bluuebunny/crossref_metadata_2025 huggingface dataset:
Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potato
Authors: Lomin Sergey N. , Kolachevskaya Oksana O. , Arkhipov Dmitry V. , Romanov Georgy A.
Published: July 2023

It has long been known that phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyzes of deduced proteins were supplemented by their expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. Total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to be low probable in potato. This was equally applied to all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific.
Inactivated tilapia lake virus vaccine formulated with MontanideTM ISA 763A VG adjuvant resulted in inadequate protection and poor immunity in vaccinated Nile tilapia
Authors: Mai Thao Thu , Thompson Kim D. , Senapin Saengchan , Rodkhum Channarong , Dong Ha Thanh
Published: July 2023

Tilapia tilapinevirus, or tilapia lake virus (TiLV), is a virus that has caused disease outbreaks in many countries worldwide since 2009. We recently developed two simple but effective TiLV vaccines based on heat-killed virus (HKV) and formalin-killed virus (FKV). In the present study, we evaluated the immunological response and efficacy of MontanideTM ISA 763A VG oil-based vaccines (O-HKV and O-FKV) in Nile tilapia (Oreochromis niloticus) and compared these responses in fish vaccinated with water-based formulations (W-HKV and W-FKV). Juvenile Nile tilapia were given primary and booster vaccinations with the vaccine formulations. The relative fold change in expression of five immunoglobulin genes (IgM, IgT, IgD, CD4 and CD8) was assessed before and after booster vaccination, and a challenge with TiLV was performed to evaluate the efficacy of the vaccines. The results showed that the water-based vaccines induced higher levels of Ig transcripts and conferred significantly higher levels of protection compared to the oil-based formulations, with relative percent survival (RPS) values ranging from 54.6% to 59.7% for W-HKV and W-FKV vaccinated fish, and 32% and 0% for the O-HKV and O-FKV vaccinated fish, respectively. These findings suggest that water-based vaccines are more effective at protecting tilapia against TiLV infection, and MontanideTM ISA 763A VG may not be a suitable adjuvant for formulating whole-inactivated TiLV vaccines.
The Evaluation of the FVIII Activity and Hypercoagulability in Patients Treated With FVIII Concentrate Using a Clot Waveform Analysis
Authors: Matsumoto Takeshi , Wada Hideo , Shiraki Katsuya , Suzuki Kei , Yamashita Yoshiki , Tawara Isao , Shimpo Hideto , Shimaoka Motomu
Published: July 2023

Background: Although the use of regular replacement therapy including emicizumab for severe hemophilia has been spread, the assessment of the hemostatic ability using routine activated partial thromboplastin time (APTT) is still difficult in patients being treated with emicizumab.
Methods: The hemostatic ability in patients treated with FVIII concentrate or emicizumab was evaluated by APTT, thrombin time (TT) and a small amount of tissue factor induced FIX activation assay (sTF/FIXa) using a clot waveform analysis (CWA).
Results: FVIII activities based on a CWA-TT were significantly higher than those based on a CWA-APTT or chromogenic assay. FVIII activities based on the three assays in plasma without emicizumab were closely correlated, and those in plasma with emicizumab based on a CWA-TT and chromogenic assays were also closely correlated. The CWA-APTT and CWA-TT showed different patterns in patients treated with FVIII concentrates from those treated with emicizumab. In particular, the CWA-TT in patients treated with FVIII concentrate showed that the peak heights were significantly higher in platelet-rich plasma than in platelet-poor plasma. In plasma with approximately 16% of FVIII activity based on APTT assay from patients treated with FVIII concentrate, the peak height on the CWA-sTF/FIXa showed a higher hemostatic abilitythan normal plasma.
Conclusions: The CWA-TT can measure the FVIII activity in patients treated with emicizumab. Although routine APTT evaluations demonstrate a low hemostatic ability in patients treated with FVIII concentrate, the CWA-TT and CWA-sTF/FIXa show hypercoagulability in those patients.
PlantMetSuite: A User-Friendly Web-Based Tool for Metabolomics Analysis and Visualisation
Authors: Liu Yu , Liu Hao-Zhuo , Chen Ding-Kang , Zeng Hong-Yun , Chen Yi-Li , Yao Nan
Published: July 2023

The advancement of mass spectrometry technologies has revolutionised plant metabolomics research by enabling the acquisition of raw metabolomics data. However, the identification, analysis, and visualisation of these data require specialised tools. Existing solutions lack a dedicated plant-specific metabolite database and pose usability challenges. To address these limitations, we developed PlantMetSuite, a web-based tool for comprehensive metabolomics analysis and visualisation. PlantMetSuite encompasses interactive bioinformatics tools and databases specifically tailored for plant metabolomics data, facilitating upstream-to-downstream analysis in metabolomics and supporting integrative multi-omics investigations. PlantMetSuite can be accessed directly through a user's browser without the need for installation or programming skills. The tool is freely available at https://plantmetsuite.verygenome.com/ and will undergo regular updates and expansions to incorporate additional libraries and newly published metabolomics analysis methods. The tool's significance lies in empowering researchers with an accessible and customisable platform for unlocking plant metabolomics insights.
Drosophila as model system to study Ras-mediated oncogenesis: the case of the tensin family of proteins
Authors: Martín-Bermudo Maria D. , Martínez-Abarca Millán Ana , Soler Beatty Jennifer , Valencia Expósito Andrea
Published: July 2023

Oncogenic mutations in the small GTPase Ras contributes to ~30% of human cancers. However, tissue growth induced by oncogenic Ras is restrained by induction of cellular senescence and additional mutations are required to induce tumor progression. Therefore, it is paramount to identify cooperating cancer genes. Recently, the tensin family of focal adhesion proteins, TNS1-4, have emerged as regulators of carcinogenesis, yet their role in cancer appears somewhat controversial. Around 90% of human cancers are of epithelial origin. We have used the Drosophila wing imaginal disc epithelium as model system to gain insight into the roles of two orthologs of human TNS2 and 4, blistery (by) and PVRAP, in epithelial cancer progression. We have generated null mutations in PVRAP and found that, as it is the case for by and mammalian tensins, PVRAP mutants are viable. We have also found that elimination of either PVRAP or by potentiates RasV12-mediated wing disc hyperplasia. Furthermore, our results have unravelled a mechanism by which tensins may limit Ras oncogenic capacity, the regulation of cell shape and growth. These results demonstrate that Drosophila tensins behave as suppressors of Ras-driven tissue hyperplasia, suggesting that the roles of tensins as modulators of cancer progression might be evolutionary conserved.
Emergence and Progression of Behavioral Motor Deficits and Skeletal Muscle Atrophy across Adult Lifespan of the Rat
Authors: GrönholdtKlein Max , Gorzi Ali , Wang Ling , Edström Erik , Rullman Eric , Altun Mikael , Ulfhake Brun
Published: July 2023

The facultative loss of muscle mass and function during aging (sarcopenia) poses a serious threat to our independence and health. Much of what we know about sarcopenia derive from studies on small rodents which serve as models for the human condition. Here we used outbred male rats to study the natural history of sarcopenia with the aim to compare behavioral motor deficits with degree of muscle wasting and to find processes underlying the preclinical phase of sarcopenia. Selected metrics were validated in female rats. We used the soleus muscle because of its long duty cycles in everyday life and significance for postural control. The results show that gait and coordination remain intact through middle age (12-18 months; 40%-60% of median lifespan) when muscle mass relative to body weight is largely maintained. The muscle, however, show multiple signs of remodeling with a shift in myofiber-type composition towards type I, increased number of hybrid fibers and fibers expressing embryonic myosin. In parallel with the shift in fiber type prevalence, fiber type clustering increased. The latter combined with a transcriptional upregulation of nicotinic acetylcholine receptor subunit  (CHRN ), NCAM and Myogenin (MYOG) suggests a remodeling driven by myofiber denervation. Additional stigmata were increased number of central nuclei, transcriptional upregulation of Smad3, FBXO32, and MuRF1mRNAs; unaltered density of satellite cells (SC) and Catenin mRNA. In early (25-month-old) and advanced (30-month-old) aging, gait and coordination deteriorate as loss of muscle mass progresses. In late middle age and early aging because of a type II atrophy (>50%), followed by type I atrophy (>50%). Number of myofiber did not correlate with this process. At advance age, the atrophy is accompanied by a decrease in SC and Catenin mRNA while several transcripts upregulated earlier-on were downregulated. In contrast, glial-derived nerve growth factor (GDNF) mRNA abundance peaked at endpoint. We conclude that sarcopenia in the rat as in humans, has a long preclinical phase where the muscle undergoes extensive remodeling to preserve muscle mass and function. The data supports the notion that myofiber denervation is the instigating mechanism, initially affecting large type II motor units (MUs) and at more advanced stage also the smaller type I MUs.
In vitro study of bacterial adhesion and biofilm growth on fresh, frozen, or decellularized human bone grafts
Authors: Villatte Guillaume , Fassot Guillaume , ERIVAN Roger , Nedelec Jean-Marie , Descamps Stéphane , Wittrant Yohann , BOISGARD Stéphane , Traore Ousmane
Published: July 2023

There was no significant difference in bacterial adhesion between the 3 bone graft types tested, regardless of the bacterial strain used (p > 0.22). After 72 hours of culture, there was no significant difference between the Fresh and Frozen bone groups, while the number of CFU in the Decellularised group was significantly lower (p < 0.01), averaging -0.72 +/- 0.08 lg, -0.20 +/- 0.01 lg and -0.78 +/- 0.48 lg with S. epidermidis, S. aureus and E. coli respectively. Absolute values differences are low, and considering fresh bone (equivalent to autograft) as the gold standard due to its low infection rates in clinical studies, we can conclude that adhesion and biolfilm development characteristics are similar between Fresh, Frozen and Decellularised bone grafts..
The Psychological Effects of Excessive Mobile App Usage: Reshaping Childhood
Authors: Patil Abhinandan
Published: July 2023

Concerns have been made about how children's health and psychology could be hurt by the growing number of mobile apps they use. This abstract looks at intervention methods and best practices for getting kids to use mobile apps in a healthy way, find a balance with technology, and build up their resilience. Key points include promoting digital literacy and critical thinking, setting clear boundaries and rules, encouraging digital balance, modeling healthy tech habits, building resilience and coping skills, encouraging face-to-face communication, setting up tech-free times and spaces, monitoring app usage and content, promoting mindfulness and self-reflection, and getting professional help when needed. By using these tactics, parents, teachers, and other caretakers can help kids build a healthy relationship with technology, live a balanced life, and build the resilience they need to handle the challenges of the digital world. The goal of these interventions is to make sure that kids' app use is good for their general health, helps them learn and get along with others, and sets them up for long-term success in the digital age.
Functional Evidence of CCDC186 as a New Disease Associated Gene with Endocrine and Central Nervous System Alterations
Authors: Arrabal Luisa , Muñoz-Pujol Gerard , Medina Inma , Gort Laura , Garcia-Villoria Judit , Roldan Susana , Tort Frederic , Ribes Antonia
Published: July 2023

Background: Protein CCDC186 is involved in the maturation of dense core vesicles in the trans-Golgi network in neurons and endocrine cells. To date, only one patient, within a large sequencing study of 1000 cases, and a single case report with variants in CCDC186 had previously been described. However, no functional studies in any of these two cases had been performed. Methods: Exome sequencing from one affected individual of each family was performed. In addition, Sanger sequencing of the parents and one of the affected siblings was also performed. CCDC186 protein was assessed in cultured fibroblasts or muscle tissue by western blot. Transcriptomic analysis was done by means of RNA sequencing. Results. We identified three patients from two gypsy families, unrelated to each other, with the same homozygous mutations in CCDC186 gene. Clinically, all patients presented with seizures, frontotemporal atrophy, hypomyelination, recurrent infections, and endocrine disturbances such as severe non ketotic hypoglycemia. Low levels of cortisol, insulin or growth hormone could only be verified in one patient. All of them had a neonatal onset and died between 7 months and 4 years of age. WES identified a homozygous variant in CCDC186 gene (c.2215C>T, p.Arg739Ter) in the index patients of both families. Protein expression studies demonstrated that the CCDC186 was practically undetectable in fibroblasts and muscle tissue. These observations correlated perfectly with the transcriptomic analysis performed in fibroblasts in one of the patients, which showed a significant reduction of CCDC186 mRNA levels. Conclusion. Our study provides functional evidence that mutations in this gene have a pathogenic effect on the protein and reinforces CCDC186 as a new disease-associated gene. In addition, mutations in CCDC186 could explain the combined endocrine and neurologic alterations detected in our patients
Factors Affecting Toxic and Essential Trace Element Concentrations in Cow’s Milk Produced in the State of Pernambuco, Brazil
Authors: Oliveira Filho Emanuel Felipe de , López-Alonso Marta , Vieira Marcolino Guilherme , Castro Soares Pierre , Herrero-Latorre Carlos , Lopes de Mendonça Carla , De Azevedo Costa Nivaldo , Miranda Marta
Published: July 2023

The aim of this study was to provide information on the levels of toxic (Cd and Pb) and essential (Cu, Fe and Zn) elements in cow’s milk produced in the State of Pernambuco (Brazil). A total of 142 samples of raw milk were collected, and the concentrations of essential and toxic elements were determined by inductively coupled plasma-optical emission spectrometry. In almost 30 % of the samples analyzed, the Pb content exceeded the maximum level established in the Brazilian legislation (0.05 mg/l). By contrast, in all samples the Cd content was below the maximum allowable level (0.02 mg/L). The essential trace elements Cu, Fe and Zn were generally present at lower concentrations than reported in other studies and can be considered within the deficient range for cow’s milk. Statistical and chemometric procedures were used to evaluate the main factors influencing the metal concentrations (proximity to major roads, presence of effluents, and milking method). The study findings demonstrate that the proximity of the farms to major roads influences the concentrations of Cd, Pb and Cu and that this is the main factor explaining the Pb content of milk. In addition, the presence of effluents influenced the concentrations of Cu, while no relationship between the metal content and the milking method was observed. Thus, in accordance with the study findings, consumption of cow’s milk produced in the region can be considered a risk to public health due to the high concentrations of Pb and the low concentrations of other essential minerals such as Cu, Zn and Fe in some of the milk samples.
Key Predictors and Geographic Variation of Food Security and Nutrition in Africa: A Spatio-temporal Model-Based Study
Authors: BOFA Adusei , Zewotir Temesgen
Published: July 2023

There is voluminous literature on Food Security in Africa. This study explicitly considers the spatio-temporal factors in addition to the usual FAO-based metrics in modeling and understanding the dynamics of food security and nutrition across the African continent. To better understand the complex trajectory and burden of food insecurity and nutrition in Africa, it is crucial to consider space-time factors when modeling and interpreting food security. The spatio-temporal anova model was found to be superior(employing statistical criteria) to the other there models from the spatio-temporal interaction domain models. The results of the study suggest that dietary supply adequacy, food stability, and consumption status are positively associated with severe food security, while average food supply and environmental factors have negative effects on Food Security and Nutrition. The findings also indicate that severe food insecurity and malnutrition are spatially and temporally correlated across the African continent. Spatio-temporal modeling and spatial mapping are essential components of a comprehensive practice to reduce the burden of severe food insecurity. likewise, any planning and intervention to improve the average food supply and environment to promote sustainable development should be regional instead of one size fit all.
Brainstem Haemorrhage and Amyloid-Like Cerebral Microbleeds Due to Blood Culture-Negative Coxiella burnetii Endocarditis
Authors: Manea Maria Mirabela , Dragos Dorin , Dobri Ana-Maria , Ghenu Maria Iuliana , Enache Iulia Ioana , Stoican Iulia Cosmina , Tuta Sorin
Published: July 2023

Infective endocarditis is a rare and challenging diagnosis, Q fever endocarditis being a major cause of culture-negative endocarditis (IE). The presence of multiple cerebral microbleeds (CMBs) suggests a particular vascular frailty and could be correlated to potential emergence of a haemorrhagic stroke in IE. We report a case of a 45 years-old patient with Coxiella burnetii endocarditis, with a brainstem hemorrhage and cerebral MRI CMBs resembling those of CAA. However the systemic inflammatory tests, the splenic infarct and kidney pathology could not be explained by a variant of CAA, neither the normal initial cerebral CT scan when the patient had already the brainstem clinical signs without evidencing the hemorrhage. Transthoracic and transesophageal echocardiogram revealed only calcified bicuspid aortic valve with moderate stenosis and regurgitation, without any vegetations and the blood cultures on conventional media were negative. Serology for Coxiella burnetii was positive. Inclusion of CMBs as a new minor imaging criteria for infective endocarditis could upgrade the diagnosis in almost 50% of patients.
Revisiting Retinal Degeneration Hallmarks: Insights from Molecular Markers and Therapy Perspectives
Authors: Rosa Joao Gabriel Santos , Disner Geonildo Rodrigo , Pinto Felipe Justiniano , Lima Carla , Lopes-Ferreira Monica
Published: July 2023

Visual impairment and blindness are a growing public health problem, as they reduce the quality of life of millions of people. The management and treatment of these diseases represent a scientific and therapeutic challenge, since the different cellular and molecular actors involved in the pathophysiology are still being identified. The visual system components, particularly the retinal cells, are extremely sensitive to genetic or metabolic alterations, and immune cells activated by insults contribute to biological events that culminate with vision loss and irreversible blindness. Several ocular diseases are linked to retinal cell loss, and diseases such as retinitis pigmentosa, age-related macular degeneration, glaucoma and diabetic retinopathy are characterized by pathophysiological hallmarks that represent possibilities to study and develop novel treatments for retinal cells degeneration. Here, we present a compilation of revisited information on retinal degeneration, including pathophysiologic and molecular features, biochemical hallmarks and possible directions for novel treatments, aiming to assist as a guide for innovative research. The expansion of knowledge of the mechanistic bases of the pathobiology of eye diseases, including information on the complex interactions of genetic predisposition, chronic inflammation, and environmental and aging-related factors will allow the identification of new therapeutic strategies.
Targeted Strategies for Degradation of Key Transmembrane Proteins in Cancer
Authors: Sakanyan Vehary , Iradyan Nina , Alves de Sousa Rodolphe
Published: July 2023

Targeted protein degradation is an attractive technology for cancer treatment due to its ability to overcome the unpredictability of small molecule inhibitors that cause resistance mutations. In recent years, various targeted protein degradation strategies have been developed based on the ubiquitin-proteasome system in the cytoplasm or the autophagy-lysosomal system during endocytosis. In this review, we describe and compare technologies for targeted inhibition and targeted degradation of the epidermal growth factor receptor (EGFR), one of the major proteins responsible for the onset and progression of many types of cancer. In addition, we have developed an alternative strategy, called alloAUTO, based on the binding of new heterocyclic compounds to an allosteric site located in close proximity to the EGFR catalytic site. These compounds cause targeted degradation of the transmembrane receptor, simultaneously activating both systems of protein degradation in cells. Damage to EGFR signaling pathways promotes inactivation of Bim sensor protein phosphorylation, which leads to disintegration of the cytoskeleton, followed by detachment of cancer cells from the extracellular matrix and, ultimately, to cancer cell death. This hallmark of targeted cancer cell death suggests an advantage over other targeted protein degradation strategies, namely that the fewer cancer cells survive, the fewer chemotherapy-resistant mutants appear.
Alopecias: Practical Tips For The Management Of Biopsies And Main Diagnostic Clues For The General Pathologist And Dermatopathologist
Authors: Pinedo Moraleda Fernando , Tristan Martin Belen , Dradi Giulia Greta
Published: July 2023

Accurately diagnosing specific variants of alopecia remains challenging for pathologists, potentially delaying appropriate therapeutic decisions by dermatologists. Issues such as limited knowledge on optimal biopsy types and processing methods add complexity. Understanding the normal histology of hair follicles and their changes throughout the follicular cycle further complicates microscopic evaluation. This paper aims to summarize these characteristics and highlight essential diagnostic clues for pathologists to confidently suggest a diagnosis, therefore playing a key role in alopecia diagnosis. Ongoing education, collaboration with dermatologists, and staying updated on advancements is crucial for accurate diagnosis and effective management of different types of alopecia.
A Taxonomy of AI Techniques for Security and Privacy in Cyber-Physical Systems
Authors: Bandi Ajay
Published: July 2023

Background:As cyber-physical systems (CPS) continue to grow, it is progressively crucial to address the challenges of data protection using artificial intelligence (AI). Objective:The goal of this research is to provide an up-to-date overview of the security and privacy issues of CPS that incorporate AI techniques. Method:To achieve this, the author conducted a systematic literature review, focusing on 35 relevant articles. Results:The data collected from these studies was then categorized into three main areas: 1) different security and privacy issues, 2) application areas and vulnerabilities, and 3) the AI techniques used to address security and privacy concerns. The literature review highlights that intrusion detection and cyberattacks are the most commonly studied areas in CPS, while Machine Learnning (ML)-based attacks and vessel trajectory are less explored. The review identifies various CPS applications such as water treatment, energy, healthcare, and transportation that address security and privacy concerns. However, a relatively small proportion of studies focused on the manufacturing domain. The review also notes that while supervised machine learning algorithms under the classification category are commonly used to address data protection issues, there are comparatively fewer studies that have implemented automation processes using robots and deep learning. Limitations:The articles related to blockchain-based research were not included in this review to focus solely on AI techniques. Conclusion:The results of this analysis indicate that there is a significant need for innovative AI/ML techniques to protect intelligent systems and networks from ML-based security threats.
Metronidazole Potentiation by Panax Ginseng and Symphidium Officinale: A New Strategy for P. gingivalis Infection Control
Authors: Ibrahim Salah mahdi , al-mizragchi Abass sabri , Haider Julfikar
Published: July 2023

Background: The important periodontal disease pathogen Porphyromonas gingivalis produces large biofilms that increase its pathogenicity. Finding natural antimicrobial agents is crucial because of the rise in antibiotic resistance. Objective: The purpose of this study was to determine if plant extracts such as Symphytum officinale (S) and Panax ginseng (G) were effective against P. gingivalis separately and in combination with a common antibiotic Metronidazole (F). Materials and Procedures: Six different dilutions were produced the plant extracts and antibiotic separately and in combination with G and F and S and F using two-fold serial dilution technique. To evaluate the effects of these substances biofilm inhibition experiments were conducted. Plaque samples were collected from periodontitis patients to isolate P. gingivalis and standard strain of P. gingivalis (ATCC 33277) were bought. Additionally, Acylated Homoserine Lactones (AHLs) detection was carried out to look for any activity that would interfere with quorum sensing. GraphPad prism was used for statistical analysis with p value < 0.05. Results: The combinations of Symphytum Officinale and Metronidazole (S+F) showed the maximum effectiveness in biofilm inhibition (98.7%), which was better than G+F (98.2%) with substantial variations in biofilm inhibition levels in different treatment regimes. Notably, the isolate from the patient was more active than the standard strain. Additionally, the plant extracts and their combinations at particular dilutions had notable inhibitory effects on the generation of AHL (p <0.05). Conclusion: The study highlights the possibility of Symphytum Officinale and Panax Ginseng as effective treatments for P. gingivalis biofilm and AHLs, both on their own and in combination with Metronidazole. These organic substances may open the door to cutting-edge methods of treating periodontal disorders.
The Physiological Eﬀects of Some Stress Indicators in Rainbow Trout Raised in Diﬀerent Systems
Authors: Usturoi Alexandru , Păsărin Benone , Usturoi Marius-Giorgi , Davidescu Mădălina , Radu-Rusu Răzvan-Mihail , Simeanu Daniel
Published: July 2023

The general desire of the world's population is to eat as healthily as possible, an aspect that has a direct impact on the technological complex aimed at animals raising (proper breeding systems, microclimate factors with implications for the welfare of animals, etc.), as well as on the quality of the finished products that will enter the food supply. Therefore, the authors set out to study how the growth system influences the health status of rainbow trout raised in different systems. The observed experimental factors did not undergo significant changes. However, differences were generated by the applied growth system. For the amount of glucose in the blood, no statistically significant differences were identified between the groups.
In contrast, comparison of the amount of glycogen led to obtaining very distinctly significant statistical fluctuations (the mean for P-si was 2.314±0.638 and for P-i 1.980±0.822). Growth hormone varied between 0.504±0.46 in the case of P-si and 0.694±0.22 ng/ml for P-i. The values obtained for cortisol showed a significant influence of stress factors on the studied trout.
The general conclusion of the present study is that various technological factors influence the health status of livestock.
Case Report and Mini-Review: Sarcina ventriculi in the Stomach of an 80-Year-Old Female
Authors: Kirmaier Andrea , Kubiak Jeffrey , Mahler Lily , Qian Xia , Wu Leo , Ono Yuho , Riedel Stefan , Medline Alexandra , Yang Xiao , Elamin Sami , Afdhal Nezam , Arnaout Ramy
Published: July 2023

In infectious disease and clinical microbiology, rarely encountered species are often of special concern simply by virtue of their unfamiliarity, especially in settings of complicated underlying disease. This is all the more so when the infectious agent has an appearance that distinguishes it from most commonly encountered organisms, making it a mystery that must be explained. In this context, it is rare for histopathologists to be more familiar with a bacterial species than clinical microbiologists but Sarcina ventriculi is one such example. Infrequently seen in tissue and even less often in culture, we here report a case of Sarcina ventriculi in the GI tract of a geriatric patient with complex underlying history. A brief discussion of the history, clinical presentation, treatment, and culture conditions of this organism is provided, along with clarification of nomenclature, which has changed and could otherwise be a source of additional confusion in this rarely encountered bacterium.
Rapid Chemical Profiling of Filipendula ulmaria Using CPC Fractionation, 2-D Mapping of 13C NMR Data and High-Resolution LC-MS
Authors: Pannakal Steve , Eilstein Joan , Hubert Jane , Kotland Alexis , Prasad Arpita , Gueguiniat-Prevot Amelie , Juchaux Franck , Beaumard Floriane , Seru Ganapaty , John Sherluck , Roy Dhimoy
Published: July 2023

Abstract: Filipendula ulmaria, commonly known as meadowsweet, is a wild herbaceous flowering plant widely distributed in Europe. A range of salicylic acid derivatives and flavonol glycosides have been previously associated with the antirheumatic and diuretic properties of F. ulmaria. In the present work, an hydroalcoholic extract of F. ulmaria aerial parts was extensively profiled using an efficient NMR-based dereplication strategy. The approach involves fractionation of the crude extract by centrifugal partition chromatography (CPC), 13C NMR analysis of the fractions, 2D-cluster mapping of the whole NMR dataset and finally, structure elucidation using a natural metabolite database, validated by 2D NMR data interpretation and liquid chromatography coupled to mass spectrometry. The chemodiversity of the aerial parts was quite broad, with 28 compounds unambiguously identified, belonging to various biosynthetic classes. The F.ulmaria extract and CPC fractions were screened for their potential to improve skin epidermal barrier function and also skin renewal properties using in vitro assays performed on Normal Human Epidermal Keratinocytes. Fractions containing quercetin, kaempferol glycosides, ursolic acid, pomolic acid, naringenin, β-sitosterol, and tellimagrandins I and II were found to be responsible for the up-regulation of genes related to skin barrier function, epidermal renewal and stress responses. This research is significant as it could provide a natural solution for improving hydration and skin renewal properties.
The Current Trend of Radiation Therapy for Patients with Localized Prostate Cancer
Authors: Numakura Kazuyuki , Kobayashi Mizuki , Muto Yumina , Sato Hiromi , Sekine Yuya , Sobu Ryuta , Aoyama Yu , Takahashi Yoshiko , Okada Shuhei , Sasagawa Hajime , Narita Shintaro , Kumagai Satoshi , Wada Yuki , Mori Naoko , Habuchi Tomonori
Published: July 2023

Abstract: A recent approach to radiotherapy for prostate cancer is the administration of high doses of radiation to the prostate while minimizing the risk of side effects. Thus, image-guided radiotherapy utilizes advanced imaging techniques and is a feasible strategy for increasing the radiation dose. New radioactive particles are another approach to achieving high doses and safe procedures. Prostate brachytherapy is currently considered as a combination therapy. Spacers are useful to protect adjacent organs, specifically the rectum, from excessive radiation exposure.
Individualized Vibrotactile Neurofeedback Training in Patients with Chronic Bilateral Vestibulopathy
Authors: Basta Dietmar , Rossi-Izquierdo Marcos , Wonneberger Kai , Brugnera Cibele , Bittar Roseli Saraiva Moreira , Greters Mário Edvin , Ernst Arneborg , Soto-Varela Andrés
Published: July 2023

Patients with bilateral vestibulopathy (BVP) suffer from postural imbalance during daily life conditions which in turn leads to a high frequency of falls. Unfortunately, vestibular rehabilitation has only modest and somewhat inconsistent effects in this patient group. Approximately fifty percent of BVP-patients show an improved postural control after conventional vestibular rehabilitation training. New and more promising approaches are required. The individualized vibrotactile neurofeedback training (IVNT) in stance and gait conditions has already been described as highly effective in patients with various vestibular disorders. The purpose of the present multicenter study was to determine the efficacy of the IVNT in improving balance, reducing self-perceived disability, and improving gait in patients with confirmed BVP. In total, 22 patients performed the IVNT with the Vertiguard®-system for 10 daily sessions. The dizziness handicap inventory (DHI), the stance stability score of the sensory organization test (SOT) and the score for everyday life mobility in stance and gait tasks (SBDT) were obtained immediately before and after the rehabilitation training period as well as 3 and 12 months later. All measures improved significantly after the IVNT. Between 77.3 % and 94.4 % of patients showed an individual benefit (depending on outcome measure). The effect was not significantly reduced within the follow-up period of 12 months. The results demonstrate a high efficacy of the IVNT for vestibular rehabilitation in BVP patients.
Similarities in the Behavior of Transcription Factors in Young Oil Palm (Elaeis guineensis Jacq.) Plants under Salt or Water Stress Provide Strategies to Develop Stress-Tolerant Oil Palm Plants at Once
Authors: Salgado Fernanda Ferreira , Carvalho da Silva Thalliton Luiz , Leão André Pereira , Togawa Roberto Coiti , De Sousa Carlos Antonio Ferreira , Grynberg Priscila , Souza Júnior Manoel Teixeira
Published: July 2023

In recent years, many studies have reported that several distinct families of transcription factor (TF) genes play crucial roles in the response of plants to abiotic stress. Although some of these families got systematically studied in many species, little knowledge exists about these genes in oil palm (Elaeis guineensis Jacq.). In this study, 20 genes differentially expressed in the leaves of oil palm plants subjected to salinity or drought stress and encoding TFs belonging to four families of TFs - MYB, HD-ZIP, NF-Y, and HSFF - got selected for further characterization. The genes underwent a structural and functional annotation, besides having their RNA-Seq expression profile validated by the qPCR technique, and a correlation analysis of their response under both stresses got performed. The annotation analysis of the promoter region showed the presence of seven cis-acting elements, all already reported to be involved in plants' response to abiotic stress. The structural and functional characterization of the proteins encoded by the selected genes showed that some groups present patterns of conserved regions and are orthologs to genes already linked to salinity or drought resistance in other plant species. It was possible to confirm the RNA-Seq expression profile of 19 genes, only gene 4 showed the opposite response when using qPCR. Through correlation analysis, it was possible to observe a high level of similarity in the behavior of the 20 genes in response to drought or salinity stress, a behavior already reported in other species. The results presented here shed light on the role of 20 TFs in the leaves of young oil palm plants under severe levels of soil salinity or water deprivation. The high level of similarity in the molecular response to both stresses allowed the identification of genes that might grant strategies aiming to develop oil palm plants with a tolerance to both salinity and drought at once.
A Richness Estimator Based on Integrated Data
Authors: Chiu Chun-Huo
Published: July 2023

Species richness is a widely used measure for assessing the diversity of a particular area. However, observed richness often underestimates the true richness due to resource limitations, particularly in the small-sized sample or highly heterogeneous assemblage. Estimating species richness in a large-scale region typically involves an integrated data set consisting of subsamples collected independently from different subregions. However, the pooled sample of integrated data is no longer a random sample from the entire region, and the use of different sampling schemes results in variations in data formats. Consequently, employing a single sampling distribution to model the pooled sample becomes impractical, rendering existing richness estimators inadequate. This study theoretically explains the applicability of Chao's lower bound estimators in estimating species richness for large-scale areas using the pooled sample. Additionally, a new nonparametric estimator is introduced, which adjusts the bias of Chao's lower bound estimator by leveraging the Good-Turing frequency formula. This proposed estimator only utilizes the pooled sample's singleton, doubleton, and tripleton richness. Simulated data sets across various models are employed to demonstrate the statistical performance of the estimator, showcasing its ability to reduce bias and provide accurate 95% confidence intervals. Real data sets are also utilized to illustrate the practical application of the proposed approach.
Abundance and Diversification of Repetitive Elements in Decapoda Genomes
Authors: Rutz Christelle , Kress Arnaud , Boštjančić Ljudevit Luka , Bonassin Lena , Francesconi Caterina , Merlat Dorine , Theissinger Kathrin , Lecompte Odile
Published: July 2023

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is picking up, however, current pipelines are failing to identify a significant proportion of divergent repeats in non-model organisms. The order Decapoda, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied on 20 Decapoda and 6 other crustacean genomes. With our new tool we identify 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other crustaceans, with an incredibly large number of highly repeated satDNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and a different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
Underwater Image Restoration and Enhancement: A Comprehensive Review of Recent Trends, Challenges, and Applications
Authors: Alsakar Yasmin M. , Sakr Nehal A , El-Sappagh Shaker , Abuhmed Tamer , Elmogy Mohammed
Published: July 2023

In recent years, underwater exploration for deep-sea resource utilization and development has a considerable interest. In an underwater environment, the obtained images and videos undergo several types of quality degradation resulting from light absorption and scattering, low contrast, color deviation, blurred details, and nonuniform illumination. Therefore, the restoration and enhancement of degraded images and videos are critical. Numerous techniques of image processing, pattern recognition and computer vision have been proposed for image restoration and enhancement, but many challenges remain. This survey presents a comparison of the most prominent approaches in underwater image processing and analysis. It also discusses an overview of the underwater environment with a broad classification into enhancement and restoration techniques and introduces the main underwater image degradation reasons in addition to the underwater image model. The existing underwater image analysis techniques, methods, datasets, and evaluation metrics are presented in detail. Furthermore, the existing limitations are analyzed, which are classified into image-related and environment-related categories. In addition, the performance is validated on images from the UIEB dataset for qualitative, quantitative, and computational time assessment. Areas in which underwater images have recently been applied are briefly discussed. Finally, recommendations for future research are provided and the conclusion is presented.
Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa
Authors: Gana James , Gcebe Nomakorinte , Pierneef Rian , Chen Yi , Moerane Rebome , Adesiyun Abiodun Adewale
Published: July 2023

Whole-genome sequencing (WGS) was used for genomic characterization of 110 strains of Listeria innocua isolated from 23 cattle farms, 8 beef abattoirs, and 48 retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (sources and types of samples) of the L. innocua isolates. The study detected 12 STs, 13 resistance genes, and 23 virulence genes. Of the 12 STs de-tected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (P<0.05). All 110 isolates of L. innocua were car-riers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (P<0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1.svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels (farm, abattoir, and retail outlets) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications..
Effect of Salt Stress on the Phenolic Compounds, Antioxidant Capacity, Microbial Load, and In Vitro Bioaccessibility of Two Microalgae Species (Phaeodactylum tricornutum and Spirulina platensis)
Authors: Uzlasir Turkan , Selli Serkan , Kelebek Hasim
Published: July 2023

Microalgae have gained attention as alternative food sources due to their nutritional value and biological effects. This study investigated the effect of salt stress on the antioxidant activity, phenolic profile, bioa-vailability of bioactive compounds, and microbial counts in the blue-green algae Spirulina platensis and di-atom species Phaeodactylum tricornutum. Culturing these microalgae in different salt concentrations (15 35‰), we observed the highest antioxidant activity and phenolic compounds in the control groups. S. platensis (20‰) exhibited higher antioxidant activity compared to P. tricornutum (30‰), which decreased with in-creasing salt stress. Using HPLC-DAD-ESI-MS/MS, we identified and quantified 20 phenolic compounds in P. tricornutum and 24 in S. platensis. The bioavailability of these compounds was assessed through in vitro di-gestion, with the highest amounts observed in the intestinal phase. Salt stress negatively affected the syn-thesis of bioactive substances. Microbial counts ranged from 300 to 2.78x104 cfu/g for total aerobic mesophilic bacteria and from 10 to 1.35x104cfu/g for yeast/mold in P. tricornutum samples, while S. platensis samples ranged from 300 to 1.9x104cfu/g and 10 to 104 cfu/g, respectively. This study suggests that adding salt at different ratios to the nutrient media during the production of P. tricornutum and S. platensis can impact phenolic compounds, antioxidant capacity, microbial load evaluation, and in vitro bioaccessibility of the studied microalgae.
Double Negative B lymphocytes are increased in patients with Systemic Lupus Erythematosus and they are correlated with early differentiated T lymphocyte subpopulations
Authors: Moysidou Eleni , Lioulios Georgios , Christodoulou Michalis , Xochelli Aliki , Stai Stamatia , Iosifidou Myrto , Iosifidou Artemis , Briza Sophia , Briza Dimitria Ioanna , Fylaktou Asimina , Stangou Maria
Published: July 2023

B and T lymphocytes demonstrate important alterations in patients with Systemic Lupus Erythematous (SLE), with significant up-regulation of Double Negative (DN) B cells. Aim of this study was to evaluate correlation of T cell immunity changes with the distinct B cell-pattern SLE. In the present study, Flow cytometry was performed in 30 patients with SLE, on remission, and 31 healthy controls, to detect DN B cells (CD19+IgD-CD27-) and a wide range of T lymphocyte subpopulations, based on the presence of CD45RA, CCR7, CD31, CD28, CD57, defined as naive, memory and advanced differentiated/senescent T cells. Both B and T lymphocytes were significantly reduced in SLE patients. However, the percentage of DN B cells were increased, compared to HC, 12.9(2.3-74.2) vs. 8(1.7-35), p=0.04. Distribution of CD4 and CD8 lymphocytes demonstrated a shift to advanced differentiated subsets. The population of DN B cells had significant positive correlation with most of early differentiated T lymphocytes, CD4CD31+, CD4CD45RA+CD28+, CD4CD45RA+CD57-, CD4CD45RA-CD57-, CD4CD28+CD57-, CD4CD28+CD57+, CD4 CM, CD8 CD31+, CD8 NAÏVE, CD8CD45RA-CD57-, CD8CD28+CD57-, CD8CD28+CD57+. Multiple Regression analysis revealed CD4CD31+, CD8CD45RA-CD57- and CD8CD28+CD57- cells as independent parameters contributing to DN B cells, adjusted R2=0.534, p<0.0001. The predominance of DN B cells in patients with SLE is closely associated with early differentiated T lymphocyte subsets, indicating a potential causality role of DN B cells in T lymphocyte activation.