bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semirational engineering of
Cytophaga hutchinsonii
polyphosphate kinase for developing a cost-effective, robust, and efficient adenosine 5′-triphosphate regeneration system
Authors: Shen Qi , Zhang Shi-Jia , Xu Bin-Hui , Chen Zhi-Yu , Peng Feng , Xiong Neng , Xue Ya-Ping , Zheng Yu-Guo 
Published: October 2023

ABSTRACT

Adenosine 5′-triphosphate (ATP) is a substrate for the biological synthesis of various valuable compounds, such as pharmaceuticals and agrochemicals. To make these biocatalytic processes more economically valuable, several ATP regeneration systems comprising enzymes and phosphate donors were developed. Due to their ability to synthesize ATP from both 5′-diphosphate and adenosine 5′-monophosphate, polyphosphate kinase 2 class III (PPK2-III) enzymes such as
Cytophaga hutchinsonii
PPK (
Ch
PPK) have attracted considerable attention in the construction of ATP regeneration systems. Furthermore, PPK2-III enzymes employ inorganic polyphosphate, which is a low-cost and stable substrate, as the phosphate donor. To facilitate the application of the PPK2-III ATP regeneration system in biocatalytic processes depending on ATP, a semirational strategy coupled with a high-throughput screening assay based on a fluorescent sensor was performed to engineer
Ch
PPK. Saturation mutagenesis was performed on 16 critical residues of
Ch
PPK. After screening approximately 4,800 colonies, nine single amino acid variants exhibited more than threefold increased activities than wild-type
Ch
PPK. Beneficial mutations were subsequently recombined, resulting in a quadruple variant (
Ch
PPK/A79G/S106C/I108F/L285P), compared with wild-type
Ch
PPK, displaying 18.8-fold enhanced activity and better stability at an elevated temperature and under acidic conditions. The introduction of this variant
Ch
PPK/A79G/S106C/I108F/L285P in the biological synthesis of nicotinamide mononucleotide catalyzed by phosphoribosyl pyrophosphate synthetase and nicotinamide phosphoribosyltransferase increased the yield by approximately threefold compared with wild-type
Ch
PPK. Therefore, the ATP regeneration system described may have implications for bioconversions requiring ATP.

IMPORTANCE

The adenosine 5′-triphosphate (ATP) regeneration system can significantly reduce the cost of many biocatalytic processes. Numerous studies have endeavored to utilize the ATP regeneration system based on
Cytophaga hutchinsonii
PPK (
Ch
PPK). However, the wild-type
Ch
PPK enzyme possesses limitations such as low enzymatic activity, poor stability, and limited substrate tolerance, impeding its application in catalytic reactions. To enhance the performance of
Ch
PPK, we employed a semi-rational design approach to obtain the variant
Ch
PPK/A79G/S106C/I108F/L285P. The enzymatic kinetic parameters and the catalytic performance in the synthesis of nicotinamide mononucleotide demonstrated that the variant
Ch
PPK/A79G/S106C/I108F/L285P exhibited superior enzymatic properties than the wild-type enzyme. All data indicated that our engineered ATP regeneration system holds inherent potential for implementation in biocatalytic processes.
Persistence of SARS-CoV-2 and its surrogate, bacteriophage Phi6, on surfaces and in water
Authors: Pitol Ana K. , Venkatesan Samiksha , Hoptroff Michael , Hughes Grant L. 
Published: October 2023

ABSTRACT

The COVID-19 pandemic spurred research on the persistence of infectious SARS-CoV-2 and its surrogates, including bacteriophage Phi6, in environmental reservoirs. Despite the wide use of Phi6, side-by-side comparisons between Phi6 and SARS-CoV-2 are limited. Here, we quantified the persistence of SARS-CoV-2 and Phi6 on surfaces (PVC plastic and stainless steel), using an initial inoculum of 10
3
plaque forming unit per surface, and evaluated the influence of four commonly used deposition solutions on viral persistence. In addition, we quantified the persistence of SARS-CoV-2 and Phi6 in water. Our findings revealed that Phi6 had a significantly longer half-life than SARS-CoV-2 in water and on surfaces. Phi6 persisted 34 hours in water compared with 13 hours for SARS-CoV-2. Viral persistence on surfaces was significantly influenced by the virus used and the deposition solution but not by the surface material. Phi6 remained infectious significantly longer than SARS-CoV-2 when the inoculation solution was culture media and saliva, leading to half-lives between 9 hours and 2 weeks for Phi6, compared to 0.5–2 hours for SARS-CoV-2. Using phosphate-buffered saline as a deposition solution led to half-lives shorter than 4 hours for both viruses on all surfaces. Our results indicate that bacteriophage Phi6 may lead to an overestimate of infectiousness for studies quantifying SARS-CoV-2 persistence on surfaces and water and highlight the importance of using appropriate deposition solutions when evaluating viral persistence on surfaces.

IMPORTANCE
The COVID-19 pandemic spurred research on the persistence of SARS-CoV-2 and its surrogates. Here we highlight the importance of evaluating viral surrogates and experimental methodologies when studying pathogen survival in the environment.
Evaluation of the Cepheid 3-gene host response blood test for tuberculosis diagnosis and treatment response monitoring in a primary-level clinic in rural China
Authors: Li Meng , Qiu Yong , Guo Mingcheng , Qu Rong , Tian Fajun , Wang Gengsheng , Wang Ya , Ma Jian , Liu Siyuan , Takiff Howard , Tang Yi-Wei , Gao Qian 
Published: October 2023

ABSTRACT

A rapid, accurate, non-sputum-based triage test for diagnosing tuberculosis (TB) is a high-priority need. Cepheid developed a novel prototype blood test, Xpert
Mycobacterium tuberculosis
Host Response (Xpert-MTB-HR), which generates a TB score based on the mRNA expression of three genes. We conducted a case-control study with prospective recruitment to evaluate its accuracy in the clinic of the Wusheng County Centers for Disease Prevention and Control in China. We enrolled 149 TB patients, 248 other respiratory diseases (ORD) patients, and 193 healthy controls. In addition, whole-blood samples taken from TB patients after 2, 5, and 6 months of treatment were tested with Xpert-MTB-HR to evaluate its ability to monitor treatment response. Xpert-MTB-HR discriminated between TB and healthy controls with an area under the curve (AUC) of 0.912 (95% CI, 0.878–0.945). With the specificity of 70% envisioned for a triage test, its sensitivity was 90.1% (84.9%–94.6%). Xpert-MTB-HR discriminated between TB and ORD with an AUC of 0.798 (0.750–0.847), and at specificity of 70%, the sensitivity was only 75.8% (68.5%–82.8%). In patients determined by Ultra to have medium or high sputum bacillary loads, with specificity of 70%, the sensitivity for discriminating patients with TB from healthy controls was 100.0% (100.0–100.0) and from patients with ORD, 95.1% (89.8–100.0). The TB scores generally increased by 2 months of treatment and then remained stable. Xpert-MTB-HR met the criteria for a triage test to discriminate between TB and healthy controls, but not between TB and ORD, except when limited to patients with high sputum bacillary loads. Xpert-MTB-HR showed promise for monitoring response to treatment but needs to be further evaluated in larger prospective studies.
Protein kinase Cdc7 supports viral replication by phosphorylating
Avibirnavirus
VP3 protein
Authors: Deng Tingjuan , Du Liuyang , Ding Shuxiang , Peng Xiran , Chen Wenjing , Yan Yan , Hu Boli , Zhou Jiyong 
Published: October 2023

ABSTRACT

Phosphorylation is an important post-translational modification that has crucial roles in diverse cellular biological pathways and in various viral life cycles. Here, we report that the VP3 protein, the major inner capsid protein of
Avibirnavirus
infectious bursal disease virus (IBDV), regulates viral replication by phosphorylation during infection. Our data showed that IBDV infection induced the upregulation of Cdc7 expression, followed by phosphorylation of residue serine 13 (S13) on VP3 by interaction. Virus rescue showed that phosphorylation of VP3 at site S13 enhanced the replication ability of IBDV. Moreover, further study demonstrated that the increase of IBDV replication was relevant to the addition of negative charge of phosphoserine on VP3. Meanwhile, the knockdown of Cdc7 severely blocked the phosphorylation level of VP3 S13 and impaired the replication of wild-type but not S13A mutant recombinant IBDV. Thus, we demonstrated that Cdc7 was a crucial enzyme that phosphorylated IBDV VP3 at site serine 13 for viral proliferation.

IMPORTANCE

The
Avibirnavirus
infectious bursal disease virus is still an important agent which largely threatens global poultry farming industry economics. VP3 is a multifunctional scaffold structural protein that is involved in virus morphogenesis and the regulation of diverse cellular signaling pathways. However, little is known about the roles of VP3 phosphorylation during the IBDV life cycle. In this study, we determined that IBDV infection induced the upregulation of Cdc7 expression and phosphorylated the VP3 Ser13 site to promote viral replication. Moreover, we confirmed that the negative charge addition of phosphoserine on VP3 at the S13 site was essential for IBDV proliferation. This study provides novel insight into the molecular mechanisms of VP3 phosphorylation-mediated regulation of IBDV replication.
Modern Approaches to the Extraction and Preconcentration of Biologically Active Compounds from Plant Samples by Microextraction Methods for Their Determination by Chromatography–Mass Spectrometry
Authors: Bessonova E. A. , Karpitskii D. A. , Kartsova L. A. 
Published: October 2023

Abstract
The review considers the main trends in actively developing methods of solid-phase and liquid–liquid microextraction for the extraction, purification, and preconcentration of analytes from medicinal plants and plant materials, the use of new extractants and approaches to the preparation of samples of plant origin, and their compatibility with mass-spectrometric detection. Particular attention is paid to the analytical capabilities, advantages, and limitations of each of the approaches to extracting analytes from plant materials for the subsequent analysis of the obtained extracts by chromatography–mass spectrometry.
Evaluation of a self-imaging OCT for remote diagnosis and monitoring of retinal diseases
Authors: Liu Zitian , Huang Wenyong , Wang Zhenyu , Jin Ling , Congdon Nathan , Zheng Yingfeng , Chen Shida , Liu Yizhi 
Published: October 2023

ObjectivesTo evaluate the feasibility and accuracy of a portable, self-imaging optical coherence tomography (OCT) for measuring central subfield thickness (CST) and achieving diagnostic concordance for retinal lesions compared with clinic-based spectral-domain OCT (SD-OCT).MethodsThis comparative, cross-sectional study was conducted between August 2020 and February 2021. Two groups of adult participants were recruited: (1) a selected cohort of 160 participants with confirmed diagnosis and (2) a consecutive cohort of 315 participants recruited randomly. All participants underwent self-imaging OCT examination, as well as standard OCT examination. CST was automatically calculated for comparisons between the two OCT devices. Diagnostic concordance for retinal lesions and the success rate of self-imaging were assessed within the consecutive cohort.ResultsIn the selected cohort, self-imaging OCT images yielded consistent CST with SD-OCT, with a mean difference of 0.1±7.7 µm for normal eyes, 4.9±10.6 µm for macular oedema, −1.3±9.5 µm for choroidal neovascularisation, 5.0±7.8 µm for epiretinal membrane. The self-imaging OCT also demonstrated good repeatability, with a mean test–retest difference in CST of 0.7±3.9 µm and limits of agreement ranging from −6.9 to 8.3 µm. Additionally, within the consecutive cohort, interdevice κ values ranged for detecting various retinal lesions ranged from 0.8 to 1.0, except in the cases of retinal detachment (κ=0.5). All eyes (100%) in the selected cohort and 242 eyes (76.8%) in the consecutive cohort successfully completed self-imaging. Participants spent less time on self-imaging compared with SD-OCT operated by a technician (66.7±20.1 vs 73.3±32.5, p<0.01). A majority of participants (90%) found the self-imaging process ‘easy’ and ‘comfortable’.Conclusions and relevanceThis study demonstrates that our self-imaging OCT and clinical-used SD-OCT are highly consistent not only in measuring the CST but also in identifying most retinal lesions.
Stent retriever for Tandem Acute Revascularization Technique (START): a novel technique for the endovascular management of tandem occlusions
Authors: Fageeh Areej , Zur Gil , Diouf Ange , La Russa Daniel , Drake Brian , P dos Santos Marlise , Caron Katie , Birch Nicole , Karwaski Stephen , Trussler Laurie , Miller Elizabeth , Fantaneanu Tadeu , Varghaei Parizad , Walker Gregory , Lesiuk Howard , Fahed Robert 
Published: October 2023

Tandem occlusions, characterized by the simultaneous presence of an intracranial large vessel occlusion and extracranial carotid artery stenosis or occlusion,1 pose a unique endovascular challenge.2 3 Typically, the extracranial occlusion is a result of atherosclerotic plaque; however, dissections are also a possible cause. It is currently uncertain whether an intracranial first approach or an extracranial first approach should be employed.4 5 A new technique has been developed which allows for the simultaneous treatment of both the intracranial and the extracranial lesion.6 We describe a variation of this technique: the stent retriever for tandem acute revascularization technique (START), which consists of simultaneously treating the intracranial lesion with stent retriever and contact aspiration, and the extracranial lesion with balloon angioplasty. We present a technical video explaining all the steps of START.(video 1)Video 1Description and example of the START.
Estimating own-price and cross-price elasticity of cigarette consumption by price tiers in Bangladesh
Authors: Shimul Shafiun N , Hussain A K M Ghulam , Nargis Nigar 
Published: October 2023

ObjectivesThe overall price elasticity of cigarette consumption in Bangladesh has been studied extensively. The estimates of price elasticity by price tiers are not available in the existing literature.MethodsUsing cohort data of nearly 6000 individuals from the International Tobacco Control Bangladesh survey, this study estimated the own-price and cross-price elasticity and income elasticity of cigarette demand by price tiers in Bangladesh. The elasticity was estimated in three stages of consumer decisions: whether to smoke, which brand to smoke and finally, how many cigarettes to smoke per day. The decision to smoke cigarettes and the choice of cigarette brands were modelled using instrumental variable probability regression. The cigarette consumption per day was modelled using seemingly unrelated regression.ResultsThe price elasticity of cigarette smoking prevalence with respect to the price of low-price cigarettes is −0.0487. The total elasticity for low-price cigarette consumption with respect to its own price is −0.1678. The own-price elasticity of smoking intensity of high-priced brands is −0.2512. The cross-price elasticity of low-price cigarette consumption with respect to high-price brand prices is 0.2643. The income elasticity of smoking prevalence overall is 0.0564. The income elasticity of daily consumption of low-price cigarettes is −0.1934 and for high-price cigarettes, it is 1.4044. The total income elasticity is 1.4608 for high-price cigarettes.ConclusionA cigarette tax policy that raises the prices of both low-price and high-price brands—but increases prices in the low-price tier at a faster rate than in the high-price tier and increases prices of all brands at a pace faster than income growth—can effectively reduce cigarette consumption in Bangladesh.JEL codesH29, L66, I18.
Projected Change in the Burden of Excess Cardiovascular Deaths Associated With Extreme Heat by Midcentury (2036–2065) in the Contiguous United States
Authors: Khatana Sameed Ahmed M. , Eberly Lauren A. , Nathan Ashwin S. , Groeneveld Peter W. 
Published: October 2023

BACKGROUND:
Climate change is causing an increase in extreme heat. Individuals with cardiovascular disease are at high risk of heat-related adverse health effects. How the burden of extreme heat–associated cardiovascular deaths in the United States will change with the projected rise in extreme heat is unknown.

METHODS:
We obtained data on cardiovascular deaths among adults and the number of extreme heat days (maximum heat index ≥90 °F [32.2 °C]) in each county in the contiguous United States from 2008 to 2019. Based on representative concentration pathway trajectories that model greenhouse gas emissions and shared socioeconomic pathways (SSP) that model future socioeconomic scenarios and demographic projections, we obtained county-level projected numbers of extreme heat days and populations under 2 scenarios for the midcentury period 2036 to 2065: SSP2-4.5 (representing demographic projections from a “middle-of-the-road” socioeconomic scenario and an intermediate increase in emissions) and SSP5-8.5 (demographic projections in an economy based on “fossil-fueled development” and a large increase in emissions). The association of cardiovascular mortality with extreme heat was estimated with a Poisson fixed-effects model. Using estimates from this model, the projected number of excess cardiovascular deaths associated with extreme heat was calculated.

RESULTS:
Extreme heat was associated with 1651 (95% CI, 921–2381) excess cardiovascular deaths per year from 2008 to 2019. By midcentury, extreme heat is projected to be associated with 4320 (95% CI, 2369–6272) excess deaths annually, which is an increase of 162% (95% CI, 142–182) under SSP2-4.5, and 5491 (95% CI, 3011–7972) annual excess deaths, which is an increase of 233% (95% CI, 206–259) under SSP5-8.5. Elderly adults are projected to have a 3.5 (95% CI, 3.2–3.8) times greater increase in deaths in the SSP2-4.5 scenario compared with nonelderly adults. Non-Hispanic Black adults are projected to have a 4.6 (95% CI, 2.8–6.4) times greater increase compared with non-Hispanic White adults. The projected change in deaths was not statistically significantly different for other race and ethnicity groups or between men and women.

CONCLUSIONS:
By midcentury, extreme heat is projected to be associated with a significantly greater burden of excess cardiovascular deaths in the contiguous United States.
Perceptual Cycles Travel Across Retinotopic Space
Authors: Fakche Camille , Dugué Laura 
Published: October 2023

Abstract
Visual perception waxes and wanes periodically over time at low frequencies (theta: 4–7 Hz; alpha: 8–13 Hz), creating “perceptual cycles.” These perceptual cycles can be induced when stimulating the brain with a flickering visual stimulus at the theta or alpha frequency. Here, we took advantage of the well-known organization of the visual system into retinotopic maps (topographic correspondence between visual and cortical spaces) to assess the spatial organization of induced perceptual cycles. Specifically, we tested the hypothesis that they can propagate across the retinotopic space. A disk oscillating in luminance (inducer) at 4, 6, 8, or 10 Hz was presented in the periphery of the visual field to induce perceptual cycles at specific frequencies. EEG recordings verified that the brain responded at the corresponding inducer frequencies and their first harmonics. Perceptual cycles were assessed with a concurrent detection task—target stimuli were displayed at threshold contrast (50% detection) at random times during the inducer. Behavioral results confirmed that perceptual performance was modulated periodically by the inducer at each frequency. We additionally manipulated the distance between the target and the inducer (three possible positions) and showed that the optimal phase, that is, moment of highest target detection, shifted across target distance to the inducer, specifically when its flicker frequency was in the alpha range (8 and 10 Hz). These results demonstrate that induced alpha perceptual cycles travel across the retinotopic space in humans at a propagation speed of 0.3–0.5 m/sec, consistent with the speed of unmyelinated horizontal connections in the visual cortex.
Event Probabilities Have a Different Impact on Early and Late Electroencephalographic Measures Regarded as Metrics of Prediction
Authors: Saurels Blake W. , Johnston Alan , Yarrow Kielan , Arnold Derek H. 
Published: October 2023

Abstract
The oddball protocol has been used to study the neural and perceptual consequences of implicit predictions in the human brain. The protocol involves presenting a sequence of identical repeated events that are eventually broken by a novel “oddball” presentation. Oddball presentations have been linked to increased neural responding and to an exaggeration of perceived duration relative to repeated events. Because the number of repeated events in such protocols is circumscribed, as more repeats are encountered, the conditional probability of a further repeat decreases—whereas the conditional probability of an oddball increases. These facts have not been appreciated in many analyses of oddballs; repeats and oddballs have rather been treated as binary event categories. Here, we show that the human brain is sensitive to conditional event probabilities in an active, visual oddball paradigm. P300 responses (a relatively late component of visually evoked potentials measured with EEG) tended to be greater for less likely oddballs and repeats. By contrast, P1 responses (an earlier component) increased for repeats as a goal-relevant target presentation neared, but this effect occurred even when repeat probabilities were held constant, and oddball P1 responses were invariant. We also found that later, more likely oddballs seemed to last longer, and this effect was largely independent of the number of preceding repeats. These findings speak against a repetition suppression account of the temporal oddball effect. Overall, our data highlight an impact of event probability on later, rather than earlier, electroencephalographic measures previously related to predictive processes—and the importance of considering conditional probabilities in sequential presentation paradigms.