bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of avian pathogenic Escherichia coli χ7122 lipopolysaccharide increases accessibility to glycoconjugate antigens
Authors: Smith Alexander A. , Corona-Torres Ricardo , Hewitt Rachel E. , Stevens Mark P. , Grant Andrew J. ,   the Glycoengineering of Veterinary Vaccines Consortium, Wren Brendan , Cuccui Jon 
Published: September 2022

Abstract
Background
Worldwide, an estimated 70.7 billion broilers were produced in 2020. With the reduction in use of prophylactic antibiotics as a result of consumer pressure and regulatory oversight alternative approaches, such as vaccination, are required to control bacterial infections. A potential way to produce a multivalent vaccine is via the generation of a glycoconjugate vaccine which consists of an antigenic protein covalently linked to an immunogenic carbohydrate. Protein-glycan coupling technology (PGCT) is an approach to generate glycoconjugates using enzymes that can couple proteins and glycan when produced in bacterial cells. Previous studies have used PGCT to generate a live-attenuated avian pathogenic Escherichia coli (APEC) strain capable of N-glycosylation of target proteins using a chromosomally integrated Campylobacter jejuni pgl locus. However, this proved ineffective against C. jejuni challenge.

Results
In this study we demonstrate the lack of surface exposure of glycosylated protein in APEC strain χ7122 carrying the pgl locus. Furthermore, we hypothesise that this may be due to the complex cell-surface architecture of E. coli. To this end, we removed the lipopolysaccharide O-antigen of APEC χ7122 pgl+ via deletion of the wecA gene and demonstrate increased surface exposure of glycosylated antigens (NetB and FlpA) in this strain. We hypothesise that increasing the surface expression of the glycosylated protein would increase the chance of host immune cells being exposed to the glycoconjugate, and therefore the generation of an efficacious immune response would be more likely.

Conclusions
Our results demonstrate an increase in cell surface exposure and therefore accessibility of glycosylated antigens upon removal of lipopolysaccharide antigen from the APEC cell surface.
Glucose transport engineering allows mimicking fed-batch performance in batch mode and selection of superior producer strains
Authors: Velazquez Daniela , Sigala Juan-Carlos , Martínez Luz María , Gaytán Paul , Gosset Guillermo , Lara Alvaro R. 
Published: September 2022

Abstract
Background
Fed-batch mode is the standard culture technology for industrial bioprocesses. Nevertheless, most of the early-stage cell and process development is carried out in batch cultures, which can bias the initial selection of expression systems. Cell engineering can provide an alternative to fed-batch cultures for high-throughput screening and host selection. We have previously reported a library of Escherichia coli strains with single and multiple deletions of genes involved in glucose transport. Compared to their wild type (W3110), the mutant strains displayed lower glucose uptake, growth and aerobic acetate production rates. Therefore, when cultured in batch mode, such mutants may perform similar to W3110 cultured in fed-batch mode. To test that hypothesis, we evaluated the constitutive expression of the green fluorescence protein (GFP) in batch cultures in microbioreactors using a semi defined medium supplemented with 10 or 20 g/L glucose + 0.4 g yeast extract/g glucose.

Results
The mutant strains cultured in batch mode displayed a fast-growth phase (growth rate between 0.40 and 0.60 h−1) followed by a slow-growth phase (growth rate between 0.05 and 0.15 h−1), similar to typical fed-batch cultures. The phase of slow growth is most probably caused by depletion of key amino acids. Three mutants attained the highest GFP fluorescence. Particularly, a mutant named WHIC (ΔptsHIcrr, ΔmglABC), reached a GFP fluorescence up to 14-fold greater than that of W3110. Strain WHIC was cultured in 2 L bioreactors in batch mode with 100 g/L glucose + 50 g/L yeast extract. These cultures were compared with exponentially fed-batch cultures of W3110 maintaining the same slow-growth of WHIC (0.05 h−1) and using the same total amount of glucose and yeast extract than in WHIC cultures. The WHIC strain produced approx. 450 mg/L GFP, while W3110 only 220 mg/L.

Conclusion
The combination of cell engineering and high throughput screening allowed the selection of a particular mutant that mimics fed-batch behavior in batch cultures. Moreover, the amount of GFP produced by the strain WHIC was substantially higher than that of W3110 under both, batch and fed-batch schemes. Therefore, our results represent a valuable technology for accelerated bioprocess development.
Fusing an exonuclease with Cas9 enhances homologous recombination in Pichia pastoris
Authors: Zhang Kun , Duan Xingpeng , Cai Peng , Gao Linhui , Wu Xiaoyan , Yao Lun , Zhou Yongjin J. 
Published: September 2022

Abstract
Background
The methylotrophic yeast Pichia pastoris is considered as an ideal host for the production of recombinant proteins and chemicals. However, low homologous recombination (HR) efficiency hinders its precise and extensive genetic manipulation. To enhance the homology-directed repair over non-homologous end joining (NHEJ), we expressed five exonucleases that were fused with the Cas9 for enhancing end resection of double strand breaks (DSBs) of DNA cuts.

Results
The endogenous exonuclease Mre11 and Exo1 showed the highest positive rates in seamless deletion of FAA1, and fusing the MRE11 to the C-terminal of CAS9 had the highest positive rate and relatively high number of clones. We observed that expression of CAS9-MRE11 significantly improved positive rates when simultaneously seamless deletion of double genes (from 76.7 to 86.7%) and three genes (from 10.8 to 16.7%) when overexpressing RAD52. Furthermore, MRE11 overexpression significantly improved the genomic integration of multi-fragments with higher positive rate and clone number.

Conclusions
Fusion expression of the endogenous exonuclease Mre11 with Cas9 enhances homologous recombination efficiency in P. pastoris. The strategy described here should facilitate the metabolic engineering of P. pastoris toward high-level production of value-added compounds.
Camels’ biological fluids contained nanobodies: promising avenue in cancer therapy
Authors: Al-Numair Nouf S. , Theyab Abdulrahman , Alzahrani Faisal , Shams Anwar M. , Al-Anazi Ibrahim O. , Oyouni Atif Abdulwahab A. , Al-Amer Osama M. , Mavromatis Charalampos , Saadeldin Islam M. , Abdali Wed A. , Hawsawi Yousef M. 
Published: September 2022

AbstractCancer is a major health concern and accounts for one of the main causes of death worldwide. Innovative strategies are needed to aid in the diagnosis and treatment of different types of cancers. Recently, there has been an evolving interest in utilizing nanobodies of camel origin as therapeutic tools against cancer. Nanotechnology uses nanobodies an emerging attractive field that provides promises to researchers in advancing different scientific sectors including medicine and oncology. Nanobodies are characteristically small-sized biologics featured with the ability for deep tissue penetration and dissemination and harbour high stability at high pH and temperatures. The current review highlights the potential use of nanobodies that are naturally secreted in camels’ biological fluids, both milk and urine, in the development of nanotechnology-based therapy for treating different typesQuery of cancers and other diseases. Moreover, the role of nano proteomics in the invention of novel therapeutic agents specifically used for cancer intervention is also illustrated.
Thermodiluted relative tidal volume estimation using a thermal camera in operating room under spinal anesthesia
Authors: Kwon JunHwan , Kwon Oyun , Oh KyeongTeak , Kim Jeongmin , Shin Cheung Soo , Yoo Sun K. 
Published: September 2022

Abstract
Background
Estimating relative tidal volume is an important factor when monitoring breathing status. The relationship between temperature and respiration volume has rarely been studied. In this paper, a formula was derived for calculating thermodiluted respiration volume from temperature changes in the nasal cavity. To evaluate the proposed formula, the study compared the relative tidal volume estimated by the proposed formula with that recorded by a respiration volume monitor (Exspiron1Xi, RVM). Thermal data were obtained for 8 cases at a rate of 10 measurements per second. Simultaneous recordings by the RVM are regarded as the reference.

Results
The mean of ICC coefficient is 0.948 ± 0.030, RMSE is 0.1026 ± 0.0284, R-squared value is 0.8962 ± 0.065 and linear regression coefficient $$\mathrm{\alpha }$$
α
is 0.966 ± 0.104, $$\upbeta$$
β
is 0.042 ± 0.057. Bland–Altman plot showed 96.01% of samples that the difference between the measured and estimated values exists within 2 standard deviations.

Conclusions
In this paper, a model that can thermodynamically calculate the relationship between thermal energy and respiration volume is proposed. The thermodiluted model is a feasible method for estimating relative respiration tidal volumes.
Classification of facial paralysis based on machine learning techniques
Authors: Gaber Amira , Taher Mona F. , Wahed Manal Abdel , Shalaby Nevin Mohieldin , Gaber Sarah 
Published: September 2022

AbstractFacial paralysis (FP) is an inability to move facial muscles voluntarily, affecting daily activities. There is a need for quantitative assessment and severity level classification of FP to evaluate the condition. None of the available tools are widely accepted. A comprehensive FP evaluation system has been developed by the authors. The system extracts real-time facial animation units (FAUs) using the Kinect V2 sensor and includes both FP assessment and classification. This paper describes the development and testing of the FP classification phase. A dataset of 375 records from 13 unilateral FP patients and 1650 records from 50 control subjects was compiled. Artificial Intelligence and Machine Learning methods are used to classify seven FP categories: the normal case and three severity levels: mild, moderate, and severe for the left and right sides. For better prediction results (Accuracy = 96.8%, Sensitivity = 88.9% and Specificity = 99%), an ensemble learning classifier was developed rather than one weak classifier. The ensemble approach based on SVMs was proposed for the high-dimensional data to gather the advantages of stacking and bagging. To address the problem of an imbalanced dataset, a hybrid strategy combining three separate techniques was used. Model robustness and stability was evaluated using fivefold cross-validation. The results showed that the classifier is robust, stable and performs well for different train and test samples. The study demonstrates that FAUs acquired by the Kinect sensor can be used in classifying FP. The developed FP assessment and classification system provides a detailed quantitative report and has significant advantages over existing grading scales.
Targeting RNA N6-methyladenosine modification: a precise weapon in overcoming tumor immune escape
Authors: Li Wei , Hao Yi , Zhang Xingda , Xu Shouping , Pang Da 
Published: September 2022

AbstractImmunotherapy, especially immune checkpoint inhibitors (ICIs), has revolutionized the treatment of many types of cancer, particularly advanced-stage cancers. Nevertheless, although a subset of patients experiences dramatic and long-term disease regression in response to ICIs, most patients do not benefit from these treatments. Some may even experience cancer progression. Immune escape by tumor cells may be a key reason for this low response rate. N6-methyladenosine (m6A) is the most common type of RNA methylation and has been recognized as a critical regulator of tumors and the immune system. Therefore, m6A modification and related regulators are promising targets for improving the efficacy of tumor immunotherapy. However, the association between m6A modification and tumor immune escape (TIE) has not been comprehensively summarized. Therefore, this review summarizes the existing knowledge regarding m6A modifications involved in TIE and their potential mechanisms of action. Moreover, we provide an overview of currently available agents targeting m6A regulators that have been tested for their elevated effects on TIE. This review establishes the association between m6A modifications and TIE and provides new insights and strategies for maximizing the efficacy of immunotherapy by specifically targeting m6A modifications involved in TIE.
Effect of downregulated citrate synthase on oxidative phosphorylation signaling pathway in HEI-OC1 cells
Authors: Xu Xiaowen , Liu Yue , Luan Jun , Liu Rongrong , Wang Yan , Liu Yingying , Xu Ang , Zhou Bingxin , Han Fengchan , Shang Wenjing 
Published: September 2022

Abstract
Background
Citrate Synthase (Cs) gene mutation (locus ahL4) has been found to play an important role in progressive hearing loss of A/J mice. HEI-OC1 cells have been widely used as an in vitro system to study cellular and molecular mechanisms related to hearing lose. We previously reported the increased apoptosis and the accumulation of reactive oxygen species in shRNACs-1429 cells, a Cs low-expressed cell model from HEI-OCI. The details of the mechanism of ROS production and apoptosis mediated by the abnormal expression of Cs needed to research furtherly.

Methods
iTRAQ proteomics was utilized to detect the differentially expressed proteins (DEPs) caused by low expression of Cs. The GO and KEGG pathways analysis were performed for annotation of the differentially expressed proteins. Protein–protein interaction network was constructed by STRING online database. Immunoblotting was utilized to confirm the protein levels of the the differentially expressed proteins.

Results
The differentially expressed proteins were significantly enriched in various signaling pathways mainly related to mitochondrial dysfunction diseases including Parkinson’s disease, Alzheimer’s disease, Huntington’s disease, et al. Most noteworthy, the oxidative phosphorylation pathway was most significantly suppressed in the shRNACs-1429 cells,, in which a total of 10 differentially expressed proteins were enriched and were all downregulated by the abnormal expression of Cs. The downregulations of Ndufb5, Ndufv1 and Uqcrb were confirmed by immunoblotting. Meanwhile, the ATP levels of shRNACs-1429 cells were also reduced.

Conclusions
These results suggest that low level expression of Cs induces the inhibition of oxidative phosphorylation pathway, which is responsible for the high level production of reactive oxygen species and low level of ATP, leading to the apoptosis of cochlear cells. This study may provide new theories for understanding and therapy of progressive hearing loss.
Improving WHO’s understanding of WHO guideline uptake and use in Member States: a scoping review
Authors: Saluja Kiran , Reddy K. Srikanth , Wang Qi , Zhu Ying , Li Yanfei , Chu Xiajing , Li Rui , Hou Liangying , Horsley Tanya , Carden Fred , Bartolomeos Kidist , Hatcher Roberts Janet 
Published: September 2022

AbstractBackgroundWHO publishes public health and clinical guidelines to guide Member States in achieving better health outcomes. Furthermore, WHO’s Thirteenth General Programme of Work for 2019–2023 prioritizes strengthening its normative functional role and uptake of normative and standard-setting products, including guidelines at the country level. Therefore, understanding WHO guideline uptake by the Member States, particularly the low- and middle-income countries (LMICs), is of utmost importance for the organization and scholarship.MethodsWe conducted a scoping review using a comprehensive search strategy to include published literature in English between 2007 and 2020. The review was conducted between May and June 2021. We searched five electronic databases including CINAHL, the Cochrane Library, PubMed, Embase and Scopus. We also searched Google Scholar as a supplementary source. The review adhered to the PRISMA-ScR (PRISMA extension for scoping reviews) guidelines for reporting the searches, screening and identification of evaluation studies from the literature. A narrative synthesis of the evidence around key barriers and challenges for WHO guideline uptake in LMICs is thematically presented.ResultsThe scoping review included 48 studies, and the findings were categorized into four themes: (1) lack of national legislation, regulations and policy coherence, (2) inadequate experience, expertise and training of healthcare providers for guideline uptake, (3) funding limitations for guideline uptake and use, and (4) inadequate healthcare infrastructure for guideline compliance. These challenges were situated in the Member States’ health systems. The findings suggest that governance was often weak within the existing health systems amongst most of the LMICs studied, as was the guidance provided by WHO’s guidelines on governance requirements. This challenge was further exacerbated by a lack of accountability and transparency mechanisms for uptake and implementation of guidelines. In addition, the WHO guidelines themselves were either unclear and were technically challenging for some health conditions; however, WHO guidelines were primarily used as a reference by Member States when they developed their national guidelines.ConclusionsThe challenges identified reflect the national health systems’ (in)ability to allocate, implement and monitor the guidelines. Historically this is beyond the remit of WHO, but Member States could benefit from WHO implementation guidance on requirements and needs for successful uptake and use of WHO guidelines.
In vivo assessment of Lewy body and beta-amyloid copathologies in idiopathic normal pressure hydrocephalus: prevalence and associations with clinical features and surgery outcome
Authors: Giannini Giulia , Baiardi Simone , Dellavalle Sofia , Zenesini Corrado , Cevoli Sabina , Danner Nils , Jyrkkänen Henna-Kaisa , Rossi Marcello , Polischi Barbara , Quadalti Corinne , Stefanini Camilla , Cortelli Pietro , Milletti David , Herukka Sanna-Kaisa , Palandri Giorgio , Leinonen Ville , Parchi Piero 
Published: September 2022

Abstract
Background
Idiopathic normal pressure hydrocephalus (iNPH) is a clinico-radiological syndrome of elderly individuals likely sustained by different neurodegenerative changes as copathologies. Since iNPH is a potentially reversible condition, assessing neurodegenerative pathologies in vitam through CSF biomarkers and their influence on clinical features and surgical outcome represents crucial steps.

Methods
We measured α-synuclein seeding activity related to Lewy body (LB) pathology by the real-time quaking-induced conversion assay (RT-QuIC) and Alzheimer disease core biomarkers (proteins total-tau, phospho-tau, and amyloid-beta) by immunoassays in the cerebrospinal fluid (CSF) of 293 iNPH patients from two independent cohorts. To compare the prevalence of LB copathology between iNPH participants and a control group representative of the general population, we searched for α-synuclein seeding activity in 89 age-matched individuals who died of Creutzfeldt-Jakob disease (CJD). Finally, in one of the iNPH cohorts, we also measured the CSF levels of neurofilament light chain protein (NfL) and evaluated the association between all CSF biomarkers, baseline clinical features, and surgery outcome at 6 months.

Results
Sixty (20.5%) iNPH patients showed α-synuclein seeding activity with no significant difference between cohorts. In contrast, the prevalence observed in CJD was only 6.7% (p = 0.002). Overall, 24.0% of iNPH participants showed an amyloid-positive (A+) status, indicating a brain co-pathology related to Aβ deposition. At baseline, in the Italian cohort, α-synuclein RT-QuIC positivity was associated with higher scores on axial and upper limb rigidity (p = 0.003 and p = 0.011, respectively) and lower MMSEc scores (p = 0.003). A+ patients showed lower scores on the MMSEc (p = 0.037) than A- patients. Higher NfL levels were also associated with lower scores on the MMSEc (rho = -0.213; p = 0.021). There were no significant associations between CSF biomarkers and surgical outcome at 6 months (i.e. responders defined by decrease of 1 point on the mRankin scale).

Conclusions
Prevalent LB- and AD-related neurodegenerative pathologies affect a significant proportion of iNPH patients and contribute to cognitive decline (both) and motor impairment (only LB pathology) but do not significantly influence the surgical outcome at 6 months. Their effect on the clinical benefit after surgery over a more extended period remains to be determined.
Gender differences in psychiatric outpatients: a before and during COVID-19 pandemic study in general hospitals from China
Authors: He Wenli , Xu Danhong , Wang Jiafeng , Shen Yuze , Lin Zheng , Ruan Liemin , Chen Qiaozhen 
Published: September 2022

AbstractBackgroundLittle is known about the gender characteristics and the Corona Virus Disease 2019 (COVID-19) impact on psychiatric department outpatients in general hospitals in China.MethodsWe retrospectively collected 225,947 outpatient clinic records before and during COVID-19 pandemic from January 1, 2019 to December 31, 2020 in the psychiatric clinic of 3 general hospitals, gender composition of patients was analyzed in different five age groups and nine diagnostic categories at three levels: total patient visits, number of patients and number of first-visit patients.ResultsThe total male-to-female ratio of psychiatric outpatient records in 3 general hospitals from 2019 to 2020 was 1:1.69. Women were more common in all age groups. Overall, the proportion of women was further increased in 2020 compared to that in 2019, especially in age group below 34 years and anxiety disorders category. Most mental disorders showed higher demands for females than that for males except mental and behavioral disorders due to psychoactive substance use with the male-to-female ratio was 1:0.05.ConclusionsThe demand for female psychiatric outpatient services is obviously higher than that for males. It is necessary to pay more attention to explore targeted mechanism or psychosocial service strategy for female patients with mental disorders.Trial registrationChiCTR2100044894, March 31, 2021 retrospectively registered.