bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progressive-Tension Sutures in Reconstruction of Posterior Trunk Defects in Pediatric Patients: A Prospective Series
Authors: Crowe Christopher S. , Hauptman Jason S. , Lee Amy , Ellenbogen Richard G. , Ettinger Russell E. , Susarla Srinivas M. 
Published: June 2022

Summary:
Following neurosurgical repair of spinal dysraphism defects, soft-tissue reconstruction is often required to obtain robust coverage of the dura. Layered closure utilizing local muscle and muscle fascia has proven reliable for this purpose, but it often results in significant dead space necessitating closed suction drainage. Progressive-tension sutures have been reported as an alternative to drains for prevention of fluid collection in several other procedures. In this study, the use of progressive-tension sutures for eliminating subcutaneous dead space and obtaining tension-free skin closure was prospectively evaluated in pediatric patients undergoing soft-tissue reconstruction for congenital spinal anomalies. Primary outcomes of interest included wound breakdown, seroma, hematoma, and cerebrospinal fluid leak. Patients were excluded if a lumbar, submuscular, or subcutaneous drain was placed during the index procedure. Over a 3-year period, 45 patients underwent muscle flap reconstruction for coverage of dural defects. The primary diagnoses were myelomeningocele (10 patients), lipomyelomeningocele (eight patients), myelocystocele (three patients), tethered cord release (15 patients), meningocele (three patients), spinal tumor (two patients), and hardware exposure following spinal instrumentation (three patients). During the follow-up period, three patients (6.7 percent) had postoperative wound complications. One patient had superficial dehiscence, one had cerebrospinal fluid leak requiring operative revision, and one had a surgical site infection necessitating operative drainage. No patients developed hematomas, seromas, cerebrospinal fluid fistulae, or wound breakdown requiring operative revision. The use of progressive-tension sutures is an effective method for eliminating subcutaneous dead space in pediatric soft-tissue reconstruction and eliminates the need for drain placement.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Factors Causing Variation in World Health Organization Surgical Safety Checklist Effectiveness—A Rapid Scoping Review
Authors: Wani Mudassir M. , Gilbert John H.V. , Mohammed Ciraj Ali , Madaan Sanjeev 
Published: June 2022

Introduction
This review was conducted to determine what factors might be responsible for prejudicing the outcomes after the implementation of a World Health Organization Surgical Safety Checklist (WHO SSC), grouping them appropriately and proposing strategies that enable the SSC a more helpful and productive tool in the operating room.

Methods
It was a rapid scoping review conducted as per Preferred Reporting Items for Systematic Review and Meta-analyses extension guidelines for scoping reviews (PRISMA-Scr). Comprehensive search on MEDLINE and Embase was carried out, to include all relevant studies published during last 5 years. Twenty-seven studies were included in analysis. The barriers to SSC implementation were classified into 5 main groups, with further subdivisions in each.

Results
The results of review revealed that there are 5 major barriers to SSC at the following levels: organizational, checklist, individual, technical, and implementation. Each of these major barriers, on further evaluation, was found to have more than one contributing factors. All these factors were analyzed individually.

Conclusions
This rapid scoping review has consolidated data, which may pave the way for experts to further examine steps that might be taken locally or globally in order that the WHO SSC to successfully achieve all its desired goals.
Use of Machine Learning Algorithms to Predict the Outcomes of Mechanical Thrombectomy in Acute Ischemic Stroke Patients With an Extended Therapeutic Time Window
Authors: Lu Shanshan , Zhang Jiulou , Wu Rongrong , Cao Yuezhou , Xu Xiaoquan , Li Ge , Liu Sheng , Shi Haibin , Wu Feiyun 
Published: June 2022

Objective
The aim of this study was to evaluate the performance of machine learning (ML) algorithms in predicting the functional outcome of mechanical thrombectomy (MT) outside the 6-hour therapeutic time window in patients with acute ischemic stroke (AIS).

Methods
One hundred seventy-seven consecutive AIS patients with large-vessel occlusion in the anterior circulation who underwent MT in the extended time window were enrolled. Clinical, neuroimaging, and treatment variables that could be obtained quickly in the real-world emergency settings were collected. Four machine learning algorithms (random forests, regularized logistic regression, support vector machine, and naive Bayes) were used to predict good outcomes (modified Rankin Scale scores of 0–2) at 90 days by using (1) only variables at admission and (2) both baseline and treatment variables. The performance of each model was evaluated using receiver operating characteristic (ROC) curve analysis. Feature importance was ranked using random forest algorithms.

Results
Eighty patients (45.2%) had a favorable 90-day outcome. Machine learning models including baseline clinical and neuroimaging characteristics predicted 90-day modified Rankin Scale with an area under the ROC curve of 0.80–0.81, sensitivity of 0.60–0.71 and specificity of 0.71–0.76. Further inclusion the treatment variables significantly improved the predictive performance (mean area under the ROC curve, 0.89–0.90; sensitivity, 0.77–0.85; specificity, 0.75–0.87). The most important characteristics for predicting 90-day outcomes were age, hypoperfusion intensity ratio at admission, and National Institutes of Health Stroke Scale score at 24 hours after MT.

Conclusions
Machine learning algorithms may facilitate prediction of 90-day functional outcomes in AIS patients with an extended therapeutic time window.
Immunotherapy in autoimmune encephalitis
Authors: Trewin Benjamin P. , Freeman Isaak , Ramanathan Sudarshini , Irani Sarosh R. 
Published: June 2022

Purpose of review
Autoimmune encephalitis (AE) refers to immune-mediated neurological syndromes often characterised by the detection of pathogenic autoantibodies in serum and/or cerebrospinal fluid which target extracellular epitopes of neuroglial antigens. There is increasing evidence these autoantibodies directly modulate function of their antigens in vivo. Early treatment with immunotherapy improves outcomes. Yet, these patients commonly exhibit chronic disability. Importantly, optimal therapeutic strategies at onset and during escalation remain poorly understood. In this review of a rapidly emerging field, we evaluate recent studies on larger cohorts, registries, and meta-analyses to highlight existing evidence for contemporary therapeutic approaches in AE.

Recent findings
We highlight acute and long-term treatments used in specific AE syndromes, exemplify how understanding disease pathogenesis can inform precision therapy and outline challenges of defining disability outcomes in AE.

Summary
Early first-line immunotherapies, including corticosteroids and plasma exchange, improve outcomes, with emerging evidence showing second-line immunotherapies (especially rituximab) reduce relapse rates. Optimal timing of immunotherapy escalation remains unclear. Routine reporting of outcome measures which incorporate cognitive impairment, fatigue, pain, and mental health will permit more accurate quantification of residual disability and comprehensive comparisons between international multicentre cohorts, and enable future meta-analyses with the aim of developing evidence-based therapeutic guidelines.
Aeromicrobium stalagmiti sp. nov., isolated from a lava cave
Authors: Byeon Yeong-Sik , Kim Sung-Min , Yang Hong Lim , Kim In Seop , Lee Soon Dong 
Published: June 2022

A Gram-reaction-positive, strictly aerobic, non-sporulating, non-motile, rod-shaped bacterium, designated YC3-14T, was isolated from pieces of stalagmite collected in a lava cave in Jeju, Republic of Korea. Cells showed growth at 15–35 °C, pH 6.0–9.0 and with 0–3 % (w/v) NaCl. Colonies of the cells were circular, smooth, convex and cream in colour. A 16S rRNA gene-based neighbour-joining tree indicated that the organism belonged to the genus

Aeromicrobium

and formed a sublineage between an Aeromicrobium endophyticum–Aeromicrobium fastidiosum cluster and an Aeromicrobium yanjiei–Aeromicrobium chenweiae cluster. The highest 16S rRNA gene similarity values of strain YC3-14T were with the type strains of

A. yanjiei

(99.2 %),

A. endophyticum

(99.1 %),

A. fastidiosum

(98.8 %),

A. ginsengisoli

(98.8 %) and

A

.

chenweiae

(98.7 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-9(H4). The predominant fatty acids were C18 : 0.10-methyl, C18 : 1
ω9c and C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and two unidentified lipids. The G+C content of the genome DNA was 69.9 mol%. These chemotaxonomic features of the isolate were typical for the genus

Aeromicrobium

. The genome-based phylogeny showed the same tree topology as the 16S rRNA gene phylogeny. The average nucleotide identity (≤84.5 %) and digital DNA–DNA hybridization (≤27.5 %) values supported that the isolate belongs to a novel species of the genus

Aeromicrobium

. On the basis of data obtained by a polyphasic approach, strain YC3-14T (=KCTC 49469T=NBRC 114653T) represents a novel species of the genus

Aeromicrobium

, for which the name Aeromicrobium stalagmiti sp. nov. is proposed.
rGREAT: an R/Bioconductor package for functional enrichment on genomic regions
Authors: Gu Zuguang , Hübschmann Daniel 
Published: June 2022

AbstractSummaryGREAT is a widely used tool for functional enrichment on genomic regions. However, as an online tool, it has limitations of outdated annotation data, small numbers of supported organisms and gene set collections, and not being extensible for users. Here we developed a new R/Bioconductor package named rGREAT which implements the GREAT algorithm locally. rGREAT by default supports more than 500 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.Availability and implementationThe package rGREAT is freely available from the Bioconductor project: https://bioconductor.org/packages/rGREAT/. The development version is available at https://github.com/jokergoo/rGREAT. Gene Ontology gene sets for 556 organisms are freely available at https://jokergoo.github.io/rGREAT_genesets/.Contactz.gu@dkfz.de or d.huebschmann@dkfz.deSupplementary informationSupplementary data are available at Bioinformatics online.
Elite neutralizers of human cytomegalovirus are characterized by high magnitude plasma IgG responses against multiple glycoprotein complexes
Authors: Harnois Melissa J. , Dennis Maria , Stöhr Dagmar , Valencia Sarah M. , Rodgers Nicole , Semmes Eleanor C. , Webster Helen S. , Jenks Jennifer A. , Barfield Richard , Pollara Justin , Chan Cliburn , Sinzger Christian , Permar Sallie R. 
Published: June 2022

ABSTRACTBackgroundHuman cytomegalovirus (HCMV) is the most common infectious complication of organ transplantation and cause of birth defects worldwide. There are limited therapeutic options and no licensed vaccine to prevent HCMV infection or disease. To inform development of HCMV antibody-based interventions, a previous study identified individuals with potent and broad plasma HCMV-neutralizing activity, termed elite neutralizers (EN), from a cohort of HCMV-seropositive (SP) blood donors. Yet, the specificities and functions of plasma antibodies associated with EN status remained undefined.MethodsWe sought to determine the plasma antibody specificities, breadth, and Fc-mediated antibody effector functions associated with the most potent HCMV-neutralizing responses in plasma from EN (n=25) relative to SP (n=19). We measured antibody binding against various HCMV strains and glycoprotein targets, and evaluated Fc-mediated effector functions, antibody dependent cellular cytotoxicity (ADCC) and antibody dependent cellular phagocytosis (ADCP).ResultsWe demonstrate that elite HCMV neutralizers have elevated IgG binding responses against multiple viral glycoproteins, relative to SP. Our study also revealed potent HCMV-specific ADCC and ADCP activity of EN plasma.ConclusionsWe conclude that antibody responses against multiple glycoprotein specificities may be needed to achieve potent plasma neutralization and that potently HCMV elite-neutralizing plasma antibodies can also mediate polyfunctional responses.
Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity
Authors: Yoshiji Satoshi , Butler-Laporte Guillaume , Lu Tianyuan , Sunday Willett Julian Daniel , Su Chen-Yang , Nakanishi Tomoko , Morrison David R. , Chen Yiheng , Liang Kevin , Hultström Michael , Ilboudo Yann , Afrasiabi Zaman , Lan Shanshan , Duggan Naomi , DeLuca Chantal , Vaezi Mitra , Tselios Chris , Xue Xiaoqing , Bouab Meriem , Shi Fangyi , Laurent Laetitia , Münter Hans Markus , Afilalo Marc , Afilalo Jonathan , Mooser Vincent , Timpson Nicholas J , Zeberg Hugo , Zhou Sirui , Forgetta Vincenzo , Farjoun Yossi , Richards J. Brent 
Published: June 2022

AbstractObesity is a major risk factor for COVID-19 severity; however, the mechanisms underlying this relationship are not fully understood. Since obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index (BMI) using Mendelian randomization (MR). This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using MR. We found that a standard deviation increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71,P= 1.63 × 10−10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing,NPNTwas expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.
SynBio in 3D: the first synthetic genetic circuit as a 3D-printed STEM educational resource
Authors: Boll Heloísa Oss , Leitão Matheus de Castro , Garay Aisel Valle , Coelho Cíntia Marques 
Published: June 2022

AbstractSynthetic biology is a new area of science that operates at the intersection of engineering and biology and aims to design and synthesize living organisms and systems to perform new or improved functions. This novel biological area is considered of extreme relevance for the development of solutions to global problems. However, its teaching is often inaccessible to students, since many educational resources and methodological procedures are not available for understanding of complex molecular processes. On the other hand, digital fabrication tools, which allow the creation of 3D objects, are increasingly used for educational purposes, and several computational structures of molecular components commonly used in synthetic biology processes are deposited in open databases. Therefore, we hypothesize that the creation of biomolecular structures models by handling 3D physical objects using computer-assisted design (CAD) and additive fabrication based on 3D printing could help professors in synthetic biology teaching. In this sense, the present work describes the design and 3D print of the molecular models of the first synthetic genetic circuit, the toggle switch, which can be freely downloaded and used by teachers to facilitate the training of STEM students in synthetic biology.
Linearization Autoencoder: an autoencoder-based regression model with latent space linearization
Authors: Lee Sangyeon , Kim Hanjin , Lee Doheon 
Published: June 2022

ABSTRACTRegression analysis is one of the most widely applied methods in many fields including bio-medical study. Dimensionality reduction is also widely used for data preprocessing and feature selection analysis, to extract high-impact features from the predictions. As the complexity of both data and prediction models increases, it becomes important and difficult to interpret the model. We suggested a novel method, linearizing autoencoder, for regression analysis with high-dimensional data. Based on the autoencoder model, we introduce a novel loss function to make data points aggregate corresponding to their known labels and align them preserving linear relations of the known feature. This model can align data points to the linear relations of labels, and achieve both the prediction and feature selection performances by extracting features that are important to the label we want to predict. Also, we applied this method to the real-world data and the result indicates that this method can successfully disentangle the latent space with given centroids in a supervised manner. This method can be applied to various prediction problems in biomedical fields.
Molecular insights into intrinsic transducer-coupling bias in the CXCR4-CXCR7 system
Authors: Sarma Parishmita , Yoon Hye-Jin , Carino Carlo Marion C. , S Deeksha , Banerjee Ramanuj , Yun Yaejin , Ji Jeongsek , Min Kyungjin , Pandey Shubhi , Dwivedi-Agnihotri Hemlata , Rui Xue , Cao Yubo , Kawakami Kouki , Kumari Poonam , Chen Yu-Chih , Luker Kathryn E. , Yadav Manish K. , Ranjan Ashutosh , Chaturvedi Madhu , Maharana Jagannath , Baidya Mithu , Yadav Prem N. , Luker Gary D. , Laporte Stéphane A. , Chen Xin , Inoue Asuka , Lee Hyung Ho , Shukla Arun K. 
Published: June 2022

AbstractChemokine receptors constitute an important subfamily of G protein-coupled receptors (GPCRs), and they are critically involved in a broad range of immune response mechanisms. Ligand promiscuity among these receptors makes them an interesting target to explore novel aspects of biased agonism. Here, we comprehensively characterize two chemokine receptors namely, CXCR4 and CXCR7, which share a common chemokine agonist (CXCL12), in terms of their G-protein coupling, β-arrestin (βarr) recruitment, contribution of GRKs, and ERK1/2 MAP kinase activation. We observe that CXCR7 lacks G-protein coupling while maintaining robust βarr recruitment with a major contribution of GRK5/6. On the other hand, CXCR4 displays robust G-protein activation as expected, however, it exhibits significantly reduced βarr-coupling compared to CXCR7 in response to their shared natural agonist, CXCL12. These two receptors induce distinct βarr conformations even when activated by the same agonist, and CXCR7, unlike CXCR4, fails to activate ERK1/2 MAP kinase. We further determine the crystal structure of βarr2 in complex with a carboxyl-terminal phosphopeptide derived from CXCR7, which reveals a smaller interdomain rotation than observed previously for activated βarrs. Importantly, structure-guided cellular experiments reveal a key contribution of a single phosphorylation site in CXCR7 on βarr recruitment and endosomal trafficking. Taken together, our study provides molecular insights into intrinsic bias encoded in the CXCR4-CXCR7 system, and it has broad implications for therapeutically important framework of biased agonism.
A pandemic clonal lineage of the wheat blast fungus
Authors: Latorre Sergio M. , Were Vincent M. , Foster Andrew J. , Langner Thorsten , Malmgren Angus , Harant Adeline , Asuke Soichiro , Reyes-Avila Sarai , Gupta Dipali Rani , Jensen Cassandra , Ma Weibin , Mahmud Nur Uddin , Mehebub Md. Shåbab , Mulenga Rabson M. , Muzahid Abu Naim Md. , Paul Sanjoy Kumar , Rabby S. M. Fajle , Raha Abdullah Al Mahbub , Ryder Lauren , Shrestha Ram-Krishna , Sichilima Suwilanji , Soanes Darren M. , Singh Pawan Kumar , Bentley Alison R. , Saunders Diane G. O. , Tosa Yukio , Croll Daniel , Lamour Kurt H , Islam Tofazzal , Tembo Batiseba , Win Joe , Talbot Nicholas J. , Burbano Hernán A. , Kamoun Sophien 
Published: June 2022

ABSTRACTWheat, the most important food crop, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America, and to guide pre-emptive wheat breeding for blast resistance.
Neuroanatomical correlates of genetic risk for obesity in children
Authors: Morys Filip , Yu Eric , Shishikura Mari , Paquola Casey , Vainik Uku , Nave Gideon , Koellinger Philipp , Gan-Or Ziv , Dagher Alain 
Published: June 2022

AbstractObesity has a strong genetic component, with up to 20% of variance in body mass index (BMI) being accounted for by common polygenic variation. Most genetic polymorphisms associated with BMI are related to genes expressed in the central nervous system. At the same time, higher BMI is associated with neurocognitive changes. However, the direct link between genetics of obesity and neurobehavioral mechanisms related to weight gain is missing. Here, we use a large sample of participants (n>4,000) from the Adolescent Brain Cognitive Development cohort and investigate how genetic risk for obesity, expressed as polygenic risk score for BMI (BMI-PRS), is related to brain and behavioral differences in adolescents. In a series of analyses, we show that BMI-PRS is related to lower cortical volume and thickness in the frontal and temporal areas, relative to age-expected values. Relatedly, using structural equation modeling, we find that lower overall cortical volume is associated with higher impulsivity, which in turn is related to an increase in BMI 1 year later. In sum, our study shows that obesity might partially stem from genetic risk as expressed in brain changes in the frontal and temporal brain areas, and changes in impulsivity.