bluuebunny/crossref_metadata_2025_split huggingface dataset:
An improved residual network using deep fusion for identifying RNA 5-methylcytosine sites
Authors: Li Xinjie , Zhang Shengli , Shi Hongyan 
Published: July 2022

AbstractMotivation5-Methylcytosine (m5C) is a crucial post-transcriptional modification. With the development of technology, it is widely found in various RNAs. Numerous studies have indicated that m5C plays an essential role in various activities of organisms, such as tRNA recognition, stabilization of RNA structure, RNA metabolism and so on. Traditional identification is costly and time-consuming by wet biological experiments. Therefore, computational models are commonly used to identify the m5C sites. Due to the vast computing advantages of deep learning, it is feasible to construct the predictive model through deep learning algorithms.ResultsIn this study, we construct a model to identify m5C based on a deep fusion approach with an improved residual network. First, sequence features are extracted from the RNA sequences using Kmer, K-tuple nucleotide frequency component (KNFC), Pseudo dinucleotide composition (PseDNC) and Physical and chemical property (PCP). Kmer and KNFC extract information from a statistical point of view. PseDNC and PCP extract information from the physicochemical properties of RNA sequences. Then, two parts of information are fused with new features using bidirectional long- and short-term memory and attention mechanisms, respectively. Immediately after, the fused features are fed into the improved residual network for classification. Finally, 10-fold cross-validation and independent set testing are used to verify the credibility of the model. The results show that the accuracy reaches 91.87%, 95.55%, 92.27% and 95.60% on the training sets and independent test sets of Arabidopsis thaliana and M.musculus, respectively. This is a considerable improvement compared to previous studies and demonstrates the robust performance of our model.Availability and implementationThe data and code related to the study are available at https://github.com/alivelxj/m5c-DFRESG.
Late offspring effects of antenatal thyroid screening
Authors: Panagiotou Grigorios , Taylor Peter N , Rees D Aled , Okosieme Onyebuchi E 
Published: July 2022

AbstractBackgroundThyroid dysfunction in pregnancy is associated with adverse offspring outcomes and recent birth-cohort studies suggest that even mild degrees of thyroid dysfunction may be linked with a range of late cognitive and behavioural effects in childhood and adolescence.Sources of dataThis review summarizes recent literature of observational studies and critically appraises randomized controlled trials (RCTs) of antenatal thyroid screening and Levothyroxine intervention.Areas of agreementOvert hypothyroidism and hyperthyroidism carry significant risks for unfavourable offspring outcomes and should be appropriately corrected in pregnancy.Areas of controversyThe significance of subclinical hypothyroidism and hypothyroxinaemia is still unclear. Meta-analyses of birth-cohort studies show associations of maternal subclinical hypothyroidism and hypothyroxinaemia with intellectual deficits, attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders, while hyperthyroidism and high-normal FT4 were linked with ADHD. RCTs have shown no benefits of screening on neurodevelopmental outcomes although Levothyroxine could have been initiated too late in pregnancy in these trials.Growing pointsA small number of studies have shown inconsistent associations of maternal thyroid dysfunction with offspring cardiometabolic indices including blood pressure and body weight. Correction of maternal thyroid dysfunction was, however, associated with favourable long-term metabolic profiles in mothers, including lipid profiles, fat mass and body mass index. Antenatal thyroid screening may therefore present opportunities for optimizing a wider range of outcomes than envisaged.Areas for developing researchFuture trials with early antenatal thyroid screening and intervention are necessary to clarify the impact of screening on late offspring and maternal effects.
Ligand-free mitochondria-localized mutant AR-induced cytotoxicity in spinal bulbar muscular atrophy
Authors: Feng Xia , Cheng Xiu-Tang , Zheng Pengli , Li Yan , Hakim Jill , Zhang Shirley Q , Anderson Stacie M , Linask Kaari , Prestil Ryan , Zou Jizhong , Sheng Zu-Hang , Blackstone Craig 
Published: July 2022

AbstractSpinal bulbar muscular atrophy (SBMA), the first identified CAG-repeat expansion disorder, is an X-linked neuromuscular disorder involving CAG-repeat-expansion mutations in the androgen receptor (AR) gene. We utilized CRISPR-Cas9 gene editing to engineer novel isogenic human induced pluripotent stem cell (hiPSC) models, consisting of isogenic AR knockout, control and disease lines expressing mutant AR with distinct repeat lengths, as well as control and disease lines expressing FLAG-tagged wild-type and mutant AR, respectively. Adapting a small-molecule cocktail-directed approach, we differentiate the isogenic hiPSC models into motor neuron-like cells with a highly enriched population to uncover cell-type-specific mechanisms underlying SBMA and to distinguish gain- from loss-of-function properties of mutant AR in disease motor neurons. We demonstrate that ligand-free mutant AR causes drastic mitochondrial dysfunction in neurites of differentiated disease motor neurons due to gain-of-function mechanisms and such cytotoxicity can be amplified upon ligand (androgens) treatment. We further show that aberrant interaction between ligand-free, mitochondria-localized mutant AR and F-ATP synthase is associated with compromised mitochondrial respiration and multiple other mitochondrial impairments. These findings counter the established notion that androgens are requisite for mutant AR-induced cytotoxicity in SBMA, reveal a compelling mechanistic link between ligand-free mutant AR, F-ATP synthase and mitochondrial dysfunction, and provide innovative insights into motor neuron-specific therapeutic interventions for SBMA.
Disentangling dyskinesia from parkinsonism in motor structures of patients with schizophrenia
Authors: Sakreida Katrin , Chiu Wei-Hua , Dukart Juergen , Eickhoff Simon B , Frodl Thomas , Gaser Christian , Landgrebe Michael , Langguth Berthold , Mirlach Daniela , Rautu Ioana-Sabina , Wittmann Markus , Poeppl Timm B 
Published: July 2022

AbstractPatients with schizophrenia frequently suffer from motor abnormalities, but underlying alterations in neuroarchitecture remain unclear. Here, we aimed to disentangle dyskinesia from parkinsonism in motor structures of patients with schizophrenia and to assess associated molecular architecture. We measured grey matter of motor regions and correlated volumetric estimates with dyskinesia and parkinsonism severity. Associations with molecular architecture were identified by cross-modal spatial correlations between ensuing maps of abnormality-related volume alterations and neurotransmitter maps from healthy populations. Both phenomena were linked to (specific) striatal and basal forebrain reductions as well as to D1 receptor density. Dyskinesia also manifested in cerebellar decrease, while parkinsonism was associated with less motor cortex volume. The parkinsonism-related brain pattern was additionally associated with 5-HT1A/2A and µ-opioid receptors distribution. Findings suggest the need to develop psychopharmacological compounds that display not only selectivity for receptor subtypes but also anatomical selectivity for alleviating dyskinesia without worsening parkinsonism and vice versa.
Intratumoral microbiota: new frontiers in tumor immunity
Authors: Zhang Zhilin , Liao Yiqun , Tang Dong 
Published: July 2022

Abstract
Microbiota–host interactions are a hot topic of research because of their important role in regulating the malignant transformation of cancer cells and cancer-related immunity. The role of gut microbiota, oral microbiota and skin microbiota in cancer progression has been extensively studied. However, intratumoral microbiota is a recently discovered topic of research that is still in its infancy. This review focuses on the impact of the intratumoral microbiota on cancer immune responses and highlights how the intratumoral microbiota modulates innate and adaptive immunity to potentially impact tumor immunotherapy in the hope that it will inspire potential ideas for the application of immunotherapy in the treatment of tumors.
Sustained Within-season Vaccine Effectiveness Against Influenza-associated Hospitalization in Children: Evidence From the New Vaccine Surveillance Network, 2015–2016 Through 2019–2020
Authors: Sahni Leila C , Naioti Eric A , Olson Samantha M , Campbell Angela P , Michaels Marian G , Williams John V , Staat Mary Allen , Schlaudecker Elizabeth P , McNeal Monica M , Halasa Natasha B , Stewart Laura S , Chappell James D , Englund Janet A , Klein Eileen J , Szilagyi Peter G , Weinberg Geoffrey A , Harrison Christopher J , Selvarangan Rangaraj , Schuster Jennifer E , Azimi Parvin H , Singer Monica N , Avadhanula Vasanthi , Piedra Pedro A , Munoz Flor M , Patel Manish M , Boom Julie A 
Published: July 2022

Abstract

Background
Adult studies have demonstrated within-season declines in influenza vaccine effectiveness (VE); data in children are limited.

Methods
We conducted a prospective, test-negative study of children 6 months through 17 years hospitalized with acute respiratory illness at 7 pediatric medical centers during the 2015–2016 through 2019–2020 influenza seasons. Case-patients were children with an influenza-positive molecular test matched by illness onset to influenza-negative control-patients. We estimated VE [100% × (1 – odds ratio)] by comparing the odds of receipt of ≥1 dose of influenza vaccine ≥14 days before illness onset among influenza-positive children to influenza-negative children. Changes in VE over time between vaccination date and illness onset date were estimated using multivariable logistic regression.

Results
Of 8430 children, 4653 (55%) received ≥1 dose of influenza vaccine. On average, 48% were vaccinated through October and 85% through December each season. Influenza vaccine receipt was lower in case-patients than control-patients (39% vs 57%, P &lt; .001); overall VE against hospitalization was 53% (95% confidence interval [CI]: 46, 60%). Pooling data across 5 seasons, the odds of influenza-associated hospitalization increased 4.2% (−3.2%, 12.2%) per month since vaccination, with an average VE decrease of 1.9% per month (n = 4000, P = .275). Odds of hospitalization increased 2.9% (95% CI: −5.4%, 11.8%) and 9.6% (95% CI: −7.0%, 29.1%) per month in children ≤8 years (n = 3084) and 9–17 years (n = 916), respectively. These findings were not statistically significant.

Conclusions
We observed minimal, not statistically significant within-season declines in VE. Vaccination following current Advisory Committee on Immunization Practices (ACIP) guidelines for timing of vaccine receipt remains the best strategy for preventing influenza-associated hospitalizations in children.
Sotrovimab Resistance and Viral Persistence After Treatment of Immunocompromised Patients Infected With the Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant
Authors: Huygens Sammy , Oude Munnink Bas , Gharbharan Arvind , Koopmans Marion , Rijnders Bart 
Published: July 2022

Abstract
Viral evolution was evaluated in 47 immunocompromised patients treated with sotrovimab. Sequencing of SARS-CoV-2 following therapy was successful in 16. Mutations associated with sotrovimab resistance were documented in 6; viral replication continued after 30 days in 5. Combination antibody therapy may be required to avoid acquired resistance in immunocompromised patients.
Guideline-Concordant Antiviral Treatment in Children at High Risk for Influenza Complications
Authors: Antoon James W , Hall Matt , Feinstein James A , Kyler Kathryn E , Shah Samir S , Girdwood Sonya Tang , Goldman Jennifer L , Grijalva Carlos G , Williams Derek J 
Published: July 2022

Abstract

Background
National guidelines recommend antiviral treatment for children with influenza at high risk for complications regardless of symptom duration. Little is known about concordance of clinical practice with this recommendation.

Methods
We performed a cross-sectional study of outpatient children (aged 1–18 years) at high risk for complications who were diagnosed with influenza during the 2016–2019 influenza seasons. High-risk status was determined using an existing definition that includes age, comorbidities, and residence in a long-term care facility. The primary outcome was influenza antiviral dispensing within 2 days of influenza diagnosis. We determined patient- and provider-level factors associated with guideline-concordant treatment using multivariable logistic regression.

Results
Of the 274 213 children with influenza at high risk for influenza complications, 159 350 (58.1%) received antiviral treatment. Antiviral treatment was associated with the presence of asthma (aOR, 1.13; 95% confidence interval [CI], 1.11–1.16), immunosuppression (aOR, 1.10; 95% CI, 1.05–1.16), complex chronic conditions (aOR, 1.04; 95% CI, 1.01–1.07), and index encounter in the urgent care setting (aOR, 1.3; 95% CI, 1.26–1.34). Factors associated with decreased odds of antiviral treatment include age 2–5 years compared with 6–17 years (aOR, 0.95; 95% CI, .93–.97), residing in a chronic care facility (aOR, .61; 95% CI, .46–.81), and index encounter in an emergency department (aOR, 0.66; 95% CI, .63–.71).

Conclusions
Among children with influenza at high risk for complications, 42% did not receive guideline-concordant antiviral treatment. Further study is needed to elucidate barriers to appropriate use of antivirals in this vulnerable population.
Coping with drought? Effects of extended drought conditions on soil invertebrate prey and diet selection by a fossorial amphisbaenian reptile
Authors: Martín José , Ortega Jesús , García-Roa Roberto , Rodríguez-Ruiz Gonzalo , Pérez-Cembranos Ana , Pérez-Mellado Valentín 
Published: July 2022

Abstract
Arid climates are characterized by a summer drought period to which animals seem adapted. However, in some years, the drought can extend for unusually longer periods. Examining the effects of these current extreme weather events on biodiversity can help to understand the effects of climate change, as models predict an increase in drought severity. Here, we examined the effects of “unusual” extended drought on soil invertebrate prey availability and on diet composition (based on fecal contents) and diet selection of a fossorial amphisbaenian, the checkerboard worm lizard Trogonophis wiegmanni. Weather data show interannual variations in summer drought duration. The abundance and diversity of soil invertebrates in spring were high, and similar to those found in a “normal” early autumn, after some rain had ended with the summer drought. In contrast, in years with “unusual” extended drought, abundance, and diversity of soil invertebrates in early autumn were very low. Also, there were seasonal changes in amphisbaenians’ diet; in autumn with drought, prey diversity, and niche breadth decreased with respect to spring and autumns after some rain had fallen. Amphisbaenians did not eat prey at random in any season, but made some changes in prey selection that may result from drought-related restrictions in prey availability. Finally, in spite that amphisbaenians showed some feeding flexibility, their body condition was lower in autumn than in spring, and much lower in autumn with drought. If extended drought became the norm in the future, amphisbaenians might suffer important negative effects for their health state.
Echo-Doppler and strain assessment of filling pressures in adults with congenitally corrected transposition and systemic right ventricles
Authors: Charles Jain C , Egbe Alexander C , Oh Jae K , Connolly Heidi M , Miranda William R 
Published: July 2022

AbstractAimsSystolic dysfunction of the systemic right ventricle (sRV) is common in adults with transposition of the great arteries and sRV. In acquired disease, diastology analysis for assessment of filling pressures (FP) is paramount in patient care.Methods and resultsRetrospective analysis of 47 adults with sRV without prior systemic tricuspid valve surgery undergoing catheterization and echocardiography within 7 days (median −2 [−1, −3]) from January 2000 to February 2021 at our institution. Median age was 48 (31, 55) years, and 16 (34.0%) patients were female. FPs were normal in 21 patients (44.7%). Left atrial size was enlarged in most patients (83.0%) with mean indexed value 58.3 ± 23.4 mL/m2. Tissue Doppler e′ was not significantly different between those with high FPs vs. normal (medial 0.07 ± 0.03 vs. 0.08 ± 0.03 m/s, P = 0.63; lateral 0.08 ± 0.04 vs. 0.08 ± 0.04 m/s, P = 0.88). E velocity and subpulmonic mitral regurgitant velocity were higher in those with high FPs (0.9 ± 0.3 vs. 0.6 ± 0.2 m/s, P = 0.005; 3.8 ± 1.1 vs. 2.8 ± 0.9 m/s, P = 0.004). Left atrial reservoir strain, sRV global longitudinal strain, and subpulmonic left ventricular strain were worse in those with high FP (18.0 ± 7.6 vs. 27.9 ± 10.2%, P = 0.0009; −13.0 ± 4.4 vs. −17.9 ± 5.0%, P = 0.002; −16.8 ± 5.7 vs. −23.0 ± 3.8%, P = 0.001).ConclusionDespite the complex anatomy, FPs can be assessed non-invasively in adults with sRV without prior systemic tricuspid valve surgery. The current guideline algorithm for diastolic dysfunction in acquired heart disease has limited applicability in this population. Given the limitations of Doppler in this heterogeneous population, strain analysis can be a helpful adjunct for estimation of FPs.
Extrapulmonary sarcoidosis involving only the heart and guts: a case report
Authors: Sasaki Shun , Hayashi Takaharu , Tateishi Emi , Higuchi Yoshiharu 
Published: July 2022

Abstract

Background
The respiratory tract is the most commonly affected organ system in sarcoidosis. Purely extrapulmonary sarcoidosis is rare. There have been no reports of extrapulmonary sarcoidosis with lesions only in the heart and guts.

Case summary
A 19-year-old male was admitted for chest symptoms accompanied by remarkably elevated troponin T and creatinine kinase levels. Electrocardiogram (ECG) showed sinus rhythm with a right bundle branch block, broad ST segment elevation, and abnormal Q waves. Endoscopic biopsy revealed granuloma formation in the transverse colon. Based on multimodal imaging, we made a clinical diagnosis of extrapulmonary sarcoidosis involving only the heart and guts. One year of immunosuppressive therapy with prednisolone resolved the inflammation in the guts but not in the heart. He experienced runs of sustained ventricular tachycardia with loss of consciousness and was admitted to our hospital again. The addition of methotrexate markedly reduced cardiac accumulation of fluorodeoxyglucose. No life-threatening ventricular arrhythmias have been recorded afterwards.

Discussion
This unusual case of cardiac sarcoidosis not only involved rare lesions only in the heart and guts but also presented with ST elevation on ECG. This case suggests that the gastrointestinal tract is a site of effective antigen capture outside of the respiratory tract that can affect the heart.
The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso
Authors: Barro Mariam , Wonni Issa , Simonin Marie , Kassankogno Abalo Itolou , Klonowska Agnieszka , Moulin Lionel , Béna Gilles , Somda Irénée , Brunel Caroline , Tollenaere Charlotte 
Published: July 2022

Abstract
Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant samples per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.
United States Family Forest Owners’ Awareness of and Participation in Carbon Sequestration Programs: Initial Findings from the USDA Forest Service National Woodland Owner Survey
Authors: Sass Emma M , Caputo Jesse , Butler Brett J 
Published: July 2022

AbstractFamily forest owners (FFOs) hold a plurality of forestland in the United States, and programs and markets exist that compensate landowners for sequestering and storing increased carbon through extended rotations, improved forest management, and increased forest cover. We used USDA Forest Service National Woodland Owner Survey (NWOS) data from 2018 to estimate the number of ownerships and their associated acreage that are enrolled, that are familiar but not enrolled, and that are unfamiliar with these programs, as well as differences in attributes among these groups. As of 2018, less than 0.1% (SE &lt; 0.1%) of FFOs are enrolled in carbon sequestration programs, and collectively they hold an estimated 400,000 ha (SE = 100,000). FFOs who are enrolled have larger holdings, are more likely to participate in other programs, and are more concerned about climate change, among other characteristics. Most FFO holdings are too small to be viable in traditional carbon programs, although new and evolving programs might enable smaller landholdings to be feasible to enroll. Knowing the characteristics of ownerships that are enrolled or aware of programs will allow for more informed design and implementation; future monitoring will be important to identify trends as these programs become more widespread.