bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community Engagement in Kidney Research: Guatemalan Experience
Authors: Aguilar-González Angie , Lou-Meda Randall , Chocó André , Moist Louise 
Published: March 2022

Abstract
Background: Community engagement is essential for effective research when addressing issues important to the community and researchers. Despite its effectiveness, there is limited published evidence concerning the evaluation of community engagement in research projects, especially in the area of nephrology. Methods: We developed a community engagement program in Guatemala to address the role of hydration in chronic kidney disease of unknown origin, using five key engagement principles: 1. Local relevance and determinants of health. 2. Acknowledgment of the community. 3. Dissemination of findings and knowledge gained to all partners. 4. Usage of community partners’ input. 5. Involvement of a cyclical and iterative process in the pursuit of goals. The effectiveness of community engagement was measured by a structured questionnaire on a 5-point likert scale. This measure determined how well and how often the research team adhered to the five engagement principles. Results: Sixty-two community leaders completed the questionnaire. Seventy-five percent were female, with a mean age of 37 years. All 5 engagement principles scored highly on the 5-point likert scale. Conclusion: Community leaders and researchers developed a relationship in which commitment and empowerment facilitated the participation in all aspects of the research process. This program is a useful tool for researchers, especially in low-middle income countries, to start research in a community.
Cyclophilin A contributes to shikonin-induced glioma cell necroptosis via promotion of chromatinolysis
Authors: Wang Xinyu , Fan Liwen , Wang Xuanzhong , Ge Pengfei , Liu Linlin 
Published: March 2022

Abstract
Shikonin induces glioma cell death via necroptosis, a caspase-independent programmed cell death pathway that is chiefly regulated by receptor-interacting serine/threonine protein kinase1 (RIP1) and 3 (RIP3). Chromatinolysis is considered as one of the key events leading to cell death during necroptosis. It is usually accompanied with nuclear translocation of AIF and formation of γ-H2AX. Cyclophilin A (CypA) is reported to participate in the nuclear translocation of AIF during apoptosis. However, it remains unclear whether CypA contributes to necroptosis via regulation of chromatinolysis. In this study, our results revealed for the first time that shikonin promoted time-dependent CypA activation, which contributed to nuclear translocation of AIF and γ-H2AX formation. In vitro studies showed that knockdown of CypA by siRNA or inhibition of CypA by its specific inhibitor, cyclosporine A (CsA), not only significantly mitigated shikonin-induced glioma cell death, but also prevented chromatinolysis. Mechanisticlly, activated CypA targeted mitochondria and triggered mitochondrial superoxide overproduction, which then promoted AIF translocation from mitochondria into the nucleus by depolarizing the mitochondria and intensified the formation of γ-H2AX by promoting intracellular accumulation of ROS. Additionally, the CypA in the nucleus can form DNA degradation complexes with AIF and γ-H2AX, which also promote the execution of chromatinolysis. Thus, we demonstrate that CypA contributes to shikonin-induced glioma cell necroptosis via promotion of chromatinolysis.
Heart-targeted Amelioration of Sepsis-induced Myocardial Dysfunction by Microenvironment Responsive Nitric Oxide Nanogenerators in Situ
Authors: Ouyang Minzhi , Ouyang Xiangnan , Peng Zefang , Liu Minghui , Xu Ganqiong , Zou Zhen , Zhang Ming , Shang Quanliang 
Published: March 2022

Abstract
Background: Reduced levels of bioavailable nitric oxide (NO) plays a key role in maintaining cardiovascular homeostasis. However, it is clinically proven that the lack of spatial and temporal control of release restrict the application of NO.Destination: The purpose of this study is to design the heart-targeted and infection microenvironment-responsive NO-releasing biomaterials to efficiently ameliorate lipopolysaccharide (LPS)-induced cardiac dysfunction.Methods and Results: The heart-targeted NO delivery and in situ release system was synthesized using hollow mesoporous silica (MSN) as the carrier and L-arginine (LA) as the NO donor. PCM-MSN@LA was characterized by several analytical techniques. The directed myocardial delivery was successfully accomplished by primary cardiomyocyte-specific peptide (PCM) targeting and low-intensity focused ultrasound (LIFU) guidance. Upon the LIFU irradiation, although the concentrations of LA released from PCM-MSN@LA was low, the research exhibited high sensitivity to the increased nitric oxide synthase (NOS) activity in the infection microenvironment. Rapid targeting of the heart and in situ NO release enabled PCM-MSN@LA in combined with LIFU exerted extraordinary protective effects against LPS-challenged myocardial injury by reducing the recruitment of inflammatory cells, inhibiting oxidative stress and maintaining the mitochondria integrity. In particular, PCM-MSN@LA+LIFU relieved but not aggravated the circulation collapse in the infection environment.Conclusion: PCM-MSN@LA+LIFU exhibited significant cardioprotective effects against severe sepsis found in the hearts of the tested mice and reduced the side effects of NO diffusion. This technique could possibly be served as a new therapeutic method for sepsis-induced myocardial injury.
Integrative nascent RNA methods to reveal cell-type specific transcription programs in peripheral blood and its derivative cells
Authors: Kwak Hojoong , Kimm Aileen , Kim Samantha , Kim Eunyoo 
Published: March 2022

Abstract
Nascent RNA sequencing is a powerful method to measure transcription with high resolution, sensitivity, and directional information. We present an integrated package of nascent RNA-seq methods composed of ultrafast Precision Run On (uPRO) combined with deep learning and hierarchical co-expression network analysis to discover enhancers, promoters, and transcription factor networks that define cell-type specific transcription programs. We generated nascent transcription profiles using one-day uPRO in human blood-derived cell lines and raw whole blood of ~ 1 ml. Transcription sites at enhancers and genes were conserved in positions but varied in expression levels across cell types. Transcription factors such as TCF-3 and OCT1 were pivotally associated with enhancer-gene networks. Intriguingly, transcription factors related to cell stress and inflammation are associated with inter-individual variation of leukocyte transcription in whole blood. Our integration of experimental and computational nascent RNA methods will provide an efficient strategy to identify specific transcriptional programs with minimal sample requirements.
Analysis of risk factors associated with average hospitalization duration and cost in pulmonary abscess patients
Authors: Zhu Tianyi , Yang Wei , Lu Wei 
Published: March 2022

Abstract
Background: This study aimed to explore the differences of average hospitalization duration and cost in various groups of pulmonary abscess patients. Methods: The hospitalization durations and costs of 190 patients with a pulmonary abscess in our department during the past five years were retrospectively analyzed.Results: Regardless of the patient’s sex or age, the average hospitalization duration of the pulmonary abscess patients was longer than that of the overall patient population by 9 days (P < 0.05). Among the hospitalized patients with a pulmonary abscess, the average hospitalization duration of male patients was 5.3 days longer than that of female patients. Also, the average inpatient cost was 15,726.4 RMB higher than that of female patients (P < 0.05). Moreover, the existence of underlying diseases was associated with a significantly longer hospitalization duration among inpatients with a pulmonary abscess (P < 0.05). Furthermore, the patients with concomitant symptoms had a significantly longer hospitalization duration than those without concomitant symptoms (P < 0.05). Conclusions: The hospitalization duration was longer for patients with a pulmonary abscess compared to those without one in the Respiratory Department of our hospital during the same period. In addition, the male sex as well as the coexistence of underlying conditions and concomitant symptoms were risk factors for a prolonged hospitalization stay among patients with a pulmonary abscess. The male sex was also a risk factor for a higher hospitalization cost among pulmonary abscess patients. Our findings suggest the importance of early detection and good control of basic diseases for certain populations of pulmonary abscess patients.
The association between clinical features at the time of non-hysteroscopic myomectomy before pregnancy and adverse obstetric and perinatal outcomes: a single-center retrospective cohort study
Authors: Kim Young Ran , Na Eun Duc , Jung Jae Eun , Lee Ji Yeon 
Published: March 2022

Abstract
BackgroundTo investigate the association of clinical characteristics at the time of non-hysteroscopic myomectomy before pregnancy and adverse obstetric outcomes in the next pregnancy.MethodsIn this retrospective cohort study, we identified 248 women who underwent abdominal or laparoscopic myomectomy for intramural (IM) and/or subserosal (SS) uterine myomas in Bundang CHA Medical Center before pregnancy and delivered at the same hospital between 2010 and 2020. The association between clinical characteristics at the time of myomectomy and subsequent obstetric outcomes were analyzed. ResultsThere was one case of uterine rupture. The gestational age at delivery was 37.7±2.4 weeks. There were 2 (0.8%) cases of fetal loss before 23 weeks, but there were no cases of perinatal death. The risk of transfusion during or after delivery was higher in the group in which multiple myomas were removed compared to the group in which only one was removed (aOR=2.41, 95% CI [1.20-4.86], p=0.014). The risk of neonatal composite morbidity was higher in the group in which myomas including the IM type were removed, than in the group in which only SS myomas were removed (aOR=14.29, 95% CI [1.82-99.57], p=0.012). Although not statistically significant, the group in which the sum of the diameters of the three largest myomas was greater than 15 cm showed a higher frequency of preterm birth (19.3% vs. 10.1%, p=0.001) and lower birth weight (2901± 625 g vs. 3063± 576 g, p=0.001) compared to the group with diameters less than 15 cm. Placenta accreta/increta (7.9% vs. 3.8%, p=0.043) and lower placental weight (646± 170 g vs. 750± 232 g, p=0.034) were more common in patients with an interval between myomectomy and pregnancy of less than 12 months compared to more than 12 months.ConclusionsTo our knowledge, this is the first study to investigate the association between clinical features at the time of myomectomy before pregnancy and various adverse obstetric and perinatal outcomes. If the removed myomas are multiple, IM, large, or the interval between myomectomy and pregnancy is short, the risk of obstetric and neonatal complications may increase.
Fluorescence in Situ Hybridisation in Carnoy’s Fixed Tonsil Tissue
Authors: Clark Sita Tarini , Waldvogel-Thurlow Sharon , Mackenzie Brett Wagner , Douglas Richard George , Biswas Kristi 
Published: March 2022

Abstract
Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy’s fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy’s fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy’s fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy’s fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques.
An analysis of BGP updates dynamics during Slammer worm attack
Authors: Matcharashvili Teimuraz , Elmokashﬁ Ahmed , Zhukova Natalia 
Published: March 2022

Abstract
In present work we investigated the character of dynamical changes in the border gateway protocol (BGP) updates process in Internet during the Slammer worm attack that occurred on 25.01.2003. We analysed BGP updates time series recorded at 8 RIPE RIS collectors located in different parts of world. Time series have been recorded before, during and after Slammer worm attack. Methods of data complex analysis, effective to discern dynamical changes in the considered process, have been used. Lempel and Ziv complexity measure, Local variation, Tsallis entropy, composite multiscale entropy and recurrence quantification analysis have been carried out on BGP updates time series in 24 hour windows shifted by 1 minute step.In spite of intense interest to the question of stability of Internet, dynamical features of BGP updates process under different harmful influences presently remain not fully understood. We showed that, the extent of order in the process of BGP updates variability increased during the Slammer worm attack. Such dynamical change lasted about 20 hours and impacted the BGP updates at all considered 8 locations. It was also shown that changes occurred in the process of BGP updates variation long before and after of worm attack are of different character when compared to period during worm attack. Based on the results of present analysis we conjecture that the observed increase in the regularity of BGP updates is caused by the influence of slammer worm.Our findings will help in further understanding of dynamics of unwanted influences on Internet processes.
Sensorineural Hearing Loss and Hypothyroidism in A Patient with Cernunnos Deficiency; A Case Report
Authors: Farsi Yeganeh , Hojabri Mahsa , Eslamian Golnaz , Shamsian Bibi Shahin , Ghanaie Roxana Mansour , Keramatipour Mohammad , Chavoshzadeh Zahra , Eskandarzadeh Shabnam 
Published: March 2022

Abstract
Cernunnos deficiency is a rare radiosensitive form of severe combined immunodeficiency (SCID). Herein, we report a patient with recurrent infections, birdlike face, microcephaly, Failure to thrive (FTT), and hypogammaglobinemia accompanied by considerable and rare features of sensorineural hearing loss and hypothyroidism with a mutation in splicing site of the third intron of non-homologous end joining 1 (NHEJ1) gene. The mutation was associated with T-B-NK + in flowcytometry. Distinct clinical manifestation along with a rarely reported genetic site mutation was noticeable in the reported case. The clinicians should be sensitive enough to suspect SCID in any patient with recurrent infections, microcephaly, FTT, and hypogammaglobinemia. Also, it is highlightable that every case of SCID with microcephaly should prompt us to the SCIDs with genetic mutations sensitive to radiation and further investigations are mandatory in highly suspicious patients.
Transcriptome analysis reveals the differentially expressed genes associated with growth in Guangxi Partridge chickens
Authors: Feng Chungang , Shao Minghui , Shi Kai , Zhao Qian , Duan Ying , Shen Yangyang , Tian Jinjie , He Kun , Li Dongfeng , Yu Minli , Lu Yangqing , Tang Yanfei 
Published: March 2022

Abstract
Background: The Guangxi Partridge chicken is a well-known chicken breed in southern China with excellent production performance, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with the original population (line D), the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. Results: The body weight of line S chickens showed a significant increase at 90 d of age, although only the internal organ ratio of lung and kidney to total body weight changed after standardizing by weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine-cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction.Conclusions: Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improvement of Guangxi partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.
Rapid screening assays of N501Y and E484K SARS-CoV-2 variants and identification of an emerging N501T variant in France
Authors: FRANCOIS Catherine , Descamps Véronique , Combremont André-Guy , Morel Virginie , Brochot Etienne , Demey Baptiste , Castelain Sandrine 
Published: March 2022

Abstract
From September 2020, new variants of concern of SARS-CoV-2 were detected in Europe. In this context, our hospital center has led us to be particularly vigilant in the search for and detection of these variants. To this end, two SARS-CoV-2 Mutation Discrimination assays for the detection of 501 and 484 mutations on spike protein were developed. It allowed to quickly identify the United Kingdom variant 20I/501Y.V1 and the south-african variant 20H/501Y.V2 that were circulating in our region and surprisingly identify a mutation of interest (N501T), which reported for the first time the A.28 lineage in France.
DAS28-P Index as a Discriminatory Measure of Poor Subjective Response to Disease-Modifying Rheumatic Drug Therapy in Early Rheumatoid Arthritis
Authors: Pisaniello Huai Leng , Whittle Samuel L. , Lester Susan , Menz Fiona , Metcalf Robert , McWilliams Leah , Hill Catherine , Proudman Susanna 
Published: March 2022

Abstract
Background: The DAS28-P index, defined as the proportion of patient-reported components (joint tenderness and visual analogue scale) of the Disease Activity Score in 28 joints (DAS28), has been proposed as a useful discriminatory measure of central pain mechanisms in RA. This study aimed to evaluate the use of the DAS28-P index as a predictor of poor subjective response in early rheumatoid arthritis (RA).Methods: Patients with early RA enrolled in a supplemental fish oil clinical trial received a combination of disease-modifying anti-rheumatic drugs (DMARDs) according to ‘treat-to-target’ protocol. Consecutive measures of the DAS28-P index for each visit over a 1-year period were estimated for each patient. Using joint longitudinal trajectories of the objective (swollen joint count and erythrocyte sedimentation rate) and subjective (tender joint count and patient global assessment) components, distinct subgroups of patients were identified using bivariate k-means cluster analysis. Baseline predictors for each subgroup were examined, and various longitudinal outcomes of disease activity and disease impact were analyzed using a random intercept, population-averaged generalized estimating equation model.Results: 121 patients were included (74% female; mean age of 57; median of 16 weeks of active disease) and a 3-cluster model was identified – the ‘Responders’ group (n=58; 48%), the ‘Partial Responders’ group (n=32; 26%), and the ‘Non-Responders’ group (n=31; 26%). The ‘Partial Responders’ group had consistently higher proportions of the DAS28-P index throughout the study period, with the lowest joint erosion score of 0.9 [95% confidence interval (CI) 0.2, 1.6] at year 3. At 52 weeks, the methotrexate dose was higher for both ‘Partial Responders’ and ‘Non-Responders’ groups (18.5mg [95% CI 15.5, 21.5] and 18.6mg [95% CI 15.3, 21.8] respectively), when compared with the ‘Responders’ group (12.8mg [95% CI 14.7, 20.9]). Conclusions: Persistently high DAS28-P index scores are useful to distinguish poor patient global assessment and excessive treatment escalation in early RA, suggestive of underlying non-inflammatory pain contributing to higher disease activity score. Early identification of this pain phenotype with detailed assessment and subsequent adjuvant non-immunosuppressive interventions are warranted for better disease outcome and symptom remission.
Screening of a FDA-Approved Compound Library Identifies Menadione in Regulating Colon Cancer Programmed Death via MAPK8 Cascades
Authors: Song Weiwei , Cao Liyuan , Ding Lei , Ma Xueqi , Gu Pengfei , Wang Wenbo , Sun Jinli , Mu Wei 
Published: March 2022

Abstract
Colorectal cancer (CRC) is a conventional gastrointestinal malignant tumor, ranking third among all type of tumors and the fifth in clinical mortality. Programed cell death including apoptosis, autophagy and necroptosis that can be distinguished by their morphological and physiological differences. Although various researches and strategies were developed for anti-cancer drugs, there still lack of the effective therapies trigger cell programmed death to eliminate malignant colon tumor cells. In this study, we explored novel agents for inducing the programmed cell death through drug repurposing. We generated a high-throughput screening of a FDA Approved Drug Library, and identified Menadione, a synthetic analogue of vitamin K, as a promising candidate in regulating colon tumor programmed death. To further investigate the underlying mechanisms of Menadione in tumor programmed death, the selected gene of PCR array were performed and the data analysis showed significantly up-regulated gene by Menadione were ATG7 and MAPK8. The Go enrichment analysis also certify that MAPK8 may be an important regulation gene for Menadione induced cell apoptosis and necrosis in colorectal cancer. MAPK8 participated in multiple signaling pathways in GO enrichment analysis and KEGG pathway enrichment analysis, further demonstrated the key regulatory role of MAPK8. Thus, we identified Menadione may be a potential compound for MAPK8-targeting cascade. Owing to their FDA-approved status, Menadione might be used rapidly in the clinical treatment of tumor therapy. We demonstrated and provided new insights into the anti-cancer drug strategies.