bluuebunny/crossref_metadata_2025_split huggingface dataset:
Through virtual saturation mutagenesis and rational design for superior substrate conversion in engineered d‐amino acid oxidase
Authors: Tang Heng , Zhu Hong‐Li , Zhao Jin‐Qiao , Wang Liu‐Yu , Xue Ya‐Ping , Zheng Yu‐Guo 
Published: July 2024

AbstractThe d‐amino acid oxidase (DAAO) is pivotal in obtaining optically pure l‐glufosinate (l‐PPT) by converting d‐glufosinate (d‐PPT) to its deamination product. We screened and designed a Rasamsonia emersonii DAAO (ReDAAO), making it more suitable for oxidizing d‐PPT. Using Caver 3.0, we delineated three substrate binding pockets and, via alanine scanning, identified nearby key residues. Pinpointing key residues influencing activity, we applied virtual saturation mutagenesis (VSM), and experimentally validated mutants which reduced substrate binding energy. Analysis of positive mutants revealed elongated side‐chain prevalence in substrate binding pocket periphery. Although computer‐aided approaches can rapidly identify advantageous mutants and guide further design, the mutations obtained in the first round may not be suitable for combination with other advantageous mutations. Therefore, each round of combination requires reasonable iteration. Employing VSM‐assisted screening multiple times and after four rounds of combining mutations, we ultimately obtained a mutant, N53V/F57Q/V94R/V242R, resulting in a mutant with a 5097% increase in enzyme activity compared to the wild type. It provides valuable insights into the structural determinants of enzyme activity and introduces a novel rational design procedure.
Isolation and identification of primary cells: A comprehensive primary cell culture experiment for graduate students
Authors: Cao Jixiang , Chen Hao , Song Qing , Sun Hong , Yang Hua , Bai Yun 
Published: July 2024

AbstractExperimental teaching is an important part of postgraduate training in basic and clinical medicine. While primary cell isolation and identification are among the most important research techniques for medical graduate students, most graduate students do not understand and master these techniques before starting their research experience. In particular, many students lack training in this field, and high‐quality teaching and learning materials are still very sparse. Here, we designed a practical experiment course for graduate students engaged in research. The target students usually have research projects involving primary cell culture in their future research, making the course highly applicable for the students. The lab exercise focused on the methods of primary cell isolation (including mechanical grinding method, explant culture method and enzymatic digestion method) and identification (including flow cytometry, immunofluorescence, and periodic acid‐Schiff (PAS) staining). It aimed to help students master the conceptual, principle, technical, operation, and analytical skills related to primary cell culture and contributed to their foundation for future research. Students generally reflect that they have initially mastered the isolation and identification of primary cell culture as a result of the course. Student feedback also indicates significantly increased confidence in the practical application of primary cell culture in the future. Here, we provide our experience for others who may want to implement similar courses.
Proteomics‐based method to comprehensively model the removal of host cell protein impurities
Authors: Disela Roxana , Keulen Daphne , Fotou Eleni , Neijenhuis Tim , Le Bussy Olivier , Geldhof Geoffroy , Pabst Martin , Ottens Marcel 
Published: July 2024

AbstractMechanistic models mostly focus on the target protein and some selected process‐ or product‐related impurities. For a better process understanding, however, it is advantageous to describe also reoccurring host cell protein impurities. Within the purification of biopharmaceuticals, the binding of host cell proteins to a chromatographic resin is far from being described comprehensively. For a broader coverage of the binding characteristics, large‐scale proteomic data and systems level knowledge on protein interactions are key. However, a method for determining binding parameters of the entire host cell proteome to selected chromatography resins is still lacking. In this work, we have developed a method to determine binding parameters of all detected individual host cell proteins in an Escherichia coli harvest sample from large‐scale proteomics experiments. The developed method was demonstrated to model abundant and problematic proteins, which are crucial impurities to be removed. For these 15 proteins covering varying concentration ranges, the model predicts the independently measured retention time during the validation gradient well. Finally, we optimized the anion exchange chromatography capture step in silico using the determined isotherm parameters of the persistent host cell protein contaminants. From these results, strategies can be developed to separate abundant and problematic impurities from the target antigen.
Real‐world data on ALK rearrangement test in Chinese advanced non‐small cell lung cancer (RATICAL): a nationwide multicenter retrospective study
Authors: Li Lin , Li Wencai , Wu Chunyan , Xi Yanfeng , Guo Lei , Ji Yuan , Jiang Lili , Li Ji , Yun Jingping , Chen Gang , Li Yuan , Liu Yueping , Mu Dianbin , Han Yuchen , Sun Leina , Xia Qingxin , Teng Xiaodong , Che Nanying , Wu Wei , Qiu Xueshan , Liu Chao , Yan Xiaochu , Li Daiqiang , Zhang Zhihong , Wang Zhe , Li Yujun , Wang Zheng , Guo Lingchuan , Nie Xiu , Geng Jingshu , Zhou Jianhua , Ying Jianming 
Published: July 2024

AbstractBackgroundAnaplastic lymphoma kinase (ALK) test in advanced non‐small cell lung cancer (NSCLC) can help physicians provide target therapies for patients harboring ALK gene rearrangement. This study aimed to investigate the real‐world test patterns and positive rates of ALK gene rearrangements in advanced NSCLC.MethodsIn this real‐world study (ChiCTR2000030266), patients with advanced NSCLC who underwent an ALK rearrangement test in 30 medical centers in China between October 1, 2018 and December 31, 2019 were retrospectively analyzed. Interpretation training was conducted before the study was initiated. Quality controls were performed at participating centers using immunohistochemistry (IHC)‐VENTANA‐D5F3. The positive ALK gene rearrangement rate and consistency rate were calculated. The associated clinicopathological characteristics of ALK gene rearrangement were investigated as well.ResultsThe overall ALK gene rearrangement rate was 6.7% in 23,689 patients with advanced NSCLC and 8.2% in 17,436 patients with advanced lung adenocarcinoma. The quality control analysis of IHC‐VENTANA‐D5F3 revealed an intra‐hospital consistency rate of 98.2% (879/895) and an inter‐hospital consistency rate of 99.2% (646/651). IHC‐VENTANA‐D5F3 was used in 53.6%, real‐time polymerase chain reaction (RT‐PCR) in 25.4%, next‐generation sequencing (NGS) in 18.3%, and fluorescence in‐situ hybridization (FISH) in 15.9% in the adenocarcinoma subgroup. For specimens tested with multiple methods, the consistency rates confirmed by IHC‐VENTANA‐D5F3 were 98.0% (822/839) for FISH, 98.7% (1,222/1,238) for NGS, and 91.3% (146/160) for RT‐PCR. The overall ALK gene rearrangement rates were higher in females, patients of ≤ 35 years old, never smokers, tumor cellularity of > 50, and metastatic specimens used for testing in the total NSCLC population and adenocarcinoma subgroup (all P < 0.05).ConclusionsThis study highlights the real‐world variability and challenges of ALK test in advanced NSCLC, demonstrating a predominant use of IHC‐VENTANA‐D5F3 with high consistency and distinct clinicopathological features in ALK‐positive patients. These findings underscore the need for a consensus on optimal test practices and support the development of refined ALK test strategies to enhance diagnostic accuracy and therapeutic decision‐making in NSCLC.
Cancer mortality by country of birth and cancer type in Sweden: A 25‐year registry‐based cohort study
Authors: Tollosa Daniel Nigusse , Zendehdel Kazem , Procopio Alessandro , Cederström Agneta , Boffetta Paolo , Pukkala Eero , Rostila Mikael 
Published: July 2024

AbstractNumerous studies have reported lower overall cancer mortality rates among immigrants compared to native populations. However, limited information exists regarding cancer mortality among immigrants based on specific birth countries and cancer types. We used population‐based registries and followed 10 million individuals aged 20 years or older in Sweden between 1992 and 2016. The Cox proportional hazard model was used to explore the disparities in cancer mortality by country of birth and cancer type, stratified by gender. Age‐standardized mortality rates were also computed using the world standard population. Hazard ratio (HR) of all‐site cancer was slightly lower among immigrants (males: HRm = 0.97: 95% confidence interval: 0.95, 0.98; females: HRf = 0.93: 0.91, 0.94) than Swedish‐born population. However, the immigrants showed higher mortality for infection‐related cancers, including liver (HRf = 1.10: 1.01, 1.19; HRm = 1.10: 1.02, 1.17), stomach (HRf = 1.39: 1.31, 1.49; HRm = 1.33: 1.26, 1.41) cancers, and tobacco‐related cancers, including lung (HRm = 1.44: 1.40, 1.49), and laryngeal cancers (HRm = 1.47: 1.24, 1.75). The HR of mesothelioma was also significantly higher in immigrants (HRf = 1.44: 1.10, 1.90). Mortality from lung cancer was specifically higher in men from Nordic (HRm = 1.41: 1.27, 1.55) and non‐Nordic Europe (HRm = 1.49: 1.43, 1.55) countries and lower in Asian (HRm = 0.78: 0.66, 0.93) and South American men (HRm = 0.70: 0.57, 0.87). In conclusion, there are large variations in cancer mortality by country of birth, and cancer type and require regular surveillance. Our detailed analyses lead to some novel findings such as excess mortality rate of mesothelioma and laryngeal cancers in Immigrants in Sweden. A targeted cancer prevention program among immigrants in Sweden is needed.
Trace elements in pancreatic cancer
Authors: Yanjun Yao , Jing Zhuang , Yifei Song , Gangzhao Gu , Chenxin Yan , Qiang Wei , Qiang Yan , Shuwen Han 
Published: July 2024

AbstractBackgroundPancreatic cancer (PCA) is an extremely aggressive malignant cancer with an increasing incidence and a low five‐year survival rate. The main reason for this high mortality is that most patients are diagnosed with PCA at an advanced stage, missing early treatment options and opportunities. As important nutrients of the human body, trace elements play an important role in maintaining normal physiological functions. Moreover, trace elements are closely related to many diseases, including PCA.ReviewThis review systematically summarizes the latest research progress on selenium, copper, arsenic, and manganese in PCA, elucidates their application in PCA, and provides a new reference for the prevention, diagnosis and treatment of PCA.ConclusionTrace elements such as selenium, copper, arsenic and manganese are playing an important role in the risk, pathogenesis, diagnosis and treatment of PCA. Meanwhile, they have a certain inhibitory effect on PCA, the mechanism mainly includes: promoting ferroptosis, inducing apoptosis, inhibiting metastasis, and inhibiting excessive proliferation.
Reliability, diagnostic value, and diagnostic yield of ultrasound‐guided percutaneous core needle biopsy for peritoneal lesions
Authors: Arslan Muhammet , Aslan Halil Serdar , Utebey Ayse Ruksan , Vurgun Sercan , Comut Erdem , Degirmencioglu Serkan , Kılıc Derya 
Published: July 2024

AbstractIntroductionPeritoneal lesions cannot be definitively distinguished based on clinical and imaging characteristics alone. This study aimed to evaluate the reliability, diagnostic value, and diagnostic yield of ultrasound‐guided percutaneous core needle biopsy (PCNB) for peritoneal lesions.MethodsA retrospective analysis of 129 patients who underwent PCNB for peritoneal lesions was performed to assessed technical completion and diagnostic yield.ResultsThe results showed that ultrasound‐guided PCNB is a safe and reliable diagnostic tool with high diagnostic yield for peritoneal lesions. Technical feasibility and diagnostic yield rates were 100% and 89.9%, respectively. The diagnostic yield was lower for patients with a known history of cancer and a short anteroposterior diameter of the target lesion.ConclusionsThese findings suggest that ultrasound‐guided PCNB could be considered as a first‐line diagnostic tool for peritoneal lesions, as it offers a minimally invasive and accurate means of obtaining tissue samples for diagnosis.
Emerging roles of tripartite motif family proteins (TRIMs) in breast cancer
Authors: Cao Jianing , Yang Mengdi , Guo Duancheng , Tao Zhonghua , Hu Xichun 
Published: July 2024

AbstractBreast cancer (BC) is the most common malignant tumor worldwide. Despite enormous progress made in the past decades, the underlying mechanisms of BC remain further illustrated. Recently, TRIM family proteins proved to be engaged in BC progression through regulating various aspects. Here we reviewed the structures and basic functions of TRIM family members and first classified them into three groups according to canonical polyubiquitination forms that they could mediate: K48‐ only, K63‐ only, and both K48‐ and K63‐linked ubiquitination. Afterwards, we focused on the specific biological functions and mechanisms of TRIMs in BCs, including tumorigenesis and invasiveness, drug sensitivity, tumor immune microenvironment (TIME), cell cycle, and metabolic reprogramming. We also explored the potential of TRIMs as novel biomarkers for predicting prognosis and future therapeutic targets in BC.
Are apps for urban food purchasing and consumption meeting Italian consumers' needs? A mixed‐methods analysis
Authors: Monticone Francesca , Samoggia Antonella , Viti Elena 
Published: July 2024

AbstractThe number of mobile phone apps downloads, especially those in the food and drink category, is growing worldwide. Such growth in digitalisation has brought the food industry and retailers to try and understand consumers new shopping needs and preferences to offer the best virtual experience to purchase food online. Past research rarely explore the features of the currently available apps for purchasing and consumption of agro‐food products compared with consumers' perception, barriers and drivers of online purchasing. The present research aims to fill this gap, in three steps. First, investigating consumers' perceptions of apps currently available for food purchasing and consumption, as well as drivers and barriers towards of online food purchasing and towards online food shopping from (peri)urban initiatives using the theory of consumer values as a theoretical framework (Study 1). Second, analysing the features of existent apps used at (peri)urban level and/or supporting (peri)urban food purchasing and consumption adopting the technology acceptance model as a theoretical framework (Study 2). Third, cross‐analysing consumer needs emerging from the survey with apps features. Quantitative data elaboration included a cluster analysis to group apps based on their features, and principal component analysis to identify consumers' key barriers and drivers. Results support how the desire to eat fresh and seasonal food is the main driver for buying from (peri)urban agriculture initiatives, whereas a more rational and aware food consumption are the drivers for choosing online over in person shopping. The most common type of apps are those aimed at food delivery, and those selling and buying food and providing food information. Restaurants and cafes are the main market channels for consumers' food online purchasing. When consumer needs (Study 1) and apps features (Study 2) are compared, a mismatch of the two emerges. Sustainability food profile and information on seasonal food are consumers' favourite features, but they are present in a limited number of apps. Results provide insights for marketing strategies and future research.
Neuropsychiatric manifestations of anti‐N‐methyl‐D‐aspartate receptor encephalitis in a 14‐year‐old female: A case report
Authors: Ali Masab , Naveed Haris , Sheikh Ateeq Ur Rehman , Ahmad Muhammad Husnain 
Published: July 2024

Key Clinical MessageThis case underscores the critical importance of timely recognition and management of NMDAR encephalitis in adolescents to mitigate potential long‐term sequelae. If a pediatric patient presents with suspected viral encephalitis, autoimmune etiology must be excluded via cerebrospinal fluid antibody assay to guide appropriate immunosuppressive therapy, and improve patient outcomes.AbstractAutoimmune encephalitis particularly involving the n‐methyl‐d‐aspartate receptor (NMDAR) is recognized as a rare cause of acute encephalopathy in pediatric patients. The following case is of a 14‐year‐old female diagnosed with anti‐NMDAR encephalitis who initially presented with fever, episodic convulsions, and loss of consciousness. She subsequently developed right‐sided body weakness, expressive aphasia, and visual hallucinations. Clinical examination revealed prominent neuropsychiatric manifestations such as altered sensorium, motor deficits, hallucinations, and visual disturbances. Cerebello‐bulbar signs were not appreciable in this particular case. She was treated for viral encephalitis but showed no improvement. Laboratory investigations revealed the presence of NMDAR antibodies in the cerebrospinal fluid confirming the diagnosis of autoimmune etiology. The patient demonstrated notable improvement following immunosuppressive treatment.
An unusual presentation of craniopharyngioma in an adult with nasal bloackade
Authors: Gohri Jay , Chaurasia Mayuri , Sheoran Varun , Kanwrani Vishal 
Published: July 2024

Key Clinical MessageEarly biopsy and multidisciplinary collaboration with imaging and physical examination are crucial for the diagnosis of such rare tumor presenations. Highlighting the importance of maintaining a broad differential for intra‐nasal lesions given the rare presentation of craniopharyngioma as nasal mass.
Is there a relationship between clipping weight and volume on golf course fairways?
Authors: Pritchard Benjamin D. , Kahiu Maureen M. , Vargas José J. , Breeden Gregory K. , Dant Lukas A. , Brosnan James T. 
Published: July 2024

AbstractPlant growth regulators (PGRs) are regularly used on golf courses to reduce mowing requirements. PGR efficacy is commonly assessed via measurements of clipping weight; however, this process is time consuming and requires specialized equipment. Golf course superintendents have started to evaluate PGR efficacy via measurements of clipping volume. Field research was conducted in Knoxville, TN, during June 2022 and 2023 to evaluate the relationship between clipping weight and volume following trinexapac‐ethyl applications to hybrid bermudagrass (C. dactylon × C. transvaalensis Burtt‐Davy, cv. ‘Latitude 36’) and manilagrass (Zoysia matrella, cv. ‘Trinity’ and ‘Zorro’) golf course fairways. Four experimental formulations of trinexapac‐ethyl [97 g ha−1 (11.4 fl oz/A)] were applied to plots 16 ft2 (1.5 m2) organized in a randomized complete block design with four replications. Clippings were collected twice weekly with volume assessed via a graduated cylinder; weight was quantified after drying clippings in a forced‐air oven for 48 hours. For hybrid bermudagrass, clipping weight and volume measurements returned similar conclusions regarding trinexapac‐ethyl efficacy for growth regulation. On dates where both metrics resulted in treatment differences, a linear relationship was present between clipping weight and volume data (R2 = 0.84). Similar responses were observed on manilagrass; however, clipping weight and volume were less closely associated (R2 = 0.78). This difference could be related to growth rate, as well as clipping size and mass differences between species. Overall, results indicate that either metric could be used to study efficacy of trinexapac‐ethyl for regulating growth of these species maintained as golf course fairways.
Assessing the impact of organic resources and phosphorus on nutrient uptake, soil traits and seed potato productivity
Authors: Singh Amanpreet , Aulakh C. S. , Sidhu A. S. , Chawla Neena 
Published: July 2024

AbstractImproving tuber yield size to boost seed potato (Solanum tuberosum) production efficiency is a paramount goal, particularly in Punjab, India, a major contributor to the nation's seed supply. To optimize nutrient absorption, soil quality, and yield of seed‐sized tubers, research was conducted in Ludhiana and Jalandhar over two years. Employing a split‐plot design, three organic treatments (farmyard manure [FYM], biofertilizer, control) were tested in main plots, while five phosphorus fertilizer levels (46.9, 62.5, 93.8, 125, 0 kg ha−1 P2O5) were examined in subplots. Results revealed that FYM notably enhanced nitrogen, phosphorus, and potassium uptake in both haulm and tubers compared to other organics. Moreover, higher phosphorus levels, particularly 125 kg ha−1 P2O5, maximized nutrient uptake. Soil attributes like available nitrogen remained unaffected, whereas phosphorus availability increased with FYM and higher phosphorus levels. Available potassium remained consistent across treatments. Soil pH, electrical conductivity, and organic carbon were unchanged with 125 kg ha−1 P2O5 treatments. FYM and biofertilizer significantly increased total tuber yields, with FYM showing a remarkable 30% boost compared to the control, and 125 kg ha−1 P2O5 phosphorus levels resulting in a notable 24% increase, indicating enhanced seed potato production strategies. Principal component analysis underscored the positive correlation between tuber yield and soil attributes, particularly favoring FYM and 125 kg ha−1 P2O5 treatments. Overall, FYM application and optimal phosphorus fertilizer levels are pivotal for augmenting nutrient uptake, soil health, and yield in seed potato cultivation.
A modified simplified SAFT EOS for VLE study of associating fluids
Authors: Hadipanah Mohammad Hossein , Mazloumi Seyed Hossein 
Published: July 2024

AbstractIn this study, the simplified version of statistical associating fluid theory (SAFT) equation of state (EOS) developed by Fu and Sandler is modified by replacing the dispersion term of this EOS with the Haghtalab–Mazloumi equation. This new SAFT‐based EOS has three adjustable parameters for non‐associating compounds and five adjustable parameters for associating compounds. The adjustable parameters of the new EOS are obtained by simultaneously fitting vapour pressures and liquid densities of pure substances. The new EOS shows better results in correlating vapour pressure and saturated liquid densities than SSAFT EOS for a selection of non‐associating and associating substances. Then, by using proper mixing rules, the new EOS is extended for mixtures. Both self‐associating and cross associating binary mixtures are used to test the capability of the new EOS in vapour–liquid equilibrium (VLE) calculations, and the results demonstrate good accuracy of the new EOS.