Life Sciences Commons^™

Oregon State Rank Assessment For Pit Roach (Hesperoleucus Mitrulus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for pit roach (Hesperoleucus mitrulus) using NatureServe methodology, 2023.

Compcorona: A Web Application For Comparative Transcriptome Analyses Ofcoronaviruses Reveals Sars-Cov-2-Specific Host Response, Rana Sali̇hoğlu, Fati̇h Saraçoğlu, Mustafa Si̇bai̇, Tali̇p Zengi̇n, Başak Abak Masud, Onur Karasoy, Tuğba Önal Süzek

Turkish Journal of Biology

Background/aim: Understanding the mechanism of host transcriptomic response to infection by the SARS-CoV-2 virus is crucial, especially for patients suffering from long-term effects of COVID-19, such as long COVID or pericarditis inflammation, potentially linked to side effects of the SARS-CoV-2 spike proteins. We conducted comprehensive transcriptome and enrichment analyses on lung and peripheral blood mononuclear cells (PBMCs) infected with SARS-CoV-2, as well as on SARS-CoV and MERS-CoV, to uncover shared pathways and elucidate their common disease progression and viral replication mechanisms. Materials and methods: We developed CompCorona, the first interactive online tool for visualizing gene response variance among the family …

Svm-Do: Identification Of Tumor-Discriminating Mrna Signatures Via Support Vectormachines Supported By Disease Ontology, Mustafa Erhan Özer, Pemra Özbek Sarica, Kazim Yalçin Arğa

Turkish Journal of Biology

Background/aim: The complicated nature of tumor formation makes it difficult to identify discriminatory genes. Recently, transcriptome-based supervised classification methods using support vector machines (SVMs) have become popular in this field. However, the inclusion of less significant variables in the construction of classification models can lead to misclassification. To improve model performance, feature selection methods such as enrichment analysis can be used to extract useful variable sets. The detection of genes that can discriminate between normal and tumor samples in the association of cancer and disease remains an area of limited information. We therefore aimed to discover novel and practical sets …

Stemnesscore: An R Package To Estimate The Stemness Of Glioma Cancer Cells At Single-Cell Resolution, Necla Koçhan, Yavuz Oktay, Gökhan Karakülah

Turkish Journal of Biology

Background/aim: Glioblastoma is the most heterogeneous and the most difficult-to-treat type of brain tumor and one of the deadliest among all cancers. The high plasticity of glioma cancer stem cells and the resistance they develop against multiple modalities of therapy, along with their high heterogeneity, are the main challenges faced during treatment of glioblastoma. Therefore, a better understanding of the stemness characteristics of glioblastoma cells is needed. With the development of various single-cell technologies and increasing applications of machine learning, indices based on transcriptomic and/or epigenomic data have been developed to quantitatively measure cellular states and stemness. In this study, …

Suma: A Lightweight Machine Learning Model Powered Shared Nearest Neighbour Based Clustering Application Interface Of Scrna-Seq, Hamza Umut Karakurt, Pınar Pir

Turkish Journal of Biology

Background/aim: Single-cell transcriptomics (scRNA-Seq) explores cellular diversity at the gene expression level. Due to the inherent sparsity and noise in scRNA-Seq data and the uncertainty on the types of sequenced cells, effective clustering and cell type annotation are essential. The graph-based clustering of scRNA-Seq data is a simple yet powerful approach which presents data as a “shared nearest neighbour” graph and clusters the cells using graph clustering algorithms. These algorithms are dependent on several user-defined parameters. Here we present SUMA, a lightweight tool that uses a random forest model to predict the optimum number of neighbours to have the optimum …

Physicochemical Differences Between Camelid Single-Domain Antibodies And Mammalian Antibodies, Nazli Eda Eski̇er, Doğa Eski̇er, Esi̇n Fi̇ruzan, Si̇bel Kalyoncu

Turkish Journal of Biology

Background/aim: In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VHHs) and humans (VHs), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VHs and VHHs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity while preserving stability, functionality, …

Glp1 Receptor Agonists-Effects Beyond Obesity And Diabetes, Sydney S Wilbon, Mikhail G Kolonin

Faculty, Staff and Student Publications

Glucagon-like peptide-1 receptor agonists (GLP1RA) have been transformative for patients and clinicians in treating type-2 diabetes and obesity. Drugs of this class, the bioavailability of which is continuously improving, enable weight loss and control blood glucose with minimal unwanted side effects. Since adopting GLP1RA for treating metabolic diseases, animal and clinical studies have revealed their beneficial effects on several other pathologies, including cardiovascular diseases, neurodegeneration, kidney disease, and cancer. A notable commonality between these diseases is their association with older age. Clinical trials and preclinical data suggest that GLP1RA may improve outcomes in these aging-related diseases. Some of the benefits …

Patient-Reported Sexual Function, Bladder Function And Quality Of Life For Patients With Low Rectal Cancers With Or Without A Permanent Ostomy, Michael K Rooney, Melisa Pasli, George J Chang, Prajnan Das, Eugene J Koay, Albert C Koong, Ethan B Ludmir, Bruce D Minsky, Sonal S Noticewala, Oliver Peacock, Grace L Smith, Emma B Holliday

Faculty, Staff and Student Publications

BACKGROUND: Despite the increasing utilization of sphincter and/or organ-preservation treatment strategies, many patients with low-lying rectal cancers require abdominoperineal resection (APR), leading to permanent ostomy. Here, we aimed to characterize overall, sexual-, and bladder-related patient-reported quality of life (QOL) for individuals with low rectal cancers. We additionally aimed to explore potential differences in patient-reported outcomes between patients with and without a permanent ostomy.

METHODS: We distributed a comprehensive survey consisting of various patient-reported outcome measures, including the FACT-G7 survey, ICIQ MLUTS/FLUTS, IIEF-5/FSFI, and a specific questionnaire for ostomy patients. Descriptive statistics and univariate comparisons were used to compared demographics, treatments, …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Comprehensive Assessment Of Economic, Productive, Phenotypic, And Morphometric Traits In Azikheli Buffalo Breed Of Northern Pakistan, Nadar Khan, Bakhtawara Bibi, Tariq Ahmad, Salman Khan, Aamir Khan, Muhammad Ibrahim

Journal of Bioresource Management

The study was conducted to illuminate the phenotypic, morphometric, and productive characteristics of the Azikheli buffalo breed. One thousand two hundred pure Azikheli buffaloes (male: female) were randomly selected from the main hub of the Azikheli buffalo breed in Swat (Azikhel). The data were analyzed for comparison and frequency distribution. Phenotypic characteristic of the female buffalo shows that more than 73 % of the body color was golden yellowish. In contrast, in males, this value was 83 %, followed by white-albino and grayish colors. The shape of horns were semi sickle and grayish in color. Morphometric parameters of the breed …

Ethnobotanical Study Of Antihemorrhagic Plants In The Skikda Region (North East Of Algeria), Nabila Souilah, Hamdi Bendif, Abdelkrim Benaradj, Abdelouaheb Belaid, Scherazad Mekious

Journal of Bioresource Management

Our survey was carried out at the level of 17 Municipalities of the Province of Skikda. Questionnaire sheets were distributed to 55 herbalists and 350 locale population (informants). The processing of survey data with the local population shows us that women (52 %) have more knowledge of phytotherapy compared to men (48 %) with a fairly high level of education. For the herbalists, we found that most are men (85.45 %) aged between 31-40 years (29.09 %) and 41-50 years (25.45 %), and with level of university study (36.36 %). On the other hand, 52.73 % of herbalists said they …

Structural Basis For Dna Proofreading, Gina Buchel, Ashok Nayak, Karl Herbine, Azadeh Sarfallah, Viktoriia Sokolova, Angelica Zamudio-Ochoa, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement …

Description Of Sivalhippus (Equidae: Perissodactyla) From The Late Miocene Siwalik Sub-Group Of Pakistan, Muhammad Tahir Waseem, Ayesha Iqbal, Sania Zubaid, Abdul Majid Khan, Muhammad Ammar

Journal of Bioresource Management

New fossil mandible as well as isolated upper and lower dentitions of the late Miocene Hipparionine species, have been discovered from a locality of Chakwal, Punjab, Pakistan. By using morphometric and morphologic analysis, we have deduced that these specimens belong to Sivalhippus theobaldi. The body size of this species was intermediate between Sivalhippus perimensis and Hipparion antilopinum while its hypsodonty indicates that this species was a grazer to a larger extent which existed in mosaic of woodland and grassland in the Latest Miocene. However, the comparison with the recent horse (Equus caballus) mandible indicates some differences in …

Hepatoprotective Effect Of Berberis Lycium In Αlpha-Naphthylisothiocyanate Induced Cholestatic Mouse Models, Shamaila Bashir, Hassan Hameed, Nida Irshad, Aqsa Ashraf, Muhammad Faizan, Saiyada Fatima Maida Halim, Hafiz M. Mazhar Asjad, Andleeb Batool, Imran Sohail

Journal of Bioresource Management

Cholestasis is characterized by the obstruction of bile flow from hepatocytes to the intestine. It results in accumulation of bile acids in the liver, which cause oxidative stress, inflammation, apoptosis, fibrosis, and cirrhosis. Till now, the treatment options against cholestasis are limited. Therefore, there is an utmost requirement to develop and evaluate the drugs with potential anti-cholestatic effects. In the current study, the drug-induced cholestasis mouse models were generated via oral administration of α-naphthylisothiocyanate (ANIT). The mice were placed into three groups of six animals each. Group I was the control group and was given saline. The cholestasis model Group …

Evaluating Microbial Contamination Of Bakeries, Wheat Flour In Ghaemshahr, Iran, Reyhaneh Gouran, Nazanin Khakipour

Journal of Bioresource Management

Although flour is regarded as a safe product from the perspective of microbiology due to its low water activity, it can be a suitable environment for the growth of microorganisms if suitable conditions are provided for their growth and reproduction. The objective of this study was to examine the microbial quality of 82 % and 78 % flours distributed in 5 bakeries in the city of Ghaemshahr. The evaluation of the results of the physicochemical tests on the samples revealed that sample No.5's moisture content (82 % of the flour sample from the bakery E) was significantly higher than other …

Purification And Comparison Of Enzymatic Properties Of Endogenous Transglutaminase Between Silver Carp And Black Carp, Yi Lin, An Yueqi, Liu Ru, Hu Yang, Xiong Shanbai

Food and Machinery

Objective: This study aimed to investigate the differences in enzymatic properties of endogenous transglutaminase （TGase） in silver carp and black carp. Methods: STG and BTG were purified from the muscle of silver carp and black carp, respectively, by 80% ammonium sulfate precipitation, Q-Sepharose FF, and Sephacryl S-200 HR chromatographies. Two enzymes were analyzed for relative molecular weights, peptide sequences, secondary structures, optimal reaction conditions, and thermal inactivation kinetics. Results: The purified STG and BTG showed similar relative molecular weights, of which the enzyme activities were 14.34 U/mg and 12.67 U/mg, respectively. Both enzymes showed differences in peptide sequences. The secondary …

Effect Of Different Processing Temperature On Texture Profile And Flavor Of The Edible Bird's Nest, Shang Kexin, Qiu Shuang, Zhang Lan, Cheng Xiangrong, Wang Dongliang

Food and Machinery

Objective: This study aimed to investigate the effects of different processing temperature on texture profile and flavor of dried edible bird's nest. Methods: With dried edible bird's nest as the main raw material, the texture profile analysis of edible bird's nest at different processing temperature was carried out by physical property analyzer. The volatile components of edible bird's nest at different processing temperature were determined by electronic nose and solid phase microextraction gas chromatography-mass spectrometry (SPME-GC-MS). Results: It was found that the adhesion of cooked edible bird's nest decreased significantly (P<0.01), but its resilience increased significantly (P<0.05) with the increase of temperature. 12 kinds of effective flavor substances were detected in the cooked edible bird's nest by SPME-GC-MS, including: 3 alcohols, 2 aldehydes, 2 esters, 3 ketones, 1 acid, and 1 ether, accounting for 6.23%, 49.34%, and 54.85% of the total detected substances in the cooked edible bird's nest at 95 ℃, 105 ℃ and 115 ℃, respectively. Conclusion: Different processing temperature affects the taste of edible bird's nest and the overall odor profile after processing. Moreover, higher cooking temperature tends to make the egg white-like flavor stronger. The volatile substances in the bird's nest stew at 95 ℃ are mainly acids, the bird's nest cooked at 105 ℃ mainly produces alcohols, and the edible bird's nest cooked at 115 ℃ mainly produces ketones and alcohols.

Research On Trajectory Planning Method For Camellia Oleifera Fruit Sorting Robot Based On Multi-Objective Optimization, Fu Mingdi, Li Zhong, Wang Qianru, Zhao Fei

Food and Machinery

Objective: Solved the problems of poor motion stability and accuracy in the food sorting process of parallel robots. Methods: Based on the analysis of the three degree of freedom food sorting robot system, a method proposed which combined polynomial interpolation and improve multi-objective particle swarm optimization algorithm for Delta robot trajectory optimization. As a parallel robot, the optimization of the shortest operation time, lowest energy consumption, and minimal motion impact were taken as multiple objectives. The improved multi-objective particle swarm optimization algorithm was applied to optimize the polynomial interpolation method, and its performance was validated. Results: The planning trajectory of …

Prediction Of Moisture Content Of Hummus Peach Based On Multi-Burr Hyperspectral Data, Gao Aidi, Qiao Fengzhang, Zhu Wenxuan, Zhong Xiaopin, Deng Yuanlong

Food and Machinery

Objective: To propose a new solution to overcome the two challenges of data with spikes and small sample sizes in nectarine hyperspectral measurement. Methods: Based on hyperspectral imaging technology, image processing methods were used to identify the area of nectarines in the hyperspectral image, and the spectral reflectance data of the area was calculated to form a hyperspectral curve image. For hyperspectral image data with spikes and noise, compared the effects of several data preprocessing methods, including polynomial smoothing algorithm (SG), multivariate scatter correction algorithm (MSC), standard normal variate algorithm (SNV), first-order derivative operator (D1), and second-order derivative operator (D2) …

Determination And Comprehensive Evaluation Of Nutritional Quality Of 12 Kinds Of Potatoes, Shao Guoli, Tan Zhanming, Cheng Yunxia, Li Wenbo, Sun Wanting

Food and Machinery

Objective: This study aimed to screen potato varieties suitable for cultivation in southern Xinjiang. Methods: By combining factor analysis and cluster analysis, a comprehensive evaluation of the nutritional quality of 12 kinds of introduced potato species was conducted using them as test materials. Results: S1 contained the most protein, and S5 included the most soluble sugar content and vitamin C; S12 contained the least nitrate, and S10 contained the most reduced sugar and starch. Nutritional quality indicators differ significantly among potato varieties. The coefficients of variation of soluble sugar content, vitamin C content, and nitrate content were 47.13%, 37.03% and …

Formula Optimization And Volatile Flavor Substance Analysis Of Extruded Corn Flour Composite Powder, Liu Xiaoqin, Ye Yang, Zeng Deyu, Yang Zhengang, Lin Fengmei

Food and Machinery

Objective: This study aimed to improve the flavor and solubility of extruded corn flour by compounding. Methods: D-optimal mixture design was used to add different proportions of puffed millet flour, fried red rice flour, puffed rice flour, and puffed black rice flour, into puffed corn flour. The composite powder was analyzed and evaluated from the perspectives of caking rate, viscosity, sensory score, and volatile flavor substance changes. The aroma components of different samples were analyzed by gas chromatography-mass spectrometry. Results: The formula of compound powder was as follows: expanded corn flour 50.8%, expanded millet flour 8.8%, fried red rice flour …

Effects Of Whey Protein Addition On The Quality Of Fried Potato Balls, Liu E, Guan Yufang, Li Jun, Wang Mei, Huang Shan, Liu Yongxiang

Food and Machinery

Objective: This stydy aimed to develop a new type of fried potato ball and evaluate its quality. Methods: In this study, potatoes were used as the main raw materials to make mashed potatoes after cooking and then fried into potato balls. The effects of whey protein addition on color difference, texture properties, rheological properties, sensory quality and starch digestibility of fried potato balls were explored. Results: Compared with non-whey protein addition, the supplementation of whey protein could significantly improve the L^* （brightness value）, a^* （redness value）, and the cohesion, adhesion, and elasticity of potato balls （P＜0.05）. …

Effects Of Sublimation Temperature On Cell Microstructure Of Pear Melon During Vacuum Freeze Drying, Tian Jinjin, Yao Chaoyang, Zhang Zhiqiang, Zhang Zhe, Ji Hongwei, Wu Jinyu

Food and Machinery

Objective: This study aimed to obtain optimal sublimation temperature of pear melon cells. Methods: The pre-freezing cooling rate and vacuum pressure were selected by optimization method to be 25 ℃/min and 10 Pa, respectively, based on cryogenic microscope imaging and vacuum freeze-drying technology. Then, sublimation temperatures of 10, 5, 0, -4, -7 and -10 ℃ were used for experimental research. The morphological parameters (equivalent diameter, area, circumference, volume), internal pressure, and porosity of cells during the process of dehydration and drying were analyzed. Results: As the sublimation temperature rose, the morphological parameters of different dimensions of cells first decreased and …

Research On Image Recognition Of Cracked Eggs Based On Convolutional Neural Network Model, Li Shu, Tang Mengdi, Tong Siyuan, Sun Ke

Food and Machinery

Objective: In order to improve the accuracy and operating efficiency of the egg crack detection method based on computer vision. Methods: Used poultry egg simulation impact equipment to obtain cracked eggs, and collected images of cracked eggs and intact eggs from different angles through egg dynamic image acquisition equipment. Then, the YOLO-v5, ResNet and SuffleNet models for cracked egg image recognition were established for the original and the preprocessed egg images, respectively. After that, the recognition accuracy and the adaptability for original egg images recognition of different models were compared. Results: The YOLO-v5, ResNet and SuffleNet models could effectively identify …

Design And Application Of Portable Intelligent Rice Freshness Detection System, Shao Xiaokang, Lin Hao, Wang Zhuo, Li Yibing, Chen Quansheng

Food and Machinery

Objective: To realize rapid nondestructive testing of rice freshness. Methods: A portable device system based on nano color-sensitive sensors combined with near-infrared spectroscopy was developed. The spectral data of the corresponding color-sensitive sensors were collected for the identification of multi-gradient rice adulteration and the prediction of freshness across batches of rice. Results: Using Si-CARS-PLS to extract spectral characteristic variables, the recognition rate of discriminative model was the highest after modeling by LDA algorithm, and the recognition rate of training set and prediction set were 97.22% and 95.83%, respectively. At the same time, PLSR model predicted that cross-batch data had stronger …

Determination Of 27 Antiparasitic Drug Residues In Penaeus Vannamei By Liquid Chromatography-Tandem Mass Spectrometry Simultaneously, Zhang Lifang, Ma Ruixin, Zheng Baiqin, Song Wang, Zhou Xin

Food and Machinery

Objective: An ultra-high performance liquid chromatography-tandem mass spectrometry method was established for the simultaneous determination of 27 antiparasitic drug residues in Litopenaeus vannamei. Methods: The solution was used to extract antiparasitic drugs in the samples of L. vannamei. The supernatant after centrifugation was purified by C₁₈ and neutral alumina powder. The sample solution was analyzed by ultra-high performance liquid chromatography-tandem mass spectrometry and applied to the instrument workstation to perform data analysis. A Thermo Hypersil Gold aQ column was used as the separation column, and 0.1% formic acid acetonitrile and 10 mmol/L ammonium formate solution （containing 0.1% formic …

Rapid Detection Of Moisture Content Of Pineapple Based On Near Infrared Spectroscopy And Ssa-Relm, Zhao Yanli, Zhao Qian, Li Zhiqiang

Food and Machinery

Objective: A method for a fast and non-destructive detection of pineapple moisture content was established. Methods: A novel detection model of pineapple moisture content was proposed based on continuous projection feature wavelength selection and Sparrow search algorithm. Firstly, according to the characteristic of pineapple NIR data with high dimension and redundant information, the results of feature wavelength selection such as successive projections algorithm, principal component analysis and full-band were compared, the selection method of characteristic wavelength of pineapple near infrared spectrum was determined. Secondly, considering that the performance of RELM model was affected by the selection of input layer weight …

Study On The Integration Model Of Port Clearance In Food Supervision In The Guangdong Hong Kong Macao Greater Bay Area, Zhang Yiming

Food and Machinery

At present, the integration construction of the Guangdong Hong Kong Macao Greater Bay Area is deepening. Among them, the port customs integration model in food supervision in the Guangdong Hong Kong Macao Greater Bay Area has problems such as inconsistent regulatory standards, cumbersome customs clearance procedures, and information asymmetry, which have led to increasingly prominent issues of low food supervision efficiency. In this regard, effective innovation in the integration model of port clearance can be promoted by unifying the food safety supervision standards of Guangdong, Hong Kong, and Macao, constructing an integrated port clearance procedure mechanism, and strengthening information sharing …

Establishment Of Quechers-Uplc-Ms/Ms Method To Determine Three Kinds Of Ochratoxins In Coffee, Gao Yunkai, Chen Xiaomei, Chen Chunqian, Zhou Lingyu, Deng Yinglin, Yin Qingchun

Food and Machinery

Objective： A new method was developed for the simultaneous determination of three kinds of ochratoxins in coffee by ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with QuEChERS pretreatment. Methods： Samples were extracted by acetonitri-water-formic acid solution (55∶40∶5) with ultrasonic, salted out with a QuEChERS salt pocket, and then purified with a (ZanChERS-Myco17) column. The chromatographic separation was performed on an ACQUITY UPLC BEH C₁₈ (1.7 μm, 2.1 mm×100 mm) column by gradient elution using a mobile phase comprising 0.2% formic acid aqueous solution and acetonitrile. In the positive ion mode of electric spray, the samples detected were used …

Food Packaging Defect Detection By Improved Network Model Of Faster R-Cnn, Xia Junyong, Wang Kangyu, Zhou Hongdi

Food and Machinery

Objective: Accurate identification and location of paper packaging box defects. Methods: The improved network model of Faster R-CNN was applied to automatically detect box defects. The data of the training set picture was enhanced and noise was added to improve the training accuracy and robustness of the model. The feature extraction network was replaced with ResNet50, and the feature pyramid network （FPN） was fused to improve the multi-scale detection ability of the model. K-means++ was used to cluster the defect scale in the dataset and optimize the anchor box scheme. Results: The average accuracy （AP） of the improved Faster R-CNN …