bluuebunny/crossref_metadata_2025 huggingface dataset:
Kırgız Türk Akın/Âşık Şiiri Geleneğinde Dine Analitik Bir Bakış
Authors: YILMAZ Mustafa
Published: May 2022

Türk ve Kırgız edebiyatı söz konusu olduğunda 20.yy’e kadar daha çok şiir akla gelmektedir. Bunun sebebi hem sözlü hem de yazılı edebiyatta eserlerin daha çok şiir formatında olmasıdır. Kırgız ve Türk Âşık şiir geleneğinde din, başat bir unsurdur. İslâm, Türk edebiyatının devirlere ayrılmasındaki en önemli faktördür. Bu sebeple âşık şiir geleneğinde din olgusunun iki ayrı dönemde ele alınması doğru olacaktır. Birincisi iki toplumun İslâmiyet öncesi âşıklık geleneğinde din olgusudur. Bu noktada iki toplumun şiir tarihine bakıldığında başlangıcından beri dinin, şiirin yani âşıklık geleneğinin oluşumunda etkili olduğu görülmektedir. İki halkın dini şiirleri mukayeseli olarak incelendiğinde benzer tarihlerde aynı dine inandıkları, bunları âşıklık (akın) geleneğiyle şiirlerine yansıttıkları, bir kısmını da bugünlere kadar saklamayı başardıkları görülmektedir. İkinci olarak İslâmiyet sonrası âşıklık geleneğinde dinin kuvvetli bir şekilde varlığı görülmektedir. İki toplumun İslamlaşma sürecinin farklı olduğunu, şiirlere de farklı yansıdığını görmekteyiz. Bu tebliğde özellikle Türk âşıklık geleneğinin oluşmasında İslâm’ın dolayısıyla tasavvuf düşüncesinin ve tekke pratiğinin üzerinde durulacaktır. Bu tarzın temsilcileri 19. yy sonuna kadar bir tekke ve tarikatla olan irtibatını devam ettirmiştir. Âşık kavramı, başından bugüne kadar Allah/Hakk âşığı anlamında kullanılmıştır. Bu konunun seçilme nedenlerinden biri de başlangıcından günümüze kadar bu geleneğin halkı çok etkilemiş olmasıdır. İki toplumun geleneğinde de bu şiirlerin içinde hurafe ve batıl inançların yer alması önemlidir. Kırgızlar bu ritüellere ırım-cırım der. Bugün Kırgızistan’da eski dinlerle İslam inancının senkronize olarak kullanıldığı, bunun da zenginlik olarak kabul edildiği görülmektedir. Oysa İslâm inancı bunu kabul etmemektedir.
Osmanlı Devleti’nin Afrika Siyasetinde İnsani Değerlerin Analizi Ve Libya Örneği
Authors: KARATEPE Gıyaseddin
Published: May 2022

Afrika’da antik çağlardan itibaren yaklaşık kırk beş kadar güçlü medeniyet tesbit edilmiştir. Afrika, Mısır, Habeş, Kartaca, Gao, Zulu gibi örnekler dahil, sosyal değerler, kültürel birikim ve sanatsal zenginliğe sahiptir. İslam Medeniyeti farklı kültür ve medeniyetleri yok etmeksizin, onları zenginlik olarak kabul ederek dönüştürme kabiliyetine sahiptir. Afrika’nın İslam medeniyetiyle tanışması, kaynaşmasıyla Sicilya ve Endülüs başta olmak üzere çok sayıda mamur şehirler ve ilim merkezleri kurulmuştur. Afrika Bu medeniyet Orta çağın kaotik çatışmaları ve skolastik felsefenin kıskacındaki Avrupa’yı derinden etkilemiş ve Rönesans hareketlerine ilham kaynağı olmuştur. Afrika İslam medeniyeti tarihte önemli bir yer edinmiştir. Osman’lının Afrika ile temasında 1492’de son Endülüs Emirliğinin yıkılması ile savunmasız duruma düşen Endülüs Müslümanları’nın yardım çağrısı kilit bir dönemdir. ll.Beyazıt döneminde gönderilen yardım gemileriyle müslümanlar Kuzey Afrika bölgelerine nakledilmişlerdir. Osmanlılar, 1517 tarihinde Mısır’ı fethederek İslam hilafetini Memlukler’den devralmışlardır. Fas, Cezayir, Tunus, Trablusgarb Osmanlı hakimiyetine geçmiştir. Böylece Kuzey Afrika’ya yönelen İspanyol saldırıları önlenmiştir. Kuzey Afrika mahalli yöneticilerinin çağrıları üzerine Kanuni döneminde Bahriye kuvvetleri intikal etmiş, işgal kuvvetleri uzaklaştırılmıştır. Bilahare mahalli yönetimler Osmanlı devletine gönüllü olarak katılmışlardır. Osmanlı Devleti, Libya’da, bölgenin sosyolojik ve kültürel değerlerini daima dikkate almıştır. Bingazi, Derne, Mısurata, Trablusgarp ve Zaviye gibi şehirlerde kapsamlı imar faaliyetleri gerçekleştirilmiştir. Medreseler, camiler, zaviyeler, şifahaneler, su kanalları yapılmıştır. Güvenli ticaret yolları, adalet sistemi ve kamu yönetimi teşkilatıyla bölgede derin izler bırakılmıştır. Afrika’nın bir çok yerinde aynı izleri görmek mümkündür.
LEAVE MANAGEMENT SYSTEM USING WEB SERVICE WORKER AND CHUNKING OF IMAGE SUBMISSION
Authors:   College of Information Technology Mindanao State University Marawi City, Lanao del Sur, Philippines, C. Mama Jasmin Jeanette , Garillo Christian L. ,   Computer Studies Department Mindanao State University – Iligan Institute of Technology Iligan City, Philippines.
Published: May 2022

Filing a leave of absence is typical for any employee. Employees may be required to submit applications which must be fully accomplished before approval. The aim of this project is like a document tracking system for leave applications through a web application. A responsive web application for leave management system where the applicant will know the status of his/her request. The administration will then be notified if there are requests submitted to them. What makes this project efficient is the incorporation of the service worker, a cutting-edge technology, in web development. A service worker is a type of web worker. It is essentially a JavaScript file that runs separately from the main browser thread, intercepting network requests, caching or retrieving resources from the cache, and delivering push messages. [1] Since service workers run separately from the main thread, workers are independent of the application they are associated with. Some parts of the project are usable offline using the HTTP request. Since leave applications may have image attachments, this system will make it possible to submit images by chunks. Chunking of images is important because there are instances where uploading may fail due to large files or slow internet connection. The use of web service workers provides the accessibility of the application even offline. While chunking of images makes it possible to submit images even on slow connectivity. The implementation of online leave management is geared toward making leave applications simple and convenient and is readily accessible for both the management and the employee.
Utility of the Basophil Activation Test Using Gly m 4, Gly m 5 and Gly m 6 Molecular Allergens for Characterizing Anaphylactic Reactions to Soy
Authors: Evrard Bertrand , Cosme Justine , Raveau Marion , Junda Maud , Michaud Elodie , Bonnet Benjamin
Published: May 2022

There are two major clinically described forms of IgE-dependent soy allergy: (i) a primary dietary form, linked to sensitization against soy storage proteins Gly m 5 and Glym 6, and (ii) a form included in birch-soy syndromes linked to Gly m 4, a PR-10-like allergen. This second form sometimes causes severe systemic reactions, even anaphylaxis, especially on consuming certain forms of soy such as soymilks or smoothies. Skin prick tests and specific IgE assays against soy whole extracts lack sensitivity. Assays of anti-Gly m 4, Gly m 5 and Gly m 6 specific IgEs have been developed to overcome this obstacle, but they unfortunately lack specificity, especially for anti-Gly m 4. We hypothesized that the basophil activation test (BAT) using molecular soy allergens Gly m 4, Gly m 5 and Gly m 6 would both remedy the lack of sensitivity of other tests and offer, through its mechanistic contribution, greater specificity than the assay of anti-Gly m 4 specific IgEs. This would enable the two types of soy allergy to be separately identified. In a characteristic clinical example of PR-10-induced anaphylactic reaction after consuming soymilk, we report preliminary results of Gly m 4-exclusive positivity of BAT supporting our hypothesis. It will be necessary to confirm these results on more patients in subsequent studies, and to specify the place of the BAT in an overall diagnostic strategy. Meanwhile, soy BAT using molecular allergens is a promising diagnostic tool for soy allergy and probably also for follow-up in specific immunotherapies.
MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
Authors: Saenz Carmen , Nigro Eleonora , Gunalan Vithiagaran , Arumugam Manimozhiyan
Published: May 2022

Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome’s contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.
Architecture Typology of Rural Plain Houses Based on Formal Features, Case Study: (Talesh, Iran)
Authors: Ghanbari Sousan , Yeganeh Mansour , Reza bemanian Mohammad
Published: May 2022

Housing is the most essential human need that in the past, rural houses have met this need well. Indigenous rural homes have undergone changes over time, some of which have been based on internal needs and needs, and some have been due to development and exogenous changes. One of the most critical steps to identify this type of change is the typology of indigenous homes; In this way, an essential step in the path of cognition, understanding and more coverage of this phenomenon is taken. Based on this, the present study intends to study and analyze the architectural types of houses in Talesh village, which originate from human nature, natural space and the bed in which they are formed. Therefore, to estimate the proportions and classification of the architectural plans of its houses, it is necessary to use a quantitative-qualitative research method. Mathematics is used in the Python programming language in data analysis. For this purpose, by selecting 150 samples of rural houses in the form of purposeful clusters and converting the created matrix from the dimensions and size of the plans to zero and one code, their similarity has been calculated. They are in close categories. Findings obtained by simulating the plans show that sloping roofs, building elevation, east-west orientation, porch, open plan and natural ventilation are common features in all indigenous houses. It is found in this area. Therefore, in general, the two architectural patterns in this area are one-story houses and Telar houses, in which high chair houses are a frequent type.
“Orphan” Connexin43 in Plakophilin-2 Deficient Hearts Revealed by Volume Electron Microscopy
Authors: van Opbergen Chantal J. M. , Sall Joseph , Petzold Chris , Dancel-Manning Kristen , Delmar Mario , Liang Feng-Xia
Published: May 2022

Previous studies revealed an abundance of functional Connexin43 (Cx43) hemichannels consequent to loss of plakophilin-2 (PKP2) expression in adult murine hearts. The increased Cx43-mediated membrane permeability is likely responsible for excess entry of calcium into the cells, leading to an arrhythmogenic/cardiomyopathic phenotype. The latter has translational implications to the molecular mechanisms of inheritable arrhythmogenic right ventricular cardiomyopathy (ARVC). Despite functional evidence, visualization of these “orphan” (i.e., non-paired in a gap junction configuration) Cx43 hemichannels remains lacking. Immuno-electron microscopy (IEM) remains an extremely powerful tool to localize, with nanometric resolution, a protein within its native structural landscape. Yet, challenges for IEM are to preserve the antigenicity of the molecular target and to provide access for antibodies to reach their target, while maintaining the cellular/tissue ultrastructure. Fixation is important for maintaining cell structure, but strong fixation and vigorous dehydration (as it is routine for EM) can alter protein structure, thus impairing antigen-antibody binding. Here, we implemented a method to combine pre-embedding immunolabeling (pre-embedding) with serial block-face scanning electron microscopy (SBF-SEM). We utilized a murine model of cardiomyocyte-specific, Tamoxifen (TAM) activated knockout of PKP2. Adult hearts were harvested 14 days post-TAM, at this time hearts present a phenotype of concealed ARVC (i.e., an arrhythmogenic phenotype but no overt structural disease). Thick (200 µm) vibratome slices were immunolabelled for Cx43 and treated with nanogold or FluoroNanogold, coupled with a silver enhancement. Left or right ventricular free walls were dissected and three-dimensional (3D) localization of Cx43 in cardiac muscle was performed using SBF-SEM. Reconstructed images allowed us to visualize the entire length of gap junction plaques, seen as two parallel, closely packed strings of Cx43-immunoreactive beads at the intercalated disc. In contrast, in PKP2-deficient hearts we observed bulging of the intercellular space, and entire areas where only one of the two strings could be observed, indicating the presence of orphan Cx43. We conclude that pre-embedding and SBF-SEM allowed visualization of cardiac Cx43 plaques in their native environment, providing for the first time a visual complement of functional data indicating the presence of orphan Cx43 hemichannels resulting from loss of desmosomal integrity in the heart.
Specificity of Nuclear Size Scaling in Frog Erythrocytes
Authors: Niide Tetsufumi , Asari Saki , Kawabata Kosuke , Hara Yuki
Published: May 2022

In eukaryotes, the cell has the ability to modulate the size of the nucleus depending on the surrounding environment, to enable nuclear functions such as DNA replication and transcription. From previous analyses of nuclear size scaling in various cell types and species, it has been found that eukaryotic cells have a conserved scaling rule, in which the nuclear size correlates with both cell size and genomic content. However, there are few studies that have focused on a certain cell type and systematically analyzed the size scaling properties in individual species (intra-species) and among species (inter-species), and thus, the difference in the scaling rules among cell types and species is not well understood. In the present study, we analyzed the size scaling relationship among three parameters, nuclear size, cell size, and genomic content, in our measured datasets of terminally differentiated erythrocytes of five Anura frogs and collected datasets of different species classes from published papers. In the datasets of isolated erythrocytes from individual frogs, we found a very weak correlation between the measured nuclear and cell cross-sectional areas. Within the erythrocytes of individual species, the correlation of the nuclear area with the cell area showed a very low hypoallometric relationship, in which the relative nuclear size decreased when the cell size increased. These scaling trends in intra-species erythrocytes are not comparable to the known general correlation in other cell types. When comparing parameters across species, the nuclear areas correlated with both cell areas and genomic contents among the five frogs and the collected datasets in each species class. However, the contribution of genomic content to nuclear size determination was smaller than that of the cell area in all species classes. In particular, the estimated degree of the contribution of genomic content was greater in the amphibian class than in other classes. Together with our imaging analysis of structural components in nuclear membranes, we hypothesized that the observed specific features in nuclear size scaling are achieved by the weak interaction of the chromatin with the nuclear membrane seen in frog erythrocytes.
AM1241-Loaded Poly(ethylene glycol)–Dithiothreitol Hydrogel Repairs Cranial Bone Defects by Promoting Vascular Endothelial Growth Factor and COL-1 Expression
Authors: Ai Yilong , She Wenting , Wu Siyuan , Shao Qing , Jiang Ziran , Chen Pengcheng , Mei Li , Zou Chen , Peng Youjian , He Yan
Published: May 2022

Objective: To explore the repair effect of the prepared drug-loaded AM1241 poly(ethylene glycol)–dithiothreitol (PEG-DTT) hydrogel on cranial bone defects in SD rats.

Methods: The PEG-DTT hydrogel under borax catalysis was quickly prepared, and the characterization of the material was observed by a scanning electron microscope. The effect of AM1241 on cell activity and bone tissue differentiation was tested. The SD rat model of cranial bone defect was established, and the defect was repaired by injecting the prepared hydrogel into the defect. The defect was divided into four groups, namely, sham group, blank group, PEG-DTT group, and PEG-DTT + AM1241 group. The rats were euthanized, and whole cranial bone was taken out for micro-CT and histological observation.

Results: The prepared hydrogel is porous; it is liquid when heated to 80°C and a hydrogel when cooled to 25°C. 5–10 μM AM1241 increased osteoblast activity. A moderate amount of AM1241 can promote osteogenic differentiation. Both the PEG-DTT group and PEG-DTT + AM1241 group showed obvious new bone tissue formation, but the PEG-DTT + AM1241 group had a better effect. In addition, the new bone tissue in the PEG-DTT + AM1241 group was significantly more than that in the other groups.

Conclusion: The prepared AM1241-loaded PEG-DTT hydrogel showed a good repair effect on SD rats with cranial bone defects. It can be used as materials for cranial bone repair in SD rats with cranial bone defects, but the repair effect is weaker than that of normal bone. These results provide a theoretical and practical basis for its further clinical application.
Design, Synthesis, and Apoptosis-Promoting Effect Evaluation of Rhopaladins’ Analog 4-Arylidene-5-Oxopyrrolidine Derivatives
Authors: Zhu Jun , Kong Ling-Qi , Chen Qin-Hua , Li Bin , Wu Lun , Ran Feng-Ying , Ke Li-Na , Zeng Xiao-Hua , Wang Hong-Mei
Published: May 2022

Marine alkaloids have novel structures and antitumor activities. Therefore, we synthesized rhopaladins’ analogs from marine alkaloids rhopaladins A-D and modified their structures to synthesize 4-benzylidene-5-pyrrolidone derivatives. Among the compounds, (2E, 4E)-4-(4-chlorobenzylidene)-2-(4-chlorostyryl)-N-cyclohexyl-1-(4-fluorophenyl)-5-oxopyrrolidine-2-carboxamide (RPDPRH) has high efficiency and less hepatotoxicity, with IC50 values of 4.66, 6.42, 17.66, 15.2, 12.36, 22.4, and 243.2 μM in vitro anti-proliferative activity testing against cervical cancer C-33A, CaSki, SiHa, and HeLa cells, human hepatocarcinoma HepG2 and 7402 cells, and human normal liver LO2 cells, respectively. In particular, RPDPRH has similar activity to cisplatin on human hepatocarcinoma cells, and cisplatin served as a positive control in our study. Next, the apoptosis of HepG2 and 7402 cells induced by RPDPRH at different concentrations was detected by Annexin V/PI flow cytometry. Moreover, the expression of apoptotic proteins was detected by Western blot analysis. Finally, the results showed that RPDPRH could induce apoptosis of hepatocarcinoma cells by regulating Bax and Bcl-2 expressions. In summary, our results indicate that RPDPRH has the potential to serve as an antitumor agent and plays a significant role in future studies.
Sex Differences in the Outcomes of Cryoablation for Atrial Fibrillation
Authors: Hermida Alexis , Burtin Jacqueline , Kubala Maciej , Fay Floriane , Lallemand Pierre-Marc , Buiciuc Otilia , Lieu Audrey , Zaitouni Mustafa , Beyls Christophe , Hermida Jean-Sylvain
Published: May 2022

Background

The literature data on the outcomes of radiofrequency catheter ablation for atrial fibrillation (AF) in women are contradictory.

Aim

To determine and compare the outcomes and complications of cryoballoon pulmonary vein isolation (cryo-PVI) in men vs. women, and to identify predictors of atrial tachyarrhythmia (ATa) recurrence.

Methods

We included all consecutive patients having undergone cryo-PVI for the treatment of symptomatic AF in our center since 2012. Peri-operative complications were documented. All patients were prospectively monitored for the recurrence of ATa, and predictors were assessed.

Results

A total of 733 patients were included (550 men (75%) and 183 (25%) women). Paroxysmal AF was recorded in 112 (61%) female patients and 252 male patients (46%; p < 0.001). Female patients were older (p < 0.001) and had a greater symptom burden (p = 0.04). Female patients were more likely to experience complications (p = 0.02). After cryo-PVI for paroxysmal AF, 66% of the female patients and 79% of the male patients were free of ATa at 24 months (p = 0.001). Female sex was the only independent predictive factor for ATa recurrence (hazard ratio [95% confidence interval] = 1.87 [1.28; 2.73]; p = 0.001). After cryo-PVI for non-paroxysmal AF, 37% of the male patients and 39% of the female patients were free of ATa at 36 months (p = 0.73). Female patients were less likely than male patients to undergo repeat ablation after an index cryo-PVI for non-paroxysmal AF (p = 0.019).

Conclusion

A single cryo-PVI procedure for paroxysmal AF was significantly less successful in female patients than in male patients. Overall, the complication rate was higher in women than in men.
Estradiol and Hyperhomocysteinemia Are Linked Predominantly Through Part Renal Function Indicators
Authors: Niu Xiao Na , Wen He , Sun Nan , Yang Yi , Du Shi Hong , Xie Rong , Zhang Yan Nan , Li Yan , Hong Xiu Qin
Published: May 2022

Background

Previous studies have shown that estrogen, kidney function, and homocysteine (Hcy) or hyperhomocysteinemia (HHcy) are related to each other. However, the underlying biological mechanisms still remain unclear. We aimed to explore the association between estradiol (E2) and HHcy in the female population, and to further evaluate the mediating role of renal function indicators.

Methods

This unmatched case–control study consisted of 1,044 female participants who were 60.60 ± 12.46 years old. Data on general demographic characteristics, such as age, smoking and drinking status, menopause and so on were collected in a personal interview, and laboratory examinations were performed by well-trained personnel. The mediating effect model was applied to analyze the direct and indirect effects of E2 on Hcy.

Results

The average levels of Hcy and E2 of the participants were 12.6 μmol/L and 14.95 pg/ml. There were statistical differences in renal indexes blood urea nitrogen (BUN), serum creatinine (Scr), uric acid (UA), glomerular filtration rate (GFR) and E2 between HHcy group and non-HHcy group. The logistic regression models showed that UA was risk factor for HHcy (P <0.001), GFR and E2 were protective factors for HHcy after adjusting for confounding factors (P <0.001). The indirect effects of E2 on Hcy through UA and GFR accounted for 14.63 and 18.29% of the total impacts of E2 on Hcy.

Conclusions

These data indicated that E2 was a protective factor of HHcy, and the effects of E2 on HHcy may be mediated by renal function indicators UA and GFR.
Placenta Accreta Spectrum Among Multiple Gestation: A Retrospective Analysis Based on a Chinese Population
Authors: Guo Zhirong , Han Xueyan , Zheng Weiran , Yang Huixia , Ma Jingmei
Published: May 2022

Background

It remained controversial whether women with multiple gestation are at higher risk of placenta accreta spectrum (PAS) disorders and large-scale studies are needed. This study aimed to assess whether PAS incidence is higher among women with multiple gestation than among singleton, as well as to compare the characteristics and outcomes of PAS in multiple and singleton gestation.

Methods

Women who underwent cesarean section with live births at Peking University First Hospital from January 2015 to December 2020 were included. Demographic and clinical information was collected through chart review. Logistic regression models were used to analyze the associations between multiple gestation and PAS. The clinical characteristics and perioperative outcomes of PAS in multiple and singleton gestation were further compared.

Results

Among the 14583 women included, 2.4% (352/14583) were diagnosed with PAS. PAS was slightly more prevalent among multiple gestations than among singletons (2.5% vs 2.4%, P=0.857). After adjusting for known risk factors and pregnancy complications, multiple gestation was associated with a higher risk of PAS (aOR=1.63, 95% CI 1.01-2.62). Among PAS patients, women who had multiple births had a significantly lower rate of previous cesarean deliveries (27.6% vs. 56.3%, P=0.003), placenta previa (17.2% vs. 56.3%, P<0.001) and invasive PAS (24.1% vs. 53.9, P=0.002) than singletons. There were no significant differences in perioperative outcomes between these two groups.

Conclusion

Multiple gestation could be independently associated with an elevated risk of PAS. The clinical characteristics of PAS in the multiple and singleton gestation groups differed significantly in cesarean delivery history and placenta previa. The results of this study may inform guidelines on the screening, early detection and timely intervention of PAS patients among women with multiple births.
Research on Countercurrent Flow Limitation in Reactor Hot Leg at the Loss of Coolant Accident-Thermohydraulic Calculation With System Code RELAP5
Authors: Li Xiang , Gao Lingyuan , Xu Caihong , Wang Ting , Sun Wan , Zhu Wen , Zhang Luteng , Ma Zaiyong , Zhu Longxiang , Pan Liangming
Published: May 2022

Since the counter current flow limitation (CCFL) of the two-phase flow has an important influence on the safety analysis of the reactor, it is also of great significance to study some characteristics and flow pattern transitions of the two-phase flow. In order to explore the characteristics and influencing factors of two-phase counter current flow in the hot leg under the condition of the Loss of Coolant Accident, this research, using RELAP5 simulation calculation, analyzed the effect of the lengths of the flow path of the hot leg, the shapes of the upper outlet of the inclined pipe, and the shapes of the elbow connecting the horizontal pipe and the inclined pipe on the characteristics of the CCFL. This research also evaluated the limitation of the model. The simulation founded that under the same liquid flow rate, the longer the horizontal pipe, the lower the gas flow rate at the beginning of the counter current flow; the effect of the elbow on the CCFL was not great; compared with the sharp outlet shape, the Jf of the gentle circle was slightly larger. The method established in this study is suitable for the prediction of CCFL in the hot leg during Loss of Coolant Accident.
Comparative Analysis of the Gut Microbiota of Mandarin Fish (Siniperca chuatsi) Feeding on Compound Diets and Live Baits
Authors: Chen Xiao , Sun Chengfei , Dong Junjian , Li Wuhui , Tian Yuanyuan , Hu Jie , Ye Xing
Published: May 2022

Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.
SPDL1 Overexpression Is Associated With the 18F-FDG PET/CT Metabolic Parameters, Prognosis, and Progression of Esophageal Cancer
Authors: Liu Hua-Song , Guo Qiang , Yang Heng , Zeng Min , Xu Li-Qiang , Zhang Qun-Xian , Liu Hua , Guo Jia-Long , Zhang Jun
Published: May 2022

Esophageal cancer (ESCA) is one of the common malignant tumors. The roles and signaling mechanisms of spindle apparatus coiled-coil protein 1 (SPDL1) in ESCA progression have not been reported previously. Therefore, the expression levels and potential clinical roles of SPDL1 were investigated using data from multiple databases and tissue samples of 53 ESCA patients who underwent 18F-FDG positron emission tomography (PET)/computed tomography (CT) before therapy. The signaling mechanisms of SPDL1 involved in ESCA progression were investigated via bioinformatics analysis. The effects of SPDL1 on the growth and migration of ESCA cells were investigated using CCK-8, Edu, and transwell assays. SPDL1 was upregulated in ESCA tissues. Increased SPDL1 expression was associated with age, grade, drinking history, cancer stage, lymph node metastasis, TP53 mutation, and poor prognosis in patients with ESCA. SPDL1 overexpression was significantly correlated with SUVmax, SUVmean, and TLG of PET/CT. SPDL1 silencing inhibited cell proliferation, migration, and invasion. SPDL1 was significantly enriched in cell cycle, spliceosome, DNA replication, and other processes. The hub genes of a constructed protein–protein interaction network included CDK1, BUB1, CCNB1, BUB1B, CCNA2, CDC20, MAD2L1, AURKB, NDC80, and PLK1, which were related to SPDL1 expression. The findings of this study suggest that SPDL1 may serve as a biomarker of ESCA prognosis.
A Prognostic Survival Model of Pancreatic Adenocarcinoma Based on Metabolism-Related Gene Expression
Authors: Xie Lin-ying , Huang Han-ying , Fang Tian , Liang Jia-ying , Hao Yu-lei , Zhang Xue-jiao , Xie Yi-xin , Wang Chang , Tan Ye-hui , Zeng Lei
Published: May 2022

Accurately predicting the survival prospects of patients suffering from pancreatic adenocarcinoma (PAAD) is challenging. In this study, we analyzed RNA matrices of 182 subjects with PAAD based on public datasets obtained from The Cancer Genome Atlas (TCGA) as training datasets and those of 63 subjects obtained from the Gene Expression Omnibus (GEO) database as the validation dataset. Genes regulating the metabolism of PAAD cells correlated with survival were identified. Furthermore, LASSO Cox regression analyses were conducted to identify six genes (XDH, MBOAT2, PTGES, AK4, PAICS, and CKB) to create a metabolic risk score. The proposed scoring framework attained the robust predictive performance, with 2-year survival areas under the curve (AUCs) of 0.61 in the training cohort and 0.66 in the validation cohort. Compared with the subjects in the low-risk cohort, subjects in the high-risk training cohort presented a worse survival outcome. The metabolic risk score increased the accuracy of survival prediction in patients suffering from PAAD.
Improvement of Genomic Predictions in Small Breeds by Construction of Genomic Relationship Matrix Through Variable Selection
Authors: Mancin Enrico , Mota Lucio Flavio Macedo , Tuliozi Beniamino , Verdiglione Rina , Mantovani Roberto , Sartori Cristina
Published: May 2022

Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value—which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models—especially those using XGBoost—in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds.
Plant Genotype to Phenotype Prediction Using Machine Learning
Authors: Danilevicz Monica F. , Gill Mitchell , Anderson Robyn , Batley Jacqueline , Bennamoun Mohammed , Bayer Philipp E. , Edwards David
Published: May 2022

Genomic prediction tools support crop breeding based on statistical methods, such as the genomic best linear unbiased prediction (GBLUP). However, these tools are not designed to capture non-linear relationships within multi-dimensional datasets, or deal with high dimension datasets such as imagery collected by unmanned aerial vehicles. Machine learning (ML) algorithms have the potential to surpass the prediction accuracy of current tools used for genotype to phenotype prediction, due to their capacity to autonomously extract data features and represent their relationships at multiple levels of abstraction. This review addresses the challenges of applying statistical and machine learning methods for predicting phenotypic traits based on genetic markers, environment data, and imagery for crop breeding. We present the advantages and disadvantages of explainable model structures, discuss the potential of machine learning models for genotype to phenotype prediction in crop breeding, and the challenges, including the scarcity of high-quality datasets, inconsistent metadata annotation and the requirements of ML models.
A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle
Authors: Alves Anderson Antonio Carvalho , da Costa Rebeka Magalhães , Fonseca Larissa Fernanda Simielli , Carvalheiro Roberto , Ventura Ricardo Vieira , Rosa Guilherme Jordão de Magalhães , Albuquerque Lucia Galvão
Published: May 2022

This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores within the tree ensemble non-linear structure. Data from Nellore cattle were used, including records of animals born between 1984 and 2015 and raised in commercial herds located in different regions of Brazil. The estimated breeding values (EBV) were computed and used as the response variable in the genomic analyses. After quality control, the remaining number of animals and SNPs considered were 3,174 and 360,130, respectively. Five independent RF analyses were carried out, considering different initialization seeds. The importance score of each SNP was averaged across the independent RF analyses to rank the markers according to their predictive relevance. A total of 117 SNPs associated with AFC were identified, which spanned 10 autosomes (2, 3, 5, 10, 11, 17, 18, 21, 24, and 25). In total, 23 non-overlapping genomic regions embedded 262 candidate genes for AFC. Enrichment analysis and previous evidence in the literature revealed that many candidate genes annotated close to the lead SNPs have key roles in fertility, including embryo pre-implantation and development, embryonic viability, male germinal cell maturation, and pheromone recognition. Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening candidate regions associated with complex traits. Complementary analyses revealed that many SNPs top-ranked in the RF-based GWAS did not present a strong marginal linear effect but are potentially involved in epistatic hotspots between genomic regions in different autosomes, remarkably in the BTAs 3, 5, 11, and 21. The reported results are expected to enhance the understanding of genetic mechanisms involved in the biological regulation of AFC in this cattle breed.
Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs
Authors: Guvenek Aysegul , Shin Jihae , De Filippis Lidia , Zheng Dinghai , Wang Wei , Pang Zhiping P. , Tian Bin
Published: May 2022

RNA stability plays an important role in gene expression. Here, using 3′ end sequencing of newly made and pre-existing poly(A)+ RNAs, we compare transcript stability in multiple human cell lines, including HEK293T, HepG2, and SH-SY5Y. We show that while mRNA stability is generally conserved across the cell lines, specific transcripts having a high GC content and possibly more stable secondary RNA structures are relatively more stable in SH-SY5Y cells compared to the other 2 cell lines. These features also differentiate stability levels of alternative polyadenylation (APA) 3′UTR isoforms in a cell type-specific manner. Using differentiation of a neural stem cell line as a model, we show that mRNA stability difference could contribute to gene expression changes in neurogenesis and confirm the neuronal identity of SH-SY5Y cells at both gene expression and APA levels. In addition, compared to transcripts using 3′-most exon cleavage/polyadenylation sites (PASs), those using intronic PASs are generally less stable, especially when the PAS-containing intron is large and has a strong 5′ splice site, suggesting that intronic polyadenylation mostly plays a negative role in gene expression. Interestingly, the differential mRNA stability among APA isoforms appears to buffer PAS choice in these cell lines. Moreover, we found that several other poly(A)+ RNA species, including promoter-associated long noncoding RNAs and transcripts encoded by the mitochondrial genome, are more stable in SH-SY5Y cells than the other 2 cell lines, further highlighting distinct RNA metabolism in neuronal cells. Together, our results indicate that distinct RNA stability control in neuronal cells may contribute to the gene expression and APA programs that define their cell identity.
Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae
Authors: Ba Hengxing , Chen Min , Li Chunyi
Published: May 2022

Antlers constitute an interesting model for basic research in regenerative biology. Despite decades of being studied, much is still unknown about the genes related to antler development. Here, we utilized both the genome and antlerogenic periosteum (AP) transcriptome data of four deer species to reveal antler-related genes through cross-species comparative analysis. The results showed that the global gene expression pattern matches the status of antler phenotypes, supporting the fact that the genes expressed in the AP may be related to antler phenotypes. The upregulated genes of the AP in three-antlered deer showed evidence of co-expression, and their protein sequences were highly conserved. These genes were growth related and likely participated in antler development. In contrast, the upregulated genes in antler-less deer (Chinese water deer) were involved mainly in organismal death and growth failure, possibly related to the loss of antlers during evolution. Overall, this study demonstrates that the co-expressed genes in antlered deer may regulate antler development.
Identification of mRNA Signature for Predicting Prognosis Risk of Rectal Adenocarcinoma
Authors: Jiang Linlin , Wang Peng , Su Mu , Yang Lili , Wang Qingbo
Published: May 2022

Background: The immune system plays a crucial role in rectal adenocarcinoma (READ). Immune-related genes may help predict READ prognoses.

Methods: The Cancer Genome Atlas dataset and GSE56699 were used as the training and validation datasets, respectively, and differentially expressed genes (DEGs) were identified. The optimal DEG combination was determined, and the prognostic risk model was constructed. The correlation between optimal DEGs and immune infiltrating cells was evaluated.

Results: Nine DEGs were selected for analysis. Moreover, ADAMDEC1 showed a positive correlation with six immune infiltrates, most notably with B cells and dendritic cells. F13A1 was also positively correlated with six immune infiltrates, particularly macrophage and dendritic cells, whereas LGALS9C was negatively correlated with all immune infiltrates except B cells. Additionally, the prognostic risk model was strongly correlated with the actual situation. We retained only three prognosis risk factors: age, pathologic stage, and prognostic risk model. The stratified analysis revealed that lower ages and pathologic stages have a better prognosis with READ. Age and mRNA prognostic factors were the most important factors in determining the possibility of 3- and 5-year survival.

Conclusion: In summary, we identified a nine-gene prognosis risk model that is applicable to the treatment of READ. Altogether, characteristics such as the gene signature and age have a strong predictive value for prognosis risk.
Engineering Human Circulating Monocytes/Macrophages by Systemic Deliverable Gene Editing
Authors: Lee So Yoon , Fierro Javier , Dipasquale Jake , Bastian Anthony , Tran An M. , Hong Deawoo , Chin Brandon , Nguyen-Lee Paul J. , Mazal Sarah , Espinal Jamil , Thomas Tima , Dou Huanyu
Published: May 2022

Delivery of plasmid DNA to transfect human primary macrophages is extremely difficult, especially for genetic engineering. Engineering macrophages is imperative for the treatment of many diseases including infectious diseases, cancer, neurological diseases, and aging. Unfortunately, plasmid does not cross the nuclear membranes of terminally differentiated macrophages to integrate the plasmid DNA (pDNA) into their genome. To address this issue, we have developed a core-shell nanoparticle (NP) using our newly created cationic lipid to deliver the anti-inflammatory cytokine IL-4 pDNA (IL-4pDNA-NPs). Human blood monocyte-derived macrophages (MDM) were effectively transfected with IL-4pDNA-NPs. IL-4pDNA-NPs were internalized in MDM within 30 minutes and delivered into the nucleus within 2 hours. Exogenous IL-4 expression was detected within 1 - 2 days and continued up to 30 days. Functional IL-4 expression led to M2 macrophage polarization in vitro and in an in vivo mouse model of inflammation. These data suggest that these NPs can protect pDNA from degradation by nucleases once inside the cell, and can transport pDNA into the nucleus to enhance gene delivery in macrophages in vitro and in vivo. In this research, we developed a new method to deliver plasmids into the nucleus of monocytes and macrophages for gene-editing. Introducing IL-4 pDNA into macrophages provides a new gene therapy solution for the treatment of various diseases.
Lessons From Transcriptome Analysis of Autoimmune Diseases
Authors: Nagafuchi Yasuo , Yanaoka Haruyuki , Fujio Keishi
Published: May 2022

Various immune cell types, including monocytes, macrophages, and adaptive immune T and B cells, play major roles in inflammation in systemic autoimmune diseases. However, the precise contribution of these cells to autoimmunity remains elusive. Transcriptome analysis has added a new dimension to biology and medicine. It enables us to observe the dynamics of gene expression in different cell types in patients with diverse diseases as well as in healthy individuals, which cannot be achieved with genomic information alone. In this review, we summarize how transcriptome analysis has improved our understanding of the pathological roles of immune cells in autoimmune diseases with a focus on the ImmuNexUT database we reported. We will also discuss the common experimental and analytical design of transcriptome analyses. Recently, single-cell RNA-seq analysis has provided atlases of infiltrating immune cells, such as pro-inflammatory monocytes and macrophages, peripheral helper T cells, and age or autoimmune-associated B cells in various autoimmune disease lesions. With the integration of genomic data, expression quantitative trait locus (eQTL) analysis can help identify candidate causal genes and immune cells. Finally, we also mention how the information obtained from these analyses can be used practically to predict patient prognosis.