bluuebunny/crossref_metadata_2025 huggingface dataset:
A hyperbaric aerodynamic levitator for containerless materials research
Authors: Boland Sydney E. , Wilke Stephen K. , Scott Jonathan A. , Schlossberg Sarah M. , Ivaschenko Alex , Weber Richard J. K. , Lipke David W.
Published: May 2023

A hyperbaric aerodynamic levitator has been developed for containerless materials research at specimen temperatures exceeding 2000 °C and pressures up to 10.3 MPa (1500 psi). This report describes the prototype instrument design and observations of the influence of specimen size, density, pressure, and flow rate on levitation behavior. The effect of pressure on heat transfer was also assessed by studying the heating and cooling behavior of levitated Al2O3 liquids. A threefold increase in the convective heat transfer coefficient was estimated as pressure increased to 10.3 MPa. The results demonstrate that hyperbaric aerodynamic levitation is a promising technique for containerless materials research at high gas pressures.
Acoustically improved performance in poly(3-hexylthiophene) based organic field effect transistor
Authors: Bhattacharjee Paromita , Mishra Himakshi , Iyer Parameswar K. , Nemade Harshal B.
Published: May 2023

Demonstration of acoustically improving charge transport characteristics of regioregular poly(3-hexylthiophene) (rrP3HT) based organic field effect transistor (OFET) fabricated on YZ lithium niobate piezoelectric substrate has been presented and analyzed. Owing to the acoustoelectric (AE) effect, a surface acoustic wave (SAW) propagating through the substrate transfers its momentum and energy to the charges in the rrP3HT channel, reducing the effective energy gap between the charge hopping states, which leads to a decrease in charge trapping and an increase in path conductivity and number of paths for charge transport. Hence, a significant increase in drain current and mobility and a substantial reduction in gate voltage were observed in the presence of SAW. The AE effect has been especially predominant in devices with smaller channel width, depicting that gate voltage brought down by 30 V provided drain current equivalent to that obtained in the absence of SAW. The bias stress analysis of the devices showed an increase in current instead of the decrease, generally seen with respect to time, reinforcing that the long term charge trapping effect in OFETs can be compensated with the propagation of SAW leading to enhanced device stability.
Are orthodox Australian rainforest seeds short-lived in storage?
Authors: Sommerville Karen D. , Newby Zoe-Joy , Martyn Yenson Amelia J. , Offord Catherine A.
Published: May 2023

Context Fifty per cent of Australian rainforest species produce orthodox seeds, but little is known about their longevity in storage. Aims To (1) estimate the longevity of seeds of 33 rainforest species using artificial aging; (2) assess the influence of habit, habitat range (restricted to rainforest or more broadly distributed), seed characteristics (endospermy, dry weight), and collection environment (e.g. precipitation, elevation and average temperature) on longevity; (3) compare longevity of rainforest seeds to previously assessed species from non-rainforest habitats; (4) compare longevity in artificial aging to real-time longevity in storage. Methods Seeds were aged at 60% relative humidity and 45°C, and tested at pre-determined intervals until germination was reduced to zero. The time taken for germination to decline to 50% (p50AA) was calculated by probit analysis. Ordinary least-squares regression was used to model p50AA for rainforest and non-rainforest species against predictor variables. Values for p50AA were then compared with the actual longevity in storage at −20°C (p50RT) using Pearson’s correlation. Key results Species restricted to rainforest exhibited a significantly lower p50AA than species with a wider distribution or those restricted to non-rainforest habitats. Collection elevation had a significant negative influence on p50AA. In all, 14 of 33 species showed a significant decline in viability after ≤12 years in storage. Values of p50AA were not correlated with p50RT. Conclusions Rainforests contain a high proportion of potentially, and actually, short-lived species; however, p50AA is not a good predictor of their real-time longevity. Implications Rainforest species should be managed as short-lived, with viability checked at least every 5 years, until real-time longevity data indicate otherwise.
Scanning electron microscopy of human islet cilia
Authors: Polino Alexander J. , Sviben Sanja , Melena Isabella , Piston David W. , Hughes Jing W.
Published: May 2023

Human islet primary cilia are vital glucose-regulating organelles whose structure remains uncharacterized. Scanning electron microscopy (SEM) is a useful technique for studying the surface morphology of membrane projections like cilia, but conventional sample preparation does not reveal the submembrane axonemal structure, which holds key implications for ciliary function. To overcome this challenge, we combined SEM with membrane-extraction techniques to examine primary cilia in native human islets. Our data show well-preserved cilia subdomains which demonstrate both expected and unexpected ultrastructural motifs. Morphometric features were quantified when possible, including axonemal length and diameter, microtubule conformations, and chirality. We further describe a ciliary ring, a structure that may be a specialization in human islets. Key findings are correlated with fluorescence microscopy and interpreted in the context of cilia function as a cellular sensor and communications locus in pancreatic islets.
Activity measurements of the radionuclides 18F, 64Cu and 99mTc for the ANSTO, Australia, in the ongoing comparisons BIPM.RI(II)-K4 series and KCRV update in the corresponding BIPM.RI(II)-K1 comparison
Authors: Michotte C , Nonis M , Wyngaardt W M Van , Tobin S , Smith M , Lee S , Jackson T , Ilter J , Howe B , Sarbutt A , Silva I Da
Published: May 2023

Main text

In 2017, comparisons of activity measurements of 18F, 64Cu, 99mTc and 11C using the Transfer Instrument of the International Reference System (SIRTI) took place at the Australian Nuclear Science and Technology Organisation (ANSTO, Australia). Ampoules containing 18F, 64Cu and 99mTc solutions were measured in the SIRTI for about 1.7 to 4 half-lives. The ANSTO carried out the primary standardization of the activity in the ampoules by 4π(LS)β—γ coincidence measurements. The comparisons, identifiers BIPM.RI(II)-K4.F-18, BIPM.RI(II)-K4.Cu-64 and BIPM.RI(II)-K4.Tc-99m are linked to the corresponding BIPM.RI(II)-K1.F-18, BIPM.RI(II)-K1.Cu-64 and BIPM.RI(II)-K1.Tc-99m comparisons. The BIPM.RI(II)-K1 18F and 99mTc key comparison reference values have been updated to include the latest BIPM.RI(II)-K4 linked results and degrees of equivalence for those three comparisons have been evaluated.

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Kinetic electron cooling in magnetic nozzles: experiments and modeling
Authors: Kim June Young , Chung Kyoung-Jae , Takahashi Kazunori , Merino Mario , Ahedo Eduardo
Published: May 2023

As long-distance space travel requires propulsion systems with greater operational flexibility and lifetimes, there is a growing interest in electrodeless plasma thrusters that offer the opportunity for improved scalability, larger throttleability, running on different propellants and limited device erosion. The majority of electrodeless designs rely on a magnetic nozzle (MN) for the acceleration of the plasma, which has the advantage of utilizing the expanding electrons to neutralize the ion beam without the additional installation of a cathode. The plasma expansion in the MN is nearly collisionless, and a fluid description of electrons requires a non-trivial closure relation. Kinetic electron effects and in particular electron cooling play a crucial role in various physical phenomena, such as energy balance, ion acceleration, and particle detachment. Based on experimental and theoretical studies conducted in recognition of this importance, the fundamental physics of the electron-cooling mechanism revealed in MNs and magnetically expanding plasmas is reviewed. In particular, recent approaches from the kinetic point of view are discussed, and our perspective on the future challenges of electron cooling and the relevant physical subject of MN is presented.
Thermal neutron reference radiation facility with high thermalization and large uniformity area
Authors: Wang Pingquan , Yang Junkai , Li Fan , Zhang Hui , Ren Zhongguo , Liu Zuoye , Zhang Hongjun , Xiong Zhonghua , Li Shicheng , Gao Fan
Published: May 2023

A new thermal neutron facility based on 12 241Am–Be neutron sources has been established at the National Institute of Metrology, China. It has two independent irradiation fields, the inner field and outer field, constructed with high-purity graphite and heavy water as moderators, respectively. Three innovative designs, including the reflection cavity, reflection layer, and homogenizing lens, were introduced to improve the performance of the facility. The reflection layer can increase the thermal neutron fluence rate by about 3–4 times, the reflection cavity also enhances thermal fluence by 3–4 times by taking advantage of multiple scattering of neutrons, and the homogenizing lens mounted on the neutron exit surface of the moderator improve the distribution of thermal neutron. The characteristics of the two fields were investigated by Monte Carlo simulations and experimental measurements. The results show that the new facility has high thermalization and large uniformity area with these innovative designs. For the inner field, the thermal neutron fluence rate at the reference position is (21 433.3 ± 407.2) cm−2 s−1, the cadmium ratio is 20.6, the non-uniformity is 0.1% over the 40 cm × 40 cm region. For the outer field, the thermal fluence rate at the reference position is (2046.0 ± 49.1) cm−2 s−1, the cadmium ratio is 1433, and the non-uniformity is 0.7% in the 70 cm × 70 cm region. The facility is expected to be suitable for the large-size detector, and its excellent performance is attractive for various thermal neutron experiments.
Soliton collisions in spin–orbit coupled spin-1 Bose–Einstein condensates
Authors: Qi Juan-juan , Zhao Dun , Liu Wu-Ming
Published: May 2023

We investigate analytically the effects of spin–orbit coupling (SOC) for the dynamics of soliton collisions in spin-1 Bose–Einstein condensates (BECs). Applying the non-standard Hirota’s bilinear method, we derive some exact one- and two-soliton solutions for the one-dimensional system of a spin–orbit coupled spin-1 BEC, which clearly shows how the dynamics of the solitons in spinor BECs can be engineered by SOC. Under SOC, the soliton collisions of ferromagnetic-polar type, ferromagnetic-ferromagnetic type and polar-polar type are discussed in details. Comparisons for the soliton states between the systems with and without SOC are displayed, a remarkable phenomenon is that the SOC can lead to the split of a soliton.
Smart screening system for breast cancer: the use of thermographic images, evolutionary algorithms, and oversampling
Authors: Queiroz Kamila Fernanda Ferreira da Cunha , de Cássia Fernandes de Lima Rita
Published: May 2023

Purpose. This study aimed to develop a computer system for automatic detection of thermographic changes indicating breast malignancy risk. Materials and methods. The database contained 233 thermograms of women, including 43 with malignant lesions and 190 with no malignant lesions. Five classifiers were evaluated (k-Nearest Neighbor, Support Vector Machine, Decision Tree, Discriminant Analysis, and Naive Bayes) in combination with oversampling techniques. An attribute selection approach using genetic algorithms was considered. Performance was assessed using accuracy, sensitivity, specificity, AUC, and Kappa statistics. Results. Support vector machines combined with attribute selection by genetic algorithm and ASUWO oversampling obtained the best performance. Attributes were reduced by 41.38%, and accuracy was 95.23%, sensitivity was 93.65%, and specificity was 96.81%. The Kappa index was 0.90, and AUC was 0.99. Conclusion. The feature selection process lowered computational costs and improved diagnostic accuracy. A high-performance system using a new breast imaging modality could positively aid breast cancer screening.
Ethanolic curcumin/silver nanoparticles suspension as antibacterial coating mixture for gutta-percha and cotton fabric
Authors: Monisha K , Antinate Shilpa S , Anandan B , Hikku G S
Published: May 2023

In recent years, the introduction of nanoparticles (NPs) in coating systems to impart antibacterial activity to substrates of interest is on the rise to counteract drug-resistant bacterial infections. In this regard, a coating system was developed using curcumin/Ag NPs (C-Ag NPs) complex in ethanolic suspension to be used as an antibacterial coating material for gutta-percha (dental filler) and cotton fabric. The prepared NPs were thoroughly characterized by employing x-ray diffraction, high-resolution scanning electron microscopy, Fourier Transform infrared spectroscopy, UV–vis spectroscopy, and particle size analysis. A simple dip coating technique with a solvent evaporation route was employed to modify the surfaces of gutta-percha and the cotton fabric. The antibacterial activity of C-Ag NPs modified gutta-percha and cotton fabric was assessed using a modified colony counting route and AATCC-147 standard, respectively, and displayed better results than curcumin-modified substrates. Therefore, the pathway for bacterial infections after root canal treatment and the spread of hospital-acquired infections in the hospital sector can be restricted with the use of C-Ag NPs modified gutta-percha and cotton fabric, respectively.
Interface and electromagnetic effects in the valley splitting of Si quantum dots
Authors: Lima Jonas R F , Burkard Guido
Published: May 2023

The performance and scalability of silicon spin qubits depend directly on the value of the conduction band valley splitting (VS). In this work, we investigate the influence of electromagnetic fields and the interface width on the VS of a quantum dot in a Si/SiGe heterostructure. We propose a new three-dimensional theoretical model within the effective mass theory for the calculation of the VS in such heterostructures that takes into account the concentration fluctuation at the interfaces and the lateral confinement. With this model, we predict that the electric field is an important parameter for VS engineering, since it can shift the probability distribution away from small VSs for some interface widths. We also obtain a critical softness of the interfaces in the heterostructure, above which the best option for spin qubits is to consider an interface as wide as possible.
Sap flow as a function of variables within nested scales: ordinary least squares vs. spatial regression models
Authors: Zabihi Khodabakhsh , Singh Vivek Vikram , Trubin Aleksei , Tomášková Ivana , Blaženec Miroslav , Surový Peter , Jakuš Rastislav
Published: May 2023

Understanding scale-dependent influential drivers of sap flow variability can help managers and policymakers to allocate resources within a particular scale to improve forest health and resiliency against water-stress stimuli such as drought and insects, e.g. bark beetle infestations. We defined a daily measure of sap flow as a function of variables within nested scales of landscape, stand, and tree, using ordinary least squares (OLS), spatial lag and error regression models. Model covariates were elevation, latitude (Y-coordinate), longitude (X-coordinate), neighborhood tree density, tree diameter at breast height, and bark temperature for 40-surveyed Norway spruce (Picea abies) in the Czech Republic, Central Europe. Trees were spatially distributed within 19-established subplots across five plots, with distances ranging 2–9 km, at which variations in soil water potential and temperature were limited. The daily measure of sap flow within the regional scale allowed us to avoid the temporal and spatial variability of climate effects on sap flow. A relatively flat terrain across subplots also allowed us to control the effects of slope, aspect, and topography-related solar incidence angle on sap flow. Sap flow was strongly spatially autocorrelated, so OLS models failed to take spatial autocorrelation into account unless to some extent, depending on the spatial distribution of samples, by including latitude and/or longitude in the models. Among spatial regression models, spatial error models performed better than lag models, allowing to capture the effects of unmeasured independent variables. Sap flow variability for the most part (∼70%) was explained by the landscape-level variable of elevation followed by the stand-level variable of tree density, and the remaining part by variables related to tree characteristics; a nested down-scaling function, defined and visualized for the first time. Therefore, thinning forest stands and future plantations with optimum distances, based on the elevation gradients, may be required to counterbalance the allocation of resources, e.g. water, nutrients, and light, among trees, leading to enhance forest health and resiliency against water-stress stimuli.
Challenges and opportunities in maintaining research momentum at a primarily undergraduate institution
Authors: Torrente Mariana , Dilek Ozlem
Published: May 2023

Conferences and meetings hosted by scientific societies usually include sessions on how to navigate the academic faculty job search and the initial setup of a laboratory, or how to identify and pursue early-career grant funding opportunities. However, there is not much professional development support available beyond this stage. Faculty may have set up the research lab and have recruited students to their groups but then might find themselves struggling to be successful in accomplishing their goals. In other words, how can we maintain the momentum once research activities are established? This Voices article summarizes a discussion carried out in the context of a round-table session at the American Society for Cell Biology’s Cell Bio 2022. We sought to identify and articulate the challenges of carrying out research at primarily undergraduate institutions (PUIs), appreciate the role of undergraduate research in the science enterprise, develop strategies to overcome research challenges and recognize unique opportunities in this setting, with the ultimate goal of launching a community of “late-early” to mid-career PUI faculty.
Latent Profiles of Fear of Cancer Recurrence and Associations with Physical and Mental Health Outcomes
Authors: Liu Jianlin , Griva Konstadina , Mahendran Rathi
Published: May 2023

Background

Fear of cancer recurrence (FCR) is a multidimensional construct; however, few studies have meaningfully integrated FCR severity (i.e., level of fear) with FCR-related concepts (e.g., triggers).

Purpose

The present study determined (a) latent profiles of FCR; (b) socio-demographic variations between identified profiles; (c) interactions between identified profiles and resilience and rumination on chronic physical disorders, depressive/anxiety symptoms, and quality of life.

Methods

The present study is a secondary data analysis of which 404 cancer survivors were included in this study. All participants completed the Fear of Cancer Recurrence Inventory and measures of resilience, rumination, depressive/anxiety symptoms, and quality of life.

Results

Latent profile analysis identified three distinct profiles based on varying levels of FCR and FCR-related concepts; Profile 1 “Low FCR” (n = 108; 26.4%), Profile 2 “Moderate FCR, High coping” (n = 197; 49.4%), and Profile 3 “High FCR, distress and impairment” (n = 99; 24.3%). Profile 3 was associated with younger age and history of radiotherapy. Latent profiles of FCR significantly interacted with resilience and rumination on depressive/anxiety symptoms.

Conclusions

Latent profile analysis integrates FCR severity and FCR-related concepts to support a nuanced understanding of FCR. Our results suggest specific points of intervention, which extend beyond addressing FCR severity.
Hook Effect in Semiquantitative SARS-CoV-2 Antispike Total Antibody Assay
Authors: Benirschke Robert C , Lee Hong Kee
Published: May 2023

Objectives

The hook effect is a common preanalytical error that results in falsely decreased analyte concentrations in immunoassays. We present here an example in a semiquantitative SARS-CoV-2 antispike total antibody assay and report the incidence of this error at our institution.

Methods

All specimens with initial results within the reportable range of the assay were diluted. Results with higher results upon dilution were determined to have the hook effect. In a subset of specimens, these results were also confirmed as elevated on an alternative SARS-CoV-2 antibody assay.

Results

Over 1 month, 12 (9.1%) of 132 results were within the analytical measuring range of the assay. Of these, 11 showed the hook effect and required dilution to obtain accurate results. These represented 8.3% of our total testing volume.

Conclusions

The hook effect was detected in a semiquantitative SARS-CoV-2 antispike total antibody assay at a high incidence. This error results in observed concentrations much lower than is accurate. Laboratories should be aware of this issue and consider manually diluting specimens within the reportable range of the assay to detect this issue.
When parents play favorites: brood demand shapes parental preference for offspring UV color
Authors: García-Campa Jorge , Müller Wendt , Rodríguez-Juncá Alicia , Morales Judith
Published: May 2023

Parents might initially produce more offspring than they might be able to raise. However, when offspring demand exceeds their parents´ rearing capacity, parents might shift care towards the offspring which yield greater fitness returns to achieve their optimal brood size via brood reduction. Such favoritism could rely on offspring signaling traits if these inform parents about offspring quality and hence about the pay-offs of their investment. Here we investigated whether favoritism of blue tit (Cyanistes caeruleus) parents for an offspring signal (i.e., ultraviolet (UV) plumage coloration) varies with brood demand. To test this, we experimentally blocked the UV reflectance of yellow breast feathers in half of the nestlings of each brood, and then we sequentially performed two opposing brood size manipulations to vary nestling demand below or above parental rearing capacity. In reduced broods, nestlings begged overall less intensely and gained more body mass, supporting that parental rearing capacities sufficed to satisfy brood demand. Moreover, in reduced broods, UV-blocked nestlings (i.e., low-quality offspring) were fed and prey-tested more often. Yet, they begged more than control nestlings, suggesting that they were perhaps treated differently by other family members or which they may exploit parental preferences beyond actual need (at least in reduced nests). Parents flexibly shifted their feeding rate and favoritism in response to short-term changes in family size, as there was no parental preference for enlarged broods. Such flexible parental feeding rules may allow parents to gain the upper hand in parent-offspring conflict. However, we did not find evidence that parental favoritism facilitated brood reduction, at least in conditions where demand was temporally enhanced.
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
Authors: Song Yidong , Yuan Qianmu , Chen Sheng , Chen Ken , Zhou Yaoqi , Yang Yuedong
Published: May 2023

Determining intrinsically disordered regions of proteins is essential for elucidating protein biological functions and the mechanisms of their associated diseases. As the gap between the number of experimentally determined protein structures and the number of protein sequences continues to grow exponentially, there is a need for developing an accurate and computationally efficient disorder predictor. However, current single-sequence-based methods are of low accuracy, while evolutionary profile-based methods are computationally intensive. Here, we proposed a fast and accurate protein disorder predictor LMDisorder that employed embedding generated by unsupervised pretrained language models as features. We showed that LMDisorder performs best in all single-sequence-based methods and is comparable or better than another language-model-based technique in four independent test sets, respectively. Furthermore, LMDisorder showed equivalent or even better performance than the state-of-the-art profile-based technique SPOT-Disorder2. In addition, the high computation efficiency of LMDisorder enabled proteome-scale analysis of human, showing that proteins with high predicted disorder content were associated with specific biological functions. The datasets, the source codes, and the trained model are available at https://github.com/biomed-AI/LMDisorder.
LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data
Authors: Chen Chia-Yu , Lӧber Ulrike , Forslund Sofia K
Published: May 2023

We introduce LongDat, an R package that analyzes longitudinal multivariable (cohort) data while simultaneously accounting for a potentially large number of covariates. The primary use case is to differentiate direct from indirect effects of an intervention (or treatment) and to identify covariates (potential mechanistic intermediates) in longitudinal data. LongDat focuses on analyzing longitudinal microbiome data, but its usage can be expanded to other data types, such as binary, categorical, and continuous data. We tested and compared LongDat with other tools (i.e., MaAsLin2, ANCOM, lgpr, and ZIBR) on both simulated and real data. We showed that LongDat outperformed these tools in accuracy, runtime, and memory cost, especially when there were multiple covariates. The results indicate that the LongDat R package is a computationally efficient and low-memory-cost tool for longitudinal data with multiple covariates and facilitates robust biomarker searches in high-dimensional datasets.

Availability and Implementation

The R package LongDat is available on CRAN (https://cran.r-project.org/web/packages/LongDat/) and GitHub (https://github.com/CCY-dev/LongDat).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
The Next Generation of Population-Based DFNB16 Carrier Screening and Diagnosis: STRC Copy-Number Variant Analysis from Genome Sequencing Data
Authors: Xiang Jiale , Peng Jiguang , Sun Xiangzhong , Lin Zibin , Li Dongdong , Ye Haodong , Wang Sibao , Bai Yushi , Wang Xiaohong , Du Peina , Gao Ya , Sun Jun , Pan Silin , Peng Zhiyu
Published: May 2023

Background

Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing.

Methods

We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number.

Results

The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%–100%) and specificity (98.8%; 95% CI, 97.7%–99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%–2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number.

Conclusions

We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit
Authors: Chen Nianhang , Zhang Rong , Zeng Tao , Zhang Xuting , Wu Ruibo
Published: May 2023

Terpenoids and their derivatives are collectively known as the terpenome and are the largest class of natural products, whose biosynthesis refers to various kinds of enzymes. To date, there is no terpenome-related enzyme database, which is a desire for enzyme mining, metabolic engineering and discovery of new natural products related to terpenoids. In this work, we have constructed a comprehensive database called TeroENZ (http://terokit.qmclab.com/browse_enz.html) containing 13 462 enzymes involved in the terpenoid biosynthetic pathway, covering 2541 species and 4293 reactions reported in the literature and public databases. At the same time, we classify enzymes according to their catalytic reactions into cyclase, oxidoreductase, transferase, and so on, and also make a classification according to species. This meticulous classification is beneficial for users as it can be retrieved and downloaded conveniently. We also provide a computational module for isozyme prediction. Moreover, a module named TeroMAP (http://terokit.qmclab.com/browse_rxn.html) is also constructed to organize all available terpenoid enzymatic reactions into an interactive network by interfacing with the previously established database of terpenoid compounds, TeroMOL. Finally, all these databases and modules are integrated into the web server TeroKit (http://terokit.qmclab.com/) to shed light on the field of terpenoid research.

Database URL  http://terokit.qmclab.com/
Impact of a sugar-sweetened beverage tax on sugar producers in Ukraine
Authors: Mandeville Kate L , Nivievskyi Oleg , Neyter Roman , Martyshev Pavlo , Vakhitov Volodymyr , Warren Bethany , Doroshenko Olena
Published: May 2023

Taxes on sugar-sweetened beverages can promote health and raise revenue. Whether these taxes negatively impact domestic sugar producers, an argument often made by opponents, is understudied. We extended a simulation model based on a uniform specific volume-based tax of UAH 4/L in Ukraine. We estimated best- and worst-case scenarios for reductions in domestic sugar demand to be 162 and 23 000 metric tons. This is at worst ∼0.5% of current exports, meaning decreases in domestic demand could easily be absorbed by export markets given export trends. Due to highly protectionist sugar sector policy, sugar producers would not be able to fully substitute domestic sales revenues through increased export revenues, but the worst-case revenue gap was <0.5% of total sectoral output in recent years. Overall, introducing a tax on sugar-sweetened beverages in Ukraine is likely to have a very limited impact on domestic sugar producers.
Theory-guided process evaluation of a multicomponent, technology-based ‘SMART Eating’ trial among Indian adults: an embedded mixed-methods study
Authors: Kaur Jasvir , Kaur Manmeet , Chakrapani Venkatesan , Kumar Rajesh
Published: May 2023

We report process evaluation findings from the ‘SMART Eating’ intervention trial, which significantly improved fat, sugar and salt (FSS), and fruits and vegetables (FVs) intake among adults. Intervention used information technology [short message service (SMS), WhatsApp and website] and interpersonal communication (distribution of SMART Eating kit) and pamphlet for comparison group. Guided by UK Medical Research Council’s framework, using embedded mixed-methods design, continuous process evaluation documented fidelity, dose, reach, acceptability and mechanisms. Intervention was implemented as intended, with high reach (91%) in both groups: ‘comparison group’ (n = 366): inadequate use of pamphlets (46%); ‘intervention group’ (n = 366): with timely remedial measures to remove implementation/usage barriers, dose of SMS (93%), WhatsApp (89%) and ‘SMART Eating’ kit (100%) was adequate, but website usage was low (50%); compliance was evident from participants’ interactions with the implementor and observations on kit usage. All these might have improved attitude, social influence, self-efficacy and household behaviours, which, in turn, mediated intervention’s effect on improving FSS and FV intake. Among poor performers, lack of effect on FV intake was perceived to be related to high cost/pesticides use and FSS intake was related to lack of family support. Low website usage, challenges with WhatsApp messaging and contextual factors (cost, pesticides abuse and family support) need to be considered while designing similar future interventions.
Molecular Pathogenesis of Colitis-associated Colorectal Cancer: Immunity, Genetics, and Intestinal Microecology
Authors: Yin Yue , Wan Jian , Yu Jingmin , Wu Kaichun
Published: May 2023

Patients with inflammatory bowel disease (IBD) have a high risk for colorectal cancer (CRC). This cancer type, which is strongly associated with chronic inflammation, is called colitis-associated CRC (CAC). Understanding the molecular pathogenesis of CAC is crucial to identify biomarkers necessary for early diagnosis and more effective treatment directions. The accumulation of immune cells and inflammatory factors, which constitute a complex chronic inflammatory environment in the intestinal mucosa, may cause oxidative stress or DNA damage to the epithelial cells, leading to CAC development and progression. An important feature of CAC is genetic instability, which includes chromosome instability, microsatellite instability, hypermethylation, and changes in noncoding RNAs. Furthermore, the intestinal microbiota and metabolites have a great impact on IBD and CAC. By clarifying immune, genetic, intestinal microecology, and other related pathogenesis, CAC may be more predictable and treatable.
Changes in Vaginal Bacteria and Inflammatory Mediators From Periconception Through the Early Postpartum Period in a Cohort of Kenyan Women Without HIV
Authors: Sabo Michelle C , Lokken Erica M , Srinivasan Sujatha , Kinuthia John , Richardson Barbra A , Fiedler Tina L , Munch Matthew , Proll Sean , Salano Clayton , John-Stewart Grace , Jaoko Walter , Fredricks David N , McClelland R Scott
Published: May 2023

Background

Women's increased risk of HIV acquisition during pregnancy and postpartum may be mediated by changes in vaginal microbiota and/or cytokines.

Methods

A cohort of 80 Kenyan women who were HIV-1 seronegative contributed 409 vaginal samples at 6 pregnancy time points: periconception, positive pregnancy test result, first trimester, second trimester, third trimester, and postpartum. Concentrations of vaginal bacteria linked with HIV risk and Lactobacillus spp were measured using quantitative polymerase chain reaction. Cytokines were measured by immunoassay.

Results

Based on Tobit regression, later pregnancy time points were associated with lower concentrations of Sneathia spp (P = .01), Eggerthella sp type 1 (P = .002), and Parvimonas sp type 2 (P = .02) and higher concentrations of Lactobacillus iners (P < .001), Lactobacillus crispatus (P < .001), Lactobacillus vaginalis (P < .001), interleukin 6 (P < .001), TNF (P = .004), C-X-C motif chemokine ligand 10 (CXCL10; P < .001), C-C motif ligand 3 (P = .009), C-C motif ligand 4 (P < .001), C-C motif ligand 5 (P = .002), interleukin 1β (P = .02), and interleukin 8 (P = .002). Most cervicovaginal cytokines and vaginal bacteria clustered separately in principal component analysis, except for CXCL10, which did not group with either cytokines or bacteria. The shift toward a Lactobacillus-dominated microbiota during pregnancy mediated the relationship between pregnancy time point and CXCL10.

Conclusions

Increases in proinflammatory cytokines, but not vaginal bacterial taxa linked with higher HIV risk, could provide an explanation for increased HIV susceptibility during pregnancy and postpartum.
Variation among populations ofTrichogramma euproctidis(Hymenoptera: Trichogrammatidae) revealed by life table parameters: perspectives for biological control
Authors: Tabebordbar Fatemeh , Formisano Giorgio , Shishehbor Parviz , Ebrahimi Ebrahim , Giorgini Massimo , Sørensen Jesper Givskov
Published: May 2023

The successful mass-rearing of potential biological control agents is a prerequisite for sustainable pest control. In this study, the performance of 3 Trichogramma euproctidis (Girault) (Hymenoptera: Trichogrammatidae) populations collected from different locations in Khuzestan (Southwest Iran) were evaluated to optimize the egg parasitoid mass-rearing for augmentative biological control of lepidopteran pests. We aimed to investigate the effects of both population origin and host quality on biological traits of ovipositing females (number of parasitized eggs) and of their progeny (development time, survival rate, sex ratio, longevity, and fecundity). The effect of host quality was assessed by allowing the parasitoid to oviposit into 1, 2, 3, or 4-day-old Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs. The 3 T. euproctidis populations developed successfully regardless the age of the host eggs. However, we found significant variation among populations and a strong influence of host quality on the traits investigated. Progeny performance in all populations decreased with increasing host age. The best-performing population (collected in Mollasani) showed the highest parasitization rate, highest survival rate, and progeny sex ratio with the greatest percentage of females. A life table corroborated these findings with superior estimates of the net reproductive rate (R0), intrinsic rate of increase (r), and reduced generation time (T) for the Mollasani population on 1-day-old host eggs. We conclude that ample variation exists among T. euproctidis populations and that rearing the Mollasani population on young rather than old eggs of E. kuehniella would be recommended to implement the biological control programs to target lepidopteran pests in Southwestern Iran.
The United Nations convention on the rights of persons with disabilities, neuroscience, and criminal legal capacity
Authors: Barsky Benjamin A , Stein Michael Ashley
Published: May 2023

The United Nations Convention on the Rights of Persons with Disabilities requires states parties to ‘recognize that persons with disabilities enjoy legal capacity on an equal basis with others in all aspects of life.’ This mandate has sparked debate about the interpretation of legal capacity, including within the criminal context as applied to the retrogressively named ‘insanity defense.’ Yet, under-examined are two questions: First, what defenses should defendants with psychosocial disabilities be able to invoke during criminal prosecutions? Second, what kind of evidence is consistent with, on the one hand, determining a defendant’s decision-making capacity to establish culpability and, on the other hand, the right to equal recognition before the law? Developments in neuroscience offer a unique prism to grapple with these issues. We argue that neuroscientific evidence of impaired decision-making, insofar as it presents valid and interpretable diagnostic information, can be a useful tool for influencing judicial decision-making and outcomes in criminal court. In doing so, we oppose the argument espoused by significant members of the global disability rights community that bioscientific evidence of psychosocial disability should be inadmissible to negate criminal responsibility. Such a position risks more defendants being punished harshly, sentenced to death, and placed in solitary confinement.
The 2022 dengue outbreak in Bangladesh: hypotheses for the late resurgence of cases and fatalities
Authors: Haider Najmul , Hasan Mohammad Nayeem , Khalil Ibrahim , Tonge Daniel , Hegde Shivanand , Chowdhury Muhammad Abdul Baker , Rahman Mahbubur , Khan Manjur Hossain , Ansumana Rashid , Zumla Alimuddin , Uddin Md Jamal
Published: May 2023

Bangladesh reported the highest number of annual deaths (n = 281) related to dengue virus infection in 2022 since the virus reappeared in the country in 2000. Earlier studies showed that >92% of the annual cases occurred between the months of August and September. The 2022 outbreak is characterized by late onset of dengue cases with unusually higher deaths in colder months, that is, October–December. Here we present possible hypotheses and explanations for this late resurgence of dengue cases. First, in 2022, the rainfall started late in the season. Compared to the monthly average rainfall for September and October between 2003 and 2021, there was 137 mm of additional monthly rainfall recorded in September and October 2022. Furthermore, the year 2022 was relatively warmer with a 0.71°C increased temperature than the mean annual temperature of the past 20 yr. Second, a new dengue virus serotype, DENV-4, had recently reintroduced/reappeared in 2022 and become the dominant serotype in the country for a large naïve population. Third, the post-pandemic return of normalcy after 2 yr of nonpharmaceutical social measures facilitates extra mosquito breeding habitats, especially in construction sites. Community engagement and regular monitoring and destruction of Aedes mosquitoes’ habitats should be prioritized to control dengue virus outbreaks in Bangladesh.
The Development and Initial Validation of Items to Assess Parent Fear of Nighttime Hypoglycemia
Authors: Monzon Alexandra D , Cushing Christopher C , McDonough Ryan , Clements Mark , Gonder-Frederick Linda , Patton Susana R
Published: May 2023

Objective

Parents of youth with type 1 diabetes (T1D) are fearful their children will experience nighttime hypoglycemia. Currently, the Hypoglycemia Fear Survey for Parents (HFS-P) lacks items that specifically assess parents’ nighttime fear. This study aimed to fill this gap by rigorously identifying new items to specifically assess parent fear of nighttime hypoglycemia and then examine the psychometric properties of the revised Hypoglycemia Fear Survey for Parents including Nighttime Fear (HFS-P-NF).

Methods

For Phase 1, we recruited 10 pediatric diabetes providers and 15 parents/caregivers of youth with T1D to generate items related to fear of nighttime hypoglycemia. For Phase 2, we recruited an additional 20 parents/caregivers to pilot-test the newly generated items. For Phase 3, we recruited another 165 parents/caregivers to evaluate structural validity via confirmatory factor analyses, reliability, and content validity of the revised HFS-P-NF.

Results

In Phase 1, we generated 54 items. In Phase 2, we removed 34 items due to violations of distributional normality and nonsignificant correlations. In Phase 3, a four-factor model reflecting behaviors maintaining high glucose, helplessness, negative social consequences, and nighttime worries was the best fitting model for the HFS-P-NF. The new items demonstrated strong internal consistency (α = 0.96) and strong to moderate relationships with criterion and content validity measures.

Conclusion

The current study provides initial evidence of validity and reliability for new items on the HFS-P-NF that broadened the conceptualization of parent fear of nighttime hypoglycemia. These findings are important to clinicians who may consider screening for parent fear of nighttime hypoglycemia more comprehensively.
Effects of low-dose/high-dose-rate X-irradiation on oxidative stress in organs following forced swim test and its combined effects on alcohol-induced liver damage in mice
Authors: Naoe Shota , Fujimoto Yuki , Murakami Kaito , Yukimine Ryohei , Tanaka Ayumi , Yamaoka Kiyonori , Kataoka Takahiro
Published: May 2023

The liver’s susceptibility to oxidative stress after a combination of forced swim test (FST) and low-dose-rate γ-irradiation has been observed. Therefore, this study aims to clarify the effects of low-dose (0.1 and 0.5 Gy)/high-dose-rate (1.2 Gy/min) irradiation on combined oxidative stressors—liver damage associated with FST and alcohol administration. In addition, the effects of similar irradiation on FST-induced immobility, which induces psychomotor retardation, and antioxidative effects on the brain, lungs, liver and kidneys were investigated, and the results were compared with those of a similar previous study that utilized low-dose-rate irradiation. Low-dose/high-dose-rate (especially 0.5 Gy) irradiation temporarily worsened liver antioxidant function and hepatic function with FST- and alcohol administration-related oxidative damage; however, the damages improved soon after. In addition, the increase in total glutathione content in the liver contributed to the early improvement of hepatic functions. However, pre-irradiation did not suppress immobility during the FST. The results also suggested that the effects of low-dose/high-dose-rate irradiation on the antioxidant functions of each organ after the FST were different from those of low-dose/low-dose-rate irradiation. Overall, this study provides further insights into the effects of low-dose irradiation on exposure to a combination of different oxidative stressors. It will also contribute to the elucidation of dose rate effects on oxidative stress in the low-dose irradiation range.
Metagenomic surveillance in Jinan, China, reveals serum microbiome and biochemistry features in fever of unknown origin (FUO) patients
Authors: Liu Ming , Liu Hui , Li Fenghua , Shen Yang , Zhang Liwen , Wang Gang , Wang Haitao , Qu Chunmei , Chen Gonghai , Zhao Xiulan , Liu Lanzheng , Zhou Jun
Published: May 2023

Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria was found, belonging to Enterobacteriaceae, Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), and Comamonadaceae (4.25%). The major virus families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae, and Herpesviridae, showing up in 34.96%, 47.37%, 30.89%, 5.69%, 3.25%, and 1.63% of patients, respectively. Using the Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in the high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, P = 0.021); tetra-PGDM (fold = 5.29, P = 0.037); and 20-HETE (fold > 10, P = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.