bluuebunny/crossref_metadata_2025 huggingface dataset:
Chiller Fault Diagnosis Based on Automatic Machine Learning
Authors: Tian Chongyi , Wang Youyin , Ma Xin , Chen Zhuolun , Xue Huiyu
Published: October 2021

Intelligent diagnosis is an important means of ensuring the safe and stable operation of chillers driven by big data. To address the problems of input feature redundancy in intelligent diagnosis and reliance on human intervention in the selection of model parameters, a chiller fault diagnosis method was developed in this study based on automatic machine learning. Firstly, the improved max-relevance and min-redundancy algorithm was used to extract important feature information effectively and automatically from the training data. Then, the long short-term memory (LSTM) model was used to mine the temporal correlation between data, and the genetic algorithm was employed to train and optimize the model to obtain the optimal neural network architecture and hyperparameter configuration. Finally, a transient co-simulation platform for building chillers based on MATLAB as well as the Engineering Equation Solver was built, and the effectiveness of the proposed method was verified using a dynamic simulation dataset. The experimental results showed that, compared with traditional machine learning methods such as the recurrent neural network, back propagation neural network, and support vector machine methods, the proposed automatic machine learning algorithm based on LSTM provides significant performance improvement in cases of low fault severity and complex faults, verifying the effectiveness and superiority of this method.
The Influence of Different Light Wavelengths of Anthropogenic Light at Night on Nestling Development and the Timing of Post-fledge Movements in a Migratory Songbird
Authors: Bani Assadi Saeedeh , Fraser Kevin C.
Published: October 2021

Many different aspects of an animal’s lifecycle such as its behavior, patterns of hormone activity, and internal clock time, can be affected by anthropogenic light at night (ALAN). Exposing an organism to ALAN during its early life could also have an impact on its development. Since photoperiod can trigger or schedule the migration timing of long-distance migratory birds, there is great potential for anthropogenic light to interact with photoperiod to affect timing. However, very little has been investigated regarding the impacts of ALAN on post-hatching development and migration timing. We investigated the impact of ALAN during nestling development in a long-distance migratory songbird to determine the potential impact on the timing of post-breeding movements in the wild. We experimentally manipulated the light by using programmable lighting, in the nest boxes of free-living nestlings of purple martin (Progne subis) in Manitoba, Canada. We exposed two groups of developing nestlings, from hatch to fledge date, to green or white LED lights (5 lux) during the night. We also included a control group that experienced natural, ambient light at night. We found that some adults abandoned their nests shortly after starting the experiment (4 of 15 nests in the white light treatment). For the nests that remained active, nestlings exposed to the white light treatment had higher weights (at day 20 or 22), later fledge dates (1.54 ± 0.37, 95% CI 0.80–2.28), and later colony departure date (2.84 ± 1.00, 95% CI 0.88–4.81), than young of the control group. Moreover, nestlings of both white and green light groups had longer nesting duration than nestlings of the control group. This study demonstrates the impact of ALAN on the development of post-breeding movement timing in nestlings of wild migratory birds. However, our results also indicate that green light may have less of an impact as compared to white light.
Sex-Specific Routes to Independent Breeding in a Polygynous Cooperative Breeder
Authors: Josi Dario , Flury Jana M. , Reyes-Contreras Maria , Tanaka Hirokazu , Taborsky Michael , Frommen Joachim G.
Published: October 2021

How can individuals obtain a breeding position and what are the benefits associated with philopatry compared to dispersal? These questions are particularly intriguing in polygamous cooperative breeders, where dispersal strategies reflect major life history decisions, and routes to independent breeding may utterly differ between the sexes. We scrutinized sex-dependent life-history routes by investigating dispersal patterns, growth rates and mortality in a wild colony of the cooperatively breeding cichlidNeolamprologus savoryi. Our data reveal that female helpers typically obtain dominant breeding positions immediately after reaching sexual maturity, which is associated with strongly reduced growth. In contrast, males obtain breeder status only at twice the age of females. After reaching sexual maturity, males follow one of two strategies: (i) they may retain their subordinate status within the harem of a dominant male, which may provide protection against predators but involves costs by helping in territory maintenance, defence and brood care; or (ii) they may disperse and adopt a solitary status, which diminishes survival chances and apparently reflects a best-of-a-bad-job strategy, as there are no obvious compensating future fitness benefits associated with this pathway. Our study illustrates that sex-dependent life history strategies strongly relate to specific social structures and mating patterns, with important implications for growth rates, the age at which breeding status is obtained, and survival.
Male Barn Swallows Tolerate Nestling-Like Courtship Calls of Rival Males
Authors: Hasegawa Masaru
Published: October 2021

Animals often exhibit conspicuous, and sometimes curious, courtship traits, such as nestling-like courtship display in birds, though modern studies of nestling-like courtship display (and calls) are virtually lacking. An exception is previous experiments on the barn swallowHirundo rustica, demonstrating that females are equally attracted to playback of two structurally similar calls, nestling-like male courtship calls and nestling food-begging calls. The experiments support the sensory trap hypothesis, i.e., that male signals mimic nestling stimuli to exploit female parental care for nestlings. However, female attraction might not be the sole function of nestling-like traits, and males might also have a sensory bias toward nestling-like traits, in which males would be less aggressive toward characteristics typical of immature individuals. Here, I conducted playback experiments to study the function of nestling-like male courtship calls in the context of male–male interactions. Playback of male courtship songs induced frequent approaches by neighbouring males, while nestling-like male courtship calls or nestling food-begging calls induced fewer approaches, though male responses to the latter two vocalisations increased when approaching the nestling period. The observed pattern indicates that, by mimicking immature individuals, males attract intended signal receivers (i.e., females) while avoiding interference from eavesdroppers (i.e., neighbouring males). This unique function can explain why species with parental care exhibit immature-like behaviour.
Total Ecosystem Carbon Stocks of Mangroves in Lamu, Kenya; and Their Potential Contributions to the Climate Change Agenda in the Country
Authors: Kairo James , Mbatha Anthony , Murithi Martin M. , Mungai Fredrick
Published: October 2021

Mangroves are carbon-rich ecosystems found in tropical and subtropical areas around the world. However, they are threatened by a combination of natural and human-induced factors. When mangroves are lost or degraded, their co-benefits to human society are greatly diminished along with the ecosystem’s ability to sequester carbon. The current study assessed mangrove cover and cover change, as well as measuring carbon stocks and their emissions levels from the mangroves of Lamu County, Kenya. We sampled above-and below-ground carbon pools, including soil organic carbon (SOC), in 191 plots distributed throughout the study area. Lastly, we evaluated the economics of avoiding mangrove deforestation based on the carbon-offset market. The total carbon stock of mangroves in Lamu was estimated at 20 million Mg C, with an average density of 560.22 ± 79.79 Mg C ha–1. Southern swamps recorded significantly higher carbon densities (p < 0.05) than other mangrove management blocks in Lamu. At least 1,739 ha of mangroves in Lamu were lost between 1990 and 2019 due to anthropogenic activities, representing a decline of 60 ha yr–1. Total emissions from loss and degradation of mangroves in Lamu is estimated at 140.1 Mg C ha–1; which translates to 30,840.1 Mg CO2e yr–1. Assuming an offset price of US$10/Mg CO2e, the estimated costs of avoided emissions in Lamu is US$308,401 yr–1 plus other co-benefits such as fishery functions and shoreline protection. Mainstreaming mangroves and associated blue carbon ecosystems into national development and climate change agenda could accelerate Kenya’s achievements of both Sustainable Development Goals (SDGs) and the Paris Agreement.
Aspects of Molecular Genetics in Dromedary Camel
Authors: Piro Mohammed
Published: October 2021

Dromedary camels are unique in their morphological and physiological characteristics and are capable of providing milk and meat even under extreme environmental conditions. Like other species, the dromedary camel has also benefitted from the development of the molecular genetics to increase the knowledge about different aspect in camel genetics (genetic variation, molecular marker, parentage control, gene of interest, whole genome, dating…etc.). In this paper we review the different molecular genetic technics used in this particular species and future prospects. Dromedary genetic studies started in the end of the 1980s with phenotypic evaluation and the attempts to highlight the protein and biochemical diversity. In the 2000s, with the development of molecular markers such as microsatellites, genetic diversity of different types in several countries were estimated and microsatellites were also used for parentage control. In terms of genetic characterization, microsatellites revealed a defined global structure, differentiating East African and South Arabian dromedaries from North African, North Arabian, and South Asian individuals, respectively. Also, mitochondrialDNA sequence analysis of ancient DNA proved to be crucial in resolving domestication processes in dromedaries. Ancient and modern DNA revealed dynamics of domestication and cross-continental dispersion of the dromedary. Nuclear SNPs, single nucleotide polymorphisms changes that occur approximately each 1000 bps in the mammalian genome were also applied in some studies in dromedary. These markers are a very useful alternative to microsatellites and have been employed in some studies on genetic diversity and relevant phenotypic traits in livestock. Finally, thanks to the use of Next Generation Sequencing (NGS) the whole-genome assemblies of the dromedary (Camelus dromedarius) and a work to establish the organization of the dromedary genome at chromosome level were recently published.
A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins
Authors: Zhu Xianyou , He Xin , Kuang Linai , Chen Zhiping , Lancine Camara
Published: October 2021

Considering that traditional biological experiments are expensive and time consuming, it is important to develop effective computational models to infer potential essential proteins. In this manuscript, a novel collaborative filtering model-based method called CFMM was proposed, in which, an updated protein–domain interaction (PDI) network was constructed first by applying collaborative filtering algorithm on the original PDI network, and then, through integrating topological features of PDI networks with biological features of proteins, a calculative method was designed to infer potential essential proteins based on an improved PageRank algorithm. The novelties of CFMM lie in construction of an updated PDI network, application of the commodity-customer-based collaborative filtering algorithm, and introduction of the calculation method based on an improved PageRank algorithm, which ensured that CFMM can be applied to predict essential proteins without relying entirely on known protein–domain associations. Simulation results showed that CFMM can achieve reliable prediction accuracies of 92.16, 83.14, 71.37, 63.87, 55.84, and 52.43% in the top 1, 5, 10, 15, 20, and 25% predicted candidate key proteins based on the DIP database, which are remarkably higher than 14 competitive state-of-the-art predictive models as a whole, and in addition, CFMM can achieve satisfactory predictive performances based on different databases with various evaluation measurements, which further indicated that CFMM may be a useful tool for the identification of essential proteins in the future.
Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics
Authors: Miao He , Chen Song , Ding Renyu
Published: October 2021

Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.
DNA Methylation and Recurrent Pregnancy Loss: A Mysterious Compass?
Authors: Zhou Qi , Xiong Yunhe , Qu Bing , Bao Anyu , Zhang Yan
Published: October 2021

Recurrent pregnancy loss (RPL) is a common and severe pathological pregnancy, whose pathogenesis is not fully understood. With the development of epigenetics, the study of DNA methylation, provides a new perspective on the pathogenesis and therapy of RPL. The abnormal DNA methylation of imprinted genes, placenta-specific genes, immune-related genes and sperm DNA may, directly or indirectly, affect embryo implantation, growth and development, leading to the occurrence of RPL. In addition, the unique immune tolerogenic microenvironment formed at the maternal-fetal interface has an irreplaceable effect on the maintenance of pregnancy. In view of these, changes in the cellular components of the maternal-fetal immune microenvironment and the regulation of DNA methylation have attracted a lot of research interest. This review summarizes the research progress of DNA methylation involved in the occurrence of RPL and the regulation of the maternal-fetal immune microenvironment. The review provides insights into the personalized diagnosis and treatment of RPL.
IL-40: A New B Cell-Associated Cytokine Up-Regulated in Rheumatoid Arthritis Decreases Following the Rituximab Therapy and Correlates With Disease Activity, Autoantibodies, and NETosis
Authors: Navrátilová Adela , Andrés Cerezo Lucie , Hulejová Hana , Bečvář Viktor , Tomčík Michal , Komarc Martin , Veigl David , Tegzová Dana , Závada Jakub , Olejárová Marta , Pavelka Karel , Vencovský Jiří , Šenolt Ladislav
Published: October 2021

Background

Interleukin 40 (IL-40) is a newly identified B cell-associated cytokine implicated in humoral immune responses and B cell homeostasis. As B cells play a pivotal role in autoimmunity, we investigated the function of IL-40 in rheumatoid arthritis (RA).

Methods

IL-40 expression was determined in the synovial tissue from RA and osteoarthritis (OA) patients. IL-40 was analysed in the serum/synovial fluid of patients with RA (n=50), systemic lupus erythematosus (SLE, n=69), OA (n=44), and healthy controls (HC, n=50). We assessed the changes of IL-40 levels in RA patients following the B cell depletion by rituximab (n=29) or after the TNF inhibition by adalimumab (n=25). We examined the relationship between IL-40, disease activity, autoantibodies, cytokines, and NETosis markers. Effect of IL-40 on synovial fibroblasts was determined.

Results

IL-40 was overexpressed in RA synovial tissue, particularly by synovial lining and infiltrating immune cells. The levels of IL-40 were up-regulated in the synovial fluid of RA versus OA patients (p<0.0001). Similarly, IL-40 was increased in the serum of RA patients compared to HC, OA, or SLE (p<0.0001 for all) and decreased after 16 and 24 weeks (p<0.01 and p<0.01) following rituximab treatment. No significant effect of adalimumab on IL-40 was observed. IL-40 levels in RA patients correlated with rheumatoid factor-IgM and anti-cyclic citrullinated peptides (anti-CCP) in the serum (p<0.0001 and p<0.01), as well as in the synovial fluid (p<0.0001 and p<0.001). Synovial fluid IL-40 was also associated with disease activity score DAS28 (p<0.05), synovial fluid leukocyte count (p<0.01), neutrophil attractants IL-8 (p<0.01), MIP-1α (p<0.01), and markers of neutrophil extracellular traps externalization (NETosis) such as proteinase 3 (p<0.0001) and neutrophil elastase (p<0.0001). Synovial fibroblasts exposed to IL-40 increased the secretion of IL-8 (p<0.01), MCP-1 (p<0.05), and MMP-13 (p<0.01) compared to the unstimulated cells.

Conclusions

We show the up-regulation of IL-40 in RA and its decrease following B cell depleting therapy. The association of IL-40 with autoantibodies, chemokines, and markers of NETosis may imply its potential involvement in RA development. Moreover, IL-40 up-regulates the secretion of chemokines and MMP-13 in synovial fibroblasts, indicating its role in the regulation of inflammation and tissue destruction in RA.
Downregulation of Renal Hsa-miR-127-3p Contributes to the Overactivation of Type I Interferon Signaling Pathway in the Kidney of Lupus Nephritis
Authors: Wu Lingling , Han Xiao , Jiang Xiaoyue , Ding Huihua , Qi Chaojun , Yin Zhihua , Xiao Jianwei , Xiong Le , Guo Qiang , Ye Zhizhong , Qu Bo , Shen Nan
Published: October 2021

MicroRNAs are involved in the pathogenesis of systemic lupus erythematosus (SLE) and dysregulated in the kidneys of lupus nephritis (LN) patients, but their pathogenic roles in LN are largely unknown. Janus Kinase 1 (JAK1) mediates the activation of the downstream signaling pathways of many inflammatory cytokines, including type I interferon (IFN-I) signaling pathway which is critical to the development of SLE and LN. Thus, JAK1 is a potent therapeutic target for these autoimmune diseases. However, there are few studies demonstrating the dysregulation of JAK1 in autoimmune diseases and the molecular mechanism behind it. In this concise report, we show an inhibitory effect of hsa-miR-127-3p, a microRNA that is downregulated in the renal tissues of LN patients, on IFN-I signaling. We found the overexpression of hsa-miR-127-3p could inhibit the induction of ISRE and GAS mediated gene expression, the phosphorylation of STAT1 and STAT2, and the upregulation of IFN stimulated genes (ISGs) stimulated by IFN-I. While, hsa-miR-127-3p antagonist enhanced the activation of IFN-I signaling in primary renal mesangial cells. Subsequently, we identified JAK1 as a bona fide target gene of hsa-miR-127-3p and showed hsa-miR-127-3p targeted JAK1 through binding to its 3’UTR and coding region. Consistently, we found the downregulation of hsa-miR-127-3p was associated with the upregulation of JAK1 and ISGs in kidney tissues of LN patients. Our data indicate renal downregulation of hsa-miR-127-3p contributes to the overactivation of IFN-I signaling pathway in the kidneys of LN patients through promoting the expression of JAK1, suggesting hsa-miR-127-3p mimics may be used to inhibit JAK1 and IFN-I signaling pathway in LN.
Anti-Phosphatidylserine/Prothrombin Antibodies at Two Points: Correlation With Lupus Anticoagulant and Thrombotic Risk
Authors: Egri Natalia , Bentow Chelsea , Rubio Laura , Norman Gary L. , López-Sañudo Susana , Mahler Michael , Pérez-Isidro Albert , Cervera Ricard , Viñas Odette , Espinosa Gerard , Ruiz-Ortiz Estíbaliz
Published: October 2021

Antibodies to phospholipids (aPL) and associated proteins are a hallmark in the diagnosis of anti-phospholipid syndrome (APS). Those included in the classification criteria are the lupus anticoagulant (LA) and the IgG and IgM isotypes of anticardiolipin (aCL) and anti-beta-2 glycoprotein I (β2GPI) antibodies. Non-classification criteria markers such as autoantibodies that recognize the phosphatidylserine/prothrombin (aPS/PT) complex have been proposed as biomarkers for APS. Studies of aPS/PT antibodies have shown a strong correlation to clinical manifestations and LA. We aimed to study the value and the persistence of aPS/PT IgG and IgM antibodies in a cohort of consecutive patients with clinical suspicion of APS and their utility as thrombotic risk markers. Our study, with 103 patients, demonstrates that persistently positive results for aPS/PT IgG antibodies were significantly associated with APS classification, thrombosis, triple aPL positivity, LA positive result, and the Global APS Score (GAPSS) > than 9 points (p < 0.01, for each condition). On the other hand, no association was seen with pregnancy morbidity (p = 0.56) and SLE (p = 0.07). Persistence of aPS/PT antibodies, defined according to the current laboratory classification criteria, likely improves the diagnosis and clinical assessment of patients with APS.
Dietary Filamentous Fungi and Duration of Feeding Modulates Gut Microbial Composition in Rainbow Trout (Oncorhynchus mykiss)
Authors: Singh Aprajita , Karimi Sajjad , Vidakovic Aleksandar , Dicksved Johan , Langeland Markus , Ferreira Jorge A. , Taherzadeh Mohammad J. , Kiessling Anders , Lundh Torbjörn
Published: October 2021

Changes in gut microbial composition over time in rainbow trout fed differentially processed diets supplemented with the filamentous fungi Neurospora intermedia were investigated in a 30-day feeding trial. Fish were fed a reference diet, non-preconditioned diet (NPD), or preconditioned (heat-treated) diet (PD), with the same inclusion level of N. intermedia in diets NPD and PD. Gut microbiota were analyzed on day 0, 10, 20, and 30. Gut microbial composition was similar for all diets on day 0, but was significantly different at day 10 and day 20. On day 30, the gut again contained similar communities irrespective of diet. The overall gut microbiota for each diet changed over time. Abundance of Peptostreptococcus and Streptococcus was higher in the initial days of feeding in fish fed on commercial diet, while a significant increase in lactic acid bacteria (Lactococcus lactis) was observed on day 30. Feed processing (preconditioning) did not contribute largely in shaping the gut microbiome. These results indicate that dietary manipulation and duration of feeding should be considered when evaluating gut microbial composition in cultured fish. A minimum 30-day feeding trial is suggested for gut microbiome, host and diet interaction studies.
Relationship of Motility Activation to Lipid Composition, Protein Profile, and Swelling Rate of Burbot Lota lota Spermatozoon Following Change of Temperature and Osmolality
Authors: Dadras Hadiseh , Policar Tomas , Loginov Dmitry , Boryshpolets Sergii , Loginova Yana , Sampels Sabine , Sotnikov Anatolii , Kholodnyy Vitaliy , Sterba Jan , Xin Miaomiao , Dzyuba Borys
Published: October 2021

Despite available information on the roles of osmotic pressure, potassium (K+), and calcium (Ca2+) in activation of Eurasian burbot spermatozoon motility, the changes in milt biochemical composition and mechanisms underlying their activation at temperatures above optimal spawning temperature is still unclear. We explored spermatozoon swelling, lipid composition and proteome in relation to osmolality and temperature of swimming medium. The result revealed that temperature increment from 4 to 30°C increases burbot spermatozoa vulnerability to osmotic pressure, decreasing motility in extremely hypotonic media, and the presence of Ca2+decreases swelling of spermatozoa. No spermatozoon swelling was observed in non-ionic isotonic media at all studied temperatures. A role of swelling in activation of spermatozoa motility at 30°C was rejected. No differences were found in protein profile and lipid composition with respect to activation of burbot spermatozoa at 30°C. Burbot spermatozoon activation occurs at 30°C without modification of the spermatozoon membrane. Elucidation of the intrinsic signaling pathway of burbot spermatozoon spontaneous activation requires further study.
Effects of Low Temperature on Shrimp and Crab Physiology, Behavior, and Growth: A Review
Authors: Ren Xianyun , Wang Qiong , Shao Huixin , Xu Yao , Liu Ping , Li Jian
Published: October 2021

As important aquaculture species worldwide, shrimps and crabs are thermophilic animals with a feeble thermoregulation ability. Changes in environmental factors are the main reason for the decrease in the immunity and disease resistance ability of cultured organisms. Water temperature is one of the most common abiotic stress factors for aquatic ectotherms. It influences nearly all biochemical and physiological processes in crustaceans, resulting in an imbalance in ion and water homeostasis, neuromuscular function loss, cellular dehydration, and altered metabolic pathways. The present review summarizes the current knowledge on the effects of low temperature on the physiological response, and the behavior, development, and growth of shrimp and crab. We suggest a deeper research to understand the physiological processes involved in thermoregulation; this knowledge could be used to reduce the adverse effects in the shrimps and crabs during the culture.
Temporal Variability of Thermohaline Fine-Structure Associated With the Subtropical Front Off the Southeast Coast of New Zealand in High-Frequency Short-Streamer Multi-Channel Seismic Data
Authors: Cooper Joanna K. , Gorman Andrew R. , Bowman M. Hamish , Smith Robert O.
Published: October 2021

Seismic oceanography generally makes use of multi-channel seismic reflection data sourced by air gun arrays and long hydrophone streamers to image oceanographic water masses and processes—often piggybacking on surveys that target deeper geological features below the seafloor. However, due to the acquisition methods employed, shallow (upper 200 m or so) regions of the ocean can be poorly imaged with this technique, and resolution is often lower than desirable for imaging fine-structure within the water column. In 2012, we collected a set of higher-resolution seismic lines off the southeast coast of New Zealand, with a generator-injector airgun source and hydrophone streamer configuration designed to improve images of shallower water masses and their boundaries. The seismic lines were acquired with coincident expendable bathythermograph deployments which provides direct ties between physical oceanographic data and seismic data, allowing for definitive identification of the Subtropical Front and associated water masses in the subsurface. Repeat acquisition along the same transect shows significant temporal variability on the scale of hours, illustrating the highly dynamic nature of this important ocean boundary. Comparisons to conventional low-frequency seismic data in the same location show the value of high-resolution acquisition methods in imaging the near-surface of the ocean and allowing subsurface features to be linked to their expressions at the surface.
Environmental Factors and Genetic Diversity as Drivers of Early Gonadal Maturation: A Gonadosomatic Index Based Investigation on Indian Shad, Tenualosa ilisha Population of Bangladesh
Authors: Ahammad A. K. Shakur , Hasan Neaz A. , Haque Mohammad Mahfujul , Bashar Abul , Ahmed Md. Borhan Uddin , Alam Mohammad Ashraful , Asaduzzaman Md. , Bashar Md. Abul , Mahmud Yahia
Published: October 2021

In recent years, attaining gonadal maturation in smaller Hilsa (Tenualosa ilisha) has become a burning issue for Hilsa fishery of Bangladesh. Causes of early maturation are not yet clearly understood. Along with environmental parameters, genetic differentiation within the population was hypothesized as the main driver, and therefore, assessing the correlation between gonadosomatic index (GSI) and environmental factors and analyzing genetic diversity were set as objectives of the present study. To address these complex issues, six diverse habitats across Bangladesh were chosen for Hilsa sample collection. For GSI, gonad was dissected from fresh fish and preserved in Bouin’s fluid for histological observation. Water quality parameters such as temperature, dissolved oxygen, pH, and salinity were also assessed. 35 fish from each habitat were used to extract and amplify DNA through the PCR technique, and genetic diversity was examined. Further, to draw a firm conclusion, the phylogenetic tree of the Hilsa population was developed by the unweighted pair-group method of arithmetic mean method based on the Cyt b gene of mitochondrial DNA. Results of GSI studies revealed that peak spawning months of T. ilisha were in October and February, where October showed the highest values in all six habitats. Histological examination showed different stages of gonadal development in different sizes and ages of Hilsa. Among all sampling sites, no statistical difference was observed for GSI value; however, smaller sized and aged Hilsa being ripped were evident in Gaglajur Haor and Kali River. Among the observed water quality parameters, temperature correlated with GSI strongly. Increased GSI was observed with temperature augmentation from downstream to upper stream, irrespective of body size and age. A perplex correlation between dissolved oxygen of observed habitats and GSI was executed. Other physico-chemical parameters viz. pH and salinity exhibited weak and moderate positive association with the GSI, respectively. Haplotype diversity of mitochondrial DNA divided the Hilsa population into three possible sub-populations, where the most distant group (Gaglajur Haor and Kali River) was subjected to early gonadal maturity. Results of this study make clear conclusions regarding the role of environmental and genetic factors on early gonadal maturations, pointing fingers at the curse of climate change and anthropogenic stressors for the migration of the Hilsa fishery of Bangladesh.
CRISPR/Cas9 System-Mediated Gene Editing in the Fujian Oysters (Crassostrea angulate) by Electroporation
Authors: Jin Kaidi , Zhang Baolu , Jin Qianqian , Cai Zhongqiang , Wei Lei , Wang Xiaomei , Zheng Yanxin , Huang Baoyu , Zhang Meiwei , Qi Yitao , Liu Yaqiong , Wang Xiaotong
Published: October 2021

The Fujian oyster (Crassostrea angulate) is an important marine bivalve mollusk with high economic value. Gene function research and gene editing techniques have broad application prospects in oyster. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been widely used for genome engineering in many species. CRISPR-mediated gene editing has also been used successfully in the Pacific oyster through direct delivery of the CRISPR/Cas9 components into oyster embryos by microinjection. However, the low throughput and operational difficulties associated with microinjection is one of the factors limiting the widespread application of CRISPR/Cas9 in oysters. In this study, we attempted to deliver the CRISPR/Cas9-system into the embryos of C. angulate by electroporation. An all-in-one CRISPR/Cas9 vector plasmid was used as CRISPR/Cas9 system in this study. Electroporation was carried out using both eggs and blastula larvae. A large number of larvae became malformed or die after electroporation. A single base substitution mutation was detected in the D-larvae developed from electroporated eggs. Our results demonstrate that the CRISPR/Cas9 system can be delivered into embryos of C. angulate for gene editing by electroporation, which provides a reference and will further contribute to the future application of electroporation in mollusks.
Implications of Isolated Para-Aortic Lymph Node Metastasis in Endometrial Cancer: A Large-Scale, Multicenter, and Retrospective Study
Authors: Li Wenting , Jiang Jie , Fu Yu , Shen Yuanming , Zhang Chuyao , Yao Shuzhong , Xu Congjian , Xia Min , Lou Ge , Liu Jihong , Lin Bei , Wang Jianliu , Zhao Weidong , Zhang Jieqing , Cheng Wenjun , Guo Hongyan , Guo Ruixia , Xue Fengxia , Wang Xipeng , Han Lili , Zhao Xia , Li Xiaomao , Zhang Ping , Zhao Jianguo , Ma Jiezhi , Yao Qin , Yang Xiaohang , Dou Yingyu , Wang Zizhuo , Liu Jingbo , Fang Yong , Li Kezhen , Wang Beibei , Chen Gang , Cheng Xiaodong , Sun Chaoyang , Kong Beihua
Published: October 2021

Objective: To systematically evaluate lymph node metastasis (LNM) patterns in patients with endometrial cancer (EC) who underwent complete surgical staging, which included systematic pelvic and para-aortic lymphadenectomy.

Methods: Four thousand and one patients who underwent complete surgical staging including systematic pelvic and para-aortic lymphadenectomy for EC were enrolled from 30 centers in China from 2001 to 2019. We systematically displayed the clinical and prognostic characteristics of patients with various LNM patterns, especially the PLN-PAN+ [para-aortic lymph node (PAN) metastasis without pelvic lymph node (PLN) metastasis]. The efficacy of PAN+ (para-aortic lymph node metastasis) prediction with clinical and pathological features was evaluated.

Results: Overall, 431 of the 4,001 patients (10.8%) showed definite LNM according to pathological diagnosis. The PAN+ showed the highest frequency (6.6%) among all metastatic sites. One hundred fourteen cases (26.5%) were PLN-PAN+ (PAN metastasis without PLN metastasis), 167 cases (38.7%) showed PLN+PAN-(PLN metastasis without PAN metastasis), and 150 cases (34.8%) showed metastasis to both regions (PLN+PAN+). There was also 1.9% (51/2,660) of low-risk patients who had PLN-PAN+. There are no statistical differences in relapse-free survival (RFS) and disease-specific survival (DSS) among PLN+PAN-, PLN-PAN+, and PLN+PAN+. The sensitivity of gross PLNs, gross PANs, and lymphovascular space involvement (LVSI) to predict PAN+ was 53.8 [95% confidence interval (CI): 47.6–59.9], 74.2 95% CI: 65.6–81.4), and 45.8% (95% CI: 38.7–53.2), respectively.

Conclusion: Over one-fourth of EC patients with LMN metastases were PLN-PAN+. PLN-PAN+ shares approximate survival outcomes (RFS and DSS) with other LNM patterns. No effective clinical methods were achieved for predicting PAN+. Thus, PLN-PAN+ is a non-negligible LNM pattern that cannot be underestimated in EC, even in low-risk patients.
Current and Future Perspectives on the Role of Probiotics, Prebiotics, and Synbiotics in Controlling Pathogenic Cronobacter Spp. in Infants
Authors: Ke Alfred , Parreira Valeria R. , Goodridge Lawrence , Farber Jeffrey M.
Published: October 2021

Cronobacter species, in particular C. sakazakii, is an opportunistic bacterial pathogen implicated in the development of potentially debilitating illnesses in infants (<12months old). The combination of a poorly developed immune system and gut microbiota put infants at a higher risk of infection compared to other age groups. Probiotics and prebiotics are incorporated in powdered infant formula and, in addition to strengthening gut physiology and stimulating the growth of commensal gut microbiota, have proven antimicrobial capabilities. Postbiotics in the cell-free supernatant of a microbial culture are derived from probiotics and can also exert health benefits. Synbiotics, a mixture of probiotics and prebiotics, may provide further advantages as probiotics and gut commensals degrade prebiotics into short-chain fatty acids that can provide benefits to the host. Cell-culture and animal models have been widely used to study foodborne pathogens, but sophisticated gut models have been recently developed to better mimic the gut conditions, thus giving a more accurate representation of how various treatments can affect the survival and pathogenicity of foodborne pathogens. This review aims to summarize the current understanding on the connection between Cronobacter infections and infants, as well as highlight the potential efficacy of probiotics, prebiotics, and synbiotics in reducing invasive Cronobacter infections during early infancy.
Functions of the Essential Gene mraY in Cellular Morphogenesis and Development of the Filamentous Cyanobacterium Anabaena PCC 7120
Authors: Liu Jing , Xing Wei-Yue , Zhang Ju-Yuan , Zeng Xiaoli , Yang Yiling , Zhang Cheng-Cai
Published: October 2021

Bacterial cell shape is determined by the peptidoglycan (PG) layer. The cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a filamentous strain with ovoid-shaped cells connected together with incomplete cell constriction. When deprived of combined nitrogen in the growth medium, about 5–10% of the cells differentiate into heterocysts, cells devoted to nitrogen fixation. It has been shown that PG synthesis is modulated during heterocyst development and some penicillin-binding proteins (PBPs) participating in PG synthesis are required for heterocyst morphogenesis or functioning. Anabaena has multiple PBPs with functional redundancy. In this study, in order to examine the function of PG synthesis and its relationship with heterocyst development, we created a conditional mutant of mraY, a gene necessary for the synthesis of the PG precursor, lipid I. We show that mraY is required for cell and filament integrity. Furthermore, when mraY expression was being limited, persistent septal PG synthetic activity was observed, resulting in increase in cell width. Under non-permissive conditions, filaments and cells were rapidly lysed, and no sign of heterocyst development within the time window allowed was detected after nitrogen starvation. When mraY expression was being limited, a high percentage of heterocyst doublets were found. These doublets are formed likely as a consequence of delayed cell division and persistent septal PG synthesis. MraY interacts with components of both the elongasome and the divisome, in particular those directly involved in PG synthesis, including HetF, which is required for both cell division and heterocyst formation.
Biomolecular Perturbations in In-Cell Dynamic Nuclear Polarization Experiments
Authors: Overall Sarah A. , Barnes Alexander B.
Published: October 2021

In-cell DNP is a growing application of NMR to the study of biomolecular structure and function within intact cells. An important unresolved question for in-cell DNP spectroscopy is the integrity of cellular samples under the cryogenic conditions of DNP. Despite the rich literature around cryopreservation of cells in the fields of stem cell/embryonic cell therapeutics, cell line preservation and in cryo-EM applications, the effect of cryopreservation procedures on DNP parameters is unclear. In this report we investigate cell survival and apoptosis in the presence of cryopreserving agents and DNP radicals. We also assess the effects of these reagents on cellular enhancements. We show that the DNP radical AMUPol has no effect on membrane permeability and does not induce apoptosis. Furthermore, the standard aqueous glass forming reagent, comprised of 60/30/10 d8-glycerol/D2O/H2O (DNP juice), rapidly dehydrates cells and induces apoptosis prior to freezing, reducing structural integrity of the sample prior to DNP analysis. Preservation with d6-DMSO at 10% v/v provided similar DNP enhancements per √unit time compared to glycerol preservation with superior maintenance of cell size and membrane integrity prior to freezing. DMSO preservation also greatly enhanced post-thaw survival of cells slow-frozen at 1°C/min. We therefore demonstrate that in-cell DNP-NMR studies should be done with d6-DMSO as cryoprotectant and raise important considerations for the progression of in-cell DNP-NMR towards the goal of high quality structural studies.
Which Is the Best In Silico Program for the Missense Variations in IDUA Gene? A Comparison of 33 Programs Plus a Conservation Score and Evaluation of 586 Missense Variants
Authors: Borges Pâmella , Pasqualim Gabriela , Matte Ursula
Published: October 2021

Mucopolysaccharidosis type I (MPS I) is an autosomal recessive disease characterized by the deficiency of alpha-L-iduronidase (IDUA), an enzyme involved in glycosaminoglycan degradation. More than 200 disease-causing variants have been reported and characterized in the IDUA gene. It also has several variants of unknown significance (VUS) and literature conflicting interpretations of pathogenicity. This study evaluated 586 variants obtained from the literature review, five population databases, in addition to dbSNP, Human Genome Mutation Database (HGMD), and ClinVar. For the variants described in the literature, two datasets were created based on the strength of the criteria. The stricter criteria subset had 108 variants with expression study, analysis of healthy controls, and/or complete gene sequence. The less stringent criteria subset had additional 52 variants found in the literature review, HGMD or ClinVar, and dbSNP with an allele frequency higher than 0.001. The other 426 variants were considered VUS. The two strength criteria datasets were used to evaluate 33 programs plus a conservation score. BayesDel (addAF and noAF), PON-P2 (genome and protein), and ClinPred algorithms showed the best sensitivity, specificity, accuracy, and kappa value for both criteria subsets. The VUS were evaluated with these five algorithms. Based on the results, 122 variants had total consensus among the five predictors, with 57 classified as predicted deleterious and 65 as predicted neutral. For variants not included in PON-P2, 88 variants were considered deleterious and 92 neutral by all other predictors. The remaining 124 did not obtain a consensus among predictors.
Lack of Parkinsonian Pathology and Neurodegeneration in Mice After Long-Term Injections of a Proteasome Inhibitor in Olfactory Bulb and Amygdala
Authors: del Rey Natalia Lopez-Gonzalez , Balzano Tiziano , Martin-Rodriguez Lucia , Salinas-Rebolledo Constanza , Trigo-Damas Ines , Rojas-Fernandez Alejandro , Alvarez-Erviti Lydia , Blesa Javier
Published: October 2021

Proteinaceous inclusions, called Lewy bodies (LBs), are used as a pathological hallmark for Parkinson’s disease (PD). Recent studies suggested a prion-like spreading mechanism for α-synucleinopathy where early neuropathological deposits occur, among others, in the olfactory bulb (OB) and amygdala. LBs contain insoluble α-synuclein and many other ubiquitinated proteins, suggesting a role of protein degradation system failure in PD pathogenesis. Therefore, we wanted to study the effects of a proteasomal inhibitor, lactacystin, on the aggregability and transmissibility of α-synuclein in the OB and amygdala. We performed injections of lactacystin in the OB and amygdala of wild-type mice. Motor behavior, markers of neuroinflammation, α-synuclein, and dopaminergic integrity were assessed by immunohistochemistry. Overall, there were no differences in the number of neurons and α-synuclein expression in these regions following injection of lactacystin into either the OB or amygdala. Microglial and astroglial labeling appeared to be correlated with surgery-induced inflammation or local effects of lactacystin. Consistent with the behavior and pathological findings, there was no loss of dopaminergic cell bodies in the substantia nigra and terminals in the striatum. Our data showed that long-term lactacystin injections in extra nigrostriatal regions may not mimic spreading aspects of PD and reinforce the special vulnerability of dopaminergic neurons of the substantia nigra pars compacta (SNc).
Working Memory Training and Cortical Arousal in Healthy Older Adults: A Resting-State EEG Pilot Study
Authors: Spironelli Chiara , Borella Erika
Published: October 2021

The current pilot study aimed to test the gains of working memory (WM) training, both at the short- and long-term, at a behavioral level, and by examining the electrophysiological changes induced by training in resting-state EEG activity among older adults. The study group included 24 older adults (from 64 to 75 years old) who were randomly assigned to a training group (TG) or an active control group (ACG) in a double-blind, repeated-measures experimental design in which open eyes, resting-state EEG recording, followed by a WM task, i.e., the Categorization Working Memory Span (CWMS) task, were collected before and after training, as well as at a 6-month follow-up session. At the behavioral level, medium to large Cohen's d effect sizes was found for the TG in immediate and long-term gains in the WM criterion task, as compared with small gains for the ACG. Regarding intrusion errors committed in the CWMS, an index of inhibitory control representing a transfer effect, results showed that medium to large effect sizes for immediate and long-term gains emerged for the TG, as compared to small effect sizes for the ACG. Spontaneous high-beta/alpha ratio analyses in four regions of interest (ROIs) revealed no pre-training group differences. Significantly greater TG anterior rates, particularly in the left ROI, were found after training, with frontal oscillatory responses being correlated with better post-training CWMS performance in only the TG. The follow-up analysis showed similar results, with greater anterior left high-beta/alpha rates among TG participants. Follow-up frontal high-beta/alpha rates in the right ROI were correlated with lower CWMS follow-up intrusion errors in only the TG. The present findings are further evidence of the efficacy of WM training in enhancing the cognitive functioning of older adults and their frontal oscillatory activity. Overall, these results suggested that WM training also can be a promising approach toward fostering the so-called functional cortical plasticity in aging.
Contributions of Luminance and Motion to Visual Escape and Habituation in Larval Zebrafish
Authors: Mancienne Tessa , Marquez-Legorreta Emmanuel , Wilde Maya , Piber Marielle , Favre-Bulle Itia , Vanwalleghem Gilles , Scott Ethan K.
Published: October 2021

Animals from insects to humans perform visual escape behavior in response to looming stimuli, and these responses habituate if looms are presented repeatedly without consequence. While the basic visual processing and motor pathways involved in this behavior have been described, many of the nuances of predator perception and sensorimotor gating have not. Here, we have performed both behavioral analyses and brain-wide cellular-resolution calcium imaging in larval zebrafish while presenting them with visual loom stimuli or stimuli that selectively deliver either the movement or the dimming properties of full loom stimuli. Behaviorally, we find that, while responses to repeated loom stimuli habituate, no such habituation occurs when repeated movement stimuli (in the absence of luminance changes) are presented. Dim stimuli seldom elicit escape responses, and therefore cannot habituate. Neither repeated movement stimuli nor repeated dimming stimuli habituate the responses to subsequent full loom stimuli, suggesting that full looms are required for habituation. Our calcium imaging reveals that motion-sensitive neurons are abundant in the brain, that dim-sensitive neurons are present but more rare, and that neurons responsive to both stimuli (and to full loom stimuli) are concentrated in the tectum. Neurons selective to full loom stimuli (but not to movement or dimming) were not evident. Finally, we explored whether movement- or dim-sensitive neurons have characteristic response profiles during habituation to full looms. Such functional links between baseline responsiveness and habituation rate could suggest a specific role in the brain-wide habituation network, but no such relationships were found in our data. Overall, our results suggest that, while both movement- and dim-sensitive neurons contribute to predator escape behavior, neither plays a specific role in brain-wide visual habituation networks or in behavioral habituation.