bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence and Structure Characteristics of 22 Deletion Breakpoints in Intron 44 of the DMD Gene Based on Long-Read Sequencing
Authors: Geng Chang , Tong Yuanren , Zhang Siwen , Ling Chao , Wu Xin , Wang Depeng , Dai Yi 
Published: April 2021

Purpose: Exon deletions make up to 80% of mutations in the DMD gene, which cause Duchenne and Becker muscular dystrophy. Exon 45-55 regions were reported as deletion hotspots and intron 44 harbored more than 25% of deletion start points. We aimed to investigate the fine structures of breakpoints in intron 44 to find potential mechanisms of large deletions in intron 44.Methods: Twenty-two dystrophinopathy patients whose deletion started in intron 44 were sequenced using long-read sequencing of a DMD gene capture panel. Sequence homology, palindromic sequences, and polypyrimidine sequences were searched at the breakpoint junctions. RepeatMasker was used to analyze repetitive elements and Mfold was applied to predict secondary DNA structure.Results: With a designed DMD capture panel, 22 samples achieved 2.25 gigabases and 1.28 million reads on average. Average depth was 308× and 99.98% bases were covered at least 1×. The deletion breakpoints in intron 44 were scattered and no breakpoints clustered in any region less than 500 bp. A total of 72.7% of breakpoints located in distal 100 kb of intron 44 and more repetitive elements were found in this region. Microhomologies of 0–1 bp were found in 36.4% (8/22) of patients, which corresponded with non-homologous end-joining. Microhomologies of 2–20 bp were found in 59.1% (13/22) of patients, which corresponded with microhomology-mediated end-joining. Moreover, a 7 bp insertion was found in one patient, which might be evidence of aberrant replication origin firing. Palindromic sequences, polypyrimidine sequences, and small hairpin loops were found near several breakpoint junctions. No evidence of large hairpin loop formation in deletion root sequences was observed.Conclusion: This study was the first to explore possible mechanisms underlying exon deletions starting from intron 44 of the DMD gene based on long-read sequencing. Diverse mechanisms might be associated with deletions in the DMD gene.
Anti-HIV-1 ADCC and HIV-1 Env Can Be Partners in Reducing Latent HIV Reservoir
Authors: Suryawanshi Poonam , Bagul Rajani , Shete Ashwini , Thakar Madhuri 
Published: April 2021

BackgroundPersistence of HIV reservoir even in suppressive ART is the key obstacle in HIV-1 cure. We evaluated the ability of HIV-1 C Env to reactivate the latently infected resting memory CD4 cells and the ability of polyclonal HIV antibodies mediating ADCC to lyse the reactivated targets.MethodologyHIV-1 antibodies from 25 HIV infected individuals (14 ADCC responders and 11 non-responders) were tested against the Env-C reactivated primary cells; CD4+ and CD4+CD45RO+ memory T cells in the presence of autologous or heterologous effector cells using multicolor flow cytometry. The frequencies of p24+ve target cells were measured to determine the reactivation and antibody mediated lysis.ResultsIncrease in the frequency of p24 expressing cells (P &lt; 0.01 in all cases) after Env-C stimulation of target cells indicated reactivation. When these reactivated targets were mixed with effector cells and HIV-1 antibodies, the frequencies of p24 expressing targets were decreased significantly when the ADCC mediating antibodies (P &lt; 0.01 in all cases) were added but not when the antibodies from ADCC non-responders or HIV negative individuals were added. In parallel, the NK cell activation was also increased only when ADCC mediating antibodies were added.ConclusionThe study showed that the HIV-1 Env could act as latency reversal agent (LRA), and only ADCC mediating antibodies could lyse the reactivated HIV reservoirs. The short stimulation cycle used in this study could be useful in testing LRAs as well as immune mediated lysis of reactivated reservoirs. The observations have further implication in designing antibody mediated immunotherapy for eradication of latent HIV reservoir.
Novel TNIP2 and TRAF2 Variants Are Implicated in the Pathogenesis of Pulmonary Arterial Hypertension
Authors: Pienkos Shaun , Gallego Natalia , Condon David F. , Cruz-Utrilla Alejandro , Ochoa Nuria , Nevado Julián , Arias Pedro , Agarwal Stuti , Patel Hiral , Chakraborty Ananya , Lapunzina Pablo , Escribano Pilar , Tenorio-Castaño Jair , de Jesús Pérez Vinicio A. 
Published: April 2021

Background: Pulmonary arterial hypertension (PAH) is a rare disease characterized by pulmonary vascular remodeling and right heart failure. Specific genetic variants increase the incidence of PAH in carriers with a family history of PAH, those who suffer from certain medical conditions, and even those with no apparent risk factors. Inflammation and immune dysregulation are related to vascular remodeling in PAH, but whether genetic susceptibility modifies the PAH immune response is unclear. TNIP2 and TRAF2 encode for immunomodulatory proteins that regulate NF-κB activation, a transcription factor complex associated with inflammation and vascular remodeling in PAH.Methods: Two unrelated families with PAH cases underwent whole-exome sequencing (WES). A custom pipeline for variant prioritization was carried out to obtain candidate variants. To determine the impact of TNIP2 and TRAF2 in cell proliferation, we performed an MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay on healthy lung pericytes transfected with siRNA specific for each gene. To measure the effect of loss of TNIP2 and TRAF2 on NF-kappa-beta (NF-κB) activity, we measured levels of Phospho-p65-NF-κB in siRNA-transfected pericytes using western immunoblotting.Results: We discovered a novel missense variant in the TNIP2 gene in two affected individuals from the same family. The two patients had a complex form of PAH with interatrial communication and scleroderma. In the second family, WES of the proband with PAH and primary biliary cirrhosis revealed a de novo protein-truncating variant in the TRAF2. The knockdown of TNIP2 and TRAF2 increased NF-κB activity in healthy lung pericytes, which correlated with a significant increase in proliferation over 24 h.Conclusions: We have identified two rare novel variants in TNIP2 and TRAF2 using WES. We speculate that loss of function in these genes promotes pulmonary vascular remodeling by allowing overactivation of the NF-κB signaling activity. Our findings support a role for WES in helping identify novel genetic variants associated with dysfunctional immune response in PAH.
Circadian Rhythm Disorders and Corresponding Functional Brain Abnormalities in Young Female Nurses: A Preliminary Study
Authors: Wu Xiaoli , Bai Fan , Wang Yunlei , Zhang Lu , Liu Lixu , Chen Yudong , Li Hanzhi , Zhang Tong 
Published: April 2021

Objective: Shift work is associated with a decrease in melatonin level and perturbation of the circadian rhythm; however, it is unknown if these lead to functional brain changes. In this study, we investigated whether circadian rhythm disorders caused by shift work are related to changes in brain functional connectivity (FC) and regional homogeneity (ReHo) using whole-brain resting-state functional magnetic resonance imaging (fMRI).Methods: This prospective case-control study included nine female night shift nurses and nine age-matched female day work nurses with normal sleep rhythms. To assess sleep quality and mood, participants were asked to complete questionnaires. Serum melatonin and cortisol levels were measured. ReHo of whole-brain resting-state function and seed-based FC of the bilateral hypothalamus were compared between groups. Variables that differed significantly between groups were used to examine the association between questionnaire scores and hormone levels and fMRI data.Results: The night shift nurses had significantly lower sleep quality and melatonin levels; lower ReHo activation in the bilateral cerebellar hemisphere and higher ReHo in the bilateral occipital lobe and left parietal lobe; and higher FC from the hypothalamus to the right cingulate gyrus, right putamen, and vermis than did the day shift nurses. Activation of the right cerebellar hemisphere left superior parietal gyrus, and the right superior occipital gyrus was correlated with sleep quality scores. Moreover, activation of the right cerebellar hemisphere (r = 0.583, P = 0.011) was correlated with melatonin levels, and higher sleepiness scores were associated with stronger FC between the hypothalamus and vermis (r = 0.501, P = 0.034).Conclusions: Circadian rhythm disorder caused by night shift work can lead to a decrease in sleep quality and melatonin level, as well as a series of changes in brain FC and ReHo.
Efficacy of Liver Resection for Single Large Hepatocellular Carcinoma in Child-Pugh A Cirrhosis: Analysis of a Nationwide Cancer Registry Database
Authors: Hong Suk Kyun , Lee Kwang-Woong , Hong Su young , Suh Sanggyun , Hong Kwangpyo , Han Eui Soo , Lee Jeong-Moo , Choi YoungRok , Yi Nam-Joon , Suh Kyung-Suk 
Published: April 2021

BackgroundTherapeutic strategies and good prognostic factors are important for patients with single large hepatocellular carcinoma (HCC). This retrospective study aimed to identify the prognostic factors in patients with single large HCC with good performance status and Child-Pugh A cirrhosis using a large national cancer registry database and to recommend therapeutic strategies.MethodsAmong 12139 HCC patients registered at the Korean Primary Liver Cancer Registry between 2008 and 2015, single large (≥ 5 cm) HCC patients with Eastern Cooperative Oncology Group (ECOG) performance status 0 and Child-Pugh score A were selected.ResultsOverall, 466 patients were analyzed. The 1-,2-,3-, and 5-year survival rates after initial treatment were 84.9%, 71.0%, 60.1%, and 51.6%, respectively, and progression-free survival rates were 43.6%, 33.0%, 29.0%, and 26.8%, respectively. Platelet count &lt; 100 × 109/L (P &lt; 0.001), sodium level &lt; 135 mmol/L (P = 0.002), maximum tumor diameter ≥ 10 cm (P = 0.001), and treatment other than resection (transarterial therapy vs. resection: P &lt; 0.001, others vs. resection: P = 0.002) were significantly associated with poorer overall survival; sodium &lt; 135 mmol/L (P = 0.015), maximum tumor diameter ≥ 10 cm (P &lt; 0.001), and treatment other than resection (transarterial therapy vs. resection: P &lt; 0.001, others vs. resection: P = 0.001) were independently associated with poorer progression-free survival.ConclusionResection as an initial treatment should be considered when possible, even in patients with single large HCC with good performance status and mild cirrhosis. Caution should be exercised in patients with low platelet level (&lt; 100 × 109/L), low serum sodium level (&lt; 135 mmol/L), and maximum tumor diameter ≥ 10 cm.
Outcome of Very Premature Newborn Receiving an Early Second Dose of Surfactant for Persistent Respiratory Distress Syndrome
Authors: Greiner Eva , Wittwer Apolline , Albuisson Eliane , Hascoët Jean-Michel 
Published: April 2021

Background:Infants presenting respiratory distress syndrome (RDS) not responding to surfactant often receive a second instillation. Few studies evaluated the consequences of this second administration. This study aimed at determining the outcome of infants presenting persistent RDS and receiving an early second dose of surfactant.Methods:Infants below 32 weeks' gestation who received a second dose of 100mg/kg of surfactant within the first 72 h of life, were retrospectively involved in this 42 months' study. They were matched to two controls receiving a single dose of 200mg/Kg based upon gender and gestational age.Results:52/156 infants receiving two doses (Group 2-doses) were significantly more often SGA [22 (42%) vs. 21 (20%)p= 0.04] and outborn [29 (56%) vs. 13 (12%)p= 0.001]. They had received antenatal corticos teroid therapy less often [26 (50%) vs. 89 (86%)p= 0.001] and presented more severe RDS based upon FiO2 level, oxygenation index and radiography. Group 2-doses survival was lower (65.4% vs. 79.6 %p&lt; 0.1) but surviving infants did not have different morbidity than controls.Discussion:Premature newborn receiving a second dose of surfactant had adverse antenatal characteristics, presented more severe RDS and only partially responded to the first dose. Outcomes of surviving infants who received 2 doses of surfactant were comparable to others.
Ultrasound Monitoring of Umbilical Catheters in the Neonatal Intensive Care Unit—A Prospective Observational Study
Authors: Sobczak Alina , Dudzik Aleksandra , Kruczek Piotr , Kwinta Przemko 
Published: April 2021

Introduction:Umbilical catheterization provides a quick yet demanding central line that can lead to complications seen nowhere else. The aim of our study was to determine whether the repeated ultrasound scanning can influence the catheterization time, prevent some of the catheter-related complications, support the decision-making process and allow prolonged catheterization in patients without an alternative central access route.Methods:A prospective observational study was performed in a tertiary neonatal intensive care unit. A total of 129 patients and 194 umbilical catheters (119 venous and 75 arterial) were analyzed with a total of 954 scans. Ultrasound screening consisted of 1) assessing the catheter tip, location, movability, and surface and 2) analyzing the catheter trajectory. The outcome variables were defined as 1) catheter dislocation and 2) associated thrombosis.Results:Dislocation of catheter throughout the whole catheterization period was observed in 68% (81/119) of UVCs and 23% (17/75) of UACs. Thrombotic complications were observed in 34.5% (41/119) of UVCs and 12% (9/75) of UACs. 1/3 of UAC-associated thrombi were visible only after catheter removal. 51% (61/119) of UVC patients and 8% (6/75) of UAC patients made a clinical decision regarding the obtained catheter image.Conclusion:Bedside ultrasound imaging of catheters supports the decision-making process related to the catheterization duration, shortening the time if abnormalities are detected and allowing a safer prolonged UC stay when an alternative central line cannot be inserted.
Timing, Dosage, and Adherence of Antiretroviral Therapy and Risk of Osteoporosis in Patients With Human Immunodeficiency Virus Infection in Taiwan: A Nested Case-Control Study
Authors: Chiu Mu-Lin , Liang Wen-Miin , Li Ju-Pi , Cheng Chi-Fung , Chiou Jian-Shiun , Ho Mao-Wang , Wu Yang-Chang , Lin Ting-Hsu , Liao Chiu-Chu , Huang Shao-Mei , Tsai Fuu-Jen , Lin Ying-Ju 
Published: April 2021

The progression of acquired immunodeficiency syndrome is delayed in patients with human immunodeficiency virus (HIV) infection receiving antiretroviral therapy (ART). However, long-term ART is associated with adverse effects. Osteoporosis is one of the adverse effects and is a multifactorial systemic skeletal disease associated with bone fragility and an increased risk of fracture. We performed a longitudinal, comprehensive, nested case-control study to explore the effect of ART on the risk of osteoporosis in 104 osteoporotic and 416 non-osteoporotic patients with HIV infection at their average age about 29 years old in Taiwan. Patients with history of ART, current exposure to ART, higher cumulative defined daily doses (DDDs), or higher ART adherence were at a higher risk of osteoporosis (p &lt; 0.05). Patients receiving nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-containing regimen (zidovudine-lamivudine combination, lamivudine-abacavir combination, and abacavir alone) and protease inhibitor (PI)-containing regimen (lopinavir-ritonavir combination, ritonavir, and atazanavir) had a higher risk of osteoporosis (p &lt; 0.05). Especially, patients receiving high doses of the PIs lopinavir-ritonavir combination had an increased risk of osteoporosis (p &lt; 0.05). In conclusion, history of ART, current exposure to ART, higher cumulative DDDs, and higher ART adherence were associated with an increased risk of osteoporosis. Furthermore, NRTI- and PI-containing regimens and high doses of PIs lopinavir-ritonavir combination may be associated with an increased risk of osteoporosis in patients with HIV infection in Taiwan.
Boosting Akt Pathway by Rupatadine Modulates Th17/Tregs Balance for Attenuation of Isoproterenol-Induced Heart Failure in Rats
Authors: Ahmed Lamiaa A. , Mohamed Ahmed F. , Abd El-Haleim Enas A. , El-Tanbouly Dalia M. 
Published: April 2021

Disruption of Th17/Tregs homeostasis plays a crucial role in governing the immune response during myocardial fibrosis and its progression to heart failure. The present study aimed to assess for the first time the possible protection afforded by rupatadine against isoproterenol-induced heart failure in rats. It also explored the role of PI3k/Akt as a possible mechanistic pathway, through which rupatadine could modulate Th17/Tregs balance to display its effect. Isoproterenol (85 and 170 mg/kg/day) was injected subcutaneously for 2 successive days, respectively and rupatadine (4 mg/kg/day) was then given orally for 14 days with or without wortmannin (PI3K/Akt inhibitor). Rupatadine succeeded to completely ameliorate isoproterenol-induced cardiac dysfunction as demonstrated by improvements of electrocardiographic and echocardiographic measurements. Moreover, rupatadine prevented the marked elevation of PAF and oxidative stress in addition to Th17 promoting cytokines (IL-6, IL-23, and TGF-β). Accordingly, rupatadine prevented Th17 stimulation or expansion as indicated by increased Foxp3/RORγt ratio and decreased production of its pro-inflammatory cytokine (IL-17). Rupatadine treatment mitigated isoproterenol-induced activation of STAT-3 signaling and the imbalance in p-Akt/total Akt ratio affording marked decrease in atrogin-1 and apoptotic biomarkers. Finally, this therapy was effective in averting cardiac troponin loss and reverting the histological alterations as assessed by myocardial fibrosis and hypertrophy grading. Contrariwise, co-administration of wortmannin mostly attenuated the protective effects of rupatadine affording more or less similar results to that of isoproterenol-untreated rats. In conclusion, rupatadine could be an effective therapy against the development of isoproterenol-induced heart failure where PI3K/Akt pathway seems to play a crucial role in its protective effect.
Outcome of Non-small Cell Lung Cancer Patients With N3 Stage: Survival Analysis of Propensity Score Matching With a Validated Predictive Nomogram
Authors: Han Chang , Wu Yijun , Sun Xu , Chong Yuming , Kang Kai , Liu Zhikai , Zhang Fuquan 
Published: April 2021

Background and Objectives: N3-positive non-small cell lung cancer (NSCLC) is usually regarded as inoperable. There were very few studies that focused on N3-NSCLC patients. This study aims to analyze prognosis of NSCLC patients with N3 disease and provides retrospective indications.Methods: NSCLC patients staged as N3 were retrospectively reviewed from the Surveillance, Epidemiology, and End Results database. Univariate and multivariate Cox regression were used for identifying prognostic factors. The selected predictive parameters by the least absolute shrinkage and selection operator (LASSO) regression were used to develop predictive nomogram models for overall survival (OS) and lung cancer-specific survival (CSS). The C-index values were calculated to assess the models' predictive ability, while calibration curves were plotted to evaluate the agreement between the predicted and the actual survival. Survival curves were plotted by Kaplan-Meier method and were compared by log-rank test. Propensity score matching (PSM) was used to balance the baseline characteristics between treatment groups.Results: A total of 24,747 N3-NSCLC patients were enrolled. The 1-, 3-, and 5-year OS rates were 35.8, 6.8, and 1.7%, respectively, while the corresponding CSS rates was 36.6, 6.9, and 1.8%, respectively. The nomogram models were developed using 11 significant prognostic parameters, including age, sex, race, histology, stage, T stage, bone, brain and liver metastases, surgery, and chemotherapy. Both of them demonstrated great predictive ability and performed well in the calibration curves. After PSM, patients receiving surgery demonstrated significantly better survival than those who did not. Besides, there was no significant difference of survival between patients receiving chemotherapy with and without radiotherapy.Conclusions: The nomogram models for predicting survival outcome of N3-NSCLC patients can be clinically used. Surgery may be beneficial to the survival for these patients, while radiotherapy may not have additional survival benefits in patients receiving chemotherapy.
Organic Farming Practices and Shade Trees Reduce Pest Infestations in Robusta Coffee Systems in Amazonia
Authors: Piato Kevin , Subía Cristian , Pico Jimmy , Calderón Darío , Norgrove Lindsey , Lefort François 
Published: April 2021

Coffee agroforestry systems could reconcile agricultural and environmental objectives. While pests and diseases can reduce yield, their interactions with shade and nutrition have been rarely researched, and are particularly lacking in perennial systems. We hypothesized that intermediate shade levels could reduce coffee pests while excess shade could favor fungal diseases. We hypothesized that organic rather than mineral fertilization would better synchronize with nutrient uptake and higher nutrient inputs would be associated with reduced pest and disease damage due to higher plant vigor, yet effects would be less obvious in shaded plots as coffee growth would be light-limited. Using three-year-old trees of Coffea canephora var. Robusta (robusta coffee) in the Ecuadorian Amazon, we compared a full-sun system with four shading methods creating different shade levels: (1) Myroxylon balsamum; (2) Inga edulis; (3) Erythrina spp.; or, (4) Erythrina spp. plus Myroxylon balsamum. Conventional farming at either (1) moderate or (2) intensified input and organic farming at (3) low or (4) intensified input were compared in a split-plot design with shade as the main plot factor and farming practice as the sub-plot factor. The infestation of the following pests and disease incidences were evaluated monthly during the dry season: brown twig beetle (Xylosandrus morigerus), coffee leaf miner (Leucoptera coffeella), coffee berry borer (Hypothenemus hampei), anthracnose disease (Colletotrichum spp.), thread blight (Pellicularia koleroga), and cercospora leaf spot (Cercospora coffeicola). Coffee berry borer and brown twig beetle infestation were both reduced by 7% in intensified organic treatments compared to intensified conventional treatments. Colonization of coffee berry borer holes in coffee berries by the entomopathogenic fungus Beauveria bassiana was also assessed. Brown twig beetle infestation was significantly higher under full sun than under Inga edulis, yet no other shade effects were detected. We demonstrate for the first time how intensified input use might promote pest populations and thus ultimately lead to robusta coffee yield losses.