bluuebunny/crossref_metadata_2025 huggingface dataset:
Rescuing the Brazilian Agave breeding program: morphophysiological and molecular characterization of a new germplasm
Authors: Raya Fabio Trigo , de Carvalho Lucas Miguel , José Juliana , da Cruz Larissa Prado , Almeida Rafael Leonardo , Delevatti Heliur Alves de Almeida , Silveira Neidiquele Maria , da Silva Simone Ferreira , Pissolato Maria Dolores , de Oliveira Adriele Bárbara , dos Reis Wagner José Villela , de Abreu Luís Guilherme Furlan , Gutiérrez Jesús , Carazzolle Marcelo Falsarella , Soares Ana Cristina Fermino , Nieto Sotelo Jorge , Ribeiro Rafael Vasconcelos , Pereira Gonçalo Amarante Guimarães
Published: September 2023

Agaves have been a valuable resource in dryland areas for centuries, providing fibers (sisal), food, and beverages. However, the advent of synthetic fibers has led to a decrease in research on Agave, resulting in the cessation of breeding programs in Brazil. With the rise of climate change, there is renewed interest in Agave for its potential as a biofuel feedstock in semiarid regions. Since 2016, we have been collecting Agave accessions throughout the country and retrieving what is left of Brazil’s original breeding program to establish a new germplasm bank. Here, we evaluated 21 of those accessions growing in the field. We used molecular markers and morphophysiological traits to characterize the plants. Based on the Mayahuelin molecular marker, we were able to reconstruct a phylogeny for the Brazilian accessions. The morphophysiological traits explained 34.6% of the phenotypic variation in the dataset, with physiological traits such as leaf water content, effective quantum efficiency of photosystem II (ΦPSII), and specific leaf mass (SLM) as the most significant traits. Specifically, we evaluated nine Agave species and found that the physiological traits, rather than the morphological ones, were the most significant. Leaf water content was negatively correlated with specific leaf mass, which could be used as a marker for selecting cultivars with higher biomass accumulation. Interestingly, ΦPSII and chlorophyll content were negatively correlated, suggesting photochemical adaptations throughout the rosette. Molecular and phenotypic data suggest that A. amaniensis, which is frequently considered a synonym of A. sisalana, is effectively another species. Overall, this study provides valuable information on the physiological traits of Brazilian Agave accessions and is a starting point for selecting more productive and climate-resilient cultivars for biorenewables production.
The role of DC-SIGN as a trans-receptor in infection by MERS-CoV
Authors: Labiod Nuria , Luczkowiak Joanna , Tapia María M. , Lasala Fátima , Delgado Rafael
Published: September 2023

DC-SIGN is a C-type lectin expressed in myeloid cells such as immature dendritic cells and macrophages. Through glycan recognition in viral envelope glycoproteins, DC-SIGN has been shown to act as a receptor for a number of viral agents such as HIV, Ebola virus, SARS-CoV, and SARS-CoV-2. Using a system of Vesicular Stomatitis Virus pseudotyped with MERS-CoV spike protein, here, we show that DC-SIGN is partially responsible for MERS-CoV infection of dendritic cells and that DC-SIGN efficiently mediates trans-infection of MERS-CoV from dendritic cells to susceptible cells, indicating a potential role of DC-SIGN in MERS-CoV dissemination and pathogenesis.
Graduate teaching assistants' challenges, conflicts, and strategies for navigating COVID-19
Authors: Acheme Doris Ehi , Biwa Valerie
Published: September 2023

COVID-19 imparted unprecedented changes to higher education. Overnight, institutions were required to transition to online instruction, which brought about numerous challenges for instructors. This study examines the experiences of an often-overlooked instructor; graduate student assistants (GTAs). Their challenges and conflicts encountered with online instruction during COVID-19 and conflict management strategies are investigated. Sixteen (N= 18) GTAs from six universities in various regions of the United States were interviewed and constant comparative analysis was used to analyze data. Findings revealed that GTAs experienced challenges with (a) online instruction, (b) students, and (c) personal challenges. Also, GTAs encountered conflicts regarding (a) safety concerns and precautions and (b) online-related proficiency, support, and expectations. Lastly, GTAs (a) employed empathy and flexibility, and (b) created boundaries and consulted others as conflict management strategies. Findings are discussed and theoretical and practical implications are advanced.
Impact of body mass index on worsening of diastolic function and impairment of left atrial strain in the general female urban population: a subanalysis of the Berlin female risk evaluation echocardiography follow-up study
Authors: Romero Dorta Elena , Wolf Adrian , Hübscher Anne , Blaschke-Waluga Daniela , Seeland Ute , Crayen Claudia , Bischoff Sven , Mattig Isabel , Dreger Henryk , Stangl Karl , Regitz-Zagrosek Vera , Landmesser Ulf , Knebel Fabian , Stangl Verena , Brand Anna
Published: September 2023

Background

The association of body mass index (BMI) with diastolic dysfunction (DD) is well described in the literature. However, there is conflicting evidence and long-term follow-up data regarding effects of BMI on preclinical DD and left atrial (LA) function are scarce, highlighting the importance of early detection tools, such as myocardial strain.

Purpose

The aim of our study was to prospectively analyze the impact of clinical and demographic parameters, especially of BMI, on worsening of diastolic function and left atrial strain (LAS) in an urban population of women with a low prevalence of cardiovascular risk factors.

Methods and Results

An extensive clinical and echocardiographic assessment comprising the analysis of phasic LAS using two-dimensional speckle-tracking echocardiography (2D STE) was performed in 258 participants of the Berlin Female Risk Evaluation (BEFRI) trial between October 2019 and December 2020 after a mean follow-up period of 6.8 years. We compared clinical and echocardiographic parameters stratifying women by BMI < or ≥25 kg/m2, and we analyzed the impact of demographic characteristics on the worsening of DD and LA mechanics in the longer-term follow-up using univariate and multivariate regression analyses. 248 women were suitable for echocardiographic analysis of LAS using 2D STE. After a mean follow-up time of 6.8 years, LA reservoir strain (LASr) and LA conduit strain (LAScd) were significantly reduced in participants with a BMI ≥25 kg/m2 compared with women with a BMI <25 kg/m2 at baseline (30 ± 8% vs. 38 ± 9%, p < 0.0001; −14 ± 7% vs. −22 ± 8%, p < 0.0001). 28% of the overweighted women presented a deterioration of diastolic function at the time of follow-up in contrast with only 7% of the group with a BMI <25 kg/m2 (p < 0.0001). BMI remained significantly associated with LAS reductions after adjustment for other risk factors in multivariate regression analyses.

Conclusion

Overweight and obesity are related to impaired LAS and to a worsening of diastolic function after a long-term follow-up in a cohort of randomly selected women.
Interobserver variability in target definition for stereotactic arrhythmia radioablation
Authors: van der Ree Martijn H. , Cuculich Phillip S. , van Herk Marcel , Hugo Geoffrey D. , Balt Jippe C. , Bates Matthew , Ho Gordon , Pruvot Etienne , Herrera-Siklody Claudia , Hoeksema Wiert F. , Lee Justin , Lloyd Michael S. , Kemme Michiel J. B. , Sacher Frederic , Tixier Romain , Verhoeff Joost J. C. , Balgobind Brian V. , Robinson Clifford G. , Rasch Coen R. N. , Postema Pieter G.
Published: September 2023

Background

Stereotactic arrhythmia radioablation (STAR) is a potential new therapy for patients with refractory ventricular tachycardia (VT). The arrhythmogenic substrate (target) is synthesized from clinical and electro-anatomical information. This study was designed to evaluate the baseline interobserver variability in target delineation for STAR.

Methods

Delineation software designed for research purposes was used. The study was split into three phases. Firstly, electrophysiologists delineated a well-defined structure in three patients (spinal canal). Secondly, observers delineated the VT-target in three patients based on case descriptions. To evaluate baseline performance, a basic workflow approach was used, no advanced techniques were allowed. Thirdly, observers delineated three predefined segments from the 17-segment model. Interobserver variability was evaluated by assessing volumes, variation in distance to the median volume expressed by the root-mean-square of the standard deviation (RMS-SD) over the target volume, and the Dice-coefficient.

Results

Ten electrophysiologists completed the study. For the first phase interobserver variability was low as indicated by low variation in distance to the median volume (RMS-SD range: 0.02–0.02 cm) and high Dice-coefficients (mean: 0.97 ± 0.01). In the second phase distance to the median volume was large (RMS-SD range: 0.52–1.02 cm) and the Dice-coefficients low (mean: 0.40 ± 0.15). In the third phase, similar results were observed (RMS-SD range: 0.51–1.55 cm, Dice-coefficient mean: 0.31 ± 0.21).

Conclusions

Interobserver variability is high for manual delineation of the VT-target and ventricular segments. This evaluation of the baseline observer variation shows that there is a need for methods and tools to improve variability and allows for future comparison of interventions aiming to reduce observer variation, for STAR but possibly also for catheter ablation.
Benchmarking open source and paid services for speech to text: an analysis of quality and input variety
Authors: Ferraro Antonino , Galli Antonio , La Gatta Valerio , Postiglione Marco
Published: September 2023

Introduction

Speech to text (STT) technology has seen increased usage in recent years for automating transcription of spoken language. To choose the most suitable tool for a given task, it is essential to evaluate the performance and quality of both open source and paid STT services.

Methods

In this paper, we conduct a benchmarking study of open source and paid STT services, with a specific focus on assessing their performance concerning the variety of input text. We utilizes ix datasets obtained from diverse sources, including interviews, lectures, and speeches, as input for the STT tools. The evaluation of the instruments employs the Word Error Rate (WER), a standard metric for STT evaluation.

Results

Our analysis of the results demonstrates significant variations in the performance of the STT tools based on the input text. Certain tools exhibit superior performance on specific types of audio samples compared to others. Our study provides insights into STT tool performance when handling substantial data volumes, as well as the challenges and opportunities posed by the multimedia nature of the data.

Discussion

Although paid services generally demonstrate better accuracy and speed compared to open source alternatives, their performance remains dependent on the input text. The study highlights the need for considering specific requirements and characteristics of the audio samples when selecting an appropriate STT tool.
The reentry of Asian kinesiology professionals after obtaining a doctorate at higher education institutions in the U.S.
Authors: Park Seungyeon
Published: September 2023

With the large increase in international doctorates at higher education institutions in the United States, little attention is being paid to former doctoral students’ cross-cultural experiences during their reentry to their home countries. Based on the re-acculturation theory as a conceptual framework, this qualitative inquiry aimed to explore how study participants perceive their reentry. The findings were explained using six subthemes: (a) the renewal process, (b) ambivalence of reentry, (c) homing instinct, (d) environmental context, (e) midpoint of repatriation, and (f) different research atmospheres. The findings reveal the importance of doctorates’ flexibility to cope with each country’s academic atmosphere and respect academic cultural differences. The findings provide insight into the challenges that international kinesiology professionals face during their reentry and how they resolve these difficulties for readjustment to the academic atmosphere of their home countries.
Academic co-creation: development and validation of a short scale
Authors: Ventura-León José , Sánchez-Villena Andy Rick , Caycho-Rodríguez Tomás , White Michael
Published: September 2023

Introduction

Given the profound changes caused in higher education by the COVID-19 pandemic, affecting 1.6 billion students and 63 million educators globally, there arises the necessity for quantifiable measures that capture the essence of academic co-creation. This study aimed to develop and validate a short scale that measures academic co-creation (AC-S) in a sample of higher education students.

Methods

A total of 3,169 students from three Peruvian cities participated in the study (Mean Age = 25.77 years old; SD = 8.92 years); 1889 were female (59.60%) and 1,280 (40.40%) males. Qualitative and quantitative procedures were used for test construction. Item response theory (IRT) under the two-parameter graded response model (GRM-2PL) and test information function were used to examine reliability; additionally, a brief measure of academic satisfaction was used to provide evidence of relationship with another variable.

Results

The AC-S displayed strong fit and reliability, assessed through the test information function and standard error. It also showed a moderate correlation with academic satisfaction, bolstering its validity by linking with a pertinent variable. Its brevity enhances its practicality for education and research, efficiently fitting explanatory models and educational contexts. Despite substantial sample size and advanced psychometric methods, the study acknowledges limitations in sample representativeness and cross-sectional design. In conclusion, IRT and SEM techniques compellingly support the AC-S’s reliability and validity.

Conclusion

The scale’s one-dimensionality, local independence, reliability, and academic satisfaction relationship form a foundation for future exploration of co-creation-based educational models. Further studies should evaluate its performance across diverse cultural contexts.
Association between blood glucose levels and arterial stiffness marker: comparing the second derivative of photoplethysmogram and cardio-ankle vascular index scores
Authors: Park Young-Jae
Published: September 2023

Objective

This study aimed to compare the association between fasting plasma glucose (FPG) and glycosylated hemoglobin A1c (HbA1c) levels using the second derivative of photoplethysmogram (SDPTG) index and the cardio-ankle vascular index (CAVI).

Methods

Electronic medical records of 276 participants (160 men, 116 women) who visited the health promotion center of a university hospital were examined. Age, sex, body mass index (BMI), blood pressure, and lipid profile were considered as risk factors for arterial stiffness, together with the FPG, HbA1c, CAVI, and SDPTG indices. Hierarchical regression models were constructed, and all participants were divided into low-normal, high-normal, prediabetic, and diabetic groups to examine the group-based differences in CAVI and SDPTG indices.

Results

FPG and HbA1c were independently predictive of increased CAVI, and their predictive powers for CAVI were equivalent (β = 0.214 and 0.200, respectively). Risk factors, including age, BMI, and male sex, were also predictive of CAVI (β= 0.593-0.630, -0.256 – -0.280, and 0.142-0.178, respectively). None of the FPG and HbA1c values were predictive of the SDPTG indices. The CAVI was higher in the diabetes group than in the other three groups according to HbA1c level, while the d/a index of the SDPTG decreased in the prediabetes group and increased in the diabetes group.

Conclusions

CAVI may not be substituted for SDPTG indices when evaluating arterial stiffness based on the glucose level. Moreover, the progression rate of arterial stiffness may differ between the diabetic and nondiabetic stages.
Battery charger load-following controller for over-voltage and under-voltage conditions
Authors: Shahid Arqum , Manzoor Sajjad , Khan Uzair , Majeed Afraz Hussain , Khan Ilyas , Mohamed Abdullah
Published: September 2023

Battery charging systems are integral to the efficient operation and economic benefit of various applications, from electric vehicles to renewable energy storage. However, maintaining battery charging according to specifications during voltage variations, including short or prolonged under-voltage and over-voltage conditions, presents a significant challenge. These voltage variations can impact the thermal safety and charging time of batteries, potentially affecting their overall performance and life span. In order to address these challenges, this paper proposes a smart charging control method designed to control both the battery charging voltage and load voltages. This method is equipped to handle utility interruptions by using regulated AC–DC converters, while an automatic interconnected DC regulator controls the battery state of charge (SOC) and load supply. This dual control mechanism ensures efficient performance under various conditions. Extensive simulations validate the effectiveness of the proposed method, demonstrating its ability to maintain a constant voltage supplied to the load and ensures the thermal safety of the system during under- and over-voltage conditions. Additionally, an analysis of the thermal effect of the charger under these voltage conditions provides valuable insights into the thermal performance of the system, which is a critical aspect of battery charging systems. The proposed charging control method offers a comprehensive solution for efficient battery charging under various voltage conditions, thus contributing to the better performance, thermal safety, and longevity of batteries.
Nonparametric probabilistic forecasting based stochastic optimal scheduling of integrated electricity and gas systems
Authors: Chen Jinyu , Chen Dawei
Published: September 2023

The volatility and sporadic availability of renewable energy create significant challenges to the optimal scheduling of integrated electricity and gas systems (IEGS). This paper develops a nonparametric probabilistic forecasting based stochastic scheduling approach of IEGS. The quantile at a series of quantile levels can be generated by direct quantile regression method. Given the set of predicted quantiles, a set of representative scenarios for wind power uncertainty can be obtained by using Monte Carlo simulation method and scenario reduction approach. Based on the implicit finite difference scheme, the original partial differential equations of the gas network are discretized to establish an algebraic model, which provide possibility for efficient solution. Then, the nonconvexity caused by the momentum equation is eliminated by the second-order core relaxation. Finally, the stochastic optimal scheduling model is reformulated as a second-order core programming problem. Numerical simulations are performed to showcase the superiority of the established stochastic optimal scheduling model.
Gentrification and its association with health inequalities in Barcelona (2011–2017)
Authors: González-Marín Patricia , Vásquez-Vera Hugo , López-Gay Antonio , Peralta Andrés , Solana-Solana Miguel , Fernández Ana
Published: September 2023

Background

Prior studies have reported conflicting findings on the impact of gentrification of neighborhood residents. While some suggest it could worsen mental health, others indicate improved self-perceived health, although this effect may vary among social groups. This study aimed to determine health inequities, according to socioeconomic position, among residents of different neighborhoods of Barcelona between 2011 and 2017, considering the intensity of the gentrification process.

Methods

Observational study with two transversal cuts (2011 and 2017). Neighborhoods were categorized into three groups based on the intensity of gentrification: intensive, moderate-mild, and no gentrification processes. We fitted Poisson robust models to estimate the prevalence ratio (PR) of poor self-reported and poor mental health according to socioeconomic position (social class III vs. I). We then calculated relative differences between 2011 and 2017 through the interaction between the year and socioeconomic position (PRi). The calculations were adjusted for age and household disposable income in the neighborhood and were stratified by sex.

Results

In neighborhoods undergoing moderate or mild gentrification during the study period, we found widening inequities in mental health between the most disadvantaged social class and the most privileged social class. Between 2011 and 2017, relative differences in poor mental health increased in moderate-low gentrification neighborhoods [women: PRi: 2.51 (1.52–4.17); men: PRi: 1.99 (1.09–3.61)], equivalent to an increase of 12.9 and 11.5 percentage points, respectively. No statistically significant differences were found in the other neighborhoods.

Discussion

The increase in mental health inequalities observed among residents of transitional neighborhoods could be explained by factors such as residential insecurity, eviction from the neighborhood, and rising housing prices.
A survey of blow fly (Diptera: Calliphoridae) populations in Phoenix, Arizona
Authors: Meeds Andrew W. , Rusch Travis W. , Falcone Danielle L. , Weidner Lauren M.
Published: September 2023

Utilizing insects in legal investigations as a tool for estimating forensically important timelines (e.g., minimum post-mortem interval (min-PMI)) is becoming more commonly used and accepted throughout the world. In the United States much of the climate is temperate, however, the Sonoran Desert is an arid location with extreme heat and irregular rainfall. Work on forensically relevant insects in this region is severely understudied. This study surveyed the populations of forensically important blow flies (Diptera: Calliphoridae) in Phoenix, Arizona for one year using traps baited with four different food sources. Nine species across four genera were collected with Lucilia sericata, Calliphora latifrons, and Lucilia mexicana accounting for 98.6% of total blow flies captured in the baited traps. Abundance drastically changed throughout the year, ranging from 500+ flies to 0 flies captured in a month, with species abundance correlating with temperature and humidity. These results reveal that environmental conditions (i.e., maximum temperature and relative humidity) may limit blow fly activity or seasonally remove (or make inactive) entire local populations, thus affecting their ability to colonize remains and produce an accurate min-PMI.
Efficient sequencing data compression and FPGA acceleration based on a two-step framework
Authors: Chen Shifu , Chen Yaru , Wang Zhouyang , Qin Wenjian , Zhang Jing , Nand Heera , Zhang Jishuai , Li Jun , Zhang Xiaoni , Liang Xiaoming , Xu Mingyan
Published: September 2023

With the increasing throughput of modern sequencing instruments, the cost of storing and transmitting sequencing data has also increased dramatically. Although many tools have been developed to compress sequencing data, there is still a need to develop a compressor with a higher compression ratio. We present a two-step framework for compressing sequencing data in this paper. The first step is to repack original data into a binary stream, while the second step is to compress the stream with a LZMA encoder. We develop a new strategy to encode the original file into a LZMA highly compressed stream. In addition an FPGA-accelerated of LZMA was implemented to speedup the second step. As a demonstration, we present repaq as a lossless non-reference compressor of FASTQ format files. We introduced a multifile redundancy elimination method, which is very useful for compressing paired-end sequencing data. According to our test results, the compression ratio of repaq is much higher than other FASTQ compressors. For some deep sequencing data, the compression ratio of repaq can be higher than 25, almost four times of Gzip. The framework presented in this paper can also be applied to develop new tools for compressing other sequencing data. The open-source code of repaq is available at: https://github.com/OpenGene/repaq.
Pulmonary exacerbations in early cystic fibrosis lung disease are marked by strong modulation of CD3 and PD-1 on luminal T cells
Authors: Giacalone Vincent D. , Giraldo Diego Moncada , Silva George L. , Hosten Justin , Peng Limin , Guglani Lokesh , Tirouvanziam Rabindra
Published: September 2023

Background

In chronic cystic fibrosis (CF) lung disease, neutrophilic inflammation and T-cell inhibition occur concomitantly, partly due to neutrophil-mediated release of the T-cell inhibitory enzyme Arg1. However, the onset of this tonic inhibition of T cells, and the impact of pulmonary exacerbations (PEs) on this process, remain unknown.

Methods

Children with CF aged 0-5 years were enrolled in a longitudinal, single-center cohort study. Blood (n = 35) and bronchoalveolar lavage (BAL) fluid (n = 18) were collected at stable outpatient clinic visits or inpatient PE hospitalizations and analyzed by flow cytometry (for immune cell presence and phenotype) and 20-plex chemiluminescence assay (for immune mediators). Patients were categorized by PE history into (i) no prior PE, (ii) past history of PE prior to stable visit, or (iii) current PE.

Results

PEs were associated with increased concentration of both pro- and anti-inflammatory mediators in BAL, and increased neutrophil frequency and G-CSF in circulation. PE BAL samples showed a trend toward an increased frequency of hyperexocytic “GRIM” neutrophils, which we previously identified in chronic CF. Interestingly, expression levels of the T-cell receptor associated molecule CD3 and of the inhibitory programmed death-1 (PD-1) receptor were respectively decreased and increased on T cells from BAL compared to blood in all patients. When categorized by PE status, CD3 and PD-1 expression on blood T cells did not differ among patients, while CD3 expression was decreased, and PD-1 expression was increased on BAL T cells from patients with current PE.

Conclusions

Our findings suggest that airway T cells are engaged during early-life PEs, prior to the onset of chronic neutrophilic inflammation in CF. In addition, increased blood neutrophil frequency and a trend toward increased BAL frequency of hyperexocytic neutrophils suggest that childhood PEs may progressively shift the balance of CF airway immunity towards neutrophil dominance.
Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin
Authors: Anderson-Crannage Morgan , Ascensión Alex M. , Ibanez-Solé Olga , Zhu Hongwen , Schaefer Edo , Ottomanelli Darcy , Hochberg Bruno , Pan Jian , Luo Wen , Tian Meijuan , Chu Yaya , Cairo Mitchell S. , Izeta Ander , Liao Yanling
Published: September 2023

Inflammation is known to play a critical role in all stages of tumorigenesis; however, less is known about how it predisposes the tissue microenvironment preceding tumor formation. Recessive dystrophic epidermolysis bullosa (RDEB), a skin-blistering disease secondary to COL7A1 mutations and associated with chronic wounding, inflammation, fibrosis, and cutaneous squamous cell carcinoma (cSCC), models this dynamic. Here, we used single-cell RNA sequencing (scRNAseq) to analyze gene expression patterns in skin cells from a mouse model of RDEB. We uncovered a complex landscape within the RDEB dermal microenvironment that exhibited altered metabolism, enhanced angiogenesis, hyperproliferative keratinocytes, infiltration and activation of immune cell populations, and inflammatory fibroblast priming. We demonstrated the presence of activated neutrophil and Langerhans cell subpopulations and elevated expression of PD-1 and PD-L1 in T cells and antigen-presenting cells, respectively. Unsupervised clustering within the fibroblast population further revealed two differentiation pathways in RDEB fibroblasts, one toward myofibroblasts and the other toward a phenotype that shares the characteristics of inflammatory fibroblast subsets in other inflammatory diseases as well as the IL-1-induced inflammatory cancer-associated fibroblasts (iCAFs) reported in various cancer types. Quantitation of inflammatory cytokines indicated dynamic waves of IL-1α, TGF-β1, TNF, IL-6, and IFN-γ concentrations, along with dermal NF-κB activation preceding JAK/STAT signaling. We further demonstrated the divergent and overlapping roles of these cytokines in inducing inflammatory phenotypes in RDEB patients as well as RDEB mouse-derived fibroblasts together with their healthy controls. In summary, our data have suggested a potential role of inflammation, driven by the chronic release of inflammatory cytokines such as IL-1, in creating an immune-suppressed dermal microenvironment that underlies RDEB disease progression.
The role of APOBEC3C in modulating the tumor microenvironment and stemness properties of glioma: evidence from pancancer analysis
Authors: Zhang Shoudu , Guo Yugang , Hu Yuanzheng , Gao Xiaofang , Bai Fanghui , Ding Qian , Hou Kaiqi , Wang Zongqing , Sun Xing , Zhao Hui , Qu Zhongyu , Xu Qian
Published: September 2023

Background

It is now understood that APOBEC3 family proteins (A3s) are essential in tumor progression, yet their involvement in tumor immunity and stemness across diverse cancer types remains poorly understood.

Methods

In the present study, comprehensive genome-wide statistical and bioinformatic analyses were conducted to elucidate A3 family expression patterns, establishing clinically relevant correlations with prognosis, the tumor microenvironment(TME), immune infiltration, checkpoint blockade, and stemness across cancers. Different experimental techniques were applied, including RT–qPCR, immunohistochemistry, sphere formation assays, Transwell migration assays, and wound-healing assays, to investigate the impact of A3C on low-grade glioma (LGG) and glioblastoma multiforme (GBM), as well as its function in glioma stem cells(GSCs).

Results

Dysregulated expression of A3s was observed in various human cancer tissues. The prognostic value of A3 expression differed across cancer types, with a link to particularly unfavorable outcomes in gliomas. A3s are associated with the the TME and stemness in multiple cancers. Additionally, we developed an independent prognostic model based on A3s expression, which may be an independent prognostic factor for OS in patients with glioma. Subsequent validation underscored a strong association between elevated A3C expression and adverse prognostic outcomes, higher tumor grades, and unfavorable histology in glioma. A potential connection between A3C and glioma progression was established. Notably, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses implicated A3C in immune system-related diseases, with heightened A3C levels contributing to an immunosuppressive tumor microenvironment (TME) in glioma. Furthermore, in vitro experiments substantiated the role of A3C in sustaining and renewing glioma stem cells, as A3C deletion led to diminished proliferation, invasion, and migration of glioma cells.

Conclusion

The A3 family exhibits heterogeneous expression across various cancer types, with its expression profile serving as a predictive marker for overall survival in glioma patients. A3C emerges as a regulator of glioma progression, exerting its influence through modulation of the tumor microenvironment and regulation of stemness.
Clinical applications of radiomics in non-small cell lung cancer patients with immune checkpoint inhibitor-related pneumonitis
Authors: Shu Yang , Xu Wei , Su Rui , Ran Pancen , Liu Lei , Zhang Zhizhao , Zhao Jing , Chao Zhen , Fu Guobin
Published: September 2023

Immune checkpoint inhibitors (ICIs) modulate the body’s immune function to treat tumors but may also induce pneumonitis. Immune checkpoint inhibitor-related pneumonitis (ICIP) is a serious immune-related adverse event (irAE). Immunotherapy is currently approved as a first-line treatment for non-small cell lung cancer (NSCLC), and the incidence of ICIP in NSCLC patients can be as high as 5%-19% in clinical practice. ICIP can be severe enough to lead to the death of NSCLC patients, but there is a lack of a gold standard for the diagnosis of ICIP. Radiomics is a method that uses computational techniques to analyze medical images (e.g., CT, MRI, PET) and extract important features from them, which can be used to solve classification and regression problems in the clinic. Radiomics has been applied to predict and identify ICIP in NSCLC patients in the hope of transforming clinical qualitative problems into quantitative ones, thus improving the diagnosis and treatment of ICIP. In this review, we summarize the pathogenesis of ICIP and the process of radiomics feature extraction, review the clinical application of radiomics in ICIP of NSCLC patients, and discuss its future application prospects.
Development and evaluation of nanobody tracers for noninvasive nuclear imaging of the immune-checkpoint TIGIT
Authors: Zeven Katty , De Groof Timo W.M. , Ceuppens Hannelore , Awad Robin Maximilian , Ertveldt Thomas , de Mey Wout , Meeus Fien , Raes Geert , Breckpot Karine , Devoogdt Nick
Published: September 2023

Introduction

T cell Ig and ITIM domain receptor (TIGIT) is a next-generation immune checkpoint predominantly expressed on activated T cells and NK cells, exhibiting an unfavorable prognostic association with various malignancies. Despite the emergence of multiple TIGIT-blocking agents entering clinical trials, only a fraction of patients responded positively to anti-TIGIT therapy. Consequently, an urgent demand arises for noninvasive techniques to quantify and monitor TIGIT expression, facilitating patient stratification and enhancing therapeutic outcomes. Small antigen binding moieties such as nanobodies, are promising candidates for such tracer development.

Methods

We generated a panel of anti-human or anti-mouse TIGIT nanobodies from immunized llamas. In addition, we designed a single-chain variable fragment derived from the clinically tested monoclonal antibody Vibostolimab targeting TIGIT, and assessed its performance alongside the nanobodies. In vitro characterization studies were performed, including binding ability and affinity to cell expressed or recombinant TIGIT. After Technetium-99m labeling, the nanobodies and the single-chain variable fragment were evaluated in vivo for their ability to detect TIGIT expression using SPECT/CT imaging, followed by ex vivo biodistribution analysis.

Results

Nine nanobodies were selected for binding to recombinant and cell expressed TIGIT with low sub-nanomolar affinities and are thermostable. A six-fold higher uptake in TIGIT-overexpressing tumor was demonstrated one hour post- injection with Technetium-99m labeled nanobodies compared to an irrelevant control nanobody. Though the single-chain variable fragment exhibited superior binding to TIGIT-expressing peripheral blood mononuclear cells in vitro, its in vivo behavior yielded lower tumor-to-background ratios at one hour post- injection, indicating that nanobodies are better suited for in vivo imaging than the single-chain variable fragment. Despite the good affinity, high specificity and on-target uptake in mice in this setting, imaging of TIGIT expression on tumor- infiltrating lymphocytes within MC38 tumors remained elusive. This is likely due to the low expression levels of TIGIT in this model.

Discussion

The excellent affinity, high specificity and rapid on-target uptake in mice bearing TIGIT- overexpressing tumors showed the promising diagnostic potential of nanobodies to noninvasively image high TIGIT expression within the tumor. These findings hold promise for clinical translation to aid patient selection and improve therapy response.
Using Photo-ID to document and monitor the prevalence of fibropapilloma tumours in a foraging aggregation of green turtles
Authors: Hancock Joana M. , Choma Jenni , Mainye Leah , Wambi Paul , Stelfox Martin R. , Polyak Maximilian M. R. , Wambua Sammy , Köhnk Stephanie
Published: September 2023

Sea turtle in-water monitoring has been conducted in Diani-Chale National Marine Reserve (DCMR) in Kenya’s South Coast since 2018, where green sea turtles (Chelonia mydas) may be found resting or foraging. Underwater surveys are conducted at a regular basis to collect data on sea turtle occurrence, abundance, and distribution, incorporating photographic identification (Photo-ID) as a capture-mark-recapture method. Photo-ID is a non-invasive, low-cost, citizen-science-friendly approach that allows researchers to obtain discrete information about individuals’ locations and health status at a given time, which is essential knowledge for spatial planning and conservation management of endangered species. When visible in the photos collected on a single individual, the occurrence of external tumours is noted, and the turtle is flagged for fibropapilloma (FP) monitoring. From July 2018 to December 2022, 2757 green turtle encounters were recorded, resulting in the identification of 571 individuals. External tumours were observed in 75 individuals. The temporal progression of the tumour’s growth was monitored through subsequent re-sightings of 47 of the affected individuals, with evidence of tumour progression and regression. Documenting the incidence of this disease on sea turtles usually involves the manipulation of captured animals, and is quite possibly under-documented in foraging grounds. Tracking the evolution of this disease using Photo-ID can be a useful, non-invasive method to understand its extent in foraging aggregations where turtles can be easily observed underwater.
Distal end of a ureteral double-J stent displaced into the contralateral ureter after percutaneous nephrolithotripsy: a case report
Authors: Chen Junyong , Xie Tao , Xu Ya , Deng Jian , Zhang Jie , Zhu Yumo , Li Guiyuan
Published: September 2023

We report displacement of the distal end of a ureteral double-J stent into the contralateral ureter after percutaneous nephrolithotripsy (PCNL) in a 71-year-old man with a history of left kidney stones. Postoperative computed tomography imaging showed that the distal end of the left ureteral double-J stent was displaced into the right ureter, which resulted in persistent right renal colic when the nephrostomy tube was clipped and continuous urine leakage from the nephrostomy opening after the nephrostomy tube was removed. After the cystoscopic adjustment of the ureteral stent, the patient recovered uneventfully and was discharged home the next day.
Medical education in Latvia: an overview of current practices and systems
Authors: Jain Nityanand , Jersovs Kirils , Safina Taira , Pilmane Mara , Jansone-Ratinika Nora , Grike Ieva , Petersons Aigars
Published: September 2023

Located in northern Europe, Latvia is one of the three Baltic States with a population of 1.9 million. The country has a rich history of medical education spanning a century and is becoming an emerging global hub for medical education. Although the surge in international students has been beneficial for the development of educational and research infrastructure, increasing demands from local students, along with institutional capacity constraints, have overburdened the available resources. Substantial investments are being made to adapt to the rapidly changing geopolitical and techno-biomedical landscape. This perspective paper presents an overview of the country’s medical education system, its challenges, and prospects from pre-university to doctoral level.
Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes
Authors: Yan Yueyang , Shi Tao , Bao Xin , Gai Yunpeng , Liang Xingxing , Jiang Yu , Li Qiushi
Published: September 2023

Background

The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host’s productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems.

Results

Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair.

Conclusion

Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.
Metabolic versatility of Caldarchaeales from geothermal features of Hawai’i and Chile as revealed by five metagenome-assembled genomes
Authors: Balbay Manolya Gul , Shlafstein Maximillian D. , Cockell Charles , Cady Sherry L. , Prescott Rebecca D. , Lim Darlene S. S. , Chain Patrick S. G. , Donachie Stuart P. , Decho Alan W. , Saw Jimmy H.
Published: September 2023

Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai‘i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai‘i are high quality bins with completeness >95% and contamination <1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota.
Peppermint extract improves egg production and quality, increases antioxidant capacity, and alters cecal microbiota in late-phase laying hens
Authors: Bai Miaomiao , Liu Hongnan , Zhang Yihui , Wang Shanshan , Shao Yirui , Xiong Xia , Hu Xin , Yu Rongyao , Lan Wei , Cui Yadong , Kong Xiangfeng
Published: September 2023

Introduction

Peppermint contains substantial bioactive ingredients belonging to the phytoestrogens, and its effects on the production of late-laying hens deserve more attention. This study evaluated the effects of dietary peppermint extract (PE) supplementation on egg production and quality, yolk fatty acid composition, antioxidant capacity, and cecal microbiota in late-phase laying hens.

Method

PE powder was identified by UPLC-MS/MS analysis. Two hundred and sixteen laying hens (60 weeks old) were randomly assigned to four treatments, each for 28 days: (i) basal diet (control group, CON); (ii) basal diet + 0.1% PE; (iii) basal diet + 0.2% PE; and (iv) basal diet + 0.4% PE. Egg, serum, and cecal samples were collected for analysis.

Results

Dietary PE supplementation increased the laying rate, serum triglyceride, immunoglobulin G, and total antioxidant capacity, while 0.2 and 0.4% PE supplementation increased eggshell thickness, serum total protein level, and superoxide dismutase activity of laying hens compared with the CON group (P < 0.05). PE addition in diets increased the C14:0, C18:3n3, C18:3n6, C23:0, C24:0, and C24:1n9 contents in the yolk. In addition, the egg yolk saturated fatty acid content was higher (P < 0.05) in the 0.2 and 0.4% PE groups compared with the CON and 0.1% PE groups. The microbiota analysis revealed that the cecal phylum Proteobacteria was decreased (P < 0.05) in the PE-supplemented groups. A total of 0.4% PE supplementation increased the cecal richness of gram-positive bacteria and decreased the richness of gram-negative and potentially pathogenic bacteria compared with the 0.1% PE group (P < 0.05). Microbial function prediction analysis showed that the cecal microbiota of the PE group was mainly enriched by fatty acid degradation, fatty acid metabolism, amino sugar metabolism, nucleotide sugar metabolism, and other pathways. Regression analysis suggested that 0.28–0.36% PE supplementation was the optimal level for improving egg production and quality, antioxidant capacity, and yolk fatty acid in late-phase laying hens.

Discussion

Dietary PE supplementation improved egg production and quality (including yolk fatty acid composition) by increasing serum IgG and antioxidant capacity and modulating the intestinal microbiota in late-phase laying hens.