bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine vision-based high-precision and robust focus detection for femtosecond laser machining
Authors: Xu Si-Jia , Duan Yan-Zhao , Yu Yan-Hao , Tian Zhen-Nan , Chen Qi-Dai
Published: September 2021

We propose a machine vision-based focus detection method (MVFD) for femtosecond laser machining. By analyzing the laser focus pattern, the defocus direction and distance are obtained simultaneously. The proposed technique presents high precision with an average error of 0.047 µm and a root mean square error (RMSE) of 0.055 µm. Moreover, the method is robust and is less affected by the tilted sample. For the curved surface sample, the average error and RMSE are 0.093 and 0.145 µm, respectively. Thus, the proposed focus detection method can be easily combined with laser processing equipment, which is widely used in large-range and high-precision femtosecond laser processing.
Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves
Authors: Bauer Simon , Contreras Sebastian , Dehning Jonas , Linden Matthias , Iftekhar Emil , Mohr Sebastian B. , Olivera-Nappa Alvaro , Priesemann Viola
Published: September 2021

Mass vaccination offers a promising exit strategy for the COVID-19 pandemic. However, as vaccination progresses, demands to lift restrictions increase, despite most of the population remaining susceptible. Using our age-stratified SEIRD-ICU compartmental model and curated epidemiological and vaccination data, we quantified the rate (relative to vaccination progress) at which countries can lift non-pharmaceutical interventions without overwhelming their healthcare systems. We analyzed scenarios ranging from immediately lifting restrictions (accepting high mortality and morbidity) to reducing case numbers to a level where test-trace-and-isolate (TTI) programs efficiently compensate for local spreading events. In general, the age-dependent vaccination roll-out implies a transient decrease of more than ten years in the average age of ICU patients and deceased. The pace of vaccination determines the speed of lifting restrictions; Taking the European Union (EU) as an example case, all considered scenarios allow for steadily increasing contacts starting in May 2021 and relaxing most restrictions by autumn 2021. Throughout summer 2021, only mild contact restrictions will remain necessary. However, only high vaccine uptake can prevent further severe waves. Across EU countries, seroprevalence impacts the long-term success of vaccination campaigns more strongly than age demographics. In addition, we highlight the need for preventive measures to reduce contagion in school settings throughout the year 2021, where children might be drivers of contagion because of them remaining susceptible. Strategies that maintain low case numbers, instead of high ones, reduce infections and deaths by factors of eleven and five, respectively. In general, policies with low case numbers significantly benefit from vaccination, as the overall reduction in susceptibility will further diminish viral spread. Keeping case numbers low is the safest long-term strategy because it considerably reduces mortality and morbidity and offers better preparedness against emerging escape or more contagious virus variants while still allowing for higher contact numbers (freedom) with progressing vaccinations.
Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
Authors: González-Ramírez Mar , Ballaré Cecilia , Mugianesi Francesca , Beringer Malte , Santanach Alexandra , Blanco Enrique , Di Croce Luciano
Published: September 2021

The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters.
Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans
Authors: Foss Eric J. , Sripathy Smitha , Gatbonton-Schwager Tonibelle , Kwak Hyunchang , Thiesen Adam H. , Lao Uyen , Bedalov Antonio
Published: September 2021

The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed similar individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution: Footprints in budding yeast were more sharply focused compared to the other three organisms, consistent with the relative sequence specificity of replication origins in S. cerevisiae. Nonetheless, with some clear exceptions, most notably the inactive X-chromosome, much of the fluctuation in replication timing along the chromosomes in all four organisms reflected uneven chromosomal distribution of pre-replication complexes.
DHA but not EPA induces the trans-differentiation of C2C12 cells into white-like adipocytes phenotype
Authors: Ghnaimawi Saeed , Rebello Lisa , Baum Jamie , Huang Yan
Published: September 2021

Muscle derived stem cells (MDSCs) and myoblast play an important role in myotube regeneration when muscle tissue is injured. However, these cells can be induced to differentiate into adipocytes once exposed to PPARγ activator like EPA and DHA that are highly suggested during pregnancy. The objective of this study aims at determining the identity of trans-differentiated cells by exploring the effect of EPA and DHA on C2C12 undergoing differentiation into brown and white adipocytes. DHA but not EPA committed C2C12 cells reprograming into white like adipocyte phenotype. Also, DHA promoted the expression of lipolysis regulating genes but had no effect on genes regulating β-oxidation referring to its implication in lipid re-esterification. Furthermore, DHA impaired C2C12 cells differentiation into brown adipocytes through reducing the thermogenic capacity and mitochondrial biogenesis of derived cells independent of UCP1. Accordingly, DHA treated groups showed an increased accumulation of lipid droplets and suppressed mitochondrial maximal respiration and spare respiratory capacity. EPA, on the other hand, reduced myogenesis regulating genes, but no significant differences were observed in the expression of adipogenesis key genes. Likewise, EPA suppressed the expression of WAT signature genes indicating that EPA and DHA have an independent role on white adipogensis. Unlike DHA treatment, EPA supplementation had no effect on the differential of C2C12 cells into brown adipocytes. In conclusion, DHA is a potent adipogenic and lipogenic factor that can change the metabolic profile of muscle cells by increasing myocellular fat.
Interaction of the causal agent of apricot bud gall Acalitus phloeocoptes (Nalepa) with apricot: Implications in infested tissues
Authors: Li Shijuan , Khurshid Muhammad , Yao Junsheng , Zhang Jin , Dawuda Mohammed Mujitaba , Hassan Zeshan , Ahmad Shahbaz , Xu Bingliang
Published: September 2021

Apricot bud gall mite, Acalitus phloeocoptes (Nalepa), is a destructive arthropod pest that causes significant economic losses to apricot trees worldwide. The current study explores the ways to understand the mode of dispersal of A. phloeocoptes, the development and ultrastructure of apricot bud gall, and the role of phytohormones in the formation of the apricot bud galls. The results demonstrated that the starch granules in the bud axon were extended at the onset of the attack. During the later stages of the attack, the cytoplasm was found to deteriorate in infected tissues. Furthermore, we have observed that the accumulation of large amounts of cytokinin (zeatin, ZT) and auxin (indoleacetic acid, IAA) led to rapid bud proliferation during rapid growth period, while abscisic acid (ABA) controls the development of gall buds and plays a vital role in gall bud maturity. The reduction of gibberellic acid (GA3) content led to rapid lignification at the later phase of bud development. Overall, our results have revealed that the mechanism underlying the interaction of apricot bud gall with its parasite and have provided reliable information for designing valuable Apricot breeding programs. This study will be quite useful for pest management and will provide a comprehensive evaluation of ecology-based cost-effective control, life history and demographic parameters of A. phloeocoptes.
Exploring the cytotoxic mechanisms of Pediocin PA-1 towards HeLa and HT29 cells by comparison to known bacteriocins: Microcin E492, enterocin heterodimer and Divercin V41
Authors: Buss George P. , Wilson Cornelia M.
Published: September 2021

The purpose of this study was to explore potential mechanisms of cytotoxicity towards HeLa and HT29 cells displayed by Pediocin PA-1. We did this by carrying out sequence alignments and 3D modelling of related bacteriocins which have been studied in greater detail: Microcin E492, Enterocin AB heterodimer and Divercin V41. Microcin E492 interacts with Toll-Like Receptor 4 in order to activate an apoptosis reaction, sequence alignment showed a high homology between Pediocin PA-1 and Microcin E492 whereas 3D modelling showed Pediocin PA-1 interacting with TLR-4 in a way reminiscent of Microcin E492. Furthermore, Pediocin PA-1 had the highest homology with the Enterocin heterodimer, particularly chain A; Enterocin has also shown to cause an apoptotic response in cancer cells. Based on this we are led to strongly believe Pediocin PA-1 interacts with TLRs in order to cause cell death. If this is the case, it would explain the difference in cytotoxicity towards HeLa over HT29 cells, due to difference in expression of particular TLRs. Overall, we believe Pediocin PA-1 exhibits a dual effect which is dose dependant, like that of Microcin. Unfortunately, due to the COVID-19 pandemic, we were unable to carry out experiments in the lab, and the unavailability of important data meant we were unable to provide and validate out solid conclusions, but rather suggestions. However, bioinformatic analysis is still able to provide information regarding structure and sequence analysis to draw plausible and evidence based conclusions. We have been able to highlight interesting findings and how these could be translated into future research and therapeutics in order to improve the quality of treatment and life of cancer patients.
Differential impact of clinicopathological risk factors within the 2 largest ProMisE molecular subgroups of endometrial carcinoma
Authors: Pasanen Annukka , Loukovaara Mikko , Ahvenainen Terhi , Vahteristo Pia , Bützow Ralf
Published: September 2021

Objective

To assess whether the prognostic impact of conventional risk factors and ancillary biomarkers differs across the 2 largest ProMisE molecular subgroups of endometrial carcinoma (EC).

Methods

Direct sequencing of POLE exonuclease domain hot spots and immunohistochemistry for MLH1, PMS2, MSH2, MSH6 and p53 were performed on 745 unselected endometrioid ECs to identify mismatch repair deficient (MMR-D, n = 264) and no specific molecular profile (NSMP, n = 206) ECs. Molecular group-specific survival analyses and interaction analyses were performed to determine the prognostic relevance of clinicopathological factors and various biomarkers (L1 cell adhesion molecule, estrogen and progesterone receptor, beta-catenin, p16, E-cadherin, KRAS) within the subgroups.

Results

Molecular subgroup did not have an independent effect on disease-specific survival after adjustment for conventional risk factors (P = 0.101). High grade (G3) and p16 hyperexpression remained significant predictors of survival in NSMP. Stage II-IV, ≥50% myometrial invasion, lymphovascular space invasion and loss of E-cadherin were independent predictors in the MMR-D group. In the interaction analysis, molecular subclass significantly modified the prognostic effect of high grade and p16 hyperexpression, which showed a stronger negative effect on survival in NSMP as compared to MMR-D (P for interaction = 0.016 for grade and 0.033 for p16).

Conclusions

Grade of differentiation and p16 hyperexpression appear to have a stronger prognostic impact in NSMP as compared to MMR-D EC. While these results need to be confirmed in a larger study population, they indicate that differential impact of risk factors needs to be taken into account when developing new molecular class-integrated risk stratification algorithms for EC.
Attitude, preparedness, and perceived self-efficacy in controlling COVID-19 pandemics and associated factors among university students during school reopening
Authors: Tadese Mesfin , Mihretie Abebe
Published: September 2021

Introduction

The coronavirus disease 2019 (COVID-19) pandemic remains a significant public health problem globally. In Ethiopia, the number of infected peoples and deaths due to COVID-19 has increased dramatically in the past. Currently, students are resuming to face to face education with strict prevention measures. University students are more dynamic and more susceptible to acquiring and spreading the virus.

Objective

To assess the attitude, preparedness, and self-efficacy to prevent and control COVID-19 and associated factors among university students during school reopening, Northeast Ethiopia.

Method

A cross-sectional study was conducted among Debre Berhan University (DBU) students from December 1 to 15/2020, when students return to campus. A multistage sampling technique was applied to recruit 682 participants. The ReadyScore criteria were used to classify the level of preparedness. Epi-Data version 4.6 was used for data entry, while SPSS version 25 for analysis. Descriptive and Binary logistic regression analysis was computed, and a p-value < 0.05 was considered statistically significant.

Result

The overall level of favourable attitude, good preparedness, and high self-efficacy among students were 67.2%, 17.9%, and 50.4%, respectively. Only mothers’ education was associated with attitude. Female gender, open relationships, health science faculty, heart disease, and favourable attitude were significant preparedness factors. Whereas being undergraduate, parents’ education, residing in dorm being four and above, having kidney disease, having friend/family history of COVID-19 infection and death, favourable attitude, and good preparedness were predictors of self-efficacy.

Conclusion

The level of attitude, preparedness, and self-efficacy towards COVID-19 among students during campus re-entry were low. Managing chronic illnesses and raising the attitude and preparedness of students is essential to reduce the burden of COVID-19 pandemics. Besides, emphasis should be placed on male, unmarried, postgraduate, and non-health science students to increase the level of preparedness and self-efficacy.
Novel diagnostic and prognostic biomarkers of colorectal cancer: Capable to overcome the heterogeneity-specific barrier and valid for global applications
Authors: Hameed Yasir , Usman Muhammad , Liang Shufang , Ejaz Samina
Published: September 2021

Introduction

The heterogeneity-specific nature of the available colorectal cancer (CRC) biomarkers is significantly contributing to the cancer-associated high mortality rate worldwide. Hence, this study was initiated to investigate a system of novel CRC biomarkers that could commonly be employed to the CRC patients and helpful to overcome the heterogenetic-specific barrier.

Methods

Initially, CRC-related hub genes were extracted through PubMed based literature mining. A protein-protein interaction (PPI) network of the extracted hub genes was constructed and analyzed to identify few more closely CRC-related hub genes (real hub genes). Later, a comprehensive bioinformatics approach was applied to uncover the diagnostic and prognostic role of the identified real hub genes in CRC patients of various clinicopathological features.

Results

Out of 210 collected hub genes, in total 6 genes (CXCL12, CXCL8, AGT, GNB1, GNG4, and CXCL1) were identified as the real hub genes. We further revealed that all the six real hub genes were significantly dysregulated in colon adenocarcinoma (COAD) patients of various clinicopathological features including different races, cancer stages, genders, age groups, and body weights. Additionally, the dysregulation of real hub genes has shown different abnormal correlations with many other parameters including promoter methylation, overall survival (OS), genetic alterations and copy number variations (CNVs), and CD8+T immune cells level. Finally, we identified a potential miRNA and various chemotherapeutic drugs via miRNA, and real hub genes drug interaction network that could be used in the treatment of CRC by regulating the expression of real hub genes.

Conclusion

In conclusion, we have identified six real hub genes as potential biomarkers of CRC patients that could help to overcome the heterogenetic-specific barrier across different clinicopathological features.
Historical changes in plant water use and need in the continental United States
Authors: Tercek Michael T. , Thoma David , Gross John E. , Sherrill Kirk , Kagone Stefanie , Senay Gabriel
Published: September 2021

A robust method for characterizing the biophysical environment of terrestrial vegetation uses the relationship between Actual Evapotranspiration (AET) and Climatic Water Deficit (CWD). These variables are usually estimated from a water balance model rather than measured directly and are often more representative of ecologically-significant changes than temperature or precipitation. We evaluate trends and spatial patterns in AET and CWD in the Continental United States (CONUS) during 1980–2019 using a gridded water balance model. The western US had linear regression slopes indicating increasing CWD and decreasing AET (drying), while the eastern US had generally opposite trends. When limits to plant performance characterized by AET and CWD are exceeded, vegetation assemblages change. Widespread increases in aridity throughout the west portends shifts in the distribution of plants limited by available moisture. A detailed look at Sequoia National Park illustrates the high degree of fine-scale spatial variability that exists across elevation and topographical gradients. Where such topographical and climatic diversity exists, appropriate use of our gridded data will require sub-setting to an appropriate area and analyzing according to categories of interest such as vegetation communities or across obvious physical gradients. Recent studies have successfully applied similar water balance models to fire risk and forest structure in both western and eastern U.S. forests, arid-land spring discharge, amphibian colonization and persistence in wetlands, whitebark pine mortality and establishment, and the distribution of arid-land grass species and landscape scale vegetation condition. Our gridded dataset is available free for public use. Our findings illustrate how a simple water balance model can identify important trends and patterns at site to regional scales. However, at finer scales, environmental heterogeneity is driving a range of responses that may not be simply characterized by a single trend.
A novel angiotensin I-converting enzyme inhibitory peptide derived from the trypsin hydrolysates of salmon bone proteins
Authors: Kaewsahnguan Thanakrit , Noitang Sajee , Sangtanoo Papassara , Srimongkol Piroonporn , Saisavoey Tanatorn , Reamtong Onrapak , Choowongkomon Kiattawee , Karnchanatat Aphichart
Published: September 2021

When fish are processed, fish bone becomes a key component of the waste, but to date very few researchers have sought to use fish bone to prepare protein hydrolysates as a means of adding value to the final product. This study, therefore, examines the potential of salmon bone, through an analysis of the benefits of its constituent components, namely fat, moisture, protein, and ash. In particular, the study seeks to optimize the process of enzymatic hydrolysis of salmon bone with trypsin in order to produce angiotensin-I converting enzyme (ACE) inhibitory peptides making use of response surface methodology in combination with central composite design (CCD). Optimum hydrolysis conditions concerning DH (degree of hydrolysis) and ACE-inhibitory activity were initially determined using the response surface model. Having thus determined which of the salmon bone protein hydrolysates (SBPH) offered the greatest level of ACE-inhibitory activity, these SBPH were duly selected to undergo ultrafiltration for further fractionation. It was found that the greatest ACE-inhibitory activity was achieved by the SBPH fraction which had a molecular weight lower than 0.65 kDa. This fraction underwent further purification using RP-HPLC, revealing that the F7 fraction offered the best ACE-inhibitory activity. For ACE inhibition, the ideal peptide in the context of the F7 fraction comprised eight amino acids: Phe-Cys-Leu-Tyr-Glu-Leu-Ala-Arg (FCLYELAR), while analysis of the Lineweaver-Burk plot revealed that the FCLYELAR peptide can serve as an uncompetitive ACE inhibitor. An examination of the molecular docking process showed that the FCLYELAR peptide was primarily able to provide ACE-inhibitory qualities as a consequence of the hydrogen bond interactions taking place between ACE and the peptide. Furthermore, upon isolation form the SBPH, the ACE-inhibitory peptide demonstrated ACE-inhibitory capabilities in vitro, underlining its potential for applications in the food and pharmaceutical sectors.
Influence of the visuo-proprioceptive illusion of movement and motor imagery of the wrist on EEG cortical excitability among healthy participants
Authors: Le Franc Salomé , Fleury Mathis , Jeunet Camille , Butet Simon , Barillot Christian , Bonan Isabelle , Cogné Mélanie , Lécuyer Anatole
Published: September 2021

Introduction

Motor Imagery (MI) is a powerful tool to stimulate sensorimotor brain areas and is currently used in motor rehabilitation after a stroke. The aim of our study was to evaluate whether an illusion of movement induced by visuo-proprioceptive immersion (VPI) including tendon vibration (TV) and Virtual moving hand (VR) combined with MI tasks could be more efficient than VPI alone or MI alone on cortical excitability assessed using Electroencephalography (EEG).

Methods

We recorded EEG signals in 20 healthy participants in 3 different conditions: MI tasks involving their non-dominant wrist (MI condition); VPI condition; and VPI with MI tasks (combined condition). Each condition lasted 3 minutes, and was repeated 3 times in randomized order. Our main judgment criterion was the Event-Related De-synchronization (ERD) threshold in sensori-motor areas in each condition in the brain motor area.

Results

The combined condition induced a greater change in the ERD percentage than the MI condition alone, but no significant difference was found between the combined and the VPI condition (p = 0.07) and between the VPI and MI condition (p = 0.20).

Conclusion

This study demonstrated the interest of using a visuo-proprioceptive immersion with MI rather than MI alone in order to increase excitability in motor areas of the brain. Further studies could test this hypothesis among patients with stroke to provide new perspectives for motor rehabilitation in this population.
Bioengineered phytomolecules-capped silver nanoparticles using Carissa carandas leaf extract to embed on to urinary catheter to combat UTI pathogens
Authors: Rahuman Haajira Beevi Habeeb , Dhandapani Ranjithkumar , Palanivel Velmurugan , Thangavelu Sathiamoorthi , Paramasivam Ragul , Muthupandian Saravanan
Published: September 2021

Rising incidents of urinary tract infections (UTIs) among catheterized patients is a noteworthy problem in clinic due to their colonization of uropathogens on abiotic surfaces. Herein, we have examined the surface modification of urinary catheter by embedding with eco-friendly synthesized phytomolecules-capped silver nanoparticles (AgNPs) to prevent the invasion and colonization of uropathogens. The preliminary confirmation of AgNPs production in the reaction mixture was witnessed by the colour change and surface resonance plasmon (SRP) band at 410nm by UV–visible spectroscopy. The morphology, size, crystalline nature, and elemental composition of attained AgNPs were further confirmed by the transmission electron microscopy (TEM), selected area electron diffraction (SAED), X-ray diffraction (XRD) technique, Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The functional groups of AgNPs with stabilization/capped phytochemicals were detected by Fourier-transform infrared spectroscopy (FTIR). Further, antibiofilm activity of synthesized AgNPs against biofilm producers such as Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa were determined by viability assays and micrographically. AgNPs coated and coating-free catheters performed to treat with bacterial pathogen to analyze the mat formation and disruption of biofilm formation. Synergistic effect of AgNPs with antibiotic reveals that it can enhance the activity of antibiotics, AgNPs coated catheter revealed that, it has potential antimicrobial activity and antibiofilm activity. In summary, C. carandas leaf extract mediated synthesized AgNPs will open a new avenue and a promising template to embed on urinary catheter to control clinical pathogens.
Technical fishway passage structures provide high passage efficiency and effective passage for adult Pacific salmonids at eight large dams
Authors: Keefer Matthew L. , Jepson Michael A. , Clabough Tami S. , Caudill Christopher C.
Published: September 2021

Fishways have been widely used for upstream passage around human-built structures, but ‘success’ has varied dramatically. Evaluation of fishway success has typically been conducted at local scales using metrics such as fish passage efficiency and passage time, but evaluations are increasingly used in broader assessments of whether passage facilities meet population-specific conservation and management objectives. Over 15 years, we monitored passage effectiveness at eight dams on the Columbia and Snake rivers for 26,886 radio-tagged spring-summer and fall Chinook SalmonO.tshwaytscha, Sockeye SalmonO.nerka, and summer steelheadO.mykissduring their migrations to spawning sites. Almost all fish that entered dam tailraces eventually approached and entered fishways. Tailrace-to-forebay passage efficiency estimates at individual dams were consistently high, averaging 0.966 (SD= 0.035) across 245 run×year×dam combinations. These estimates are among the highest recorded for any migratory species, which we attribute to the scale of evaluation, salmonid life history traits (e.g., philopatry), and a sustained adaptive management approach to fishway design, maintenance, and improvement. Full-dam fish passage times were considerably more variable, with run×year×dam medians ranging from 5–65 h. Evaluation at larger scales provided evidence that fishways were biologically effective, e.g., we observed rapid migration rates (medians= 28–40 km/d) through river reaches with multiple dams and estimated fisheries-adjusted upstream migration survival of 67–69%. However, there were substantive uncertainties regarding effectiveness. Uncertainty about natal origins confounded estimation of population-specific survival and interpretation of apparent dam passage ‘failure’, while lack of post-migration reproductive data precluded analyses of delayed or cumulative effects of passing the impounded system on fish fitness. Although the technical fishways are effective for salmonids in the Columbia-Snake River system, other co-migrating species have lower passage rates, highlighting the need for species-specific design and evaluation wherever passage facilities impact fish management and conservation goals.
Self-collection and pooling of samples as resources-saving strategies for RT-PCR-based SARS-CoV-2 surveillance, the example of travelers in French Polynesia
Authors: Aubry Maite , Teiti Iotefa , Teissier Anita , Richard Vaea , Mariteragi-Helle Teheipuaura , Chung Kiyojiken , Deen Farah , Paoaafaite Tuterarii , Cao-Lormeau Van-Mai
Published: September 2021

In French Polynesia, the first case of SARS-CoV-2 infection was detected on March 10th, 2020, in a resident returning from France. Between March 28th and July 14th, international air traffic was interrupted and local transmission of SARS-CoV-2 was brought under control, with only 62 cases recorded. The main challenge for reopening the air border without requiring travelers to quarantine on arrival was to limit the risk of re-introducing SARS-CoV-2. Specific measures were implemented, including the obligation for all travelers to have a negative RT-PCR test for SARS-CoV-2 carried out within 3 days before departure, and to perform another RT-PCR testing 4 days after arrival. Because of limitation in available medical staff, travelers were provided a kit allowing self-collection of oral and nasal swabs. In addition to increase our testing capacity, self-collected samples from up to 10 travelers were pooled before RNA extraction and RT-PCR testing. When a pool tested positive, RNA extraction and RT-PCR were performed on each individual sample. We report here the results of COVID-19 surveillance (COV-CHECK PORINETIA) conducted between July 15th, 2020, and February 15th, 2021, in travelers using self-collection and pooling approaches. We tested 5,982 pools comprising 59,490 individual samples, and detected 273 (0.46%) travelers positive for SARS-CoV-2. A mean difference of 1.17 Ct (CI 95% 0.93–1.41) was found between positive individual samples and pools (N = 50), probably related to the volume of samples used for RNA extraction (200 μL versus 50 μL, respectively). Retrospective testing of positive samples self-collected from October 20th, 2020, using variants-specific amplification kit and spike gene sequencing, found at least 6 residents infected by the Alpha variant. Self-collection and pooling approaches allowed large-scale screening for SARS-CoV-2 using less human, material and financial resources. Moreover, this strategy allowed detecting the introduction of SARS-CoV-2 variants of concern in French Polynesia.
Using climatic variables alone overestimate climate change impacts on predicting distribution of an endemic species
Authors: Zangiabadi Somayeh , Zaremaivan Hassan , Brotons LIuis , Mostafavi Hossein , Ranjbar Hojjatollah
Published: September 2021

Plant species distribution is constrained by both dynamic and static environmental variables. However, relative contribution of dynamic and static variables in determining species distributions is not clear and has far reaching implications for range change dynamics in a changing world. Prunus eburnea (Spach) Aitch. & Hemsl. is an endemic and medicinal plant species of Iran. It has rendered itself as ecologically important for its functions and services and is currently in need of habitat conservation measures requiring investigation of future potential distribution range. We conducted sampling of 500 points that cover most of Iran plateau and recorded the P. eburnea presence and absence during the period 2015–2017. In this study, we evaluated impacts of using only climatic variables versus combined with topographic and edaphic variables on accuracy criteria and predictive ability of current and future habitat suitability of this species under climate change (CCSM4, RCP 2.6 in 2070) by generalized linear model and generalized boosted model. Models’ performances were evaluated using area under the curve, sensitivity, specificity and the true skill statistic. Then, we evaluated here, driving environmental variables determining the distribution of P. eburnea by using principal component analysis and partitioning methods. Our results indicated that prediction with high accuracy of the spatial distribution of P. eburnea requires both climate information, as dynamic primary factors, but also detailed information on soil and topography variables, as static factors. The results emphasized that environmental variable grouping influenced the modelling prediction ability strongly and the use of only climate variables would exaggerate the predicted distribution range under climate change. Results supported using both dynamic and static variables improved accuracy of the modeling and provided more realistic prediction of species distribution under influence of climate change.
Association between adherence to Antiretroviral Therapy and place of residence among adult HIV infected patients in Ethiopia: A systematic review and meta-analysis
Authors: Fite Robera Olana
Published: September 2021

Background

According to the World Health Organization, optimal adherence to Antiretroviral Therapy (ART) improves quality of life. Patients who use ART have varying characteristics in terms of where they live. The effect of place of residence on ART adherence is unclear in Ethiopia. Therefore, the aim of this systematic review and meta-analysis was to estimate the pooled association between place of residence and adherence to ART.

Methods

Articles were retrieved from PubMed, Scopus, African Journals Online (AJOL), Journal Storage (JSTOR), and Web of Science. The data was extracted using Microsoft Excel 2016 spreadsheet. Review Manager 5.3 and STATA version 14 were used for the analysis. The Cochrane Q statistic was used to assess between-study heterogeneity. I2was used to quantify between-study heterogeneity. A weighted inverse variance random-effects model was used to calculate the pooled odds ratio with 95% confidence interval.

Results

Seven studies were included in this systematic review and meta-analysis. The Begg’s test (Z = 0.15, P = 0.881) and Egger’s test (t = 0.14, P = 0.894) revealed no evidence of publication bias. Urban residence was associated with an increased likelihood of good adherence (OR 2.07, 95%CI 1.22–3.51).

Conclusions

The study recommends that policy-makers should enact policies that increase access to ART services in a rural area in order to improve adherence. It is recommended that implementation studies be conducted in order to identify practical and affordable interventions.
The concept of “whole perforator system” in the lateral thoracic region for latissimus dorsi muscle-preserving large flaps: An anatomical study and case series
Authors: Kagaya Yu , Arikawa Masaki , Sekiyama Takuya , Mitsuwa Hideyuki , Takanashi Ryo , Taga Marie , Akazawa Satoshi , Miyamoto Shimpei
Published: September 2021

Background

Previous studies have reported on the abundant cutaneous perforating blood vessels around the latissimus dorsi (LD) lateral border, such as a thoracodorsal artery perforator (TDAP) of septocutaneous type (TDAP-sc) and muscle-perforating type (TDAP-mp), or the lateral thoracic artery perforator (LTAP). These perforators have been clinically utilized for flap elevation; however, there have been few studies that accurately examined all the cutaneous perforators (TDAP-sc, TDAP-mp, LTAP) around the LD lateral border. Here, we propose a new “whole perforator system” (WPS) concept in the lateral thoracic region and a methodology that enables elevating large flaps with reliable perfusion in a muscle-preserving manner.

Methods

We first performed an anatomical study that verified the number and perforating points of all perforators around the LD lateral border using the results of dynamic contrast-enhanced magnetic resonance imaging of patients with breast cancer. Following the anatomical evaluation, we performed large muscle-preserving flap transfer that contained all of the perforators around the LD lateral border in an actual clinical setting.

Results

A total of 175 latissimus dorsi from 98 patients were included. The mean number of perforators (TDAP-sc + TDAP-mp + LTAP) per side was 4.51±1.44 (2–9); TDAP-sc was present in 57.1% (100/175) of cases, and TDAP-mp in 76.6% (134/175); the TDAP total prevalence rate (TDAP-sc + TDAP-mp) was 96.0% (168/175). The LTAP existence rate was 94.3% (165/175). Distance from the axillary artery to the TDAP-sc was 148.7±56.3 mm, which was significantly proximal to the TDAP-mp (183.8±54.2 mm) and LTAP (172.2±81.3 mm).

Conclusion

The lateral thoracic region has an abundant cutaneous perforator system derived from the descending branch of the thoracodorsal and lateral thoracic arteries. Clinical application of the lateral thoracic WPS flap is promising, with a large survival area even with muscle-preserving procedures and requiring a relatively simple procedure.
Can co-authorship networks be used to predict author research impact? A machine-learning based analysis within the field of degenerative cervical myelopathy research
Authors: Grodzinski Noah , Grodzinski Ben , Davies Benjamin M.
Published: September 2021

Introduction

Degenerative Cervical Myelopathy (DCM) is a common and disabling condition, with a relatively modest research capacity. In order to accelerate knowledge discovery, the AO Spine RECODE-DCM project has recently established the top priorities for DCM research. Uptake of these priorities within the research community will require their effective dissemination, which can be supported by identifying key opinion leaders (KOLs). In this paper, we aim to identify KOLs using artificial intelligence. We produce and explore a DCM co-authorship network, to characterise researchers’ impact within the research field.

Methods

Through a bibliometric analysis of 1674 scientific papers in the DCM field, a co-authorship network was created. For each author, statistics about their connections to the co-authorship network (and so the nature of their collaboration) were generated. Using these connectedness statistics, a neural network was used to predict H-Index for each author (as a proxy for research impact). The neural network was retrospectively validated on an unseen author set.

Results

DCM research is regionally clustered, with strong collaboration across some international borders (e.g., North America) but not others (e.g., Western Europe). In retrospective validation, the neural network achieves a correlation coefficient of 0.86 (p<0.0001) between the true and predicted H-Index of each author. Thus, author impact can be accurately predicted using only the nature of an author’s collaborations.

Discussion

Analysis of the neural network shows that the nature of collaboration strongly impacts an author’s research visibility, and therefore suitability as a KOL. This also suggests greater collaboration within the DCM field could help to improve both individual research visibility and global synergy.
Characterization of the spontaneous degenerative mitral valve disease in FVB mice
Authors: Ayme-Dietrich Estelle , Da Silva Sylvia , Bouabout Ghina Alame , Arnoux Alizée , Guyonnet Jérôme , Becker Guillaume , Monassier Laurent
Published: September 2021

Background

The development of new non-surgical treatments dedicated to mitral valve degeneration is limited by the absence of relevant spontaneous and rapidly progressing animal experimental models.

Animals

We characterized the spontaneous mitral valve degeneration in two inbred FVB mouse strains compared to C57BL/6J and investigated a contribution of the serotonergic system.

Methods

Males and females FVB/NJ and FVB/NRj were compared to the putative C57BL/6J control at 12, 16, 20 and 24 weeks of age. Body weight, systolic blood pressure, heart rate, urinary 5-hydroxyindoleacetic acid (5-HIAA), whole blood and plasma serotonin, tail bleeding time, blood cell count, plasma TGF-β1 and plasma natriuretic peptide concentrations were measured. Myocardium and mitral valves were characterized by histology. mRNA mitral expression of 5-HT2A and 5-HT2B receptors was measured in the anterior leaflet. Cardiac anatomy and function were assessed by echocardiography.

Results

Compared to C57BL/6J, FVB mice strains did not significantly differ regarding body weight increase, arterial blood pressure and heart rate. A progressive augmentation of plasma pro-ANP was observed in FVB mice. Nevertheless, no cardiac hypertrophy or left-ventricular fibrosis were observed. Accordingly, plasma TGF-β1 was not different among the three strains. Conversely, FVB mice demonstrated a high prevalence of fibromyxoid highly cellularized and enriched in glycosaminoglycans lesions, inducing major mitral leaflets thickening without increase in length. The increased thickness was correlated with urinary 5-HIAA and blood platelet count. Whole blood serotonin concentration was similar in the two strains but, in FVB, a reduction of plasma serotonin was observed together with an increase of the bleeding time. Finally, echocardiography identified left atrial and left ventricular remodeling associated with thickening of both mitral leaflets and mitral insufficient in 30% of FVB mice but no systolic protrusion of mitral leaflets towards the atrium.

Conclusion

The FVB mouse strain is highly prone to spontaneous mitral myxomatous degeneration. A contribution of the peripheral serotonergic system is suggested.
Regional heterogeneity in violence and individual characteristics associated with recent transactional sex among Ugandan girls and young women: A national and regional analysis of data from the Violence Against Children and Youth Survey
Authors: Stamatakis Caroline , Howard Ashleigh , Chiang Laura , Massetti Greta M. , Apondi Rose , Stoebenau Kirsten , Hegle Jennifer , Wasula Lydia , Patel Pragna
Published: September 2021

Objectives

This study assessed associations between recent transactional sex (TS) and potential determinants and variations in patterns across two geographic regions with high HIV burden compared to the rest of Uganda, among adolescent girls and young women (AGYW).

Methods

In 2015, a nationally representative cross-sectional household survey was conducted in Uganda. A stratified multi-stage cluster sample design produced nationally representative estimates and sub-national estimates for AGYW in two high HIV burden regions, DREAMS Central 1 (Bukomansimbi, Ssembabule, and Rakai districts) and DREAMS Central 2 (Mubende, Mityana, Gomba, and Mukono districts), and the rest of Uganda. To identify associations between recent TS (defined as sex in the past 12 months in exchange for material support or help) and risk factors, multivariable logistic regressions were conducted. Interaction terms assessed the associations between violence and recent TS across geographic regions.

Results

Nationally, 14.2% of sexually active AGYW engaged in recent TS. Region-specific significant associations emerged between recent TS and marriage, family wealth, friendship, orphanhood, and sexual debut. In DREAMS Central 1 and 2, AGYW who witnessed violence in the home or community, or experienced sexual, physical, or emotional violence had higher odds of recent TS than AGYW who did not experience that form of violence (adjusted odds ratio ranged between 2.10 (95% CI, 1.07, 4.13) and 8.25 (95% CI, 3.40, 20.06)). The magnitude of association between recent TS and types of violence varied by region.

Conclusions

Violence is strongly and consistently associated with recent TS, and patterns in prevalence and risk factors vary across regions in Uganda. Given the high risk of HIV association with recent TS, HIV epidemic control efforts may benefit from focus on comprehensive violence prevention and target persons who engage in TS. Comprehensive HIV prevention programming aimed at keeping AGYW HIV-negative should incorporate prevention of violence and TS as key components to facilitate HIV epidemic control in this vulnerable population.
Rab11a mediates cell-cell spread and reassortment of influenza A virus genomes via tunneling nanotubes
Authors: Ganti Ketaki , Han Julianna , Manicassamy Balaji , Lowen Anice C.
Published: September 2021

Influenza A virus [IAV] genomes comprise eight negative strand RNAs packaged into virions in the form of viral ribonucleoproteins [vRNPs]. Rab11a plays a crucial role in the transport of vRNPs from the nucleus to the plasma membrane via microtubules, allowing assembly and virus production. Here, we identify a novel function for Rab11a in the inter-cellular transport of IAV vRNPs using tunneling nanotubes [TNTs]as molecular highways. TNTs are F-Actin rich tubules that link the cytoplasm of nearby cells. In IAV-infected cells, Rab11a was visualized together with vRNPs in these actin-rich intercellular connections. To better examine viral spread via TNTs, we devised an infection system in which conventional, virion-mediated, spread was not possible. Namely, we generated HA-deficient reporter viruses which are unable to produce progeny virions but whose genomes can be replicated and trafficked. In this system, vRNP transfer to neighboring cells was observed and this transfer was found to be dependent on both actin and Rab11a. Generation of infectious virus via TNT transfer was confirmed using donor cells infected with HA-deficient virus and recipient cells stably expressing HA protein. Mixing donor cells infected with genetically distinct IAVs furthermore revealed the potential for Rab11a and TNTs to serve as a conduit for genome mixing and reassortment in IAV infections. These data therefore reveal a novel role for Rab11a in the IAV life cycle, which could have significant implications for within-host spread, genome reassortment and immune evasion.
What is the risk of a deadly adenovirus pandemic?
Authors: Kremer Eric J.
Published: September 2021

Many of us had refresher courses in virology, immunology, and epidemiology in 2020, and we were reminded of the fact that Homo sapiens, the wiliest predator on the planet, has been hunting everything that moves for millennia. These repeated interspecies contacts inherently lead to recurrent zoonosis (nonhuman to human) and anthroponosis (human to nonhuman). Given the accelerating changes in our ecosystems since the neolithic revolution, it was not surprising to see a virus that spreads via aerosolization and liquid droplets cause a pandemic in a few months. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic begs the question—which viruses could cause a global threat? In this Opinion, the characteristics that make adenoviruses a risk, which include efficient intra- and interspecies transmission, thermostable particles, persistent/latent infections in diverse hosts, and the ability to readily recombine and escape herd immunity, are discussed.