bluuebunny/crossref_metadata_2025 huggingface dataset:
Increase of glutamate in satellite glial cells of the trigeminal ganglion in a rat model of craniofacial neuropathic pain
Authors: Cho Yi Sul , Mah Won , Youn Dong Ho , Kim Yu Shin , Ko Hyoung-Gon , Bae Jin Young , Kim Yun Sook , Bae Yong Chul
Published: December 2023

Introduction

Satellite glial cells (SGCs) that envelop the cell bodies of neurons in sensory ganglia have been shown to both release glutamate, and be activated by glutamate in the context of nociceptive signaling. However, little is known about the subpopulations of SGCs that are activated following nerve injury and whether glutamate mechanisms in the SGCs are involved in the pathologic pain.

Methods

To address this issue, we used light and electron microscopic immunohistochemistry to examine the change in the glutamate levels in the SGCs and the structural relationship between neighboring neurons in the trigeminal ganglion (TG) in a rat model of craniofacial neuropathic pain, CCI-ION.

Results

Administration of ionomycin, ATP and Bz-ATP induced an increase of extracellular glutamate concentration in cultured trigeminal SGCs, indicating a release of glutamate from SGCs. The level of glutamate immunostaining in the SGCs that envelop neurons of all sizes in the TG was significantly higher in rats with CCI-ION than in control rats, suggesting that SGCs enveloping nociceptive as well as non-nociceptive mechanosensitive neurons are activated following nerve injury, and that the glutamate release from SGCs increases in pathologic pain state. Close appositions between substance-P (SP)-immunopositive (+) or calcitonin gene-related peptide (CGRP)+, likely nociceptive neurons, between Piezo1+, likely non-nociceptive, mechanosensitive neurons and SP+ or CGRP+ neurons, and between SGCs of neighboring neurons were frequently observed.

Discussion

These findings suggest that glutamate in the trigeminal SGCs that envelop all types of neurons may play a role in the mechanisms of neuropathic pain, possibly via paracrine signaling.
Oscillatory network spontaneously recovers both activity and robustness after prolonged removal of neuromodulators
Authors: More-Potdar Smita , Golowasch Jorge
Published: December 2023

Robustness of neuronal activity is a property necessary for a neuronal network to withstand perturbations, which may otherwise disrupt or destroy the system. The robustness of complex systems has been shown to depend on a number of features of the system, including morphology and heterogeneity of the activity of the component neurons, size of the networks, synaptic connectivity, and neuromodulation. The activity of small networks, such as the pyloric network of the crustacean stomatogastric nervous system, appears to be robust despite some of the factors not being consistent with the expected properties of complex systems, e.g., small size and homogeneity of the synaptic connections. The activity of the pyloric network has been shown to be stable and robust in a neuromodulatory state-dependent manner. When neuromodulatory inputs are severed, activity is initially disrupted, losing both stability and robustness. Over the long term, however, stable activity homeostatically recovers without the restoration of neuromodulatory input. The question we address in this study is whether robustness can also be restored as the network reorganizes itself to compensate for the loss of neuromodulatory input and recovers the lost activity. Here, we use temperature changes as a perturbation to probe the robustness of the network’s activity. We develop a simple metric of robustness, i.e., the variances of the network phase relationships, and show that robustness is indeed restored simultaneously along with its stable network activity, indicating that, whatever the reorganization of the network entails, it is deep enough also to restore this important property.
Repetitive spreading depolarization induces gene expression changes related to synaptic plasticity and neuroprotective pathways
Authors: Dell’Orco Michela , Weisend Jordan E. , Perrone-Bizzozero Nora I. , Carlson Andrew P. , Morton Russell A. , Linsenbardt David N. , Shuttleworth C. William
Published: December 2023

Spreading depolarization (SD) is a slowly propagating wave of profound depolarization that sweeps through cortical tissue. While much emphasis has been placed on the damaging consequences of SD, there is uncertainty surrounding the potential activation of beneficial pathways such as cell survival and plasticity. The present study used unbiased assessments of gene expression to evaluate that compensatory and repair mechanisms could be recruited following SD, regardless of the induction method, which prior to this work had not been assessed. We also tested assumptions of appropriate controls and the spatial extent of expression changes that are important for in vivo SD models. SD clusters were induced with either KCl focal application or optogenetic stimulation in healthy mice. Cortical RNA was extracted and sequenced to identify differentially expressed genes (DEGs). SDs using both induction methods significantly upregulated 16 genes (vs. sham animals) that included the cell proliferation-related genes FOS, JUN, and DUSP6, the plasticity-related genes ARC and HOMER1, and the inflammation-related genes PTGS2, EGR2, and NR4A1. The contralateral hemisphere is commonly used as control tissue for DEG studies, but its activity could be modified by near-global disruption of activity in the adjacent brain. We found 21 upregulated genes when comparing SD-involved cortex vs. tissue from the contralateral hemisphere of the same animals. Interestingly, there was almost complete overlap (21/16) with the DEGs identified using sham controls. Neuronal activity also differs in SD initiation zones, where sustained global depolarization is required to initiate propagating events. We found that gene expression varied as a function of the distance from the SD initiation site, with greater expression differences observed in regions further away. Functional and pathway enrichment analyses identified axonogenesis, branching, neuritogenesis, and dendritic growth as significantly enriched in overlapping DEGs. Increased expression of SD-induced genes was also associated with predicted inhibition of pathways associated with cell death, and apoptosis. These results identify novel biological pathways that could be involved in plasticity and/or circuit modification in brain tissue impacted by SD. These results also identify novel functional targets that could be tested to determine potential roles in the recovery and survival of peri-infarct tissues.
Excitatory subtypes of the lateral amygdala neurons are differentially involved in regulation of synaptic plasticity and excitation/inhibition balance in aversive learning in mice
Authors: Morishima Mieko , Matsumura Sohta , Tohyama Suguru , Nagashima Takashi , Konno Ayumu , Hirai Hirokazu , Watabe Ayako M.
Published: December 2023

The amygdala plays a crucial role in aversive learning. In Pavlovian fear conditioning, sensory information about an emotionally neutral conditioned stimulus (CS) and an innately aversive unconditioned stimulus is associated with the lateral amygdala (LA), and the CS acquires the ability to elicit conditioned responses. Aversive learning induces synaptic plasticity in LA excitatory neurons from CS pathways, such as the medial geniculate nucleus (MGN) of the thalamus. Although LA excitatory cells have traditionally been classified based on their firing patterns, the relationship between the subtypes and functional properties remains largely unknown. In this study, we classified excitatory cells into two subtypes based on whether the after-depolarized potential (ADP) amplitude is expressed in non-ADP cells and ADP cells. Their electrophysiological properties were significantly different. We examined subtype-specific synaptic plasticity in the MGN-LA pathway following aversive learning using optogenetics and found significant experience-dependent plasticity in feed-forward inhibitory responses in fear-conditioned mice compared with control mice. Following aversive learning, the inhibition/excitation (I/E) balance in ADP cells drastically changed, whereas that in non-ADP cells tended to change in the reverse direction. These results suggest that the two LA subtypes are differentially regulated in relation to synaptic plasticity and I/E balance during aversive learning.
The identification of new roles for nicotinamide mononucleotide after spinal cord injury in mice: an RNA-seq and global gene expression study
Authors: Zhang Chunjia , Li Yan , Bai Fan , Talifu Zuliyaer , Ke Han , Xu Xin , Li Zehui , Liu Wubo , Pan Yunzhu , Gao Feng , Yang Degang , Wang Xiaoxin , Du Huayong , Guo Shuang , Gong Han , Du Liangjie , Yu Yan , Li Jianjun
Published: December 2023

Background

Nicotinamide mononucleotide (NMN), an important transforming precursor of nicotinamide adenine dinucleotide (NAD+). Numerous studies have confirmed the neuroprotective effects of NMN in nervous system diseases. However, its role in spinal cord injury (SCI) and the molecular mechanisms involved have yet to be fully elucidated.

Methods

We established a moderate-to-severe model of SCI by contusion (70 kdyn) using a spinal cord impactor. The drug was administered immediately after surgery, and mice were intraperitoneally injected with either NMN (500 mg NMN/kg body weight per day) or an equivalent volume of saline for seven days. The central area of the spinal cord was harvested seven days after injury for the systematic analysis of global gene expression by RNA Sequencing (RNA-seq) and finally validated using qRT-PCR.

Results

NMN supplementation restored NAD+ levels after SCI, promoted motor function recovery, and alleviated pain. This could potentially be associated with alterations in NAD+ dependent enzyme levels. RNA sequencing (RNA-seq) revealed that NMN can inhibit inflammation and potentially regulate signaling pathways, including interleukin-17 (IL-17), tumor necrosis factor (TNF), toll-like receptor, nod-like receptor, and chemokine signaling pathways. In addition, the construction of a protein-protein interaction (PPI) network and the screening of core genes showed that interleukin 1β (IL-1β), interferon regulatory factor 7 (IRF 7), C-X-C motif chemokine ligand 10 (Cxcl10), and other inflammationrelated factors, changed significantly after NMN treatment. qRT-PCR confirmed the inhibitory effect of NMN on inflammatory factors (IL-1β, TNF-α, IL-17A, IRF7) and chemokines (chemokine ligand 3, Cxcl10) in mice following SCI.

Conclusion

The reduction of NAD+ levels after SCI can be compensated by NMN supplementation, which can significantly restore motor function and relieve pain in a mouse model. RNA-seq and qRT-PCR systematically revealed that NMN affected inflammation-related signaling pathways, including the IL-17, TNF, Toll-like receptor, NOD-like receptor and chemokine signaling pathways, by down-regulating the expression of inflammatory factors and chemokines.
Progression and regression of kidney disease in type 1 diabetes
Authors: Jansson Sigfrids Fanny , Groop Per-Henrik
Published: December 2023

Diabetic kidney disease is distinguished by the presence of albuminuria, hypertension, declining kidney function, and a markedly elevated cardiovascular disease risk. This constellation of clinical features drives the premature mortality associated with type 1 diabetes. The first epidemiological investigations concerning type 1 diabetes-related albuminuria date back to the 1980s. The early studies found that proteinuria – largely equivalent to severe albuminuria – developed in 35 to 45% of individuals with type 1 diabetes, with the diabetes duration-specific incidence rate pattern portraying one or two peaks. Furthermore, moderate albuminuria, the first detectable sign of diabetic kidney disease, was found to nearly inexorably progress to overt kidney disease within a short span of time. Since the early reports, studies presenting more updated incidence rates have appeared, although significant limitations such as study populations that lack broad generalizability, study designs vulnerable to substantive selection bias, and constrained follow-up times have been encountered by many. Nevertheless, the most recent reports estimate that in modern times, moderate – instead of severe – albuminuria develops in one-third of individuals with type 1 diabetes; yet, a considerable part (up to 40% during the first ten years after the initial albuminuria diagnosis) progresses to more advanced stages of the disease over time. An alternative pathway to albuminuria progression is its regression, which affects up to 60% of the individuals, but notably, the relapse rate to a more advanced disease stage is high. Whether albuminuria regression translates into a decline in cardiovascular disease and premature mortality risk is an area of debate, warranting more detailed research in the future. Another unclear but alarming feature is that although the incidence of severe albuminuria has fallen since the 1930s, the decline seems to have reached a plateau after the 1980s. This stagnation may be due to the lack of kidney-protective medicines since the early 1980s, as the recent breakthroughs in type 2 diabetes have not been applicable to type 1 diabetes. Therefore, novel treatment strategies are at high priority within this patient population.
Causal relationship between levels of myeloperoxidase and obstructive sleep apnea: a bidirectional two-sample Mendelian randomization study
Authors: Tang Weihua , Li Fang , Huang Rui , Liu Peijun
Published: December 2023

Background

Several observational studies have investigated the association between myeloperoxidase (MPO) and obstructive sleep apnea (OSA). However, the nature of this relationship remains uncertain due to potential selection and confounding biases. To resolve this, we conducted a bidirectional two-sample Mendelian randomization (MR) study to scrutinize the causal relationship between MPO and OSA.

Methods

Instrumental variables (IVs) for OSA were sourced from the publicly available FinnGen dataset, encompassing 38,998 OSA cases and 336,659 controls. Data on MPO were sourced from a study of 21,758 individuals conducted by the European Bioinformatics Institute (EBI). The primary MR analysis utilized the inverse-variance weighted (IVW) method, with MR–Egger intercept and leave-one-out methods assessing pleiotropy and Cochran’s Q test determining heterogeneity.

Results

The IVW analysis indicated a causal relationship between heightened MPO levels and an increased incidence of OSA. Individuals with elevated MPO levels manifested a higher propensity to develop OSA, exhibiting an odds ratio (OR) of 1.075 and a 95% confidence interval (CI) of 1.011–1.143 (p = 0.021). Conversely, the reciprocal analysis unveiled no significant association between OSA and heightened MPO levels (p = 0.643). No directional pleiotropy was identified through the MR–Egger intercept test (p > 0.05).

Conclusion

Our study provides evidence of an association between elevated MPO levels and an increased incidence of OSA. However, OSA does not necessarily lead to elevated MPO levels. When patients present with high MPO levels, screening for OSA may be advisable, considering their clinical characteristics.
Cortical responses time-locked to continuous speech in the high-gamma band depend on selective attention
Authors: Commuri Vrishab , Kulasingham Joshua P. , Simon Jonathan Z.
Published: December 2023

Auditory cortical responses to speech obtained by magnetoencephalography (MEG) show robust speech tracking to the speaker's fundamental frequency in the high-gamma band (70–200 Hz), but little is currently known about whether such responses depend on the focus of selective attention. In this study 22 human subjects listened to concurrent, fixed-rate, speech from male and female speakers, and were asked to selectively attend to one speaker at a time, while their neural responses were recorded with MEG. The male speaker's pitch range coincided with the lower range of the high-gamma band, whereas the female speaker's higher pitch range had much less overlap, and only at the upper end of the high-gamma band. Neural responses were analyzed using the temporal response function (TRF) framework. As expected, the responses demonstrate robust speech tracking of the fundamental frequency in the high-gamma band, but only to the male's speech, with a peak latency of ~40 ms. Critically, the response magnitude depends on selective attention: the response to the male speech is significantly greater when male speech is attended than when it is not attended, under acoustically identical conditions. This is a clear demonstration that even very early cortical auditory responses are influenced by top-down, cognitive, neural processing mechanisms.
Relationship between immune nutrition index and all-cause and cause-specific mortality in U.S. adults with chronic kidney disease
Authors: Zhang Junlin , Xiao Xiang , Han Tianzhao , Liu Yuping , Shuai Ping
Published: December 2023

Objective

The available evidence regarding the association of immune nutrition status with chronic kidney disease (CKD) is limited. Thus, the present study examined whether immunonutrition indices were associated with renal function and mortality among CKD individuals.

Research design and methods

This study enrolled 6,099 U.S. adults with CKD from the NHANES 2005–2018 database. Participants were matched with National Death Index records until 31 December 2019 to determine mortality outcomes. The time-dependent receiver operating characteristic was utilized to identify the most effective index among the prognostic nutritional index (PNI), system inflammation score (SIS), Naples prognostic score (NPS), and controlling nutritional status (CONUT) for predicting mortality. Cox regression models were employed to evaluate the associations of immunonutrition indices with mortality in participants with CKD.

Results

The PNI exhibited the strongest predictive power among the four indices evaluated and the restricted cubic spline analysis revealed a cutoff value of 51 for the PNI in predicting mortality. During a median follow-up of 72 months (39–115 months), a total of 1,762 (weighted 24.26%) CKD participants died from all causes. The Kaplan–Meier curve demonstrated a reduced risk of death for the subjects with a higher PNI compared to those in the lower group. Besides, after adjusting for multiple potential confounders, a higher PNI remained an independent predictor for lower risks of all-cause mortality (HR 0.80, 95%CI: 0.71–0.91, p < 0.001) and cardiovascular disease (CVD) mortality (HR 0.69, 95%CI: 0.55–0.88, p = 0.002) in individuals with CKD.

Conclusion

In CKD, a higher PNI level was significantly associated with lower mortality from all causes and CVD. Thus, the clinical utility of this immunonutrition indicator may facilitate risk stratification and prevent premature death among patients with CKD.
Signaling pathways regulated by natural active ingredients in the fight against exercise fatigue-a review
Authors: Zhao Rongyue , Wu Ruomeng , Jin Junjie , Ning Ke , Wang Zhuo , Yi Xuejie , Kapilevich Leonid , Liu Jiao
Published: December 2023

Exercise fatigue is a normal protective mechanism of the body. However, long-term fatigue hinders normal metabolism and exercise capacity. The generation and recovery from exercise fatigue involves alterations in multiple signaling pathways, mainly AMPK, PI3K/Akt, Nrf2/ARE, NF-κB, PINK1/Parkin, and BDNF/TrkB, as well as MAPK signaling pathways that mediate energy supply, reduction of metabolites, oxidative stress homeostasis, muscle fiber type switching, and central protective effects. In recent studies, a rich variety of natural active ingredients have been identified in traditional Chinese medicines and plant extracts with anti-fatigue effects, opening up the field of research in new anti-fatigue drugs. In this review we give an overview of the signaling pathways associated with the activity of natural food active ingredients against exercise fatigue. Such a comprehensive review is necessary to understand the potential of these materials as preventive measures and treatments of exercise fatigue. We expect the findings highlighted and discussed here will help guide the development of new health products and provide a theoretical and scientific basis for future research on exercise fatigue.
Ansofaxine hydrochloride inhibits tumor growth and enhances Anti-TNFR2 in murine colon cancer model
Authors: Jing Qianyu , Wan Quan , Nie Yujie , Luo Junqian , Zhang Xiangyan , Zhu Lan , Gui Huan , Li Linzhao , Wang Chenglv , Chen Shuanghui , Wang Mengjiao , Yuan Haohua , Lv Hang , Pan Runsang , Jing Qianjun , Nie Yingjie
Published: December 2023

Introduction: As psychoneuroimmunology flourishes, there is compelling evidence that depression suppresses the anti-tumor immune response, promotes the progression of cancer, and inhibits the effectiveness of cancer immunotherapy. Recent studies have reported that antidepressants can not only alleviate the depressant condition of cancer patients, but also strengthen the anti-tumor immunity, thus suppressing tumors. Tumor necrosis factor receptor 2 (TNFR2) antagonistic antibodies (Anti-TNFR2) targeting tumor-infiltrating regulatory T cells (Tregs) has achieved great results in preclinical studies, and with a favorable toxicity profile than existing immunotherapies, and is expected to become a new generation of more effective treatment strategies. Understanding the effects of combination therapy with antidepressants and Anti-TNFR2 may help design new strategies for cancer immunotherapy.

Methods: We treated CT26, HCT116, MCA38 and SW620 colon cancer cells with fluoxetine (0–50 µM), ansofaxine hydrochloride (0–50 µM) and amitifadine hydrochloride (0–150 µM) to examine their effects on cell proliferation and apoptosis. We explored the antitumor effects of ansofaxine hydrochloride in combination with or without Anti-TNFR in subcutaneously transplanted CT26 cells in tumor-bearing mouse model. Antitumor effects were evaluated by tumor volume. NK cell, M1 macrophage cell, CD4+ T cell, CD8+ T cell, exhausted CD8+ T and regulatory T cell (Tregs) subtypes were measured by flow cytometry. 5-hydroxytryptamine, dopamine and norepinephrine levels were measured by ELISA.

Results: Oral antidepression, ansofaxine hydrochloride, enhanced peripheral dopamine levels, promoted CD8+T cell proliferation, promoted intratumoral infiltration of M1 and NK cells, decreased the proportion of tumor-infiltrating exhausted CD8+T cells, and strengthened anti-tumor immunity, thereby inhibiting colon cancer growth. In combination therapy, oral administration of ansofaxine hydrochloride enhanced the efficacy of Anti-TNFR2, and produced long-term tumor control in with syngeneic colorectal tumor-bearing mice, which was attributable to the reduction in tumor-infiltrating Treg quantity and the recovery of CD8+ T cells function.

Discussion: In summary, our data reveal the role of ansofaxine hydrochloride in modulating the anti-tumor immunity. Our results support that exhausted CD8+T is an important potential mechanism by which ansofaxine hydrochloride activates anti-tumor immunity and enhances anti-tumor effects of anti-TNFR2.
The influence of herbal medicine on serum motilin and its effect on human and animal model: a systematic review
Authors: Cho Min-Seok , Park Jae-Woo , Kim Jinsung , Ko Seok-Jae
Published: December 2023

Introduction: Motilin (MLN) is a gastrointestinal (GI) hormone produced in the upper small intestine. Its most well understood function is to participate in Phase III of the migrating myoelectric complex component of GI motility. Changes in MLN availability are associated with GI diseases such as gastroesophageal reflux disease and functional dyspepsia. Furthermore, herbal medicines have been used for several years to treat various GI disorders. We systematically reviewed clinical and animal studies on how herbal medicine affects the modulation of MLN and subsequently brings the therapeutic effects mainly focused on GI function.

Methods: We searched the PubMed, Embase, Cochrane, and Web of Science databases to collect all articles published until 30 July 2023, that reported the measurement of plasma MLN levels in human randomized controlled trials and in vivo herbal medicine studies. The collected characteristics of the articles included the name and ingredients of the herbal medicine, physiological and symptomatic changes after administering the herbal medicine, changes in plasma MLN levels, key findings, and mechanisms of action. The frequency patterns (FPs) of botanical drug use and their correlations were investigated using an FP growth algorithm.

Results: Nine clinical studies with 1,308 participants and 20 animal studies were included in the final analyses. Herbal medicines in clinical studies have shown therapeutic effects in association with increased levels of MLN, including GI motility regulation and symptom improvement. Herbal medicines have also shown anti-stress, anti-tumor, and anti-inflammatory effects in vivo. Various biochemical markers may correlate with MLN levels. Markers may have a positive correlation with plasma MLN levels included ghrelin, acetylcholine, and secretin, whereas a negative correlation included triglycerides and prostaglandin E2. Markers, such as gastrin and somatostatin, did not show any correlation with plasma MLN levels. Based on the FP growth algorithm, Glycyrrhiza uralensis and Paeonia japonica were the most frequently used species.

Conclusion: Herbal medicine may have therapeutic effects mainly on GI symptoms with involvement of MLN regulation and may be considered as an alternative option for the treatment of GI diseases. Further studies with more solid evidence are needed to confirm the efficacy and mechanisms of action of herbal medicines.

Systematic Review Registration:https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=443244, identifier CRD42023443244.
Pharmacological approaches to understanding protein kinase signaling networks
Authors: Stephenson Elloise H. , Higgins Jonathan M. G.
Published: December 2023

Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
Forecasting infections with spatio-temporal graph neural networks: a case study of the Dutch SARS-CoV-2 spread
Authors: Croft V. Maxime , van Iersel Senna C. J. L. , Della Santina Cosimo
Published: December 2023

The spread of an epidemic over a population is influenced by a multitude of factors having both spatial and temporal nature, which are hard to completely capture using first principle methods. This paper concerns regional forecasting of SARS-Cov-2 infections 1 week ahead using machine learning. We especially focus on the Dutch case study for which we develop a municipality-level COVID-19 dataset. We propose to use a novel spatiotemporal graph neural network architecture to perform the predictions. The developed model captures the spread of infectious diseases within municipalities over time using Gated Recurrent Units and the spatial interactions between municipalities using GATv2 layers. To the best of our knowledge, this model is the first to incorporate sewage data, the stringency index, and commuting information into GNN-based infection prediction. In experiments on the developed real-world dataset, we demonstrate that the model outperforms simple baselines and purely spatial or temporal models for the COVID-19 wild type, alpha, and delta variants. More specifically, we obtain an average R2 of 0.795 for forecasting infections and of 0.899 for predicting the associated trend of these variants.
Radioassay facilities at the STFC Boulby Underground Laboratory
Authors: Scovell Paul R. , Thiesse Matthew , Ahmed Maouloud Sid , Ghag Chamkaur , Dobson James
Published: December 2023

For future low-background particle physics experiments, it will be essential to assay candidate detector materials using an array of assay techniques. To minimise the risk of sample contamination whilst moving between assay techniques, it is also sensible to minimise the distance between assay stations, particularly for non-destructive techniques where the sample may end up being installed into an experiment. The Boulby UnderGround Screening (BUGS) Facility comprises an array of germanium detectors, two XIA UltraLo-1800 surface-alpha counters, two radon emanation detectors and an Agilent ICP-MS system. This article describes each of these systems.
MegaSSR: a web server for large scale microsatellite identification, classification, and marker development
Authors: Mokhtar Morad M. , Alsamman Alsamman M. , El Allali Achraf
Published: December 2023

Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.
Reference genome of the nutrition-rich orphan crop chia (Salvia hispanica) and its implications for future breeding
Authors: Gupta Parul , Geniza Matthew , Elser Justin , Al-Bader Noor , Baschieri Rachel , Phillips Jeremy Levi , Haq Ebaad , Preece Justin , Naithani Sushma , Jaiswal Pankaj
Published: December 2023

Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
Identification and analysis of BAHD superfamily related to malonyl ginsenoside biosynthesis in Panax ginseng
Authors: Wang Ping , Yan Yan , Yan Min , Piao Xiangmin , Wang Yingping , Lei Xiujuan , Yang He , Zhang Nanqi , Li Wanying , Di Peng , Yang Limin
Published: December 2023

Introduction

The BAHD (benzylalcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase and deacetylvindoline 4-O-acetyltransferase), has various biological functions in plants, including catalyzing the biosynthesis of terpenes, phenolics and esters, participating in plant stress response, affecting cell stability, and regulating fruit quality.

Methods

Bioinformatics methods, real-time fluorescence quantitative PCR technology, and ultra-high-performance liquid chromatography combined with an Orbitrap mass spectrometer were used to explore the relationship between the BAHD gene family and malonyl ginsenosides in Panax ginseng.

Results

In this study, 103 BAHD genes were identified in P. ginseng, mainly distributed in three major clades. Most PgBAHDs contain cis-acting elements associated with abiotic stress response and plant hormone response. Among the 103 genes, 68 PgBAHDs are WGD (whole-genome duplication) genes. The significance of malonylation in biosynthesis has garnered considerable attention in the study of malonyltransferases. The phylogenetic tree results showed 34 PgBAHDs were clustered with genes that have malonyl characterization. Among them, seven PgBAHDs (PgBAHD4, 45, 65, 74, 90, 97, and 99) showed correlations > 0.9 with crucial enzyme genes involved in ginsenoside biosynthesis and > 0.8 with malonyl ginsenosides. These seven genes were considered potential candidates involved in the biosynthesis of malonyl ginsenosides.

Discussion

These results help elucidate the structure, evolution, and functions of the P. ginseng BAHD gene family, and establish the foundation for further research on the mechanism of BAHD genes in ginsenoside biosynthesis.
Transcriptome analysis and physiological changes in the leaves of two Bromus inermis L. genotypes in response to salt stress
Authors: Song Wenxue , Gao Xueqin , Li Huiping , Li Shuxia , Wang Jing , Wang Xing , Wang Tongrui , Ye Yunong , Hu Pengfei , Li Xiaohong , Fu Bingzhe
Published: December 2023

Soil salinity is a major factor threatening the production of crops around the world. Smooth bromegrass (Bromus inermis L.) is a high-quality grass in northern and northwestern China. Currently, selecting and utilizing salt-tolerant genotypes is an important way to mitigate the detrimental effects of salinity on crop productivity. In our research, salt-tolerant and salt-sensitive varieties were selected from 57 accessions based on a comprehensive evaluation of 22 relevant indexes, and their salt-tolerance physiological and molecular mechanisms were further analyzed. Results showed significant differences in salt tolerance between 57 genotypes, with Q25 and Q46 considered to be the most salt-tolerant and salt-sensitive accessions, respectively, compared to other varieties. Under saline conditions, the salt-tolerant genotype Q25 not only maintained significantly higher photosynthetic performance, leaf relative water content (RWC), and proline content but also exhibited obviously lower relative conductivity and malondialdehyde (MDA) content than the salt-sensitive Q46 (p < 0.05). The transcriptome sequencing indicated 15,128 differentially expressed genes (DEGs) in Q46, of which 7,885 were upregulated and 7,243 downregulated, and 12,658 DEGs in Q25, of which 6,059 were upregulated and 6,599 downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the salt response differences between Q25 and Q46 were attributed to the variable expression of genes associated with plant hormone signal transduction and MAPK signaling pathways. Furthermore, a large number of candidate genes, related to salt tolerance, were detected, which involved transcription factors (zinc finger proteins) and accumulation of compatible osmolytes (glutathione S-transferases and pyrroline-5-carboxylate reductases), etc. This study offers an important view of the physiological and molecular regulatory mechanisms of salt tolerance in two smooth bromegrass genotypes and lays the foundation for further identification of key genes linked to salt tolerance.
Gender stereotypes and social perception of vocal confidence is mitigated by salience of socio-indexical cues to gender
Authors: Roche Jennifer M. , Asaro Katie , Morris Bradley J. , Morgan Shae D.
Published: December 2023

Introduction

Socio-indexical cues to gender and vocal affect often interact and sometimes lead listeners to make differential judgements of affective intent based on the gender of the speaker. Previous research suggests that rising intonation is a common cue that both women and men produce to communicate lack of confidence, but listeners are more sensitive to this cue when it is produced by women. Some speech perception theories assume that listeners will track conditional statistics of speech and language cues (e.g., frequency of the socio-indexical cues to gender and affect) in their listening and communication environments during speech perception. It is currently less clear if these conditional statistics will impact listener ratings when context varies (e.g., number of talkers).

Methods

To test this, we presented listeners with vocal utterances from one female and one male-pitched voice (single talker condition) or many female/male-pitched voices (4 female voices; 4 female voices pitch-shifted to a male range) to examine how they impacted perceptions of talker confidence.

Results

Results indicated that when one voice was evaluated, listeners defaulted to the gender stereotype that the female voice using rising intonation (a cue to lack of confidence) was less confident than the male-pitched voice (using the same cue). However, in the multi-talker condition, this effect went away and listeners equally rated the confidence of the female and male-pitched voices.

Discussion

Findings support dual process theories of information processing, such that listeners may rely on heuristics when speech perception is devoid of context, but when there are no differentiating qualities across talkers (regardless of gender), listeners may be ideal adapters who focus on only the relevant cues.
Buddhist culture as a safeguard for the subjective happiness of Chinese residents: mitigating anxiety regarding housing prices, unemployment, and inequality
Authors: Tan Shuying , Fang Peijie , Shi Wenxiang , Du Shukai
Published: December 2023

Introduction

This study examines whether Buddhist culture in China can safeguard the subjective happiness of residents by mitigating the detrimental impact of adversity. Considering Chinese traditional culture and referencing Baidu Search Index data, we focus on three sources of anxiety that are currently troubling Chinese residents: housing prices, unemployment, and inequality.

Methods

We conduct logit regressiontoinvestigate the mitigating impact of Buddhist culture on anxiety. The frequency of droughts and floods that occurred during the Ming and Qing dynasties are employed as instrumental variables for the local density of Buddhist culture to avoid endogeneity problems.

Results

Empirical analysis based on microdata shows that Chinese Buddhist culture demonstrates the ability to alleviate the negative effects of housing price pressures, unemployment anxiety, and perceived inequality on subjective well-being. Mechanism analyses reveal that Chinese Buddhist culture plays a role in ameliorating the adverse impacts of housing and unemployment pressures on factors such as job satisfaction, physical health status, social trust, and expectations of future social standing. Moreover, it works to reduce inclinations toward social comparisons, thereby acting as a safeguard for happiness. Heterogeneity analysis shows that this insurance effect is more pronounced among vulnerable groups, including those in rural areas, middle-aged and elderly demographics, individuals with fewer social connections, lower social security coverage, and suboptimal health conditions.

Discussion

This study expands the landscape of happiness economics research and provides novel evidence about the correlation between religion and happiness. Psychotherapists may draw on certain aspects of religious philosophy in addressing mental disorders. From a governmental perspective, there is potential to effectively steer religious culture towards fostering social harmony and promoting economic development.
Comparing self-esteem and self-compassion: an analysis within the big five personality traits framework
Authors: Yang Fan , Hagiwara Chiaki , Kotani Tomomi , Hirao Joji , Oshio Atsushi
Published: December 2023

Self-esteem and self-compassion are two ways to relate to oneself. However, little is known about the similarities and differences between these two constructs. The current study used cross-sectional data from a Japanese sample to explore their relationship from a Big Five perspective. Results showed that differences between self-esteem and self-compassion appeared mainly in openness, agreeableness, and neuroticism. Specifically, self-esteem was uniquely associated with openness, and self-compassion was uniquely associated with agreeableness. Moreover, the negative correlation between self-compassion and neuroticism was larger than that between self-esteem and neuroticism. Implications and future directions are discussed.
Community health workers’ quality of comprehensive care: a cross-sectional observational study across three districts in South Africa
Authors: Babalola Olukemi , Levin Jonathan , Goudge Jane , Griffiths Frances
Published: December 2023

Background

Community healthcare worker (CHW) training programs are becoming increasingly comprehensive (an expanded range of diseases). However, the CHWs that the program relies on have limited training. Since CHWs’ activities occur largely during household visits, which often go unsupervised and unassessed, long-term, ongoing assessment is needed to identify gaps in CHW competency, and improve any such gaps. We observed CHWs during household visits and gave scores according to the proportion of health messages/activities provided for the health conditions encountered in households. We aimed to determine (1) messages/activities scores derived from the proportion of health messages given in the households by CHWs who provide comprehensive care in South Africa, and (2) the associated factors.

Methods

In three districts (from two provinces), we trained five fieldworkers to score the messages provided by, and activities of, 34 CHWs that we randomly selected during 376 household visits in 2018 and 2020 using a cross-sectional study designs. Multilevel models were fitted to identify factors associated with the messages/activities scores, adjusted for the clustering of observations within CHWs. The models were adjusted for fieldworkers and study facilities (n = 5, respectively) as fixed effects. CHW-related (age, education level, and phase of CHW training attended/passed) and household-related factors (household size [number of persons per household], number of conditions per household, and number of persons with a condition [hypertension, diabetes, HIV, tuberculosis TB, and cough]) were investigated.

Results

In the final model, messages/activities scores increased with each extra 5-min increase in visit duration. Messages/activities scores were lower for households with either children/babies, hypertension, diabetes, a large household size, numerous household conditions, and members with either TB or cough. Increasing household size and number of conditions, also lower the score. The messages/activities scores were not associated with any CHW characteristics, including education and training.

Conclusion

This study identifies important factors related to the messages provided by and the activities of CHWs across CHW teams. Increasing efforts are needed to ensure that CHWs who provide comprehensive care are supported given the wider range of conditions for which they provide messages/activities, especially in households with hypertension, diabetes, TB/cough, and children or babies.
Investigation of two norovirus outbreaks linked to drinking water contaminated with multiple GII strains in a rural county—Chongqing, China, 2021
Authors: Li Tingting , Peng Jingyao , Li Qin , Li Baisong , Yuan Yi , Yang Chuan , Yang Di , Tang Wenge , Qi Li
Published: December 2023

Backgrounds

Norovirus is leading cause of non-bacterial gastroenteritis outbreaks globally, characterized by different strains prevalent in different countries and regions.

Methods

Cases were defined as individuals experiencing diarrhea ≥3 times/24 h, and/or vomiting ≥2 times/24 h in two villages between January 28 and February 9, 2021. Investigations were conducted to identify causes. Cases were interviewed using a standardized in-person form to collect data on potential risk factors. A retrospective cohort study was conducted to investigate the role of the spring water supply as the outbreak source. Residents from neighboring villages with different water sources served as the unexposed population. Stool specimens, rectal swabs, and water samples were tested using quantitative real-time Polymerase Chain Reaction, with subsequent sequencing performed on pathogen-positive specimens.

Results

Village-specific attack rates were 21.93% (123/561) and 26.99% (88/326), respectively. Evidence from both epidemiological and laboratory tests was consistent. Drinking spring water was statistically associated with the two outbreaks (RR = 41.8 and 79.2, respectively). In both outbreaks, stool specimens, rectal swabs, and water samples tested positive for norovirus. Specifically, GII.2 (P16) and GII.17 (P17) were identified in outbreak A, and GII.4 Sydney (P16) and GII.1 (P16) in outbreak B.

Conclusion

These two independent gastroenteritis outbreaks share similarities, both being linked to norovirus GII strains. The contaminated spring drinking water was identified as the probable source and was promptly closed and subjected to disinfection procedures. These findings reinforce the importance of implementing sanitation and environmental disinfection measures in rural areas, especially during the periods of increased rainfall.