bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Cellular Heterogeneity in Immune Microenvironment of Primary Central Nervous System Lymphoma by Single-Cell Sequencing
Authors: Wei Boyuan , Liu Zhe , Fan Yue , Wang Shuwei , Dong Chao , Rao Wei , Yang Fan , Cheng Gang , Zhang Jianning
Published: October 2021

Background

Primary central nervous system lymphoma (PCNSL) is characterized by a lack of specificity and poor prognosis. Further understanding of the tumor heterogeneity and molecular phenotype of PCNSL is of great significance for improving the diagnosis and treatment of this disease.

Methods

To explore the distinct phenotypic states of PCNSL, transcriptome-wide single-cell RNA sequencing was performed on 34,851 PCNSL cells from patients. The cell types, heterogeneity, and gene subset enrichment of PCNSL were identified. A comparison of the PCNSL cells with 21,250 normal human fetal brain (nHFB) cells was further analyzed to reveal the differences between PCNSL and normal sample.

Results

Six cell populations were mainly identified in the PCNSL tissue, including four types of immune cells—B cell, T cell, macrophage and dendritic cell—and two types of stromal cells: oligodendrocyte and meningeal cell. There are significant cellular interactions between B cells and several other cells. Three subpopulations of B cells indicating diffident functions were identified, as well as a small number of plasma cells. Different subtypes of T cells and dendritic cells also showed significant heterogeneity. It should be noted that, compared with normal, the gene expression and immune function of macrophages in PCNSL were significantly downregulated, which may be another important feature of PCNSL in addition to B cell lesions and may be a potential target for PCNSL therapy.
Influence of American Society of Anesthesiologists Score on Oncologic Outcomes in Patients With Upper Tract Urothelial Carcinoma After Radical Nephroureterectomy: A Large-Sample Study in Two Institutions
Authors: Yuan Yichu , Wang Yiqiu , Zhang Nan , Mao Xiawa , Huang Yiran , Huang Jiwei , Ji Na
Published: October 2021

Introduction

As a research team of urologists and an anesthetist, we sought to investigate the prognostic significance of American Society of Anesthesiologists (ASA) score in patients with upper tract urothelial cancer (UTUC) after radical nephroureterectomy (RNU). ASA physical status (ASA-PS) classification not only was found to be associated with increased comorbidities but also independently factors for predicting morbidity and mortality. Accurate risk assessment was being particularly important for patients being considered for surgery.

Methods

Records for 958 patients with UTUC who underwent RNU were reviewed. Clinicopathologic variables, including ASA-PS, were assessed at two institutions. Overall survival (OS), cancer-specific survival (CSS), intravesical recurrence-free survival (IRFS), and metastasis-free survival (MFS) were estimated using the Kaplan–Meier method and Cox regression analyses. We measured the independent predictive value of ASA-PS for mortality by multivariate regression. Association of ASA-PS and clinicopathologic variables was assessed.

Results

The group of patients with ASA = 2/3 had a shorter 5-year OS (67.6% and 49.9%), CSS (72.9% and 58.1%), and MFS (75.1% and 58.5%). The median follow-up time was 39 months. Kaplan–Meier curves showed that the group with ASA = 2/3 had significantly poorer OS, CSS, and MFS. Adjusting for multiple potential confounding factors, multivariate analyses suggested that ASA score was an independent predictor of OS, CSS, and MFS (p = 0.004, p = 0.005, p < 0.001).

Conclusion

Higher ASA scores were independently associated with lower survival rate. This capability, along with its simplicity, makes it a valuable prognostic metric. It should be seriously referenced in UTUC patients being considered for RNU.
Case Report: A Pancreatic Ductal Adenocarcinoma Patient With Concurrent Targetable Somatic Novel KANK1-ALK, UPP2-NTRK3 Fusion, and Pathogenetic Germline BRCA Mutation
Authors: Meng Fan , Lu Le , Tan Yuan , Duan Qianqian , Lu Hongwei
Published: October 2021

Pancreatic ductal adenocarcinoma (PDAC) is presently one of the cancers with the worst survival rates. The current treatment options for PDAC are relatively scarce due to insufficient understanding of molecular characteristics and subtypes of PDAC. Based on next-generation sequencing (NGS), we firstly presented a case about a KRAS wild-type pancreatic ductal adenocarcinoma patient harboring a concurrent targetable rare somatic novel KANK1-ALK, UPP2-NTRK3 fusion, and pathogenetic germline BRCA mutation. These two novel fusion statuses were assayed by immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH). Our findings demonstrated that comprehensive and systematic screening of PDAC for actionable genomic alteration may substantially improve the therapeutic prospects for a sizeable fraction of patients with PDAC. To improve the management of PDAC in an era of precision medicine, it is important to identify ALK or NTRK fusion-positive and pathogenic germline mutation subsets of patients who can benefit from targeted therapies.
Transcriptome Analysis Reveals the Senescence Process Controlling the Flower Opening and Closure Rhythm in the Waterlilies (Nymphaea L.)
Authors: Li Zhaoji , Zhou Weijuan , Wang Peng , Chen Yanfu , Huo Shaojie , Wang Jian , Tian Daike , Niu Jun , Zhao Ying , Song Xiqiang
Published: October 2021

Most waterlily flowers open at dawn and close after noon usually for three to four days, and thereafter wilt. The short lifespan of flowers restricts the development of the flower postharvest industry. The termination of flower movements is a key event during flower aging process. However, it is still unclear when the senescence process initiates and how it terminates the movement rhythm. In this study, we observed that the opening diameter of flowers was the smallest on the fourth (last) flowering day. Subsequent transcriptome profiles generated from petals at different flowering stages showed that the multiple signaling pathways were activated at the last closure stage (Time 3, T3) of the flowers, including Ca2+, reactive oxygen species and far red light signaling pathways, as well as auxin, ethylene and jasmonic acid signaling pathways. Moreover, In terms of cell metabolism regulation, the genes related to hydrolase (protease, phospholipase, nuclease) were upregulated at T3 stage, indicating that petals entered the senescence stage at that time; and the genes related to water transport and cell wall modification were also differentially regulated at T3 stage, which would affect the ability of cell expand and contract, and eventually lead to petal not open after the fourth day. Collectively, our data provided a new insight into the termination of flower opening in the waterlilies, and a global understanding of the senescence process of those opening-closure rhythm flowers.
Pathogenic Microbes Increase Plant Dependence on Arbuscular Mycorrhizal Fungi: A Meta-Analysis
Authors: Qin Mingsen , Miranda Jean-Pascal , Tang Yun , Wei Wangrong , Liu Yongjun , Feng Huyuan
Published: October 2021

Numerous studies have confirmed that arbuscular mycorrhizal fungi (AMF) can promote plant nitrogen and phosphorus absorption, and prime systemic plant defense to plant pathogenic microbes. Despite that, the information on the interaction between AMF and plant pathogenic microbes is limited, especially the influence of plant pathogenic microbes on the effect of AMF promoting plant growth. In this study, 650 independent paired-wise observations from 136 published papers were collected and used to calculate the different effect of AMF with plant pathogenic microbes (DAPP) in promoting plant growth through meta-analysis. The results showed that AMF had a higher effect size on plant growth with pathogenic microbes comparing to without pathogenic microbes, including the significant effects in shoot and total fresh biomass, and shoot, root, and total dry biomass. The results of the selection models revealed that the most important factor determining the DAPP on plant dry biomass was the harm level of plant pathogenic microbes on the plant dry biomass, which was negatively correlated. Furthermore, the change of AMF root length colonization (RLC) was the sub-important factor, which was positively correlated with the DAPP. Taken together, these results have implications for understanding the potential and application of AMF in agroecosystems.
The Streptochaeta Genome and the Evolution of the Grasses
Authors: Seetharam Arun S. , Yu Yunqing , Bélanger Sébastien , Clark Lynn G. , Meyers Blake C. , Kellogg Elizabeth A. , Hufford Matthew B.
Published: October 2021

In this work, we sequenced and annotated the genome ofStreptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space.Streptochaetais similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However,Streptochaeta(and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology ofStreptochaetamay thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
Non-linear Response to Cell Number Revealed and Eliminated From Long-Term Tracheid Measurements of Scots Pine in Southern Siberia
Authors: Babushkina Elena A. , Dergunov Dmitry R. , Belokopytova Liliana V. , Zhirnova Dina F. , Upadhyay Keshav K. , Tripathi Shri K. , Zharkov Mikhail S. , Vaganov Eugene A.
Published: October 2021

Dendroclimatic research offers insight into tree growth–climate response as a solution to the forward problem and provides reconstructions of climatic variables as products of the reverse problem. Methodological developments in dendroclimatology have led to the inclusion of a variety of tree growth parameters in this field. Tree-ring traits developed during short time intervals of a growing season can potentially provide a finer temporal scale of both dendroclimatic applications and offer a better understanding of the mechanisms of tree growth reaction to climatic variations. Furthermore, the transition from classical dendroclimatic studies based on a single integral variable (tree-ring width) to the modern multitude of quantitative variables (e.g., wood anatomical structure) adds a lot of complexity, which mainly arises from intrinsic feedbacks between wood traits and muddles seasonality of registered climatic signal. This study utilized life-long wood anatomical measurements of 150- to 280-year-old trees ofPinus sylvestrisL. growing in a moisture-sensitive habitat of the forest-steppe of Southern Siberia (Russia) to investigate and eliminate legacy effect from cell production in tracheid traits. Anatomical parameters were calculated to describe the results of the three main subsequent stages of conifer xylem tracheid development, namely, cell number per radial file in the ring, mean and maximum cell radial diameter, and mean and maximum cell-wall thickness. Although tree-ring width was almost directly proportional to cell number, non-linear relationships with cell number were revealed in tracheid measurements. They exhibited a stronger relationship in the areas of narrow rings and stable anatomical structure in wider rings. The exponential models proposed in this study demonstrated these relationships in numerical terms with morphometric meaning. The ratio of anatomical measurements to their modeled values was used to develop long-term anatomical chronologies, which proved to retain information about climatic fluctuations independent of tree-ring width (cell number), despite decreased common signal.
Sex Differences in Pulmonary Hypertension
Authors: Rodriguez-Arias Juan José , García-Álvarez Ana
Published: October 2021

Pulmonary hypertension (PH) includes multiple diseases that share as common characteristic an elevated pulmonary artery pressure and right ventricular involvement. Sex differences are observed in practically all causes of PH. The most studied type is pulmonary arterial hypertension (PAH) which presents a gender bias regarding its prevalence, prognosis, and response to treatment. Although this disease is more frequent in women, once affected they present a better prognosis compared to men. Even if estrogens seem to be the key to understand these differences, animal models have shown contradictory results leading to the birth of the estrogen paradox. In this review we will summarize the evidence regarding sex differences in experimental animal models and, very specially, in patients suffering from PAH or PH from other etiologies.
The Predictive Capabilities of the Auroral Electrojet Index for Medium Energy Electron Precipitation
Authors: Tyssøy H. Nesse , Partamies N. , Babu E. M. , Smith-Johnsen C. , Salice J. A.
Published: October 2021

The chemical imprint of the energetic electron precipitation on the atmosphere is now acknowledged as a part of the natural forcing of the climate system. It has, however, been questioned to which degree current proxies are able to quantify the medium energy electron (MEE) (≳30 keV) precipitation and the associated daily and decadal variability. It is particularly challenging to model the high energy tail (≳300 keV) of MEE, both in terms of the intensity as well as the timing. This study explores the predictive capabilities of the AE index for the MEE precipitation. MEE measurements from the NOAA/POES over a full solar cycle from 2004 to 2014 are applied. We combine observations from the MEPED 0° and 90° detectors together with theory of pitch angle diffusion by wave-particle interaction to estimate the precipitating fluxes. To explore the energy dependent time scales, each of the MEPED energy channels, > 43, >114, and >292 keV are evaluated independently. While there is a strong correlation between the daily resolved AE index and >43 keV fluxes, it is a poor predictor for the >292 keV fluxes. We create new AE based MEE proxies by accumulating the AE activity over multiple days, including terms counting for the associated lifetimes. The results indicate that AE based proxies can predict at least 70% of the observed MEE precipitation variance at all energies. The potential link between the AE index, substorms and the MEE precipitation is discussed.
Comprehensive Analysis of Ferroptosis-Related LncRNAs in Breast Cancer Patients Reveals Prognostic Value and Relationship With Tumor Immune Microenvironment
Authors: Xu Zhengjie , Jiang Suxiao , Ma Juan , Tang Desheng , Yan Changsheng , Fang Kun
Published: October 2021

Background: Breast cancer (BC) is a heterogeneous malignant tumor, leading to the second major cause of female mortality. This study aimed to establish an in-depth relationship between ferroptosis-related LncRNA (FRlncRNA) and the prognosis as well as immune microenvironment of the patients with BC.

Methods: We downloaded and integrated the gene expression data and the clinical information of the patients with BC from The Cancer Genome Atlas (TCGA) database. The co-expression network analysis and univariate Cox regression analysis were performed to screen out the FRlncRNAs related to prognosis. A cluster analysis was adopted to explore the difference of immune microenvironment between the clusters. Furthermore, we determined the optimal survival-related FRLncRNAs for final signature by LASSO Cox regression analysis. Afterward, we constructed and validated the prediction models, which were further tested in different subgroups.

Results: A total of 31 FRLncRNAs were filtrated as prognostic biomarkers. Two clusters were determined, and C1 showed better prognosis and higher infiltration level of immune cells, such as B cells naive, plasma cells, T cells CD8, and T cells CD4 memory activated. However, there were no significantly different clinical characters between the clusters. Gene Set Enrichment Analysis (GSEA) revealed that some metabolism-related pathways and immune-associated pathways were exposed. In addition, 12 FRLncRNAs were determined by LASSO analysis and used to construct a prognostic signature. In both the training and testing sets, patients in the high-risk group had a worse survival than the low-risk patients. The area under the curves (AUCs) of receiver operator characteristic (ROC) curves were about 0.700, showing positive prognostic capacity. More notably, through the comprehensive analysis of heatmap, we regarded LINC01871, LINC02384, LIPE-AS1, and HSD11B1-AS1 as protective LncRNAs, while LINC00393, AC121247.2, AC010655.2, LINC01419, PTPRD-AS1, AC099329.2, OTUD6B-AS1, and LINC02266 were classified as risk LncRNAs. At the same time, the patients in the low-risk groups were more likely to be assigned to C1 and had a higher immune score, which were consistent with a better prognosis.

Conclusion: Our research indicated that the ferroptosis-related prognostic signature could be used as novel biomarkers for predicting the prognosis of BC. The differences in the immune microenvironment exhibited by BC patients with different risks and clusters suggested that there may be a complementary synergistic effect between ferroptosis and immunotherapy.
Directed Expression of Tracheal Antimicrobial Peptide as a Treatment for Bovine-Associated Staphylococcus Aureus-Induced Mastitis in Mice
Authors: Zhang Zhipeng , Chen Daijie , Lu Xubin , Zhao Ruifeng , Chen Zhi , Li Mingxun , Xu Tianle , Mao Yongjiang , Yang Yi , Yang Zhangping
Published: October 2021

Bovine mastitis is perplexing the dairy industry since the initiation of intensive dairy farming, which has caused a reduction in the productivity of cows and an escalation in costs. The use of antibiotics causes a series of problems, especially the formation of bacterial antimicrobial resistance. However, there are limited antibiotic-free therapeutic strategies that can effectively relieve bacterial infection of bovine mammary glands. Hence, in this study, we constructed a mammary gland tissue-specific expression vector carrying the antimicrobial peptide of bovine-derived tracheal antimicrobial peptide (TAP) and evaluated it in both primary bovine mammary epithelial cells (pBMECs) and mice. The results showed that the vector driven by the β-lactoglobulin gene (BLG) promoter could efficiently direct the expression of TAP in pBMECs and the mammary gland tissue of mice. In addition, significant antibacterial effects were observed in both in vitro and in vivo experiments when introducing this vector to bovine-associated Staphylococcus aureus-treated pBMECs and mice, respectively. This study demonstrated that the mammary gland tissue-specific expression vector could be used to introduce antimicrobial peptide both in in vitro and in vivo and will provide a new therapeutic strategy in the treatment of bovine mastitis.
Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org
Authors: Koo Michelle S. , Vredenburg Vance T. , Deck John B. , Olson Deanna H. , Ronnenberg Kathryn L. , Wake David B.
Published: October 2021

Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Research over the last two decades has shown that susceptibility to this disease varies greatly with respect to a suite of host and pathogen factors such as phylogeny, geography (including abiotic factors), host community composition, and historical exposure to pathogens; yet, despite a growing body of research, a comprehensive understanding of global chytridiomycosis incidence remains elusive. In a large collaborative effort, Bd-Maps was launched in 2007 to increase multidisciplinary investigations and understanding using compiled global Bd occurrence data (Bsal was not discovered until 2013). As its database functions aged and became unsustainable, we sought to address critical needs utilizing new technologies to meet the challenges of aggregating data to facilitate research on both Bd and Bsal. Here, we introduce an advanced central online repository to archive, aggregate, and share Bd and Bsal data collected from around the world. The Amphibian Disease Portal (https://amphibiandisease.org) addresses several critical community needs while also helping to build basic biological knowledge of chytridiomycosis. This portal could be useful for other amphibian diseases and could also be replicated for uses with other wildlife diseases. We show how the Amphibian Disease Portal provides: (1) a new repository for the legacy Bd-Maps data; (2) a repository for sample-level data to archive datasets and host published data with permanent DOIs; (3) a flexible framework to adapt to advances in field, laboratory, and informatics technologies; and (4) a global aggregation of Bd and Bsal infection data to enable and accelerate research and conservation. The new framework for this project is built using biodiversity informatics best practices and metadata standards to ensure scientific reproducibility and linkages across other biological and biodiversity repositories.
VSV-EBOV Induces Temporal and Dose-Dependent Transcriptional Responses in Non-human Primates
Authors: Pinski Amanda N. , Maroney Kevin J. , Marzi Andrea , Messaoudi Ilhem
Published: October 2021

Zaire Ebola virus (EBOV), the causative agent of Ebola virus disease (EVD), is a member of the Filoviridae family. EVD is characterized by innate and adaptive immune dysregulation that leads to excessive inflammation, coagulopathy, lymphopenia, and multi-organ failure. Recurrent outbreaks of EBOV emphasize the critical need for effective and deployable anti-EBOV vaccines. The FDA-approved VSV-EBOV vaccine protects non-human primates (NHPs) and humans from EBOV when given at a 10–20 million PFU dose. We recently demonstrated that a dose as small as 10 PFU protected NHPs from lethal EBOV infection. Furthermore, 1 PFU of VSV-EBOV protected 75% of vaccinated NHPs. In this study, we performed a comparative transcriptional analysis of the whole blood transcriptome in NHPs vaccinated with doses of VSV-EBOV associated with complete protection (10M PFU), protection with mild EVD (10 PFU), and break-through protection (1 PFU) before and after challenge with a lethal dose of EBOV Makona. Transcriptional findings demonstrated that, regardless of dose, vaccination significantly attenuated the upregulation of genes associated with fatal EVD. Genes involved in T- and B-cell activation were more highly expressed in groups receiving 10 or 10M PFU than in 1 PFU–vaccinated animals. Furthermore, the singular vaccinated (1 PFU) non-survivor exhibited a transcriptional signature distinct from both surviving vaccinated animals and controls that received an irrelevant vaccine. These findings provide additional insight into mechanisms of vaccine-mediated protection and informing public policy on vaccine distribution during outbreaks.
Effects of Onion Residue, Bovine Manure Compost and Compost Tea on Soils and on the Agroecological Production of Onions
Authors: Orden Luciano , Ferreiro Nicolás , Satti Patricia , Navas-Gracia Luis Manuel , Chico-Santamarta Leticia , Rodríguez Roberto A.
Published: October 2021

Organic solid wastes are rarely considered when planning for rural production in Argentina. Onion production in the low valley of Río Colorado (Buenos Aires) generates between 12,000 and 20,000 Mg year−1 of vegetal wastes (i.e., leaves, stems, skins, roots) from harvesting, cleaning and classification of bulbs, causing many problems with their management. The aim of this work is to study the effect of different doses of onion residue-bovine manure compost and onion residue-bovine manure compost tea on the soil physicochemical properties, microbial activity and agroecological onion production in sandy soil. Results showed that the highest dose of compost caused the highest effects on soil pH, electrical conductivity and nutrient content. Soil enzymatic activities were already high in the soil before the compost was applied, which may have contributed to the small effect caused by any dose on soil activity. A significant positive effect on bulb weight and organic onion yield were found as a result of the amendment and growing season. In conclusion, agroecological production of onion with the addition of a 300 kg N ha−1 compost and compost tea guarantee yields comparable to those of conventional fertilization, as occurred during the two growing seasons of this study.
Territorial Analysis of the European Rural Development Funds (ERDF) as a Driving Factor of Ecological Agricultural Production
Authors: Ferasso Marcos , Blanco Miguel , Bares Lydia
Published: October 2021

The Europe 2030 project identified the need to create a growth model that is based on a dynamic balance between economic, social, and environmental dimensions. This involves, among other objectives, redirecting the resources that are allocated to the Common Agricultural Plan (CAP) toward more ecological agriculture and livestock. In recent decades, two packages of the European Agricultural Fund for Rural Development (EAFRD) approved funds for projects related to agriculture. This study carried out a regional evaluation of the effects on production and employment that were generated in the Spanish organic farming sector. For this, a methodology that is frequently used by researchers to analyze territorial differences was used, namely, the shift-share analysis. The main results showed important differences at the regional level in the production of crops. Likewise, constant shift and constant share analyses were used to forecast the evolution of the sector from the recent data. Pending the approval of the new EAFRD 2021–2030, the results obtained in this research allowed for the identification of the regions that showed a favorable evolution to change the agricultural model and to identify the projects that generated employment and ecological production in the sector.
Efficient Biocontrol of Gaeumannomyces graminis var. Tritici in Wheat: Using Bacteria Isolated from Suppressive Soils
Authors: Méndez Isabel , Fallard Ana , Soto Isabel , Tortella Gonzalo , de la Luz Mora María , Valentine Alex J. , Barra Patricio Javier , Duran Paola
Published: October 2021

“Take-all” disease is the most important biotic factor affecting cereal productivity, causing 30–50% of crop losses. The causal agent is the ascomycete soil-borne pathogen Gaeumannomyces graminis var. tritici (Ggt). Current control measures are ineffective, because Ggt can remain saprophytic in soils for long periods. Therefore, the study of the microbiome residing in suppressive soils (SS) is a promising niche of Ggt biocontrol. Here, we evaluated the efficiency of Serratia sp., Bacillus sp., and Acinetobacter sp. isolated from SS against the incidence of Ggt on wheat. Our results demonstrated that plants inoculated with the bacterial consortium in both greenhouse and field conditions were highly efficient in Ggt biocontrol, more so than individual strains. The disease reduction was evidenced by higher biomass production, fewer copies of the Ggt genome with a concomitant curtailment of blackening of roots, a decrease of lipid peroxidation, and an increase of superoxide dismutase activity. The ability of the microbial consortium over that of single strains could be attributable to interspecies communication as a strategy to biocontrol; i.e., higher chitinase activity. In conclusion, bacterial consortia from SS are an important niche of Ggt biocontrol, serving as a model for other soil-borne pathogens.
The Diets of Companion Cats in Aotearoa New Zealand: Identification of Obesity Risk Factors
Authors: Forrest Rachel , Awawdeh Leena , Esam Fiona , Pearson Maria , Waran Natalie
Published: October 2021

One in four New Zealand cats are overweight or obese, conditions associated with poor health outcomes. As part of an online survey that was conducted from January 2019 to March 2019, NZ residents aged ≥18 years were asked demographic questions along with questions related to the body condition, breed and diet of their cat/s. From the responses, possible owner-related risk factors for developing obesity were identified. Of the respondents, 65.5% (n = 1537) owned cat/s; the owners being more likely to be female, live rurally, or live with children. Most of the respondents fed their cat/s biscuits from the supermarket (63%) and wet food (57%). Almost half (45%) fed their cat/s specialised food from a pet shop or veterinary clinic and gave them treats, with 31% of respondents feeding their cat/s raw meat. Feeding cats a variety of food types may make it difficult to estimate the appropriate amount of each needed to avoid excess caloric intake. In addition, approximately 30% of the respondents did not agree with the correct body condition statement, revealing a need for owner education. These findings highlight important areas of cat nutrition requiring future research to better inform the development of healthy weight interventions for NZ cats.
Search for Associations of FSHR, INHA, INHAB, PRL, TNP2 and SPEF2 Genes Polymorphisms with Semen Quality in Russian Holstein Bulls (Pilot Study)
Authors: Nikitkina Elena , Krutikova Anna , Musidray Artem , Plemyashov Kirill
Published: October 2021

The aim of the study was to search for new mutations in the previously studied gene loci of follicle-stimulating hormone receptor (FSHR), inhibin α (INHA), inhibin β A (INHAB), prolactin (PRL), transition protein 2 (TNP2), and sperm flagella 2 (SPEF2) by sequencing, as well as the search for associations of previously identified mutations at these loci with fresh semen quality in Russian Holstein bulls. Phenotypic data from 189 bulls was collected. Data was analyzed for most bulls for three years of semen collection. The maximum value of each semen quality indicator (doublet ejaculate volume, sperm concentration, progressive motility and total number of spermatozoa) were selected. SNPs were identified in the FSHR, INHA, INHAB, TNP2, SPEF2 genes. The PRL gene did not have polymorphism. Significant (p < 0.05) associations of polymorphisms in the FSHR gene with double ejaculate volume, concentration and total number of spermatozoa were identified. Polymorphism in the INHA gene was significantly associated (p < 0.05) with sperm concentration. Polymorphism in the INHAB gene was significantly associated (p < 0.05) with doublet ejaculate volume and total number of spermatozoa. Polymorphisms in the TNP2 and SPEF2 genes did not have significant associations with semen quality. The SNPs studied in our pilot work may be considered as candidate genetic markers in the selection of bulls.
Effects of Early Nutrition of Hatched Chicks on Welfare and Growth Performance: A Pilot Study
Authors: Lingens Jan Berend , Abd El-Wahab Amr , Ahmed Marwa Fawzy Elmetwaly , Schubert Dana Carina , Sürie Christian , Visscher Christian
Published: October 2021

This study aimed to investigate the possibility of rearing newly hatched chicks with immediate access to feed and water in the same hatching unit one week prior to transferring them to the conventional broiler house with special regards to foot pad health and growth performance. Two trials were performed with a total of 6900/6850 (trials 1/2) broiler chickens (ROSS 308). A total of 3318/3391 chicks (trials 1/2) were transported from the hatchery (duration of about 3 h) and reared in a conventional broiler house (control group: delayed nutrition on-hatchery hatched). The control group did not receive any form of nutrition until they were taken to conventional broiler housing. Additionally, a total of 3582/3459 (trials 1/2) embryonated eggs (d 18) were obtained from the same parent flock of the same commercial hatchery and taken to the farm facility. After on-farm hatch, the chicks had immediate access to water and feed (experimental group: early nutrition on-farm hatched). After d 6/7 of life, the on-farm hatched chicks (trials 1/2) were transferred to the broiler house on the same facility. The delayed nutrition on-hatchery hatched groups displayed a significantly lower dry matter content in the litter compared to the early nutrition on-farm hatched groups (two-factorial analysis) at d 6/7 and d 14 of life. However, thereafter, no significant differences were noted. Based upon two-factorial analysis, the early nutrition on-farm hatched groups revealed lower foot pad lesions from d 14 of life onwards and showed a higher body weight (BW) throughout the rearing period compared to the delayed nutrition on-hatchery hatched groups (p < 0.05). Overall, early nutrition on-farm hatched chickens is of critical importance together with using new litter at d 7 to maintain healthy foot pads as well as to enhance nutrient utilization and optimize the growth performance.
The Current State of the Protected Apis mellifera mellifera Population in Russia: Hybridization and Nosematosis
Authors: Kaskinova Milyausha , Saltykova Elena , Poskryakov Alexander , Nikolenko Alexey , Gaifullina Luisa
Published: October 2021

The Southern Urals of Russia are the habitat of one of the surviving populations of the dark forest bee—the Burzyan population of Apis mellifera mellifera. In this study, we present the results of the subspecies identification of bee colonies in the Altyn-Solok Nature Reserve in the Southern Ural Mountains using the intergenic mtDNA COI-COII locus and the assessment of the prevalence of nosematosis. Analysis of the mtDNA COI-COII intergenic locus in the studied sample showed that 30.4% of the colonies belong to the lineage C. The PCR diagnostics of nosematosis in 92 colonies selected from different sectors of the Altyn-Solok Nature Reserve showed that about half of the analyzed colonies were infected with Nosema apis. Nosema ceranae was found in eight colonies. Both of these factors can lead to the extinction of this population of the dark forest bee.
Phytochemical Constituents and Biological Activities of the Unexplored Plant Rhinanthus angustifolius subsp. grandiflorus
Authors: Zhang Leilei , Zengin Gokhan , Rocchetti Gabriele , Senkardes Ismail , Sharmeen Jugreet B. , Mahomoodally Mohamad Fawzi , Behl Tapan , Rouphael Youssef , Lucini Luigi
Published: October 2021

In the present study, a total of 12 extracts of Rhinanthus angustifolius subsp. grandiflorus, an understudied hemiparasitic species, were obtained using different extraction techniques, namely, homogenizer-assisted extraction (HAE), maceration (MAC), soxhlet (SOX), infusion, and solvents (ethyl acetate, methanol, ethanol, and water), and were evaluated for their in vitro antioxidant and enzyme-inhibiting properties. Additionally, untargeted profiling based on high-resolution mass spectrometry targeted different phytochemical classes, namely, polyphenols, terpenoids, and alkaloids. The highest total phenolic and flavonoid contents were detected using methanol as the extraction solvent. Multivariate statistics following the untargeted profiling revealed that the extraction solvent had a hierarchically higher impact than the extraction method when considering the recovery of bioactive compounds. The methanolic extracts displayed the highest radical-scavenging antioxidant capacity, as provided by CUPRAC and FRAP assays. On the other hand, the water extracts (MAC and HAE) and the infusion extract showed the highest activity as metal chelators (25.66–27.51 mg EDTAE/g). Similarly, the water extract obtained by HAE and the infusion extract revealed the highest phosphomolybdenum activity (3.92 ± 0.14 and 3.71 ± 0.01 mmol TE/g, respectively). The different extracts also exhibited different enzyme inhibition potentials. For instance, HAE and MAC ethanolic extracts inhibited only α-amylase (0.69 ± 0.01 and 0.70 ± 0.01 mmol ACAE/g), while all the other extracts showed a dual inhibition against both carbohydrate-hydrolyzing enzymes tested (i.e., α-amylase: 0.07–0.69 mmol ACAE/g; α-glucosidase: 0.03–1.30 mmol ACAE/g). Nevertheless, the other extracts inhibited acetyl-, butyryl-cholinesterases, or both; MAC–water extract displayed no inhibition against the enzymes. Additionally, all the studied extracts were found to inhibit tyrosinase, ranging from 10.62 to 52.80 mg KAE/g. In general, the water extracts showed weaker inhibition towards the enzymes than the other extracts. This study demonstrated that R. angustifolius is an excellent source of natural antioxidants and enzyme inhibitors that could be further investigated and exploited for pharmaceutical purposes.
Deep Learning-Based Segmentation of Various Brain Lesions for Radiosurgery
Authors: Wu Siangruei , Wu Yihong , Chang Haoyun , Su Florence T. , Liao Hengchun , Tseng Wanju , Liao Chunchih , Lai Feipei , Hsu Fengming , Xiao Furen
Published: October 2021

Semantic segmentation of medical images with deep learning models is rapidly being developed. In this study, we benchmarked state-of-the-art deep learning segmentation algorithms on our clinical stereotactic radiosurgery dataset. The dataset consists of 1688 patients with various brain lesions (pituitary tumors, meningioma, schwannoma, brain metastases, arteriovenous malformation, and trigeminal neuralgia), and we divided the dataset into a training set (1557 patients) and test set (131 patients). This study demonstrates the strengths and weaknesses of deep-learning algorithms in a fairly practical scenario. We compared the model performances concerning their sampling method, model architecture, and the choice of loss functions, identifying suitable settings for their applications and shedding light on the possible improvements. Evidence from this study led us to conclude that deep learning could be promising in assisting the segmentation of brain lesions even if the training dataset was of high heterogeneity in lesion types and sizes.
Variability of Diffuse Daylight Due to the Diversity of Cloud Arrays
Authors: Petržala Jaromír , Kocifaj Miroslav
Published: October 2021

Illuminance modeling that allows us to mimic or even replicate the dynamics of daylight changes is increasingly becoming a challenge for the development of more accurate prediction systems of natural light availability in building interiors or variations of insolation at arbitrarily oriented façades. We demonstrate that illuminance amplitude due to random cloud arrangement can vary over a wide range even when other atmospheric parameters remain unchanged. It follows from our systematic numerical modeling that diffuse illuminance predictions can be significantly improved by incorporating cloud coverage, mean cloud size, and cloud base altitude into daylight models. We show that any model of homogeneous luminance patterns would fail in modeling the illuminance amplitudes we can expect on horizontal and vertical planes under partial cloud coverage with individual clouds distributed randomly. However, these situations occur with high frequency in most of regions worldwide, thus the modeling results we obtained here are of high relevance to daylight modeling and solar energy systems as well.
Shafting Torsional Vibration Analysis of 1000 MW Unit under Electrical Short-Circuit Fault
Authors: Pan Honggang , Wu Yunshi , Pang Zhiyuan , Fu Yanming , Zhao Tianyu
Published: October 2021

Taking a 1000 MW turbine generator as the research object, the short-circuit fault in electrical disturbance is analyzed. Since it is very difficult to carry out fault analysis experiments and research on actual systems, simulation analysis is one of the more effective means of electrical fault diagnosis; the simulation’s results approach the actual behavior of the system and are ideal tools for power system analysis, and can provide an empirical basis for practical applications. The short-circuit fault model of the SIMULINK power system is built to analyze the two types of faults of generator terminals short-circuit and power grid short-circuit. The impact load spectrum, fault current and speed fluctuation between low-voltage rotors were extracted and analyzed. The conclusion is that the impact value of electromagnetic torque at the generator terminal is greater than that on the power grid side. The impact value of a two-phase short-circuit at the generator terminal is the largest, and that of a three-phase short-circuit on the power grid side is the smallest. The transient impulse current of a three-phase short-circuit at any fault point is greater than that of a two-phase short-circuit; the impulse current of the grid side short-circuit is much greater than that of the generator terminal short-circuit; the speed fluctuation and fluctuation difference caused by the three-phase short-circuit in the grid side are the largest. The alternating frequency of the transient electromagnetic force of the four kinds of faults avoids the natural frequency of the torsional vibration of the shaft system, and the torsional resonance of the shaft system in the time domain of the short-circuit fault will not appear. However, after the fault is removed, the residual small fluctuation torque in the system has a potential impact on the rotor system. This research shows an analysis of the structural integrity and safe operation of turbine generator units after a short-circuit fault, which can not only be applied to engineering practice, but also provide a theoretical basis for subsequent research.
Sport Performance Analysis with a Focus on Racket Sports: A Review
Authors: Krizkova Sarka , Tomaskova Hana , Tirkolaee Erfan Babaee
Published: October 2021

Athletes, both professional and amateur, are always looking for ways to improve their performance. With the introduction and increasing availability of modern technologies and smart devices arose the need to measure and analyze performance, but likewise, the use of these innovations as a competitive advantage also arose. Scientific publications reflect the wide range of available approaches and technologies, as well as the growing interest in various sports. As a result, we concentrated on a systematic review of publications that presented performance analysis tools and methods in all sports, with a final focus on racket sports. Clarivate Analytics’ Web of Science (WoS) and Elsevier Inc.’s SCOPUS databases were searched for 1147 studies that conducted performance analysis and sports research and were published in English. The data in the systematic review are current, up until 18 May 2021. A general review was performed on 759 items, and then 65 racket sports publications were thoroughly scrutinized. We concentrated on performance data, data collection and analysis tools, performance analysis methods, and software. We also talked about performance prediction. In performance research, we have identified specific approaches for specific sports as well as key countries. We are also considering expanding performance analysis in to E-sports in the future.
Prediction of Beck Depression Inventory Score in EEG: Application of Deep-Asymmetry Method
Authors: Kang Min , Kang Seokhwan , Lee Youngho
Published: October 2021

There is ongoing research on using electroencephalography (EEG) to predict depression. In particular, the deep learning method in which brain waves are used as inputs of a convolutional neural network (CNN) is being widely researched and has shown remarkable performance. We built a regression model to predict the severity score (Beck Depression Inventory [BDI]) of depressed patients as an extension of the deep-asymmetry method, which has shown promising performance in depression classification. Predicting the severity of depression is very important because the treatment and coping methods are different for each severity level. We imaged brain waves using the deep-asymmetry method, used them to train a two-dimensional CNN-based deep learning model, and achieved satisfactory performance. The EEG image-based CNN approach will make an important contribution to creating a highly interpretable model for predicting depression in the future.
Investigation of a Possible Material-Saving Approach of Sputtering Techniques for Radiopharmaceutical Target Production
Authors: Kotliarenko Alisa , Azzolini Oscar , Keppel Giorgio , Pira Cristian , Esposito Juan
Published: October 2021

Magnetron sputtering (MS) is a relatively new deposition technique, which is being considered among the cyclotron solid target (CST) manufacturing options now available, aiming at the medical radioisotopes yield for radiopharmaceutical production. However, the intrinsic high material losses during the deposition process do not permit its use with extremely expensive target materials, such as isotopically enriched metals/oxides. In this study, R&D technology for a new recovering shield is instead proposed to assess the dissipation of target material during the sputtering processes and, thus, an estimate of the material recovery that may be feasible and the related amount. The weight-loss analysis method is used to assess the material losses level inside the chamber during processing. In all tests carried out, a high-purity copper (99.99%) was used as a target material. As a result of this study, the material distribution for both magnetron and diode sputtering depositions can be calculated. The feasibility of the ultra-thick coatings growing, devoted to CST production, is demonstrated.