bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircRNA expression profile and potential role of hsa_circ_0040039 in intervertebral disc degeneration
Authors: Huang Sheng , Zhong Junlong , Qi Qihua , Liu Gangan , Gong Ming 
Published: August 2022

Purpose:
Circular RNAs (circRNAs) play an critical role in the pathological processes associated with IDD. However, the potential roles of circRNAs in IDD remain largely unclear. Here, we identify the circRNAs expression profiles and elucidate the potential role of candidate circRNAs in the pathogenesis of intervertebral disc degeneration (IDD) through microarray data and bioinformatics analyses.

Methods:
We obtained the datasets of microarrays (GSE67566 and GSE116726) from the Gene Expression Omnibus database. The differentially expressed circRNAs and miRNAs were identified using the Limma R package. The target miRNAs and target genes of the candidate circRNAs were predicted using an online tool. Functional enrichment analyses of the target genes were performed using the clusterProfiler R package. A protein-protein interaction (PPI) network was constructed using STRING.

Results:
A total of 104 differentially expressed circRNAs were identified between the IDD and the control groups, including 41 upregulated circRNAs and 63 downregulated circRNAs (cutoff criteria (|log2 fold change| > 2, P < .05)). Hsa_circ_0040039, which was the most upregulated circRNA (log2 fold change = 2.95), was selected for further analysis. The regulatory circRNA-miRNA-mRNA network comprised hsa_circ_0040039, 2 target miRNAs (hsa-miR-424-5p and hsa-miR-15b-5p), and 77 target genes. Functional enrichment analysis showed that the 77 promising target genes are mainly enriched in the ubiquitin proteasome system and Wnt signaling pathway. Further, the PPI network showed that the top 3 hub genes are BRTC, SIAH1, and UBE2V1.

Conclusions:
A total of 104 differentially expressed circRNAs were identified between the IDD and control groups. Hsa_circ_0040039 may serve as a sponge of hsa-miR-424-5p and hsa-miR-15b-5p, to regulate the expression of downstream genes (such as BRTC, SIAH1, and UBE2V1); thus, it may be involved in IDD-associated pathological processes via the Wnt/β-catenin signaling pathway. Further studies are required to confirm the potential roles of hsa_circ_0040039 in IDD.
Rational emotive health therapy for the management of depressive symptoms among parents of children with intellectual and reading disabilities in English language
Authors: Ugwuanyi Leonard Tochukwu , Egbe Cajetan Ikechukwu , Nnamani Amuche Patricia , Ubah Josephine Chioma , Adaka Terfa Ahon , Adama Grace Ngozi , Ejide Afusat B. , Uloh-Bethels Annah Chinyeaka , Emelogu Ngozi Ugonma , Ossai Rosemary Chidimma , Okoyeukwu Ngozi Georgina , Agbo Philomina Akudo , Otu Mkpoikanke Sunday 
Published: August 2022

Background:
There is little data in developing countries such as Nigeria with regard to the impact of caring for their children with intellectual and reading disability (IRD) on the quality of life of the parents and the risk of psychopathology.

Objective:
The main objective of the study was to assess the level of psychopathology, i.e., depression among parents of children with intellectual and reading disabilities.

Methods:
This was pretest/posttest control group design with 198 parents (99 fathers/99 mothers) of 100 children with the diagnosis of IRD. The measures used in this study for data collection was Beck Depression Inventory (BDI). Repeated measures analysis of variance (ANOVA) was employed for data analysis.

Results:
Result obtained showed a significant high proportion of depressive symptoms among parents of children with intellectual and reading disabilities at initial assessment. Furthermore, the REHT intervention resulted in a significant reduction in depression of parents in treatment group as compared to those in the control group.

Conclusion:
The presence of a child with intellectual and reading disabilities does not cause parents to become depressed but irrational beliefs about their children’s mental and reading deficiencies may contribute to unhealthy thinking and feelings about the future of their children. REHT is very effective in assisting depressed parents of children with intellectual and reading disabilities to think rationally about their children and work towards overcoming disability-related as well as behavior-related irrational beliefs. The mental health providers, therapists and counselors should apply the REHT in managing people with psychological distress especially parents of children with intellectual and reading disabilities who may have psychological diagnosis of depression.
Concomitant presentation of eosinophilic or oncocytic mucoepidermoid carcinoma, immunoglobulin G4–related disease, and adult-onset asthma and periocular xanthogranuloma: Case report of 3 uncommon clinical entities
Authors: Chhabra Nikita , Cebak John E. , Schmitt Alessandra , Lal Devyani , Rosenthal Allison C. , Taylor Cullen M. , Thorwarth Ryan M. , Shah Ami A. , Rodriguez-Pla Alicia 
Published: August 2022

Rationale:
Immunoglobulin (Ig) G4–related disease (IgG4-RD) reportedly has a strong relationship with adult-onset asthma and periocular xanthogranuloma (AAPOX) and may be linked to sclerosing mucoepidermoid carcinoma (MEC). We present a rare case of IgG4-RD and AAPOX occurring in a patient with resected eosinophilic or oncocytic MEC.

Patient concerns:
A 52-year-old woman was referred to our rheumatology clinic in 2020 to be evaluated for suspected IgG4-RD.

Diagnoses:
The patient had diagnoses of periorbital xanthelasmas, worsening glucocorticoid-dependent chronic rhinosinusitis and adult-onset asthma, and cervical lymphadenopathy persisting 2 years after resection of a low-grade MEC of a minor salivary gland.

Interventions:
Because the patient’s symptomatic relief was glucocorticoid dependent, IgG4-RD was suspected, and she was referred to our medical center. Her amylase and lipase levels were elevated. Serum IgG4 levels were initially within normal limits, but IgG4-RD was diagnosed because of the presence of lymphadenopathy and evidence of pancreatitis, which was shown on positron emission tomography/computed tomography. Furthermore, the IgG4 levels later increased without explanation. After the patient began combination therapy with a glucocorticoid (prednisone) and methotrexate, her symptoms improved but recurred when the daily oral glucocorticoid dosage decreased below 10 mg. An excisional biopsy of her right submandibular gland in 2021 yielded results consistent with IgG4-RD. In addition, AAPOX was diagnosed, given the presence of periocular edema and plaques, adult-onset asthma, and rhinosinusitis.

Outcome:
The patient was carcinoma free at last follow-up and was receiving medication to treat the other conditions.

Lessons:
The diagnosis of these 3 concomitant, uncommon entities required approximately 7 years of medical investigations. Clinicians should know that IgG4-RD, AAPOX, and MEC may occur together.
LONG NONCODING RNA UPREGULATES ADAPTER SHCA PROTEIN EXPRESSION TO PROMOTE COGNITIVE IMPAIRMENT AFTER CARDIAC ARREST AND RESUSCITATION
Authors: Zhang Yu-Han , Peng Fei , Zhang Lu , Kang Kang , Yang Man , Chen Chan , Yu Hai 
Published: August 2022

ABSTRACT

Aim: More patients are resuscitated from cardiac arrest and cardiopulmonary resuscitation (CA/CPR) due to advances in medical care. However, the burden now lies with post–cardiac arrest cognitive impairment in CA/CPR survivors. Based on our previous study, we aimed to further confirm the correlation between the long noncoding RNA-promoting ShcA (lncRNA-PS)/Src homology and collagen A (ShcA) axis and CA/CPR-induced cognitive impairment in molecular, cellular, and tissue levels. Methods and Results: The in vivo experiments were based on a mouse model of CA/CPR, while oxygen-glucose deprivation and reoxygenation was used as a cell model in vitro. Conditional ShcA suppression in neurons of the hippocampal CA1 region was achieved by cyclization recombinase of bacteriophage P1 recognizing DNA fragment locus of x-over P1 site (Cre/LoxP recombination system). Genetic manipulation of HT22 was achieved by lentivirus targeting lncRNA-PS and ShcA. Neurological function score was remarkably decreased, and cognitive function was affected after restoration of spontaneous circulation. LncRNA-PS and ShcA overexpression after CA/CPR, mainly happened in neurons of hippocampal CA1 region, was observed by in situ hybridization and immunofluorescence. Neuronal ShcA knockdown in hippocampal CA1 region before CA/CPR attenuated cognitive impairment after CA/CPR. ShcA deficiency protected HT22 cell line against oxygen-glucose deprivation and reoxygenation by inhibiting inflammation and apoptosis. In vitro upregulation of lncRNA-PS elevated ShcA expression, which was reversed by knockdown of ShcA. Conclusions: This study revealed that lncRNA-PS/ShcA axis is critically involved in the pathogenesis of cognitive impairment after CA/CPR. By inhibiting ShcA expression in neurons of the hippocampal CA1 region could improve the survival outcomes in mice after CA/CPR.
EVALUATING SEPSIS CRITERIA IN DETECTING ALTERATIONS IN CLINICAL, METABOLIC, AND INFLAMMATORY PARAMETERS IN BURN PATIENTS
Authors: Knuth Carly M. , Rehou Sarah , Barayan Dalia , Jeschke Marc G. 
Published: August 2022

ABSTRACT
Sepsis has become the leading cause of death in burn patients. Furthermore, sepsis and septic complications result in significant morbidities and longer hospitalization, which has profound impacts on the healthcare system. Despite this, sepsis in burn patients is surprisingly poorly understood and characterized. This retrospective, single-institution cohort study aimed to increase our understanding of the septic response after burns. We hypothesized that different sepsis definitions will results in distinctive septic trajectories and biochemical patterns after injury. Sepsis was defined by our burn center–specific prospective definition, the American Burn Association criteria, Sepsis-3 criteria, and the Mann-Salinas criteria. Applying these definitions, we compared clinical, metabolic, and inflammatory markers in septic and nonseptic burn patients. We found that the Sepsis-3 criteria are the most reliable screening tool used before clinical diagnoses for detecting sepsis trajectories and biochemical patterns. Moreover, we characterized distinct temporal alterations in biomarkers during the pre– and post–septic periods in burn patients, which may be incorporated into future sepsis definitions to improve the accuracy of a sepsis diagnosis in burn patients.
HEAD AND THORAX ELEVATION PREVENTS THE RISE OF INTRACRANIAL PRESSURE DURING EXTRACORPOREAL RESUSCITATION IN SWINE
Authors: Levy Yael , Hutin Alice , Polge Nicolas , Lidouren Fanny , Fernandez Rocio , Kohlhauer Matthias , Leger Pierre-Louis , Rambaud Jérôme , Debaty Guillaume , Lurie Keith , Ghaleh Bijan , Lamhaut Lionel , Tissier Renaud 
Published: August 2022

ABSTRACT

Aim: Head and thorax elevation during cardiopulmonary resuscitation improves cerebral hemodynamics and ultimate neurological outcome after cardiac arrest. Its effect during extracorporeal cardiopulmonary resuscitation (E-CPR) is unknown. We tested whether this procedure could improve hemodynamics in swine treated by E-CPR. Methods and Results: Pigs were anesthetized and submitted to 15 minutes of untreated ventricular fibrillation followed by E-CPR. Animals randomly remained in flat position (flat group) or underwent head and thorax elevation since E-CPR institution (head-up group). Electric shocks were delivered after 30 minutes until the return of spontaneous circulation (ROSC). They were followed during 120 minutes after ROSC. After 30 minutes of E-CPR, ROSC was achieved in all animals, with no difference regarding blood pressure, heart rate, and extracorporeal membrane of oxygenation flow among groups. The head-up group had an attenuated increase in ICP as compared with the flat group after cardiac arrest (13 ± 1 vs. 26 ± 2 mm Hg at the end of the follow-up, respectively). Cerebral perfusion pressure tended to be higher in the head-up versus flat group despite not achieving statistical difference (66 ± 1 vs 46 ± 1 mm Hg at the end of the follow-up). Carotid blood flow and cerebral oxygen saturation were not significantly different among groups. Conclusion: During E-CPR, head and thorax elevation prevents ICP increase. Whether it could improve the ultimate neurological outcome in this situation deserves further investigation.
DNASE-MEDIATED DISSOLUTION OF NEUTROPHIL EXTRACELLULAR TRAPS ACCELERATES IN VITRO THROMBIN GENERATION KINETICS IN TRAUMA PATIENTS
Authors: Goswami Julie , MacArthur Taleen A. , Mahony Cillian , Kizhakkedathu Jayachandran N. , Vappala Sreeparna , Smith Stephanie , Morrissey James H. , Spears Grant M. , Bailey Kent R. , Dong Jing-Fei , Kozar Rosemary A. , Hall Nathan , Johnstone Andrea , Park Myung S. 
Published: August 2022

ABSTRACT

Introduction: Neutrophil extracellular traps (NETs) trigger thrombin generation. We aimed to characterize the effects of deoxyribonuclease (DNAse) on NET components (cell-free DNA [cfDNA] and histones) and thrombin generation after trauma. Methods: Citrated plasma samples were collected from trauma patients and healthy volunteers. Thrombin generation (calibrated automated thrombogram) was measured as lag time (LT, in minutes), peak height (in nM), and time to peak thrombin generation (in minutes). Citrullinated histone 3 (CitH3) and 4 (CitH4) were measured by enzyme-linked immunosorbent assay; cfDNA by PicoGreen (all in nanograms per milliliter). Samples analyzed +/− DNAse (1,000 U/mL). Results expressed as median and quartiles [Q1, Q3], Wilcoxon testing, P < 0.05 significant. Results: We enrolled 46 patients (age, 48 [31, 67] years; 67% male) and 21 volunteers (age, 45 [28, 53] years; 43% male). Deoxyribonuclease treatment of trauma plasma led to shorter LT (3.11 [2.67, 3.52] min; 2.93 [2.67, 3.19] min), shorter time to peak thrombin generation (6.00 [5.30, 6.67] min; 5.48 [5.00, 6.00] min), greater peak height (273.7 [230.7, 300.5] nM; 288.7 [257.6, 319.2] nM), decreased cfDNA (576.9 [503.3, 803.1] ng/mL; 456.0 [393.5, 626.7] ng/mL), decreased CitH3 (4.54 [2.23, 10.01] ng/mL; 3.59 [1.93, 7.98] ng/mL), and increased H4 (1.30 [0.64, 6.36] ng/mL; 1.75 [0.83, 9.67] ng/mL), all P < 0.001. The effect of DNAse was greater on trauma patients as compared with volunteers for LT (ΔLT, −0.21 vs. −0.02 min, P = 0.007), cfDNA (ΔcfDNA −133.4 vs. −84.9 ng/mL, P < 0.001), and CitH3 (ΔCitH3, –0.65 vs. −0.11 ng/mL, P = 0.004). Conclusion: Deoxyribonuclease treatment accelerates thrombin generation kinetics in trauma patient samples as compared with healthy volunteers. These findings suggest that NETs may contribute to the hypercoagulable state observed in trauma patients.
Recent research advances in identification and prevention of youth suicide risk
Authors: Barzilay Shira , Apter Alan 
Published: August 2022

Purpose of the review
The rate of youth suicidal behaviors has gradually increased over the last 15 years and continues to grow during the COVID-19 pandemic. This trend burdens mental health services and demands significant developments in risk detection and delivery of interventions to reduce the risk. In this article we outline significant advances and recent findings in youth suicide research that may facilitate strategies for identifying and preventing suicide risk among youth at risk in general and in specific risk groups.

Recent findings
The rise in suicide and suicidal behaviors is most likely to affect young people of racial, ethnic, sexual, and gender identity minorities and those living in poverty or experiencing maltreatment. The suicide rate in children is rising and demands special attention. Proximal risk factors for suicidal behavior compared with suicidal ideation have been suggested to identify near-term suicidal risk. Effective and scalable prevention strategies were identified, and the role of new technologies in suicide prevention among youth is to be determined.

Summary
To reach broader suicide prevention in youth and reduce the pressure on mental healthcare, public health approaches and improved service access for minority youth and those living in underserved areas of the world are needed.
Concatenated 16S rRNA Sequence Analysis Improve Bacterial Taxonomy
Authors: Paul Bobby 
Published: August 2022

AbstractMicroscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Further, advances in DNA sequencing and bioinformatics workflows facilitated sophisticated genome-based methods for microbial taxonomy. Although sequencing of 16S rRNA gene is widely employed to identify and classify the bacterial community as a cost-effective and single-gene approach. However, the accuracy of the 16S rRNA sequence-based species identification is limited by multiple copies of the gene and their higher sequence identity between closely related species. Availability of a large volume of bacterial whole-genome data provided an opportunity to develop comprehensive species-specific 16S rRNA reference libraries. With defined rules, we have concatenated four 16S rRNA gene copy variants to develop a species-specific reference library. Using this approach, species-specific 16S rRNA gene libraries were developed for four closely related Streptococcus species (S. gordonii, S. mitis, S. oralis, and S. pneumoniae). Sequence similarity and phylogenetic analysis of concatenated 16S rRNA copies yielded better resolution than single gene copy approaches. The approach is very effective to classify genetically related species, and it may reduce misclassification of bacterial species and genome assemblies.
Harnessing Wolbachia cytoplasmic incompatibility alleles for confined gene drive: a modeling study
Authors: Li Jiahe , Champer Jackson 
Published: August 2022

AbstractWolbachia is a maternally-inherited bacteria, which can spread rapidly in populations by manipulating reproduction. CifA and CifB are genes found in Wolbachia phage that are responsible for cytoplasmic incompatibility, the most common type of Wolbachia reproductive interference. In this phenomenon, no viable offspring are produced when a male with both CifA and CifB (or just CifB in an alternative mechanism) mates with a female lacking CifA. Utilizing this feature, we propose new types of toxin-antidote gene drives that can be constructed with these genes. By using both mathematical and simulation models, we found that a drive containing CifA and CifB together create a confined drive with a moderate to high introduction threshold. When introduced separately, they act as a self-limiting drive. We observed that the performance of these drives is substantially influenced by various ecological parameters and drive characteristics. Extending our models to continuous space, we found that the drive individual release distribution has a critical impact on drive persistence. Our results suggest that these new types of drives based on Wolbachia transgenes are safe and flexible candidates for genetic modification of populations.
Epigenetic Changes in Saccharomyces cerevisiae Alters the Aromatic Profile in Alcoholic Fermentation
Authors: Kong Yanzhuo , Olejar Kenneth J. , On Stephen L.W. , Winefield Christopher , Wescombe Philip A. , Brennan Charles S. , Hider Richard N. , Chelikani Venkata 
Published: August 2022

AbstractEpigenetic changes in genomics provide phenotypic modification without DNA sequence alteration. This study shows that benzoic acid, a common food additive and known histone deacetylase inhibitor (HDACi), has an epigenetic effect on Saccharomyces cerevisiae. Benzoic acid stimulated formation of epigenetic histone marks H3K4Me2, H3K27Me2, H3K18ac and H3Ser10p in S. cerevisiae and altered their phenotypic behavior, resulting in increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation. Our study demonstrates the HDACi activity of certain dietary compounds such as sodium butyrate, curcumin and anacardic acid, suggests the potential use of these dietary compounds in altering S. cerevisiae phenotypes without altering host-cell DNA. This study highlights the potential to use common dietary compounds to exploit epigenetic modifications for various fermentation and biotechnology applications as an alternative to genetic modification. These findings indicate that benzoic acid and other food additives may have potential epigenetic effects on human gut microbiota, in which several yeast species are involved.ImportanceThis manuscript investigates and reports for the first time utilizing microbial epigentics to alter the fermentation process of Pinot noir wines. We have experimentally demonstrated that certain dietary epigenetic compounds possess histone deacetylase (HDAC) inhibiting activity and can alter the wine characteristics by altering yeast gene expression. We have coined the term ‘nutrifermentics’ to represent this newly proposed field of research, which provides insights on the effect of certain dietary compounds on microbial strains and their potential application in fermentation process. This technological approach is a novel way to manipulate microorganisms for innovative food and beverage production with quality attributes.
Light prevents pathogen-induced aqueous microenvironments via potentiation of salicylic acid signaling
Authors: Lajeunesse Gaële , Roussin-Léveillée Charles , Boutin Sophie , Fortin Élodie , Laforest-Lapointe Isabelle , Moffett Peter 
Published: August 2022

AbstractUpon establishment of an infection, many plant pathogens induce an aqueous microenvironment in the extracellular space of their host, resulting in water-soaked lesions. In the case of Pseudomonas syringae (Pst), this is accomplished through the activity of water-soaking effectors that stimulate abscisic acid (ABA) production and signaling, which results in stomatal closure. This reduces transpiration and induces a microenvironment favorable for bacterial growth. Stomata are also highly sensitive to environmental conditions, including light and circadian rhythm. Here, we show that a period of darkness is required for water-soaking, and that a constant light regime abrogates the water-soaking activity of Pst effectors. Additionally, we show that constant light induces resistance against Pst and that this effect requires salicylic acid (SA). An increase in SA production upon infection under constant light did not affect effector-induced ABA signaling, but rather abrogated ABA’s ability to induce stomatal closure. Indeed, under normal diurnal light regimes, application of a SA analog is sufficient to prevent the ability of the pathogen to induce stomatal closure and a water-rich niche in the apoplast. Our results provide a novel approach to interfering with a common virulence strategy, as well as providing a physiological mechanism by which SA functions in defense against certain pathogens.