bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetics in Ecology, Evolution, and Conservation
Authors: Lamka Gina F. , Harder Avril M. , Sundaram Mekala , Schwartz Tonia S. , Christie Mark R. , DeWoody J. Andrew , Willoughby Janna R.
Published: April 2022

Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.
The Relationship Between Hospitalization Frequency of Acute Exacerbation of Chronic Obstructive Pulmonary Disease and Anxiety and Depression
Authors: Wen-tao Ding , Xue-xiu Chen , Zun-jiang Chen , Wei Chen , Cheng-feng Pan , Xing-ken Fan
Published: April 2022

Depression and anxiety are common in patients with COPD (chronic obstructive pulmonary disease), and anxiety and depression can increase the risk of hospitalization and the acute exacerbation of chronic obstructive pulmonary disease. The relationship between the frequency of hospitalization for acute exacerbation of COPD (AECOPD) and the anxiety and depression of patients is not fully understood. This study aims to analyze the relationship between the frequency of hospitalizations and anxiety and depression of patients of acute exacerbation of chronic obstructive pulmonary disease (AECOPD). A collection of 309 AECOPD patients admitted to the emergency department in our hospital from 2019 to 2020 were divided into anxiety group A and depression group D according to the Hospital Anxiety and Depression Scale (HADS) score and divided into A1 and D1 negative groups (≤7 Score), A2 and D2 suspicious groups (8–10 points), A3 and D3 confirmed groups (≥11 points) for paired analysis of anxiety and depression correlation and difference and comparison of the frequency of hospitalization in each group within 2 years. The results found that anxiety and depression were significantly positively correlated (r = 0.654, p = 0.000). Intra-group comparison shows that the difference between the anxiety-diagnosed and non-diagnosed groups and the depression subgroups are statistically p < 0.05; the comparison between the anxiety subgroup and the depression subgroup showed that there was a statistical difference between the confirmed group and the non-diagnosed group (p < 0.01). In short, AECOPD anxiety is positively correlated with depression, and depression is affected by the frequency of hospitalization earlier and gradually, and anxiety should be prioritized in the acute phase.
Clinical and Genetic Features of Chinese Patients With NIPA1-Related Hereditary Spastic Paraplegia Type 6
Authors: Fu Jun , Ma Mingming , Li Gang , Zhang Jiewen
Published: April 2022

Background: Mutations in the NIPA1 gene cause hereditary spastic paraplegia (HSP) type 6 (SPG6), which is a rare type of HSP with a frequency of less than 1% in Europe. To date, less than 30 SPG6 families and limited NIPA1 mutations have been reported in different ethnic regions. The clinical features are variable.

Methods: We screened for NIPA1 mutations by whole exome sequencing or next generation sequencing in 35 unrelated Chinese families with HSP. The clinical manifestations were evaluated.

Results: Two variants of NIPA1 were identified in three index patients (3/35, 8.6%), two of whom carried a previously reported common variant c.316G > A (p.G106R), and the third patient harbored a novel likely pathogenic variant c.126C > G (p.N42K). Both variants were de novo in the three index patients. The phenotype was pure HSP in two patients and complicated HSP with epilepsy in the third one.

Conclusion:NIPA1-related HSP is more common in China than it in Europe. Both pure and complicated form of HSP can be found. The variant c.316G > A is a hotspot mutation, and the novel variant c.126C > G expands the mutational spectrum. The phenomenon of de novo mutations in NIPA1 emphasizes the need to consider autosomal dominant HSP-related genes in sporadic patients.
Convergence Analysis of Rust Fungi and Anther Smuts Reveals Their Common Molecular Adaptation to a Phytoparasitic Lifestyle
Authors: Zhou Xianzhen , Yu Dan , Cao Zhimin
Published: April 2022

Convergent evolution between distantly related taxa often mirrors adaptation to similar environments. Rust fungi and anther smuts, which belong to different classes in Pucciniomycotina, have independently evolved a phytoparasitic lifestyle, representing an example of convergent evolution in the fungal kingdom. To investigate their adaptations and the genetic bases underlying their phytoparasitic lifestyles, we performed genome-wide convergence analysis of amino acid substitutions, evolutionary rates, and gene gains and losses. Convergent substitutions were detected in ATPeV0D and RP-S27Ae, two genes important for the generation of turgor pressure and ribosomal biosynthesis, respectively. A total of 51 positively selected genes were identified, including eight genes associated with translation and three genes related to the secretion pathway. In addition, rust fungi and anther smuts contained more proteins associated with oligopeptide transporters and vacuolar proteases than did other fungi. For rust fungi and anther smuts, these forms of convergence suggest four adaptive mechanisms for a phytoparasitic lifestyle: 1) reducing the metabolic demand for hyphal growth and penetration at the pre-penetration stage, 2) maintaining the efficiency of protein synthesis during colonization, 3) ensuring the normal secretion of rapidly evolving secreted proteins, and 4) improving the capacity for oligopeptide metabolism. Our results are the first to shed light on the genetic convergence mechanisms and molecular adaptation underlying phytoparasitic lifestyles in fungi.
An Evaluation Framework for Risk of Coastal Marine Ecological Diversity Loss From Land-Based Impacts
Authors: Hoel Paige , Fredston Alexa , Halpern Benjamin S.
Published: April 2022

Coastal environments globally are experiencing an increase in the influence and impact of human activities. Assessing the amount of modification that anthropogenic impacts cause to coastal ecosystems is imperative for characterizing and predicting habitat loss and degradation, and prioritizing conservation measures. However, as the spatial scale and data availability of coastal ecosystems vary immensely, many of the established practices on habitat risk assessment are applicable only to small scales and regions with extensive monitoring efforts. Traditional small-scale assessments also present a challenge when trying to prioritize remediation and resources over larger areas or regions. Here we show a simplified risk assessment framework, applied to a global scenario to rank the risk of loss of ecological diversity within ecoregions. Using established knowledge on sensitivities of mangroves, seagrasses, and stony corals, we create a weighted risk scoring system for each biogenic habitat. This risk score is combined with the species richness in a given ecoregion to create a priority ranking. We find that seagrass contains the largest area at severe risk of ecological diversity loss, followed by stony corals and mangroves. This work establishes a framework for assessing risk of loss of ecological diversity within ecoregions that can be used to rank the needs of the regions, from local scale applications to global scale as presented here, without extensive computing resources or exhaustive datasets.
New Assessment of Wave Energy in Relation to Geomorphological and Demographic Characteristics on the Pacific Coast of Baja California, Mexico
Authors: Ventura Yudisleyvis , Rodríguez Yandy , Odériz Itxaso , Chávez Valeria , Mori Nobuhito , Felix Angélica , Cerdeira-Estrada Sergio , Silva Rodolfo
Published: April 2022

The electrical grid of the Baja California peninsula, Mexico, operates separately from the National Interconnected System, with Baja California connected to the Western Electricity Coordinating Council of the USA; and Baja California Sur having an isolated, independent network. Based on the need for alternative renewable sources of electricity generation in the region, this work evaluates the wave energy power at specific locations on the Pacific coast of the peninsula, and identifies wave generation sites (WEGS). The WEGS were defined as rocky shore sites associated with a wave energy potential of over 10 kW/m (where the installation of oscillating water columns (OWC) is feasible) and the presence of coastal settlements that are less than 10 km from the shoreline. It was found that 370 km of the Pacific coast of the peninsula have characteristics suitable for the installation of OWC, and up to 1.4 million inhabitants could be benefited by this wave energy harvesting.
Predictability of 6 Intraocular Lens Power Calculation Formulas in People With Very High Myopia
Authors: Chu Yi-Ching , Huang Tzu-Lun , Chang Pei-Yao , Ho Wei-Ting , Hsu Yung-Ray , Chang Shu-Wen , Wang Jia-Kang
Published: April 2022

Purpose

To investigate the accuracy of 6 intraocular lens (IOL) power calculation formulas in predicting refractive outcomes in extremely long eyes.

Setting

Department of Ophthalmology, Far Eastern Memorial Hospital, Taiwan.

Design

Retrospective comparative study.

Methods

In this retrospective single-center study, we reviewed 70 eyes of 70 patients with axial length (AL) ≥ 28 mm who had received an uneventful 2.2 mm corneal wound phacoemulsification and in-the-bag IOL placement. The actual postoperative refractive results were compared to the predicted refraction calculated with 6 formulas (Haigis, Hoffer Q, Holladay 1, SRK/T, T2, Barrett Universal II formulas) using IOLMaster 500 as optical biometry in the User Group for Laser Interference Biometry (ULIB) constants.

Results

Overall, the Haigis and Barrett formulas achieved the lowest level of mean prediction error (PE) and median absolute error (MedAE). Hoffer Q, Holladay 1, SRK/T, and T2 had hyperopic prediction errors (p < 0.05). The Hoffer Q and Holladay 1 had significantly more MedAE between the 6 formulas. After the mean PE was zeroed out, the MedAE had no significant difference between each group. The absolute error tends to be larger in patients with longer AL. The absolute errors were 30.0–37.1% and 60.0–64.3% within 1.0 D of all patients compared to predicted refraction calculated using various formulas.

Conclusion

The Haigis and Barrett Universal II formulas had a better success rate in predicting IOL power in high myopic eyes with AL longer than 28 mm using the ULIB constant in this study. The postoperative refractive results were inferior to the benchmark standards, which indicated that the precision of IOL power calculation in patients with high myopia still required improvement.
Development of a Convolutional Neural Network-Based Colonoscopy Image Assessment Model for Differentiating Crohn’s Disease and Ulcerative Colitis
Authors: Wang Lijia , Chen Liping , Wang Xianyuan , Liu Kaiyuan , Li Ting , Yu Yue , Han Jian , Xing Shuai , Xu Jiaxin , Tian Dean , Seidler Ursula , Xiao Fang
Published: April 2022

Objective

Evaluation of the endoscopic features of Crohn’s disease (CD) and ulcerative colitis (UC) is the key diagnostic approach in distinguishing these two diseases. However, making diagnostic differentiation of endoscopic images requires precise interpretation by experienced clinicians, which remains a challenge to date. Therefore, this study aimed to establish a convolutional neural network (CNN)-based model to facilitate the diagnostic classification among CD, UC, and healthy controls based on colonoscopy images.

Methods

A total of 15,330 eligible colonoscopy images from 217 CD patients, 279 UC patients, and 100 healthy subjects recorded in the endoscopic database of Tongji Hospital were retrospectively collected. After selecting the ResNeXt-101 network, it was trained to classify endoscopic images either as CD, UC, or normal. We assessed its performance by comparing the per-image and per-patient parameters of the classification task with that of the six clinicians of different seniority.

Results

In per-image analysis, ResNeXt-101 achieved an overall accuracy of 92.04% for the three-category classification task, which was higher than that of the six clinicians (90.67, 78.33, 86.08, 73.66, 58.30, and 86.21%, respectively). ResNeXt-101 also showed higher differential diagnosis accuracy compared with the best performing clinician (CD 92.39 vs. 91.70%; UC 93.35 vs. 92.39%; normal 98.35 vs. 97.26%). In per-patient analysis, the overall accuracy of the CNN model was 90.91%, compared with 93.94, 78.79, 83.33, 59.09, 56.06, and 90.91% of the clinicians, respectively.

Conclusion

The ResNeXt-101 model, established in our study, performed superior to most clinicians in classifying the colonoscopy images as CD, UC, or healthy subjects, suggesting its potential applications in clinical settings.
Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs
Authors: Field Matt A.
Published: April 2022

Precision medicine programs to identify clinically relevant genetic variation have been revolutionized by access to increasingly affordable high-throughput sequencing technologies. A decade of continual drops in per-base sequencing costs means it is now feasible to sequence an individual patient genome and interrogate all classes of genetic variation for < $1,000 USD. However, while advances in these technologies have greatly simplified the ability to obtain patient sequence information, the timely analysis and interpretation of variant information remains a challenge for the rollout of large-scale precision medicine programs. This review will examine the challenges and potential solutions that exist in identifying predictive genetic biomarkers and pharmacogenetic variants in a patient and discuss the larger bioinformatic challenges likely to emerge in the future. It will examine how both software and hardware development are aiming to overcome issues in short read mapping, variant detection and variant interpretation. It will discuss the current state of the art for genetic disease and the remaining challenges to overcome for complex disease. Success across all types of disease will require novel statistical models and software in order to ensure precision medicine programs realize their full potential now and into the future.
ADC-Net: An Open-Source Deep Learning Network for Automated Dispersion Compensation in Optical Coherence Tomography
Authors: Ahmed Shaiban , Le David , Son Taeyoon , Adejumo Tobiloba , Ma Guangying , Yao Xincheng
Published: April 2022

Chromatic dispersion is a common problem to degrade the system resolution in optical coherence tomography (OCT). This study is to develop a deep learning network for automated dispersion compensation (ADC-Net) in OCT. The ADC-Net is based on a modified UNet architecture which employs an encoder-decoder pipeline. The input section encompasses partially compensated OCT B-scans with individual retinal layers optimized. Corresponding output is a fully compensated OCT B-scan with all retinal layers optimized. Two numeric parameters, i.e., peak signal to noise ratio (PSNR) and structural similarity index metric computed at multiple scales (MS-SSIM), were used for objective assessment of the ADC-Net performance and optimal values of 29.95 ± 2.52 dB and 0.97 ± 0.014 were obtained respectively. Comparative analysis of training models, including single, three, five, seven and nine input channels were implemented. The mode with five-input channels was observed to be optimal for ADC-Net training to achieve robust dispersion compensation in OCT.
Development of Alveolar Hemorrhage After Pfizer-BioNTech COVID-19 mRNA Vaccination in a Patient With Renal-Limited Anti-neutrophil Cytoplasmic Antibody-Associated Vasculitis: A Case Report
Authors: Nishioka Ken , Yamaguchi Shintaro , Yasuda Itaru , Yoshimoto Norifumi , Kojima Daiki , Kaneko Kenji , Aso Mitsuhiro , Nagasaka Tomoki , Yoshida Eriko , Uchiyama Kiyotaka , Tajima Takaya , Yoshino Jun , Yoshida Tadashi , Kanda Takeshi , Itoh Hiroshi
Published: April 2022

Since the coronavirus disease 2019 (COVID-19) pandemic continues and a new variant of the virus has emerged, the COVID-19 vaccination campaign has progressed. Rare but severe adverse outcomes of COVID-19 vaccination such as anaphylaxis and myocarditis have begun to be noticed. Of note, several cases of new-onset antineutrophil cytoplasmic antibody-associated vasculitis (AAV) after COVID-19 mRNA vaccination have been reported. However, relapse of AAV in remission has not been recognized enough as an adverse outcome of COVID-19 vaccination. We report, to our knowledge, a first case of renal-limited AAV in remission using every 6-month rituximab administration that relapsed with pulmonary hemorrhage, but not glomerulonephritis, following the first dose of the Pfizer-BioNTech COVID-19 vaccine. The patient received the COVID-19 vaccine more than 6 months after the last dose of rituximab according to the recommendations. However, his CD19+ B cell counts were found to be increased after admission, indicating that our case might have been prone to relapse after COVID-19 vaccination. Although our case cannot establish causality between AAV relapse and COVID-19 mRNA vaccination, a high level of clinical vigilance for relapse of AAV especially in patients undergoing rituximab maintenance therapy following COVID-19 vaccination should be maintained. Furthermore, elapsed time between rituximab administration and COVID-19 mRNA vaccination should be carefully adjusted based on AAV disease-activity.
A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World
Authors: Ghosh Dilip Kumar , Kokane Amol , Kokane Sunil , Mukherjee Krishanu , Tenzin Jigme , Surwase Datta , Deshmukh Dhanshree , Gubyad Mrugendra , Biswas Kajal Kumar
Published: April 2022

Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.
Healthy Vaginal Microbiota and Influence of Probiotics Across the Female Life Span
Authors: Lehtoranta Liisa , Ala-Jaakkola Reeta , Laitila Arja , Maukonen Johanna
Published: April 2022

Vaginal microbiota plays a central role in women’s health and reproduction. Vaginal microbiota is dynamic and shaped by hormonal shifts in each stage of a woman’s life from pre-puberty to postmenopause. Current research has mainly focused on vaginal bacterial and fungal members of the community and emphasized their role in disease. However, the impact of balanced vaginal microbiota on health and its interaction with the host is yet poorly understood. High abundance of vaginal lactobacilli is most strongly associated with health, but the concept of health may vary as vaginal dysbiosis may be asymptomatic. Furthermore, there is a lot of variation between ethnic groups in terms of dominating vaginal bacteria. Probiotic lactobacilli could be a safe and natural means to balance and maintain healthy vaginal microbiota. Research evidence is accumulating on their role in supporting women’s health throughout life. This review describes the current literature on vaginal microbiota, the major factors affecting its composition, and how the communities change in different life stages. Furthermore, we focused on reviewing available literature on probiotics and their impact on vaginal microbiota and health.
Marine Vertebrates Impact the Bacterial Community Composition and Food Webs of Antarctic Microbial Mats
Authors: Almela Pablo , Velázquez David , Rico Eugenio , Justel Ana , Quesada Antonio
Published: April 2022

The biological activity of marine vertebrates represents an input of nutrients for Antarctic terrestrial biota, with relevant consequences for the entire ecosystem. Even though microbial mats assemble most of the biological diversity of the non-marine Antarctica, the effects of the local macrofauna on these microecosystems remain understudied. Using 16S rRNA gene sequencing, 13C and 15N stable isotopes, and by characterizing the P and N-derived nutrient levels, we evaluated the effects of penguins and other marine vertebrates on four microbial mats located along the Antarctic Peninsula. Our results show that P concentrations, C/N and N/P ratios, and δ15N values of “penguin-impacted” microbial mats were significantly higher than values obtained for “macrofauna-free” sample. Nutrients derived from penguin colonies and other marine vertebrates altered the trophic interactions of communities within microbial mats, as well as the relative abundance and trophic position of meiofaunal groups. Twenty-nine bacterial families from eight different phyla significantly changed with the presence of penguins, with inorganic nitrogen (NH4+ and NO3–) and δ15N appearing as key factors in driving bacterial community composition. An apparent change in richness, diversity, and dominance of prokaryotes was also related to penguin-derived nutrients, affecting N utilization strategies of microbial mats and relating oligotrophic systems to communities with a higher metabolic versatility. The interdisciplinary approach of this study makes these results advance our understanding of interactions and composition of communities inhabiting microbial mats from Antarctica, revealing how they are deeply associated with marine animals.
Gut Microbiome Analyses of Wild Migratory Freshwater Fish (Megalobrama terminalis) Through Geographic Isolation
Authors: Liu Yaqiu , Li Yuefei , Li Jie , Zhou Qiong , Li Xinhui
Published: April 2022

Gut microbiome is considered as a critical role in host digestion and metabolic homeostasis. Nevertheless, the lack of knowledge concerning how the host-associated gut microbiome underpins the host metabolic capability and regulates digestive functions hinders the exploration of gut microbiome variation in diverse geographic population. In the present study, we selected the black Amur bream (Megalobrama terminalis) that inhabits southern China drainage with multiple geographic populations and relatively high digestive plasticity as a candidate to explore the potential effects of genetic variation and environmental discrepancy on fish gut microbiome. Here, high-throughput 16S rRNA gene sequencing was utilized to decipher the distinct composition and diversity of the entire gut microbiota in wild M. terminalis distributed throughout southern China. The results indicated that mainland (MY and XR) populations exhibited a higher alpha diversity than that of the Hainan Island (WS) population. Moreover, a clear taxon shift influenced by water temperature, salinity (SA), and gonadosomatic index (GSI) in the course of seasonal variation was observed in the gut bacterial community. Furthermore, geographic isolation and seasonal variation significantly impacted amino acid, lipid, and carbohydrate metabolism of the fish gut microbiome. Specifically, each geographic population that displayed its own unique regulation pattern of gut microbiome was recognized as a specific digestion strategy to enhance adaptive capability in the resident environment. Consequently, this discovery suggested that long-term geographic isolation leads to variant environmental factors and genotypes, which made a synergetic effect on the diversity of the gut microbiome in wild M. terminalis. In addition, the findings provide effective information for further exploring ecological fitness countermeasures in the fish population.
Transcriptomic Analysis of Resistant and Wild-Type Isolates Revealed Fludioxonil as a Candidate for Controlling the Emerging Isoprothiolane Resistant Populations of Magnaporthe oryzae
Authors: Wang Zuo-Qian , Meng Fan-Zhu , Yin Liang-Fen , Yin Wei-Xiao , Lv Liang , Yang Xiao-Lin , Chang Xiang-Qian , Zhang Shu , Luo Chao-Xi
Published: April 2022

The point mutation R343W in MoIRR, a putative Zn2Cys6 transcription factor, introduces isoprothiolane (IPT) resistance in Magnaporthe oryzae. However, the function of MoIRR has not been characterized. In this study, the function of MoIRR was investigated by subcellular localization observation, transcriptional autoactivation test, and transcriptomic analysis. As expected, GFP-tagged MoIRR was translocated in the nucleus, and its C-terminal could autonomously activate the expression of reporter genes HIS3 and α-galactosidase in absence of any prey proteins in Y2HGold, suggesting that MoIRR was a typical transcription factor. Transcriptomic analysis was then performed for resistant mutant 1a_mut (R343W), knockout transformant ΔMoIRR-1, and their parental wild-type isolate H08-1a. Upregulated genes in both 1a_mut and ΔMoIRR-1 were involved in fungicide resistance-related KEGG pathways, including the glycerophospholipid metabolism and Hog1 MAPK pathways. All MoIRR deficiency-related IPT-resistant strains exhibited increased susceptibility to fludioxonil (FLU) that was due to the upregulation of Hog1 MAPK pathway genes. The results indicated a correlation between FLU susceptibility and MoIRR deficiency-related IPT resistance in M. oryzae. Thus, using a mixture of IPT and FLU could be a strategy to manage the IPT-resistant populations of M. oryzae in rice fields.
Mechanism of the Curative Effect of Wen-Shen-Jian-Pi Prescription in the Treatment of Amyotrophic Lateral Sclerosis
Authors: Gong Fan , Zhu Wei , Liao Weilong , Wang Mingzhe , Zheng Xuanlu , Wang Chenghui , Liu Te , Pan Weidong
Published: April 2022

Objective

To study the mechanism of the effect of Wen-Shen-Jian-Pi (WSJP) prescription on an ALS model comprising mice knocked out for an encoding RNA editing, mice (AR2).

Methods

Twenty-four transgenic AR2 mice were randomly divided into a vehicle group, a low dose WSJP group (15 mg), a medium-dose WSJP group (30 mg), and a high-dose WSJP group (45 mg) (all n = 6 per group). In the treatment groups, the WSJP prescription was given once a day while the vehicle group was fed the same volume of water. The weekly changes in body weight, rotarod test, and grip strength were used to detect the changes in the AR2 and changes of the number of normal mitochondria, abnormal mitochondria, and autophagosomes in injured spinal cord cells were used to evaluate the pathogenetic effects of WSJP treatment.

Results

The WSJP-treated AR2 mice gained weight more quickly from 8 weeks, and showed active behavior and displayed significantly better constant rotarod scores and grip strengths during the experiment compared with those of the vehicle AR2 mice. The number of normal mitochondria in the WSJP-treated AR2 mice had significantly more normal mitochondria than the vehicle group, while the numbers of abnormal mitochondria and autophagosomes were greatly decreased compared with those in the vehicle group.

Conclusion

The WSJP prescription could delay the decline in motor function of ALS model mice by reducing the degeneration of neurons. The potential of WSJP to treat ALS should be assessed in a clinical trial.
Immunocytochemical Localization of Enzymes Involved in Dopamine, Serotonin, and Acetylcholine Synthesis in the Optic Neuropils and Neuroendocrine System of Eyestalks of Paralithodes camtschaticus
Authors: Kotsyuba Elena , Dyachuk Vyacheslav
Published: April 2022

Identifying the neurotransmitters secreted by specific neurons in crustacean eyestalks is crucial to understanding their physiological roles. Here, we combined immunocytochemistry with confocal microscopy and identified the neurotransmitters dopamine (DA), serotonin (5-HT), and acetylcholine (ACh) in the optic neuropils and X-organ sinus gland (XO-SG) complex of the eyestalks of Paralithodes camtschaticus (red king crab). The distribution of Ach neurons was studied by choline acetyltransferase (ChAT) immunohistochemistry and compared with that of DA neurons examined in the same or adjacent sections by tyrosine hydroxylase (TH) immunohistochemistry. We detected 5-HT, TH, and ChAT in columnar, amacrine, and tangential neurons in the optic neuropils and established the presence of immunoreactive fibers and neurons in the terminal medulla in the XO region of the lateral protocerebrum. Additionally, we detected ChAT and 5-HT in the endogenous cells of the SG of P. camtschaticus for the first time. Furthermore, localization of 5-HT- and ChAT-positive cells in the SG indicated that these neurotransmitters locally modulate the secretion of neurohormones that are synthesized in the XO. These findings establish the presence of several neurotransmitters in the XO-SG complex of P. camtschaticus.
COVID-19 Quarantine Impact on Wellbeing and Cognitive Functioning During a 10-Week High-Intensity Functional Training Program in Young University Students
Authors: Ballester-Ferrer Juan Arturo , Carbonell-Hernández Laura , Pastor Diego , Cervelló Eduardo
Published: April 2022

Physical exercise can improve cognitive functioning and wellbeing; however, the degree of change in either of these two variables seems to be related to the exercise intensity or type. Therefore, new physical training (PT) programs have been developed to increase exercise efficiency. One such example is high-intensity functional training (HIFT), which has proven to be a time-efficient and highly effective strategy to improve physical fitness. This study analyzed whether HIFT can affect reaction time (RT) and vitality, as well as positive and negative affect. Forty-two college students participated in the study, 21 in the experimental group and 21 in the control group. The experimental group completed 10 weeks of training, five of which were supervised, and the remainder consisted of online training during the COVID-19 quarantine. Participants were evaluated at the beginning, at the end of the 5 weeks of supervised training, and after the 5 weeks of online training. HIFT improved RT without changes in psychological wellbeing during the entire period of training supervised and online. Therefore, during the HIFT program, the quarantine situation did not adversely affect this population’s wellbeing, but it did negatively affect adherence to the training program.
Multiple Mechanistically Distinct Timescales of Neocortical Plasticity Occur During Habituation
Authors: Chaloner Francesca A. , Cooke Sam F.
Published: April 2022

Recognizing familiar but innocuous stimuli and suppressing behavioral response to those stimuli are critical steps in dedicating cognitive resources to significant elements of the environment. Recent work in the visual system has uncovered key neocortical mechanisms of this familiarity that emerges over days. Specifically, exposure to phase-reversing gratings of a specific orientation causes long-lasting stimulus-selective response potentiation (SRP) in layer 4 of mouse primary visual cortex (V1) as the animal’s behavioral responses are reduced through habituation. This plasticity and concomitant learning require the NMDA receptor and the activity of parvalbumin-expressing (PV+) inhibitory neurons. Changes over the course of seconds and minutes have been less well studied in this paradigm, so we have here characterized cortical plasticity occurring over seconds and minutes, as well as days, to identify separable forms of plasticity accompanying familiarity. In addition, we show evidence of interactions between plasticity over these different timescales and reveal key mechanistic differences. Layer 4 visual-evoked potentials (VEPs) are potentiated over days, and they are depressed over minutes, even though both forms of plasticity coincide with significant reductions in behavioral response. Adaptation, classically described as a progressive reduction in synaptic or neural activity, also occurs over the course of seconds, but appears mechanistically separable over a second as compared to tens of seconds. Interestingly, these short-term forms of adaptation are modulated by long-term familiarity, such that they occur for novel but not highly familiar stimuli. Genetic knock-down of NMDA receptors within V1 prevents all forms of plasticity while, importantly, the modulation of short-term adaptation by long-term familiarity is gated by PV+ interneurons. Our findings demonstrate that different timescales of adaptation/habituation have divergent but overlapping mechanisms, providing new insight into how the brain is modified by experience to encode familiarity.
Reinforcement Learning for Central Pattern Generation in Dynamical Recurrent Neural Networks
Authors: Yoder Jason A. , Anderson Cooper B. , Wang Cehong , Izquierdo Eduardo J.
Published: April 2022

Lifetime learning, or the change (or acquisition) of behaviors during a lifetime, based on experience, is a hallmark of living organisms. Multiple mechanisms may be involved, but biological neural circuits have repeatedly demonstrated a vital role in the learning process. These neural circuits are recurrent, dynamic, and non-linear and models of neural circuits employed in neuroscience and neuroethology tend to involve, accordingly, continuous-time, non-linear, and recurrently interconnected components. Currently, the main approach for finding configurations of dynamical recurrent neural networks that demonstrate behaviors of interest is using stochastic search techniques, such as evolutionary algorithms. In an evolutionary algorithm, these dynamic recurrent neural networks are evolved to perform the behavior over multiple generations, through selection, inheritance, and mutation, across a population of solutions. Although, these systems can be evolved to exhibit lifetime learning behavior, there are no explicit rules built into these dynamic recurrent neural networks that facilitate learning during their lifetime (e.g., reward signals). In this work, we examine a biologically plausible lifetime learning mechanism for dynamical recurrent neural networks. We focus on a recently proposed reinforcement learning mechanism inspired by neuromodulatory reward signals and ongoing fluctuations in synaptic strengths. Specifically, we extend one of the best-studied and most-commonly used dynamic recurrent neural networks to incorporate the reinforcement learning mechanism. First, we demonstrate that this extended dynamical system (model and learning mechanism) can autonomously learn to perform a central pattern generation task. Second, we compare the robustness and efficiency of the reinforcement learning rules in relation to two baseline models, a random walk and a hill-climbing walk through parameter space. Third, we systematically study the effect of the different meta-parameters of the learning mechanism on the behavioral learning performance. Finally, we report on preliminary results exploring the generality and scalability of this learning mechanism for dynamical neural networks as well as directions for future work.
Temporal Trends of Intravenous Thrombolysis Utilization in Acute Ischemic Stroke in a Prospective Cohort From 1998 to 2019: Modeling Based on Joinpoint Regression
Authors: Olavarría Verónica V. , Hoffmeister Lorena , Vidal Carolina , Brunser Alejandro M. , Hoppe Arnold , Lavados Pablo M.
Published: April 2022

Introduction

The frequency of intravenous thrombolysis (IVT) in acute ischemic stroke (AIS) is lower than it should be in several regions of the world. It is unclear what interventions can produce significant improvements in IVT utilization. We aimed to investigate the temporal trends in IVT in AIS and identify changes in time that could be associated with specific interventions.

Methods

We included patients with AIS who were admitted from January 1998 to December 2019 in our institution. To analyze trends in utilization and time points in which they changed, we performed a Joinpoint regression analysis. Interventions were assigned to a specific category according to the Behavior Change Wheel framework intervention function criteria.

Results

A total of 3,361 patients with AIS were admitted, among which 538 (16%) received IVT. There were 245 (45.5%) women, and the mean age and median National Institutes of Health Stroke Scale (NIHSS) scores were 68.5 (17.2) years and 8 (interquartile range, 4–15), respectively. Thrombolysis use significantly increased by an average annual 7.6% (95% CI, 5.1–10.2), with one Joinpoint in 2007. The annual percent changes were.45% from 1998 to 2007 and 9.57% from 2007 to 2019, concurring with the stroke code organization, the definition of door-to-needle times as an institutional performance measure quality indicator, and the extension of the therapeutic window.

Conclusions

The IVT rates consistently increased due to a continuous process of protocol changes and multiple interventions. The implementation of a complex multidisciplinary intervention such as the stroke code, as well as the definition of a hospital quality control metric, were associated with a significant change in this trend.
Altered Spontaneous Brain Activity Patterns in Children With Strabismic Amblyopia After Low-Frequency Repetitive Transcranial Magnetic Stimulation: A Resting-State Functional Magnetic Resonance Imaging Study
Authors: Wang Yi-Ning , Pan Yi-Cong , Shu Hui-Ye , Zhang Li-Juan , Li Qiu-Yu , Ge Qian-Min , Liang Rong-Bin , Shao Yi
Published: April 2022

Objective

Previous studies have demonstrated altered brain activity in strabismic amblyopia (SA). In this study, low-frequency repetitive transcranial magnetic stimulation (rTMS) was applied in children with strabismic amblyopia after they had undergone strabismus surgery. The effect of rTMS was investigated by measuring the changes of brain features using the amplitude of low-frequency fluctuation (ALFF).

Materials and Methods

In this study, 21 SA patients (12 males and 9 females) were recruited based on their age (7–13 years old), weight, and sex. They all had SA in their left eyes and they received rTMS treatment one month after strabismus surgery. Their vision before and after surgery were categorized as pre-rTMS (PRT) and post-rTMS (POT). All participants received rTMS treatment, underwent magnetic resonance imaging (MRI), and their data were analyzed using the repeated measures t-test. The team used correlation analysis to explore the relationship between logMAR visual acuity and ALFF.

Results

Pre- versus post-rTMS values of ALFF were significantly different within individuals. In the POT group, ALFF values were significantly decreased in the Angular_R (AR), Parietal_Inf_L (PIL), and Cingulum_Mid_R (CMR) while ALFF values were significantly increased in the Fusiform_R (FR) and Frontal_Inf_Orb_L(FIL) compared to the PRT stage.

Conclusion

Our data showed that ALFF recorded from some brain regions was changed significantly after rTMS in strabismic amblyopes. The results may infer the pathological basis of SA and demonstrate that visual function may be improved using rTMS in strabismic amblyopic patients.
Reduced Radial Peripapillary Capillary in Pathological Myopia Is Correlated With Visual Acuity
Authors: Ye Jie , Lin Jue , Shen Meixiao , Chen Wen , Zhang Riyan , Lu Fan , Shao Yilei
Published: April 2022

Purpose

To quantify the radial peripapillary capillary (RPC) density and the peripapillary retinal nerve fiber layer (pRNFL) thickness in pathological myopia and examine associations among these factors and best-corrected visual acuity (BCVA).

Methods

The cohort was composed of 41 eyes as control and 79 eyes with high myopia (59 simple high myopia, 20 pathological myopia). Optical coherence tomography angiography was done to obtain RPC density and pRNFL thickness, superficial retinal capillary plexus (SRCP), and deep retinal capillary plexus (DRCP) density. The axial length (AL) was measured. Correlations among BCVA, RPC density, pRNFL thickness, AL, and other parameters were determined.

Results

For pathological myopia, the densities of RPC, SRCP, and DRCP were significantly less than those of the control and simple high myopia groups (p ≤ 0.005). There was no statistical difference in pRNFL thickness between pathological myopia and simple high myopia (p = 0.063), whereas there was significant difference in global pRNFL thickness between pathological myopia and control (p = 0.008). The global RPC density showed the greatest area under the curve (AUC = 0.962, sensitivity = 94.74%, specificity = 90.00%, cutoff value = 47.8%) for pathological myopia, whereas the AUC of pRNFL thickness, SRCP, and DRCP were only 0.675, 0.824, and 0.865, respectively. The univariate and multiple linear regression models showed that RPC density, SRCP density, and AL were correlated with BCVA (All p < 0.05). In the final BCVA model with multiple generalized estimating equation analysis, AL, RPC density and interaction between RPC and AL were shown (all p < 0.03). For an eye with AL ≥ 27.94 mm, global RPC density was predicted to be less than 48.77% with a high risk of visual impairment.

Conclusion

Peripapillary alterations, both the decreasing RPC density and pRNFL thickness, occurred in pathological myopia compared with the control. The RPC density was associated with BCVA, and this relationship was affected by AL.
Complementary Use of Super-Resolution Imaging Modalities to Study the Nanoscale Architecture of Inhibitory Synapses
Authors: Gookin Sara E. , Taylor Matthew R. , Schwartz Samantha L. , Kennedy Matthew J. , Dell’Acqua Mark L. , Crosby Kevin C. , Smith Katharine R.
Published: April 2022

The nanoscale architecture of synapses has been investigated using multiple super-resolution methods, revealing a common modular structure for scaffolds, neurotransmitter receptors, and presynaptic proteins. This fundamental organization of proteins into subsynaptic domains (SSDs) is thought to be important for synaptic function and plasticity and common to many types of synapses. Using 3D super-resolution Structured Illumination Microscopy (3D-SIM), we recently showed that GABAergic inhibitory synapses exhibit this nanoscale organizational principle and are composed of SSDs of GABAA receptors (GABAARs), the inhibitory scaffold gephyrin, and the presynaptic active zone protein, RIM. Here, we have investigated the use of 3D-SIM and dSTORM to analyze the nanoscale architecture of the inhibitory synaptic adhesion molecule, neuroligin-2 (NL2). NL2 is a crucial mediator of inhibitory synapse formation and organization, associating with both GABAARs and gephyrin. However, the nanoscale sub-synaptic distribution NL2 remains unknown. We found that 3D-SIM and dSTORM provide complementary information regarding the distribution of NL2 at the inhibitory synapse, with NL2 forming nanoscale structures that have many similarities to gephyrin nanoscale architecture.
How Does the University Food Environment Impact Student Dietary Behaviors? A Systematic Review
Authors: Li Xingbo , Braakhuis Andrea , Li Zengning , Roy Rajshri
Published: April 2022

The food environment has been implicated in creating an obesogenic generation; and while previous research has focused on population-wide initiatives, the university population resides in a research gap. To explore detailed components of the university food environment and what shaped dietary behaviors, we retrieved literature from the following databases: ScienceDirect, Scopus, PubMed, Medline, and EMBASE. Eleven studies were identified for qualitative content analysis and study quality assessment identified most of the studies as of good quality (n 8) and some as of fair quality (n 3). The certainty of evidence remained at a low level for all (n 11) studies due to the cross-sectional, observational nature of studies. Three major themes emerged: (1) food environment, (2) student perceptions (SPs), and (3) dietary outcome (DO). In a university food environment, the taste of food was paramount for the food choices of students, followed by the availability of food and the price of food. When university students perceive and choose foods and beverages, they sometimes regard unhealthy foods and beverages as healthy options. The diet quality of university students is more susceptible to living arrangements and socioeconomic status, but higher salt, fat, and added sugar consumption generally resulted in poorer quality of diet on campus. Future research could use novel methods to explore a wider range and deeper level of students' dietary behavior determinants in university food environments.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42021283562.