larger atherosclerotic lesions on both control and high‐fat/high‐cholesterol diets. Our integrated transcriptomics and gene set enrichment analyses studies show that CITED2 deficiency elevates STAT1 and interferon regulatory factor 1 (IRF1) regulated pro‐inflammatory gene expression in macrophages. At the molecular level, our studies identify that CITED2 deficiency elevates IFNγ‐induced STAT1 transcriptional activity and STAT1 enrichment on IRF1 promoter in macrophages. More importantly, siRNA‐mediated knockdown of IRF1 completely reversed elevated pro‐inflammatory target gene expression in CITED2‐deficient macrophages. Collectively, our study findings demonstrate that CITED2 restrains the STAT1‐IRF1 signaling axis in macrophages and limits the development of atherosclerotic plaques.