bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparative metagenomic approach to detect pathogenic bacteria in commercial broilers affected with respiratory disease complex
Authors: Patel J. G. , Patel B. J. , Joshi D. V. , Patel S. S. , Patel R. K. , Gandhi H. , Raval S. H. , Parmar R. S.
Published: October 2022

Respiratory disease complex is a serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide. A metagenomic approach was used to investigate bacterial abundance and diversity using Whole genome shotgun sequencing of clinically diseased and healthy broiler affected with respiratory disease complex. The data were analyzed using best hit approach through MG-RAST. Sequences predominantly aligned with the phyla Proteobacteria followed by Bacteroidetes in samples from clinically diseased broiler affected with respiratory disease complex, whereas Chlamydiae followed by Proteobacteria in sample from apparently healthy broiler birds. At the species level Escherichia coli, Ornithobacterium rhinotracheale and Pseudomonas aruginosa were predominant in diseased birds, Chlamydia psittaci, Mycoplasma gallisepticum, Lactobacillus agilis and Gallibacterium anatis were predominated bacterial species found in the apparently healthy birds. Higher alpha diversity indices and richness values were found for the bacterial communities in clinically diseased broiler birds as compared to healthy birds. The present study findings may help in formulating strategies for the prevention, control and treatment of respiratory infections in birds and consequently also reducing economic losses in poultry industries.
Switchable pH-responsive Pickering stabilizers made by sonothermal glycation of sodium caseinate with κappa- carrageenan
Authors: Tirgarian Behraad , Farmani Jamshid , Farahmandfar Reza , Milani Jafar M. , Bockstaele Filip Van
Published: October 2022

Food-approved colloidal particles that can construct stable emulsions, but destabilize on purpose using a specific stimulus like pH change would be of great importance to food and pharmaceutical industries (bioactive delivery). However, such edible Pickering stabilizers are quite rare, since they must possess superb interfacial activity (rapid, strong and reversible adsorption at oil-water interface) to be efficient in stabilization of these unique systems. Herein, we report the formation of sodium caseinate (SC)-κappa-carrageenan (kC) colloidal conjugates that can offer such Pickering ability. SC-kC conjugates were prepared by wet-heating Maillard reaction after sonication pre-treatments (400 W, 20 kHz) for 10, 20, and 30 min. The SC-kC conjugation was confirmed by Fourier transform infrared spectroscopy, CD spectra, intrinsic fluorescence analysis, and glycation degree (GD). With increased sonication duration, a higher GD (59.75 ± 0.69% in 30 min) was observed which led to improved interfacial activity (higher adsorption quantity and rate at interface), lower particle size (< 500 nm) as well as higher emulsifying activity and stability indices. It was observed that the emulsion prepared with the 30 min ultrasonic conjugate had the lowest mean droplet size (1.65 ± 0.10 µm) and polydispersity index (0.46 ± 0.00) along with the highest zeta potential (-35.76 ± 0.54 mV). Furthermore, it was found that sonothermal glycation with kC empowered the SC to fabricate emulsions with excellent pH-responsive behaviors where it can be easily switched on (pH = 7) and off (pH = 4.5) over 4 cycles and remain stable with further emulsification. Therefore, SC-kC colloidal conjugates can create novel Pickering systems with attributes desired to many applications.
Comparative effects of epidural steroid injections on disc bulging and disc protrusion in patients with discogenic low back pain
Authors: Çetin Eyüp , Şah Volkan , Zengin İrfan , Arabacı Özkan , Akyol Mehmet Edip , Yücel Murat
Published: October 2022

Objective
Discogenic low back pain is a widespread disorder around the world. Numerous methods have been developed and continue to be developed in the treatment of discogenic low back pain. In this study, we aimed to examine the effect of epidural steroid administration (ESI) on disc bulging and disc protrusion in patients with discogenic low back pain.
Materials and Methods
The prospective randomized study reviewed medical records of 71 patients with discogenic low back pain who were radiologically proven as disc bulging and disc protrusion with or without radicular pain and did not require surgery at Neurosurgery Department between June 2021 and June 2022. All the patients underwent ESI and attended regular follow-up visits for a period of 6 months. Visual Analogue Scale (VAS) and Oswestry Disability Index (ODI) scores were assessed before the procedure, one week after the procedure, one month after the procedure, and six months after the procedure.
Results
There was no significant difference between patients with disc bulging and disc protrusion in terms of demographic characteristics. In both groups, both VAS and ODI scores showed a significant decrease in the post-procedure period compared to the pre-procedure period. However, there was no significant difference between the two groups with regard to the reduction rate between post-procedure 1st week VAS scores and pre-procedure VAS scores.
Conclusion
The results indicated that lumbar interlaminar steroid injection is an effective treatment for disc bulging and discogenic pain due to protrusion and that both groups benefited from ESI administration. Additionally, except for the first week of injection, relief due to the use of epidural steroids was observed to be greater in the Disc Protrusion group compared to the Disc Bulging group.
SIRT2 inhibition rescues neurodegenerative pathology but increases systemic inflammation in a transgenic mouse model of Alzheimer’s disease
Authors: Sola-Sevilla Noemi , Mesa-Lombardo Alberto , Aleixo Mikel , Exposito Sara , Diaz-Perdigón Teresa , Azqueta Amaia , Zamani Farzad , Suzuki Takayoshi , Maioli Silvia , Eroli Francesca , Matton Anna , Solas Maite , Tordera Rosa M. , Martín Eduardo D. , Puerta Elena
Published: October 2022

Sirtuin 2 (SIRT2) has been proposed to have a central role on aging, inflammation, cancer and neurodegenerative diseases; however, its specific function remains controversial. Recent studies propose SIRT2 pharmacological inhibition as a therapeutic strategy for several neurodegenerative diseases including Alzheimer’s disease (AD). Surprisingly, none of these published studies regarding the potential interest of SIRT2 inhibition has assessed the peripheral adverse side consequences of this treatment. In the present study we demonstrate that pharmacological treatment with 33i improved cognitive dysfunction and LTP, and reduced amyloid pathology and neuroinflammation in the APP/PS1 AD mouse model. However, this treatment increased peripheral levels of inflammatory cytokines IL-1β, Tnf-α, Tgf-β, IL-6 and MCP-1. Accordingly, peripheral SIRT2 inhibition with the blood brain barrier impermeable compound AGK-2, worsened the cognitive capacities and increased systemic inflammation. These results suggest that, although SIRT2 pharmacological inhibition may have beneficial consequences in neurodegenerative diseases, its systemic adverse side effects should be taken into account. This information is essential to maximize the therapeutic potential of SIRT2 inhibition not only for AD but also for other neurodegenerative diseases.
Identification of DDIT4 as a Potential Prognostic Marker Associated with Chemotherapy and Immunotherapy Response in Triple-Negative Breast Cancer
Authors: Chen Xuanzhao , Li Zeyan , Liang Meihua , Zhang Ziyang , Zhu Di , Lin Biyun , Zhou Renyu , Lu Yuanzhi
Published: October 2022

Background
Triple-negative breast cancer (TNBC) is the most heterogenous and aggressive subtype of breast cancer. Chemotherapy remains the standard treatment option for patients with TNBC owing to the unavailability of acceptable targets and biomarkers in clinical practice. Novel biomarkers and targets for patient stratification and treatment of TNBC are urgently needed. In this study, we aimed to identify novel biomarkers and therapeutic targets using RNA sequencing (RNA-seq) and data mining using data from public databases.
Methods
RNA-sequencing (RNA-Seq) was performed to detect the different gene expression patterns in the human TNBC cell line HS578T treated with docetaxel or doxorubicin. Raw data were analyzed using the R package “edgeR” to identify the profile of differentially expressed genes (DEGs) and functionally annotated through R package “clusterProfiler.” The prognostic and predictive value of DNA damage-inducible transcript 4 gene (DDIT4) expression in patients with TNBC was further studied using published online data resources, including TIMER, UALCAN, and Kaplan-Meier Plotter. LinkedOmics and GeneMANIA were used to investigate the genes and functional networks related to DDIT4. GSCALite was used to analyze the pathway activities of DDIT4 and its hub genes.
Results
Through the integrative analyses of RNA-Seq data and public datasets, we observed the overexpression of DDIT4 in TNBC tissues(p<0.01) and found that patients with DDIT4 overexpression showed poor survival outcomes (p<0.05). Notably, immune infiltration analysis showed that the levels of DDIT4 expression correlated negatively with the abundance of tumor-infiltrating immune cells and immune biomarker expression (p<0.05), but correlated positively with immune checkpoint molecules (p<0.01). Furthermore, DDIT4 and its hub genes (ADM, ENO1, PLOD1, and CEBPB) involved in the activation of Apoptosis, Cell Cycle and EMT pathways. Eventually, we found ADM, ENO1, PLOD1 and CEBPB showed poor overall survival in BC patients (p<0.01).
Conclusion
In this study, we found that DDIT4 expression is associated with the progression, therapeutic efficacy, and immune microenvironment of patients with TNBC, and DDIT4 would be as a potential prognostic biomarker and therapeutic target. These findings will help to identify potential new molecular targets and improve therapeutic strategies against TNBC.
Advanced mathematical analysis to optimize image processing for pore size assessment of knitted fabrics
Authors: Huang Rong , DenHartog Emiel , Joines Jeff
Published: October 2022

Pore size is one of the significant factors influencing fabric performance, such as comfort and protection. The reliable measurement of pore size is fundamental to studying fabric structure and performance. Image processing is the popular method to characterize pore size because of its convenience and efficiency. However, there is no standard procedure to retrieve pores from fabric images. Furthermore, many uncertainties exist when deciding on critical thresholds, making the process subjective and less comparable. The study proposed a standardized workflow to determine the pore size and the distribution of knitted fabrics using image processing. The major contributions include discussing the impact of structuring element size on fabric structure, suggesting an objective way to select the optimal structuring element size, and proposing an approach to isolate noise pores. As a result, the measurement of pore size using image processing is more accurate and reliable, reflecting the true pore size distribution of fabrics, establishing a solid foundation for producing qualified fabrics. Moreover, the proposed method includes specific steps for image processing and objective criteria for selecting thresholds, enabling the generation of computer algorithms that automatically process fabric images on a large scale, making it more efficient and saving labor, time, and money.
Bounds on the differential uniformity of the Wan-Lidl polynomials
Authors: Chen Li-An , Coulter Robert S
Published: October 2022

We study the differential uniformity of the Wan-Lidl polynomials over finite
fields.
A general upper bound, independent of the order of the field, is established.
Additional bounds are established in settings where one of the parameters is
restricted. In particular, we establish a class of permutation polynomials
which have differential uniformity at most 5 over fields of order $3\bmod 4$,
irrespective of the field size.
Computational results are also given.
Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome
Authors: Doane Michael , Reed Michael , McKerral Jody , Lima Lais Farias Oliveira , Papudeshi Bhavya , Morris Megan , Goodman Asha , Johri Shaili , Dillon Taylor , Turnlund Abigail , Peterson Meredith , Mora Maria , Venegas Rafael de la Parra , Pillans Richard , Rohner Christoph , Pierce Simon , Legaspi Christine , Araujo Gonzalo , Ramirez-Macias Deni , Edwards Robert , Dinsdale Elizabeth
Published: October 2022

Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their functional contribution to host health. Here, we compare diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations, globally. We hypothesised co-occurrence patterns would occur independently of diversity patterns. Whale shark aggregation was the most important factor discriminating taxonomic diversity patterns. Microbiome network architecture was similar across all aggregations with degree distributions matching Erdos-Renyi graphs. However, networks had greater modularity than expected, indicating definitive microbiome structure. In addition, whale sharks hosted 35 ‘core’ microbiome members supporting the high modularity observed in microbiomes. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the microbiome in whale sharks. We suggest host-microbiome and microbe-microbe interactions which drive self-assembly of the microbiome are, in part, the result of emergent functions that support functionally redundant key core microbial members.
Teaser Sentence: The skin microbiome of whale sharks has emergent co-occurrences structure despite distinct diversity patterns.
Acute subdural haematoma exacerbates cerebral blood flow disorder and promotes the development of intraoperative brain bulge in patients with severe traumatic brain injury
Authors: Zhang Shangming , Chen Qizuan , Xian Liang , Chen Yehuang , Wei Liangfeng , Wang Shousen
Published: October 2022

Background
Decompressive craniectomy (DC) is a routine procedure used for the treatment of severe traumatic brain injury (TBI) with concomitant acute subdural haematoma (SDH). However, certain patients are prone to developing malignant brain bulge during DC, which prolongs the operative time and worsens patient outcomes. Previous studies have shown that malignant intraoperative brain bulge (IOBB) may be associated with excessive arterial hyperaemia caused by cerebrovascular system disorders. Through a clinical retrospective analysis and prospective observations, we found that the cerebral blood flow of patients who possessed risk factors manifested high resistance and low flow velocity, which severely affected brain tissue perfusion and resulted in the occurrence of malignant IOBB. In the current literature, rat models of severe brain injury-associated brain bulge have rarely been reported.
Methods
To gain an in-depth understanding of cerebrovascular changes and the cascade of responses related to brain bulge, we introduced acute SDH into the Marmarou model for the preparation of a rat model of high intracranial pressure (ICP) to simulate the pathological conditions experienced by patients with severe brain injury.
Results
With the introduction of a 400 µL haematoma, significant dynamic changes occurred in ICP, mean arterial pressure, and relative blood perfusion rate of the cerebral cortical vessels. ICP increased to 56.9 ± 2.3 mmHg, mean arterial pressure showed reactive decrease, and the blood flow of cerebral cortical arteries and veins on the non-SDH-affected side decreased to < 10%. These changes could not fully recover even after DC. This resulted in generalised damage to the neurovascular unit and a lag effect to the venous blood reflux, which triggered malignant IOBB formation during DC.
Conclusion
An excessive increase in ICP causes cerebrovascular dysfunction and brings about a cascade of damage to brain tissue, which forms the basis for the development of diffuse brain swelling. The subsequent heterogeneous responses of the cerebral arteries and veins during craniotomy may be the main cause of primary IOBB. Clinicians should pay particular attention to the redistribution of CBF to various vessels when performing DC in patients with severe TBI.
Metformin alleviates ethanol-induced cardiomyocyte injury by activating AKT/Nrf2 signaling in an ErbB2-dependent manner
Authors: chen yunjie , Zhu suyan , Lin Zhu , zhang yuanbin , he shengqu , chen xueqin , zhou xuan
Published: October 2022

Background Metformin, a first-line oral anti-diabetic drug, has recently been reported to exert protective effect on various cardiovascular diseases. However, the potential role of metformin in ethanol-induced cardiomyocyte injury is still unknown. Therefore, this study was aimed to investigate the effect of metformin on ethanol-induced cardiomyocyte injury and its underlying mechanism.
Methods and Results H9c2 cardiomyocytes were exposed to ethanol for 24 h to establish an ethanol-induced cardiomyocyte injury model, and followed by treatment with metformin in the presence or absence of Lapatinib (an ErbB2 inhibition). CCK8 and LDH assays demonstrated that metformin suppressed cardiomyocyte apoptosis induced by ethanol exposure. Furthermore, the up-regulated expressions of apoptosis-related proteins (Bax and C-CAS-3) were also reduced by metformin. In addition, our results showed that metformin activated the AKT/Nrf2 pathway, and then promoted Nrf2 nuclear translocation and the transcription of its downstream antioxidant genes (HO-1, CAT and SOD2), thereby inhibiting oxidative stress. Interestingly, we found that ErbB2 expression was significantly inhibited in ethanol-treated cardiomyocyte, which was markedly reversed by metformin. In contrast, Lapatinib largely abrogated the activation of AKT/Nrf2 signaling by metformin, accompanied by the increases in oxidative stress and cardiomyocyte apoptosis,indicating that metformin prevented ethanol-induced cardiomyocyte injury in an ErbB2-dependent manner.
Conclusions In summary, our study provides the first evidence that metformin protects cardiomyocyte against ethanol-induced oxidative stress and apoptosis by activating ErbB2-mediated AKT/Nrf2 signaling. Thus, metformin may be a potential novel treatment approach for alcoholic cardiomyopathy.
Labor Supply, Hourly Imbalances and Household consumption in Cameroon
Authors: Evou Jean-Pierre , Ntamack Simon Alain Song
Published: October 2022

This paper studies two things: first, the impact of observed labor supply constraints on the welfare of household members and, second, break down the different work times dysfunctions by comparing observed hours to the hours actually desired by individuals. Using ECAM IV data from 2014 and a discrete choice collective labour supply model, it arrives at the following results: (i) the unemployment and underemployment constraint negatively impacts household consumption and thus their material well-being; (ii) on the 25.53% of unemployed women, nearly 25% of them are forced into unemployment or inactivity. On the contrary, on the 2.54% of unemployed men, none of them wishes to remain inactive or unemployed; (iii) nearly one woman over four (26%) and one man over five (20%) are forced into underemployment.
JEL code : I1 ; D6 ; J2 ; C25
Targeting MYH9 represses USP14-mediated NAP1L1 deubiquitination and enhances temozolomide response in Glioma
Authors: Chen Zigui , Yan Xin , Miao Changfeng , Liu Longyang , Liu Su , Xia Ying , Fang Weiyi , Zheng Dandan , Luo Qisheng
Published: October 2022

Myosin heavy chain 9 (MYH9) has been significantly involved in a number of diseases. Nevertheless, the function of MYH9 in glioma is unclear. The article aims to investigate the effect of MYH9 and to determine if MYH9 is also implicated in temozolomide chemoresistance of glioma. Here, we first found that MYH9 increased cell proliferation and temozolomide resistance in glioma. Mechanistic studies showed that MYH9 bound to NAP1L1, a potential tumor promoter has been reported to promote the tumor proliferation, and further inhibited ubiquitination and degradation of NAP1L1 by recruiting USP14. The up-regulated NAP1L1 increased the binding with c-Myc and further activated c-Myc, which induce the expression of CCND1/CDK4, thereby promoting temozolomide resistance and cell proliferation in glioma. In addition, we found that up-regulated MYH9 level was strongly related to patient survival and should be demonstrated as a negative factor in patients with glioma. Taken together, our results offer a new perspective on the role of MYH9 in glioma progression by regulating NAP1L1 deubiquitination, targeting MYH9 will have the possible clinical application in glioma treatment going forward.
Construction of 3D landscape index based on oblique photogrammetry and its application in islands
Authors: Guo Zhen , Wang Jue , Liu Yinchu , Xu Hao , Ma Jinchao , Zhang Zhiwei
Published: October 2022

The landscape index is quantitative indicator to reflect the composition and spatial configuration characteristics of landscape ecological structures. Following the "P-C-L" frameworks, eight 3D landscape indexes were constructed to quantitatively describe the spatial landscape features and two sensitivity indexes were built to identify the differences between 2D and 3D. Based on two kinds of oblique photogrammetry data of Sichang Island and Tianheng Island, the results show that: 1) The shape index (TPSI) indicates the spatial shape of the patch scale. The TPSI of vegetation was generally higher than that of buildings, with a reasonable correlation (R2 = 0.698). The classification index (TCI) shows remarkable performance in patch-type identification. When the value of TCI approaches values of 100 or 33, the patch-type is probably building or vegetation, respectively, with a classification accuracy rate of 95% after verification. 2) The sensitivity indexes, GSC and ESC, provide an evaluation criterion for the attribute transformation from 2D to 3D. The dimensional change significantly affected the buildings and arbor, with a GSC of 6.697 and 2.306, respectively. The changes in low-rise ground features were not significant. On class and landscape scales, the dynamic ranges of all six 3D indexes increased compared to 2D indexes. The highest was TLSI (3D Landscape Shape Index), and the lowest was TSHEI (3D Shannon Evenness Index), with a growth rate of 349.65% and 0.3%, respectively. 3) The 3D landscape indexes can better feature the biomass and the intensity of human development and construction activities on all scales. Its combination with modern remote sensing and mapping technology can provide a more sound ecological assessment method for spatial planning of different ecosystems.
Proteomics‑based prognostic signature predicts prognosis and immunity in glioma
Authors: Shen Xinyu , Zhou Jue , Tan Haoyuan , Zhao Dongxu , Lan Jin , Guo Han , Bao Yinghui
Published: October 2022

The prognosis of glioma patients is closely associated with the expression of immune cells and oncoproteins. Therefore, protein-related signatures were conducted to improve the prediction of overall survival (OS) in glioma patients after surgery. Differential oncoproteins were selected from the Renji cohort and The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) regression model is designed to construct the multiple oncoprotein model related to OS in two test series. Furthermore, the 6-oncoprotein model was tight associated with immune cell infiltration, immune function, and immunotherapy. In summary, the 6-oncoprotein marker, a favorable biomarker for the prognosis and immune characteristics of glioma, could help individualized immunotherapy for patients with glioma.
Identification and functional annotation of hypothetical protein from the core genome of Orientia tsutsugamushi towards designing a novel drug target
Authors: Panda Subhasmita , Swain Subrat Kumar , Sahu Basanta Pravas , Sarangi Rachita
Published: October 2022

The rapid buildup of microbial genomic sequences with a large number of uncharacterized genes has resulted from advances in biological technologies. These genes encode the uncharacterized/ hypothetical and conserved proteins. Orientia tsutsugamushi, a gram negative bacterium causes scrub typhus disease in humans, contains approximately 20% of these proteins which have yet to be annotated. So in the present study, out of 292 hypothetical proteins were chosen to characterize and annotate by using different in silico techniques such as ExPASy ProtParam, VirulentPred, PSROTb, Pfam, InterproScan, PSIPred, SWISS_MODEL, CASTp and STRING. The comparative proteomics analysis revealed that, the protein which are stable, cytoplasmic and virulent, it is non homologous to human genome but essential for the function of the organism. The annotation of these proteins may disclose new information about the pathogen. The actual function of the protein will completely understand by experimental analysis. Prediction of the structure and function of this hypothetical protein should help researchers to uncover and better understand the function of Orientia tsutsugamushi, leading to the discovery of new drug targets.
The landscape of lung microbiota predicts the outcome of severe community-acquired pneumonia by interacting with the host immune response
Authors: Han Yi , Lin Mengna , Xu Feixiang , Sun Keyu , Yang Bin , Lu Su , Ding Hailin , Wang Jianli , Gu Guorong , Min Min , Kuang Zhongshu , Xue Mingming , Xing Lingyu , Zhang Yunqiang , Liu Huifang , Wang Weibing , Zhang Yun , Tong Chaoyang , Zhang Hong , Song Zhenju
Published: October 2022

Background:The lung microbiota and host immune response is thought to be a key player in the progression of pneumonia. However, the critical features of the microbiota have rarely been studied in severe community-acquired pneumonia (SCAP) patients. This study aimed to explore the correlations among the lung microbiota and the host immune defense, the disease severity, and the outcome in SCAP patients.Methods:A prospective and observational study in the intensive care unit (ICU) of four hospitals in China was performed. The lung microbiota was quantified and characterized using metagenomic next-generation sequencing (mNGS), collecting sputum and bronchoalveolar lavage fluid (BALF) in SCAP and CAP patients. Risk factors for disease progress and prognosis were investigated by logistic regression. In addition, transcriptomics was applied to explore host immune variation and the interaction between microbiota and host immune responses.Results:Our results showed that the microbiome α- and β-diversity in SCAP patients were significantly lower than those in CAP patients and lower in nonsurvivors than survivors. The Simpson index, the existence ofStreptococcus pneumonia, the delta-SOFA score, the use of immunosuppressor, and activated partial thromboplastin time (APTT) were independently associated with the 28-day mortality of SCAP patients. Furthermore, the differentially expressed genes, including Opiorphin Prepropeptide (OPRPN), Histatin 1 (HTN1), Histatin 3 (HTN3), Lipocalin 1 (LCN1), Follicular Dendritic Cell Secreted Protein (FDCSP) and Statherin (STATH) in SCAP were correlated with immune response pathways.The neutrophil proportions and degranulation were suppressed in the nonsurvivors of SCAP. At the same time, interleukin-10 signaling was activated, while interferon-α, -β, and -γ responses were suppressed in the dismal outcome patients.Conclusions:Our findings confirmed that the lung microbiota played an essential role in association with the severity of pneumonia and represented a significant contributor to heterogeneity in SCAP by altering host immune responses.
Construction and characterization of the infectious cDNA clone of the prevalent Chinese soybean mosaic virus strain SC3
Authors: Liu Hui , Zheng Huanfang , Xiang Wenyang , Song Yingpei , Li Bowen , Yin Jinlong , Liu Mengzhuo , Liu Xiaoxiang , Wang Liqun , Yang Shouping , Xu Kai , Zhi Haijian
Published: October 2022

The resistance of different soybean varieties to the Chinese isolate of soybean mosaic virus SC3 was systematically studied. However, the resistance of different germplasm sources is still poorly understood. We constructed an infectious DNA clone of Chinese SMV isolate SC3 (pSC3) and modified it to allow the expression of yellow fluorescence protein (YFP)/ red fluorescence protein (RFP) during viral infection. By using the infection of pSC3-RFP, we can classify the resistance of different soybean cultivars to SMV-SC3 to the extreme resistance that restricts initial viral replication and the resistance that allows viral replication in the initially inoculated cells but restricts further movement. Also, we tracked the SMV-SC3 infection in susceptible cultivar Nannong 1138-2 (NN1138-2) and found that the seed transmission of SMV to the offspring plants can be tracked and recorded by imaging the virus-driven expression of YFP. Overall, we reveal new aspects of soybean resistance to SMV-SC3 and provide an essential tool to study the infection and transmission of SMV-SC3, which will help decipher the genes involved in SMV pathogenesis and host resistance.
The use of artificial intelligence tools in cancer detection compared to the traditional diagnostic imaging methods: an overview
Authors: Silva Helbert Eustáquio Cardoso da , Santos Glaucia Nize Martins , Mesquita Carla Ruffeil Moreira , Leite André Ferreira , Figueiredo Paulo Tadeu de Souza , Stefani Cristine Miron , Melo Nilce de Santos
Published: October 2022

The aim of this overview article is to discuss the application of artificial intelligence (AI) tools in detecting and diagnosing malignant tumors based on different imaging modalities. The acronym PIRDs was used to create a search strategy. A comprehensive literature search was conducted on indexed databases and grey literature for systematic reviews of AI as a diagnostic model and/or detection tool for any cancer type in adult patients, compared to the traditional diagnostic radiographic imaging model. There were no limits on publishing status, publication time, or language. In total, 382 records were retrieved in the databases, 364 after removing duplicates, 32 satisfied the full-text reading criterion, and 09 papers were considered for qualitative synthesis. The studies found that several AI approaches are promising in terms of specificity, sensitivity, and diagnostic accuracy in the detection and diagnosis of malignant tumors. The Super Vector Machine algorithm method performed better in cancer detection and diagnosis. Computer-assisted detection (CAD) has shown promising in terms of aiding cancer detection, when compared to the traditional method of diagnosis. The use of AI tools benefitted less experienced radiologists more than experienced specialists on the use of machine learning and radiomic analysis in cancer identification. The combination of a CAD system, machine learning algorithms, and radiomic analysis seemed to be effective and promising in the identification and diagnosis of malignant tumors. However, further longitudinal studies with a longer follow-up duration are required for a better understanding of the clinical application of these artificial intelligence systems.
An APOBEC/Inflammation-based classifier improves the stratification of multiple myeloma patients and identifies novel risk subgroups
Authors: Grasedieck Sarah , Panahi Afsaneh , Jarvis Matthew C. , Borzooee Faezeh , Harris Reuben S. , Larijani Mani , Avet-Loiseau Hervé , Samur Mehmet , Munshi Nikhil , Song Kevin , Rouhi Arefeh , Kuchenbauer Florian
Published: October 2022

Background: Recent insights into the pathogenesis of multiple myeloma (MM) have highlighted inflammation and genome editing, e.g. by APOBEC enzymes, as major drivers of disease onset and progression. We hypothesized that inclusion of molecular features corresponding to these two mechanisms can be utilized to define novel MM risk groups at initial diagnosis.
Methods: Using two independent patient cohorts (MMRF and IFM/DFCI 2009), we developed and validated an easy-to-calculate novel risk-score that is based on mRNA expression levels of APOBEC2 and APOBEC3B, as well as inflammatory cytokines (IL11, TGFB1 and TGFB3) and serum levels of ß2-microglobulin and LDH.
Results: Performance of the Editor- and Inflammation-based score (EI-score) was superior to current cytogenetics-based risk classifiers. Moreover, the EI-score was able to identify previously unrecognized MM patients who experience favourable outcomes despite carrying adverse risk cytogenetics.
Conclusions: Through accurate risk stratification we can identify patients who are currently over-or undertreated. The EI-score is a contemporary and superior prognostic score, calculated based on transcript levels at diagnosis, allowing the identification of unrecognized MM risk subgroups potentially leading to adjustment of clinical treatment and improvement of patient outcomes.
The Difference in Personality and Self-esteem of Mono/bilinguistic and Multilinguistic Individuals
Authors: Baruah Primli
Published: October 2022

With the advancements in technology and opening borders to globalization, the world has joined hands to come together for trade, marketing, development and peace. This has led to an increase of multi linguistic people who learn more than two languages to work effectively at different locations and for other reasons. Though there is an open world, many individuals only learn upto one or two languages in the process of their development. It has been found in previous research that multilingualism has had many positive impacts, the literature to that is still limited; it has not been verified over different populations and cultures. To compare Mono/bilinguistic individuals to Multilinguistic in terms of their Personality and Self Esteem a total of 60 participants (N=60, 30 Mono/bilinguistic and 30= Multilinguistic) were included in the study. Rosenberg Self Esteem Scale (RSES) and Multicultural Personality Questionnaire (MPQ) were used to collect data. Non-random purposive sampling was used, and the data was compared using a Descriptive statistics and independent sample t-test. There was no statistically significant difference found in the two groups. There was no direct evidence of multilinguistic people having measurable higher attributes than the other group.
Helping agents to enter and exploit artificial institutions
Authors: Cunha Rafhael , Hübner Jomi , de Brito Maiquel
Published: October 2022

In this paper, we are considering agents that act to satisfy their interests in systems composed of institutions. These institutions are unknown to the agents at design time and are endowed with actions (called institutional actions) with functions that bring consequences in the environment that match the interests of the agents. However, existing models of artificial institutions do not make these consequences explicit. Agents need to know the institutions and the consequences of carrying out institutional actions before acting in the systems. Considering this problem, this paper proposes to instrument institutions with a purpose model that makes the environmental consequences of carrying out institutional actions explicit. In addition, the paper also presents some algorithms that agents can use to consider this information in their reasoning and deliberation process. The model is presented, discussed and implemented using the JaCaMo framework, highlighting its advantages for agents when reasoning about the consequences of their actions both in the institution and in the environment.
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Authors: Ammar Ammar , Cavill Rachel , Evelo Chris , Willighagen Egon
Published: October 2022

Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug's efficacy and side effects. Unfortunately, large-scale experimental screening of ligand-binding against protein variants is still time-consuming and expensive. Alternatively, in silico approaches can play a role in guiding those experiments. Methods ranging from computationally cheaper machine learning (ML) to the more expensive molecular dynamics have been applied to accurately predict the mutation effects. However, these effects have been mostly studied on limited and small datasets, while ideally a large dataset of binding affinity changes due to binding site mutations is needed. In this work, we used the PSnpBind database with six hundred thousand docking experiments to train a machine learning model predicting protein-ligand binding affinity and the effect of binding site single-point mutations on it. A numerical representation of the protein, binding site, mutation, and ligand information was encoded using 256 features among which about half of which were manually selected based on domain knowledge. A machine learning approach composed of two regression models is proposed, the first predicting wild-type protein-ligand binding affinity while the second predicting the mutated protein-ligand binding affinity. The best performance model reported an RMSE value within 0.5-0.6~kcal/mol\textsuperscript{-1} on an independent test set with an R\textsuperscript{2} value of 0.87-0.90. We report an improvement in the prediction performance compared to several reported models developed for protein-ligand binding affinity prediction. The obtained models can be used as a complementary method in early-stage drug discovery. They can be applied to rapidly obtain a better overview of the ligand binding affinity changes across protein variants carried by people in the population and narrow down the search space where more time-demanding methods can be used to identify potential leads that achieve a better affinity for all protein variants.
Sea ice and argon
Authors: Hambler Clive
Published: October 2022

1) Atmospheric argon on Earth and Mars cycles on a seasonal basis and abiotic factors will be particularly important drivers of this noble gas.
2) It is predicted and confirmed that there is similarity in the seasonality of sea ice and argon, with atmospheric argon in a Hemisphere often increasing fastest when sea ice in that Hemisphere is declining fastest.
3) There is some visual similarity between the detailed phenology of Greenland Sea ice extent and argon in some Northern Hemisphere sites, but formal analysis is required.
4) If causal, the mechanism is unclear but could involve argon bubble formation during freezing and bubble release in the spring melt.
5) Other variables with very similar phenology to sea ice, including high-latitude sea temperatures, should be investigated as potential drivers.
6) Cycling of argon by sea ice would strengthen the argument that seasonal cycling of carbon dioxide is in part driven abiotically.
Metagenomics analysis on the microbiota of chicken manure anaerobic digestion materials in biogas production
Authors: Lam Tze-Kang , Yu Chang-Ping , Wu Shih-Hsiung
Published: October 2022

Identifying the microbial composition in the evaluation of the effectiveness of anaerobic digestion for complex systems still poses a challenge with regard to the first three phases (hydrolysis, acidogenesis and acetogenesis). These phases are crucial in creating substrates for the methanogens to take in, which will affect biogas production. In this study, the microbial composition of the various chambers in the anaerobic digestion of chicken manure was investigated. The optimal living conditions of the microorganisms in the chambers corresponds well with their respective operating conditions (aerobic hydrolysis chamber to anaerobic digester chambers). Diversity of the microbial community for chicken manure was relatively simpler, consisting of mainly the genus of Lactobacillus compared to the main digestion chambers of a more complex community containing more class of Clostridia. This change in microbial diversity composition indicates on the amount and degree of anaerobic digestion occurring (chicken manure only has hydrolysis phase occurring while the main digesters has the first three phases of anaerobic digestion (hydrolysis, acidogenesis and acetogenesis) occurring). A comparison of the metagenomics vs metaproteomics mode of analysis revealed that the bacterial compositions between these two modes of analysis were quite comparable, with the main difference being the quantity of unclassified microorganisms each due to different database and techniques used. The quantity of volatile fatty acids detected in each respective chamber suggested the effectiveness of the microorganisms in assimilating the metabolites for their growth. Successful integration of these study modes would present a better understanding of the anaerobic digestion of complex systems.
Yatırım Kararlarında Yapay Zekanın Rolü ve Türk Finans Sektörü Uygulamaları
Authors: ALP COŞKUN Esra
Published: October 2022

Öz Makinelerin düşünüp düşünemeyeceğini sorgulayan ilk kişi Alan Turing değildi, ancak olumlu bir yanıt veren en yakın kişi olduğu söylenebilir. Yapay zeka (AI) teknikleri, otomatik (kendi kendine) giden arabalar, karanlık fabrikalarda üretim, sohbet robotları ve robo-danışmanlar gibi birçok amaç için kullanılmaktadır. Yapay zekanın finans sektöründe artan kullanımına paralel olarak, ampirik çalışmalar da yapay zeka tekniklerinin geleneksel modellerden daha iyi performans gösterdiğini ortaya koymaktadır. Bu çalışma, Türk finans sektörü örneğinde yapay zeka tekniklerinin yatırımcıların karar verme süreçleri üzerindeki etkilerine ışık tutmayı amaçlamaktadır. Literatürde ilk olarak bu çalışma, bazı politika önerileri geliştirmek için Türkiye ve AB uygulamalarını karşılaştırarak, Türk finans sektöründeki mevcut AI politika çerçevesini ve endüstri uygulamalarını da gözden geçirmektedir.
THE EFFECT OF ROLE AMBIGUITY ON ALIENATION FROM WORK: MEDIATOR ROLE OF WORKLOAD
Authors: FAYGANOĞLU Pınar , CAN YALÇIN Rukiye , BEĞENİRBAŞ Memduh
Published: October 2022

Bu çalışmanın amacı, çalışanların rol belirsizliği ile işe yabancılaşma algıları arasındaki ilişkide iş yükü fazlalığının düzenleyici bir rol oynayıp oynamadığının ortaya koyulmasıdır. Bu amaçla, Ankara’da faaliyet gösteren üniversite, banka, sağlık kuruluşları ile güvenlik hizmeti üreten farklı kurumlarda çalışan, 312 kişiden anket yoluyla elde edilen veriler analiz edilmiştir. Analizlerde ilk olarak çalışma kapsamında kullanılan ölçeklere AMOS kullanılarak doğrulayıcı faktör analizi yapılmış olup, ardından değişkenler arası korelasyon analizi ve çalışma bağlamında ortaya koyulan hipotezleri test etmek amacıyla hiyerarşik regresyon analizi yapılmış ve iş yükü fazlalığının düzenleyicilik rolü oynayıp oynamadığını ortaya koyabilmek adına SPSS Process v3.5 Macro yazılımı ile Bootstrap yöntemini esas alan regresyon analizi yapılmıştır. Bulgular neticesinde, çalışanların rol belirsizliği algılarının işe yabancılaşma düzeyini anlamlı ve pozitif olarak etkilediği ve iş yükü fazlalığı algısının rol belirsizliği ile işe yabancılaşma arasındaki ilişkide düzenleyici bir etkiye sahip olduğu ortaya koyulmuştur.
Presentation Context Of Art And New Media Art: Levent İskenderoğlu “One Photos Thousand Stories” YouTube Channel Example
Authors: KANLIOĞLU Alahattin , ŞEN Egemen Umut
Published: October 2022

Gelişen teknolojiler, insan hayatını kolaylaştırma özelliği sayesinde, hayatımızda her geçen gün daha çok yer edinmektedir. Teknolojik gelişmelere koşut olarak gelişen yeni medya; çok büyük kitlelere ulaşılabilir olma yönüyle kitlesizleşme sağlaması, izleyicilerin istediği zaman istediği kadar ulaşabilmesi neticesinde eş zamanlılık imkânı tanıması ve en karakteristik özelliği olan etkileşimli bir ortam olması sebebiyle geleneksel medyanın yerini almaktadır. Geleneksel sergiler kadar büyük bütçeler gerektirmemesi ve çeşitli sebeplerle küratörlerin ilgisi dışında kalan sanatçıların yapıtlarını izleyicilere sunma fırsatı vermesi gibi özellikleri nedeniyle yeni medya sanatçılara önemli bir temsil ortamı sağlama açısından büyük bir önem taşımaktadır. Ancak bugün sanatın bu yeni medya zemininde vücut bulması yalnızca böyle açıklanamaz. O muazzam merak duyguları ile sanatçıları bu alana çeken çoğu kez geleneksel imkanların eksikliği değil de sanat eseri icra etmenin bu yeni biçiminin çekiciliğidir. Bu çalışmada yeni medyanın hem sanatsal üretim pratiği hem de sunum bağlamında kullanılmasıyla oluşan yeni medya sanatı örneklerinden birini oluşturan, sanat tarihi uzmanı ve sanat eleştirmeni Levent İskenderoğlu’nun “Bir Fotoğraf Bin Öykü” YouTube kanalı örnek durum analizi ve betimleme yöntemi kullanılarak incelenmiştir.
The Transgender Experience: Cross-dressing and Sex-change in Virginia Woolf’s Orlando
Authors: ÖZTOP HANER Sezgi
Published: October 2022

Virginia Woolf’un beşinci romanı olan Orlando adlı eserindeki transgender başkahramanın potansiyel mevcudiyetiyle yaratılmış olan toplumsal cinsiyet belirsizliğinin ve değişken cinsiyetin önemi bu çalışmanın temel kapsamını oluşturmaktadır. Bu bakımdan, Virginia Woolf’un Orlanda eseri toplumsal cinsiyet kavramının nasıl tekrar biçimlendiğini ve yeniden ifade edildiğini ve hatta bir bedenin nasıl sürekli dönüşüm içinde olduğunu gösterir. Sonrasında, sürekli başkalaşım ve dönüşüm süreci içinde olan, kılıktan kılığa giren cinsiyet edimi kavramının cinsel kimliğin akışkanlığı ve çok katmanlılığı ile bir arada kullanımı romanda rastlanılan ince bir noktadır. Bu bakımdan, başkahraman Orlando hem kadın hem erkek ve aynı zamanda cinsiyetsiz biri olarak ortaya çıkmaktadır. Böylece, eserin başkahramanı Orlando kılıp değiştirip sahte tavırlarla gerçeği gizleyerek cinsel kimliğin akışkanlığını ve belirsizliğini gözler önüne sermiş olur. Bu kapsamda, bu çalışma transgender bir figürün olası varlığı ile toplumsal cinsiyet belirsizliğinin romanda nasıl oluşturulduğunu göstermiş ve bu oluşumun okuyucuların zihnindeki toplumsal cinsiyet algısı dinamiklerini sorgulamalarını ve cinsiyet ve cinsel kimlik kategorileri üzerine tekrar düşünmelerini sağlamıştır.
Accordinğ To The Quran Unbelief From The Sense And Talents of The Heart
Authors: TEBER Hatice
Published: October 2022

Kur’ân-ı Kerim’in beyan buyurduğuna göre insan, hem iyiliğe hem de kötülüğe kabiliyetli bir varlık olarak yaratılmıştır. Ne var ki lütuf ve keremi sonsuz olan Allah, insanı bu iki zıt kabiliyeti arasında şaşkın ve perişan bırakmamış, ona “akıl” gibi temyiz edici bir kuvvet vermiştir. Cenab-ı Hak Yüce Kitab’ında insanı, önüne İlâhi gerçekleri sere¬rek, devamlı aklını kullanmaya çağırmaktadır. Allah tarafından aklım kullanmayanlar zemmedilirken, akıl sahipleri yani kendilerine verilen akıl nimetini gerçek anlamda kullananlar da övülmektedirler. Kur’ân-ı Kerim’de insanları akletmeye yönelten ayetler olduğu gibi, akletme işini kalbin yaptığım, iman ve imansızlıkların kalpten çıktığım belirten ayetlerde pek çoktur. Çünkü kalp, insanı gerçek bil-giye götüren bir kaynaktır. İman, küfür, hasenat, seyyiat onun fiili erindendir. Bu yüzden kalp insanın özü ve günahın gerçek mahallidir. Bütün duyu¬lar, kalbin hizmetçileri durumundadır.

Kur’ân’da duyular ile anlamanın, akletmenin merkezi sayılan kalp arasında çok sıkı bağlar vardır. Bu sebeple Kur’ân’da duyuları olmayanın düşünemeyeceği ve kendilerine duyular verilen insanların da niçin düşünemedikleri her zaman sorgulanmıştır. sâlim düşünebilmek için duyulardan istifade edil¬mesi gerektiği ifade edildiği gibi, duyular ve kalbin görevlerini yap-madıklarından, yani anlayıp akletmediklerinden de söz edilir. Gerçekte sağır ve dilsiz olmayan insanlar sağır ve dilsiz olarak vasıflandırılırlar.