bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino Acid Adjacency in the Proteins: Non-Interdependent and Non-Reductionist
Authors: Khavinson Vladimir , Kormilets Dmitry , Maryanovich Alexander 
Published: April 2023

Abstract
BACKGROUND AND GOAL. In the chain of events “(a) codon/transcription/translation → (b) primary protein structure → (c) post-translational modification of amino acids”, the middle link (b) has been paid little attention. We sought to find out if the adjacency of amino acids in the protein structure obeys any rules.
METHOD. We have pooled the data on the primary protein structure from proteomes of more than 700,000 biological species (32,462,157 proteins and 11,117,062,854 amino acid residues) into a universal proteome (a data bank) and determined the frequency of occurrence (F) of 20 proteinogenic amino acids, 400 dimers, 8000 trimers, 160,000 tetramers, and 3,200,000 pentamers.
RESULTS AND DISCUSSION. The average length of the protein molecule comprises 342.46 ± 0.06 amino acid residues. In the universal proteome, we found all pentamers except WCMMW. In the remaining 3,199,999 pentamers, F ranged from 1 to 739,321. The pentamers with different amino acids at the same position differ significantly in the frequency of occurrence. The pentamers with the same amino acids at the different positions are statistically indistinguishable in the frequency of occurrence. In the overwhelming majority of pentamers, the observed frequency of occurrence (Fpenta observed) is significantly different from the expected frequency of occurrence (Fpenta expected) obtained by multiplying Famino acid observed of all five amino acids constituting the pentamer. In a protein molecule, amino acids do not have properties that "permit" or "forbid" the appearance of certain amino acids in neighboring positions of the polypeptide chain. The same rule applies to di-, tri-, and tetramers. In the oligomeres, of which the proteins consist, Fobserved depends less on the amino acids that make them up and more on some unknown factor. This factor, by natural selection of codons in the DNA molecule, creates for almost every amino acid in the protein a statistically significant deviation of the observed frequency of occurrence from the expected one.
CONCLUSION. The order of codons in DNA (and amino acid residues in a protein) is independent of neighboring codons (and amino acids), however, is non-reductionist and is controlled by a yet unknown factor.
Psychometric properties of the Chinese version of the Intensive Care Experience Questionnaire(ICEQ)
Authors: Hu Aiping , Yang Shuang , Ma Yonghong , Xiang Mingfang , Wang Guorong 
Published: April 2023

Abstract
Background: Negative experiences of ICU patients seriously affect the quality of life and survival outcome of patients. The application of scientific, scalable, high-quality assessment tools to understand the status of ICU patients' experience, its influencing factors, and its impact on long-term adverse outcomes is important for clinical practitionersto improve patient experience. ICEQ is an existing and mature tool for assessing ICU patient’s experience. However, there is a lack of scientific assessment tools to quantify the ICU patient experience in China. Here, we introduced the ICEQ for cross-cultural adaption, and test its reliability and validity to provide a recommend tool for future research.
Methods: After obtaining the authorization of the author of the ICEQ, the Beaton's cross-cultural guidelines was adopted to modify the ICEQ. From November 2021 to May 2022, 356 patients who met the criteria in four Grade A hospitals in Sichuan were investigated by questionnaires. Including the characteristics data of patients and ICEQ. SPSS21.0 and Amos21.0 software were used to analyze the reliability and validity of the C- ICEQ, which including the Internal consistency reliability, Split half reliability, Construct validity, Convergent validity and Content validity tests.
Results: The C-ICEQ contains 21 items and 5 dimensions: Awareness of surroundings; Frightening experiences; Satisfaction with care; Needs for cognition and Recall of experiences. There were five common factors extracted from EFA, and cumulative explanatory variation rate was 60.634%. CFA showed that CMIN/DF was 2.567, RMSEA was 0.069, GFI was 0.888. Cronbach's α coefficient of five dimensions of the C-ICEQ ranged from 0.815 to 0.888, and the split half reliability ranged from 0.806 to 0.891. The I-CVI, S-CVI and S-CVI/Ave were all 1.0; AVE value is between 0.4 and 0.6, and CR value is above 0.7.
Conclusions: The C-ICEQ demonstrated acceptable reliability and validity to assess intensive care experience of ICU patient’s in China.
Exosomes derived from LPS-preconditioned bone marrow-derived MSC modulate macrophage plasticity to promote allograft survival via the NF-κB/NLRP3 signaling pathway
Authors: Zhang Peiyao , Wu Panfeng , Khan Umar Zeb , Zhou Zekun , Sui Xinlei , Li Cheng , Dong Kangkang , Liu Yongjun , Qing Liming , Tang Juyu 
Published: April 2023

Abstract
Objectives This study investigated whether exosomes from LPS pretreated bone marrow mesenchymal stem cells (LPS pre-MSCs) could prolong skin graft survival.Methods The exosomes were isolated from the supernatant of MSCs pretreated with LPS. LPS pre-Exo and rapamycin were injected via the tail vein into C57BL/6 mice allografted with BALB/c skin; graft survival was observed and evaluated. The accumulation and polarization of macrophages were examined by immunohistochemistry. The differentiation of macrophages in the spleen was analyzed by flow cytometry. For in vitro, an inflammatory model was established. Specifically, bone marrow-derived macrophages (BMDMs) were isolated and cultured with LPS (100 ng/ml) for 3 h, and were further treated with LPS pre-Exo for 24 h or 48 h. The molecular signaling pathway responsible for modulating inflammation was examined by Western blotting. The expressions of downstream inflammatory cytokines were determined by Elisa, and the polarization of macrophages was analyzed by flow cytometry.Results LPS pre-Exo could better ablate inflammation compared to untreated MSC-derived exosomes (BM-Exo). These loaded factors inhibited the expressions of inflammatory factors via a negative feedback mechanism. In vivo, LPS pre-Exo significantly attenuated inflammatory infiltration, thus improving the survival of allogeneic skin graft. Flow cytometric analysis of BMDMs showed that LPS pre-Exo were involved in the regulation of macrophage polarization and immune homeostasis during inflammation. Further investigation revealed that the NF-κB/NLRP3/procaspase-1/IL-1β signaling pathway played a key role in LPS pre-Exo-mediated regulation of macrophage polarization. Inhibiting NF-κB in BMDMs could abolish the LPS-induced activation of inflammatory pathways and the polarization of M1 macrophages while increasing the proportion of M2 cells.Conclusion LPS pre-Exo are able to switch the polarization of macrophages and enhance the resolution of inflammation. This type of exosomes provides an improved immunotherapeutic potential in prolonging graft survival.
Biochemical, inflammatory and oxidative stress biomarkers in obese patients after COVID-19
Authors: Dyakov Denis , Spirina Lyudmila , Akbasheva Olga , Merkulov Evgeny , Samoylova Yulia , Matveeva Maria , Ermolaeva Yulia , Ponomareva Darija , Novozhilova Polina 
Published: April 2023

Abstract
The purpose of the study was to research informative biochemical, inflammatory and oxidative stress indicators after SARS-CoV2 infection in obesity.
Methods. Forty people (37.0 8.9 years old) were examined after SARS-CV2 infection and twenty people (36.0 5.4 years old) who had no documented coronavirus infection during the pandemic. The antibody to SARS-CV2 level, biochemical and oxidative stress indicators were determined. The proteolysis was assessed by the trypsin and elastase-like proteases and α1-proteins inhibitor (α1-PI) activity.
Results. All subjects, regardless the COVID-19 infection in the anamnesis, had antibodies to SARS-CoV2. We found the TNF increased content, the trypsin- and elastase-like proteases activity, the increased MDA concentration and decreased catalase activity compared with the retrospective control. The biochemical parameters did not differ significantly from the normal values. But levels of C-reactive protein were three times higher in those who were ill than who probably had the disease in asymptomatic form (not vaccinated).
Elevated levels of antibodies were found in people in post-COVID with dermatological, neurological, gastroenterological, cardiological symptoms and shortness of breath. Overweight individuals had higher antibody titer to SARS-CoV2, increase in trypsin-like protease activity, and decrease in α1-PI activity than normal weight ones. An increase in the adipose tissue percentage correlates with a decrease in α1-PI activity. Obesity causes chronic inflammation and PI deficiency in the postoperative period.
Conclusion. In the COVID long period, the trypsin-like, elastic-like proteases activity, MDA and oxidative modified proteins level increased. Overweight individuals had elevated SARS-CoV2 antibodies, trypsin-like protein activity, and decreased α1-PI activity.
Shorebird Abundance is Associated With Nutritional Quality of Intertidal Biofilm on the Fraser River Estuary
Authors: Drever Mark , Mogle Matthew J. , Douglas Tristan J. , Flemming Scott A. , Hamilton Diana J. , Liefer Justin D. , Elner Robert W. 
Published: April 2023

Abstract
Dense congregations of shorebirds forage on tidal flats during long-distance migration, and their abundance is presumed to mirror the underlying ecological conditions. We quantified the nutritional content of intertidal biofilm (a thin layer of microalgae, bacteria, and other micro-organisms embedded in a mucilaginous matrix) to assess whether biofilm biomass and the abundance of macronutrients (lipid, protein, and carbohydrate) provide a measure of habitat quality for migrating shorebirds. We compared shorebird use, biofilm biomass, nutritional quality, and stable isotope signatures at two mudflats on the Fraser River estuary, British Columbia, Canada, during summer 2020 (southward migration) and spring 2021 (northward migration). The abundances of Western Sandpipers (Calidris mauri) and Dunlin (Calidris alpina) were consistently higher (6-100×) at Brunswick Point relative to the Iona Foreshore site during both migration periods. Biofilm biomass (chlorophyll a) was 2× higher at Brunswick Point than Iona Foreshore during southward migration, and was similar between sites during northward migration. Macronutrient content (lipid, protein, and carbohydrate) in intertidal biofilm was 1.4× to 3.8× higher at Brunswick Point than Iona Foreshore during both migration periods. Carbohydrate content was higher during southward migration at both tidal flats, whereas protein and lipid content at Iona Foreshore did not show significant differences between years/migration periods. Carbon and nitrogen stable isotope signatures during spring 2021 did not differ between the two sites, suggesting that nutrients had similar origins from marine and terrestrial inputs. The findings tie shorebird use to nutrients available in intertidal biofilm during migration periods.
AUF1 modulates apoptosis via regulating transcription and alternative splicing of immune response genes in auditory hair cells
Authors: Li Lihua , Wang Zhi , Xu Kai , Bai Xue , Wu Wenjing , Zhang Zhilin , Chen Xubo 
Published: April 2023

Abstract

Background:AU-rich element RNA-binding factor 1 (AUF1) is a multifunctional RNA binding proteins (RBPs) in post-transcriptional gene regulation. However, it remains unclear whether or not AUF1 has a function in the regulation of inflammation and apoptosis as a splicing factor in presbycusis and auditory hair cells.Methods:In this study, RNA-seq was used to analyze the global transcript level and alternative splicing in AUF1 siRNA-treated HEI-OC1 cells (siAUF1) and control cells. Integration analysis was carried out using published transcriptome and AUF1-RNA interactome datasets.Results:SiAUF1 was found to promote the level of apoptosis in HEI-OC1 cells. The RNA-seq results indicated the extensive regulation of the expression of hundreds of genes by AUF1 knocked down cells. The genes down-regulated by siAUF1 were significantly involved in immune responses and cellular apoptosis. AUF1 regulated the alternative splicing of genes, such as FASTK, MAP4, and hnRNPDL, that are involved in mitochondrial functioning and cellular apoptosis. Furthermore, the published transcriptomic data of aging mice demonstrated that the expression of AUF1 and immune response were highly exhibited in aging animals. Moreover, RBMS3 was also found to be an important gene target of AUF1 to modulate apoptosis.Conclusion:To our knowledge, this is the first investigation of its kind that has described the transcriptome-wide analysis of AUF1-regulated expression and alternative splicing profiles and has demonstrated the possible mechanisms of AUF1 regulating immune response, apoptosis, and alternative splicing, which could aid future researches on cellular biology and contribute to the deciphering of the aging process and presbycusis.
Novel insight into risk of major adverse cardiovascular and cerebrovascular events of patients with central retinal artery occlusion: regarding sex differences
Authors: Chen Ting , Wang Yuedan , Li Xuejie , Feng Jiaqing , Yang Hongxia , Li Ying , Feng Hui , Xiao Xuan 
Published: April 2023

Abstract
To estimate the association between central retinal artery occlusion (CRAO) and major adverse cardiovascular and cerebrovascular events (MACCE), including their clinical characteristics, blood markers, and the contribution of CRAO to MACCE, as well as to assess any sex differences. This retrospective cohort study included continuous new-onset CRAO patients and 1:4controls during the same period. Correlations of CRAOwith the incidence of MACCE during follow-up and the sex-related differences were studied. One hundred and twenty-four CRAO patients and four hundred and ninety-six controls were enrolled. Neutrophil-to-lymphocyte ratio (NLR, P = 0.014) and high-sensitivity C-reactive protein (hs-CRP, P = 0.038) were tended to be higher in CRAO patients. After the follow-up period, 78 patients experienced MACCE. Multivariate Cox regression analysis showed that CRAO was a predictor of the occurrence of MACCE (HR: 2.321, 95% CI: 1.439 - 3.744, P = 0.001). Sex subgroups indicated that age, diabetes, current smoking, CRAO, NLR and hs-CRP increased the risk factor of MACCE in males (All P<0.05)and CRAO, NLR, low-density lipoprotein cholesterol (LDL-C)and hs-CRP were independent influencing factors for females (All P<0.05). New-onset CRAO significantly increases the probability of MACCE and is associated with a poor prognosis. The sex-related differences suggested that effective prevention of the occurrence of MACCE in high-risk patients requires that attention be given to individualized risk factors corresponding to sexes.
Assessment of the influence of non-ionizing radiation to the morbidity of MRI and ultrasound diagnostics specialists in Kazakhstan
Authors: Ibrayeva Lyazat , Grebeneva Olga , Omarkulov Bauyrzhan , Rybalkina Dina , Bacheva Irina , Minbayeva Larissa 
Published: April 2023

Abstract

The state of health of healthcare practitioners with occupational exposure to a complex of hazards may differ from the state of health of general population and justify the need to develop a number of preventive measures for healthcare practitioners. The purpose of the study was assessment of the prevalence of morbidity among medical specialists (MRI and ultrasound diagnostics). Design: retrospective (2018-2021), nonrandomized. Participants: MRI and ultrasound diagnostics specialists, ophthalmologists (as control). An analysis of data on healthcare practitioners seeking for medical care was done (diagnosis by ICD-10). Morbidity was also compared with general population of the RK. Higher morbidity of healthcare practitioners of the listed above specialties with genitourinary and musculoskeletal systems diseases, eye diseases and oncopathology was revealed. Comparing with ophthalmologists, ultrasound diagnostic specialists had higher morbidity with malignant and benign neoplasms (RR 2.74 and RR 9.58, respectively), MRI specialists had higher morbidity with malignant neoplasms and blood diseases (RR 4.73 and RR 1.89, respectively). The incidence rates of SARS-COV-2 in MRI and ultrasound diagnostic specialists and ophthalmologists exceeded those in the general population of the RK. Identified features of the morbidity of healthcare practitioners should be taken into account in labor ergonomics and organization of preventive and screening measures for diagnosing diseases.
Preoperative prediction of sinonasal papilloma by artificial intelligence using nasal video endoscopy: A retrospective study
Authors: Yui Ryosuke , Takahashi Masahiro , Noda Katsuhiko , Yoshida Kaname , Sakurai Rinko , Ohira Shinya , Omura Kazuhiro , Otori Nobuyoshi , Wada Kota , Kojima Hiromi 
Published: April 2023

Abstract
Sinonasal inverted papilloma (IP) is at risk of recurrence and malignancy, and early diagnosis using nasal endoscopy is essential. We thus developed a diagnostic system using artificial intelligence (AI) to identify nasal sinus papilloma. Endoscopic surgery videos of 53 patients undergoing endoscopic sinus surgery were edited to train and evaluate deep neural network models and then a diagnostic system was developed. The correct diagnosis rate based on visual examination by otolaryngologists was also evaluated using the same videos and compared with that of the AI diagnostic system patients. Main outcomes evaluated included the percentage of correct diagnosis compared to AI diagnosis and the correct diagnosis rate for otolaryngologist based on years of practice experience. The diagnostic system had an area under the curve of 0.874, accuracy of 0.843, false positive rate of 0.124, and false negative rate of 0.191. The average correct diagnosis rate among otolaryngologists was 69.4%, indicating that the AI was highly accurate. Evidently, although the number of cases was small, a highly accurate diagnostic system was created. Future studies with a larger sample size to improve the accuracy of the system and expand the range of diseases that can be detected for more clinical applications are warranted.
The utility of Galactomannan and Polymerase Chain Reaction Assays in Bronchoalveolar Lavage for diagnosis of Chronic Pulmonary Aspergillosis
Authors: CHOWDHURY MOHIT , Singh Gagandeep , Pandey Mragnayani , Mishra Himanshu , Meena Ved prakash , Sethi Prayas , Singh Amandeep , Prakash Bindu , upadhyay Ashish datt , Mohan Anant , Sinha Sanjeev , Xess Immaculata , Wig Naveet , Kabra Sushil Kumar , Ray Animesh 
Published: April 2023

Abstract
The diagnosis of Chronic pulmonary aspergillosis (CPA) is established by combined clinic-radio-microbiological criteria. Out of the different microbiological criteria, usually a positive serology for Aspergillus-specific IgG levels is the cornerstone of diagnosis . Alternatively, other microbiological evidence can also be employed viz. significantly positive Aspergillus antigen (broncho-alveolar lavage fluid/BALF galactomannan ≥ 1.0), histopathological demonstration of the fungi following lung biopsy or resection, or demonstration of hyaline septate hyphae in direct microscopy resembling Aspergillus spp. or its growth on respiratory specimen. However the role of BALF- GM and the newer BALF-PCR have not been confirmed by studies till date. The study enrolled 210 patients overall of suspected CPA. Of the participants, 88 patients met the criteria for chronic pulmonary aspergillosis, whereas 122 patients had an alternative diagnosis. The sensitivity - specificity of AsperGenius® PCR and "in-house” PCR were 52.27(36.69-67.54) % - 33.78(23.19-45.72) % and 36.36(22.41-52.23) % - 39.19(28.04-51.23) % respectively. The sensitivity / specificity of BALF(>1.0) and serum galactomannan(>1.0) were 46.55%(33.34-60.13) / 64.08%(54.03-73.3) and 62.96%(54.7671.17) / 62.96%(54.76-71.17) respectively. The optimal cut-off value for BALF Galactomannan and serum galactomannan in diagnosing CPA was found to be 0.69 (sensitivity: 64%; specificity: 53%) and 0.458 (sensitivity: 67%; specificity: 64%) respectively. Aspergillus PCR from BAL may not be a good “rule-in” test for diagnosing CPA. While the performances of GM in BAL and serum may be better than PCR, it is to be used in conjunction with other clinical, radiological and other microbiological characteristics.
Unusually High Room and Elevated-Temperature Tensile Properties Observed in Direct Aged Wire-Arc Directed Energy Deposited Inconel 718
Authors: Song Jie , Jimenez Xavier A. , Russell Carissa , To Albert C. , Fu Yao 
Published: April 2023

Abstract
Wire-arc directed energy deposition (DED) processed Inconel (IN) 718 is known to have coarse columnar grain, strong texture, significant chemical and microstructural inhomogeneity in as-fabricated condition. Homogenization treatment is commonly used prior to aging to eliminate the inhomogeneity and detrimental precipitation for better mechanical properties. In this study, however, direct aging (DA) at 700 °C without homogenization has resulted in room-temperature yield strength, ultimate tensile strength (UTS), and elongation that are comparable to wrought condition and among the highest reported properties for wire-arc DED IN718. The DA samples at between 650 °C and 750 °C aging also demonstrates remarkable ductility when deformed at elevated temperatures. In addition, when aged below 750 °C the DA IN718 possesses significantly higher UTS compared to those with homogenization treatment. These superior mechanical properties are highly likely due to the non-uniform and hierarchical precipitation consisting of disk-shaped γ″ in diameter from a few to tens of nm in the dendritic core area and micron-sized Laves phase and carbides in the inter-dendritic region.
Substituted salicylic acid analogs offer improved potency against multidrug-resistant Neisseria gonorrhoeae and good selectivity against commensal vaginal bacteria
Authors: Almolhim Hanan , Elhassanny Ahmed E.M. , Abutaleb Nader S. , Seleem Mohamed N. , Carlier Paul R. 
Published: April 2023

Abstract
Drug-resistant Neisseria gonorrhoeae represents a major threat to public health; without new effective antibiotics, untreatable gonococcal infections loom as a real possibility. In a previous drug-repurposing study, we reported that salicylic acid had good potency against azithromycin-resistant N. gonorrhoeae. We now report that the anti-gonococcal activity in this scaffold is easily lost by inopportune substitution, but that select substituted naphthyl analogs (3b,o,p) have superior activity to salicylic acid itself. Promisingly, these compounds also show very weak growth inhibition of commensal vaginal bacteria.