bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and Spatial Changes in the Microbiome Following Pediatric Severe Traumatic Brain Injury
Authors: Rogers Matthew B. , Simon Dennis , Firek Brian , Silfies Laurie , Fabio Anthony , Bell Michael J. , Yeh Andrew , Azar Justin , Cheek Richard , Kochanek Patrick M. , Peddada Shyamal D. , Morowitz Michael J. 
Published: March 2022

OBJECTIVES:
The microbiome may be affected by trauma and critical illness. Many studies of the microbiome in critical illness are restricted to a single body site or time point and confounded by preexisting conditions. We report temporal and spatial alterations in the microbiome of previously healthy children with severe traumatic brain injury (TBI).

DESIGN
We collected oral, rectal, and skin swabs within 72 hours of admission and then twice weekly until ICU discharge. Samples were analyzed by 16S rRNA gene amplicon sequencing. Children undergoing elective outpatient surgery served as controls. Alpha and beta diversity comparisons were performed with Phyloseq, and differentially abundant taxa were predicted using Analysis of Composition of Microbiomes.

SETTING:
Five quaternary-care PICUs.

PATIENTS:
Patients less than 18 years with severe TBI requiring placement of an intracranial pressure monitor.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Three hundred twenty-seven samples were analyzed from 23 children with severe TBI and 35 controls. The community composition of initial oral (F = 3.2756, R
2 = 0.0535, p = 0.012) and rectal (F = 3.0702, R
2 = 0.0649, p = 0.007) samples differed between TBI and control patients. Rectal samples were depleted of commensal bacteria from Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae families and enriched in Staphylococcaceae after TBI (p < 0.05). In exploratory analyses, antibiotic exposure, presence of an endotracheal tube, and occurrence of an infection were associated with greater differences of the rectal and oral microbiomes between TBI patients and healthy controls, whereas enteral nutrition was associated with smaller differences (p < 0.05).

CONCLUSIONS:
The microbiome of children with severe TBI is characterized by early depletion of commensal bacteria, loss of site specificity, and an enrichment of potential pathogens. Additional studies are needed to determine the impact of these changes on clinical outcomes.
Social Influences on Perceptions of Sense of Control and Attributed Dignity Among Older People Managing Multiple Chronic Conditions
Authors: LeBlanc Raeann G. , Jacelon Cynthia S. 
Published: March 2022

Abstract

Purpose
The aim of this study was to explore associations between social support, sense of control, and attributed dignity in persons aged 65 years and older who self-manage multiple chronic conditions while living in the community.

Design
A descriptive, nonexperimental, correlational design was used in this study.

Methods
Eighty-nine participants completed telephone surveys that measured social support, sense of control and attributed dignity. Regression analysis was used to identify associations.

Results
Participants were independent in seven of the eight instrumental activities of daily living, with participants having an average of 11 (±4) chronic conditions. Significant positive relationships between social support, perceived sense of control, and attributed dignity were identified.

Conclusions
Positive social support is strongly associated with perceived sense of control and attributed dignity.

Clinical Relevance
Healthcare professionals, especially rehabilitation nurses, can assess social support and offer ways to improve social support, thus enhancing sense of control and attributed dignity. These concepts enhance older individuals’ ability to manage multiple chronic conditions.
The expanding role of synthetic nucleic acids for diagnosis and treatment
Authors: Arinuma Yoshiyuki 
Published: March 2022

Purpose of review
The presence of autoantibodies is a characteristic and diagnostic index of systemic lupus erythematosus (SLE). Antidouble-stranded DNA (antids-DNA) antibodies are the most frequent autoantibodies found in SLE related to the diagnosis and disease activity of SLE, and are measured by established methods like ELISA as a polyclonal autoantibody. However, there is no reliable data on the relationship between the respective reactivity of these polyclonal antids-DNA antibodies against different epitopes generated from the original antigen and the disease phenotype. Of the complications in SLE, neuropsychiatric SLE (NPSLE) is a troublesome and frequent phenotype of the disease but no specific diagnostic autoantibodies in serum have been found. First in this review, the possibility of antids-DNA antibodies for identifying primary NPSLE in patients with SLE based on the reactivity of different synthetic nucleic acids is described as a diagnostic marker. The purpose of this review is to examine diagnostic and therapeutic opportunities to modulate autoimmune in the central nervous system (CNS) developing the CNS inflammatory disorders.

Recent findings
Khatri et al. investigated antids-DNA antibodies in order to develop a reliable method based on the application of synthetic nucleic acids and protein-based antigen arrays to characterize autoreactive antibodies specially for NPSLE. They found autoantibodies in three particular synthetic double stranded antigens and the antinuclear antibody patterns in ordinary lupus and NPSLE. These discoveries are leading to precision medicine in the CNS inflammatory disorders.

Summary
Verifying the similarity of antids-DNA obtained from patients with NPSLE can be useful as a diagnostic marker. mRNA vaccination can locally suppress autoimmunity in the CNS associated with critical steps for the develop of CNS autoinflammation. Synthetic nuclei acids may provide a diagnostic and therapeutic target in patients with autoimmune CNS inflammatory disorders.
Disrupted default mode network and executive control network are associated with depression severity on structural network
Authors: He Mengxin , Cheng Yuqi , Chu Zhaosong , Xu Jinlei , Lu Yi , Shen Zonglin , Xu Xiufeng 
Published: March 2022

Objective
Major depressive disorder (MDD) is a psychiatric disorder with a relatively limited response to treatment. It is necessary to better understand the neuroanatomical mechanisms of structural networks.

Methods
The current study recruited 181 first-onset, untreated adult MDD patients: slight MDD (SD, N = 23), moderate MDD (MD, N = 77), Heavy MDD (HD, N = 81) groups; along with a healthy control group (HC, N = 81) with matched general clinical data. FreeSurfer was used to preprocess T1 images for gray matter volume (GMV), and the default mode network (DMN) and the execution control network (ECN) were analyzed by structural covariance network (SCN).

Results
Present study found that the GMV of brain regions reduced with the severity of the disease. Specifically, the GMV of the left anterior cingulate gyrus (ACC.L) is negatively correlated with MDD severity. In addition, the SCN connectivity of the whole-brain network increases with the increase of severity in MDD. ACC.L is a key brain region with increased connectivity between the left orbitofrontal in DMN and between the right orbitofrontal in ECN, which leads to damage to the balance of neural circuits.

Conclusions
Patients with smaller GMV of ACC.L are more likely to develop severe MDD, and as a key region in both networks which have distinct structural network models in DMN and ECN. MDD patients with different severity have different neuroimaging changes in DMN and ECN.
“I wanna live and not think about the future” What place for advance care planning for people living with severe multiple sclerosis and their families? A qualitative study
Authors: Koffman Jonathan , Penfold Clarissa , Cottrell Laura , Farsides Bobbie , Evans Catherine J , Burman Rachel , Nicholas Richard , Ashford Stephen , Silber Eli 
Published: March 2022

ABSTRACTBackgroundLittle is known about how people with multiple sclerosis and their families comprehend advance care planning (ACP) and its relevance in their lives.AimTo explore under what situations, with whom, how, and why do people with MS and their families engage in ACPMethodsWe conducted a qualitative study comprising interviews with people living with MS and their families followed by an ethical discussion group with five health professionals representing specialties working with people affected by MS and their families. Twenty-seven people with MS and 17 family members were interviewed between June 2019 and March 2020. Interviews and the ethical discussion group were audio-recorded and transcribed verbatim. Data were analysed using the framework approach.ResultsParticipants’ narratives focused on three major themes :(i) planning for an uncertain future; (ii) perceived obstacles to engaging in ACP that included uncertainty concerning MS disease progression, negative previous experiences of ACP discussions and prioritising symptom management over future planning; (iii) Preferences for engagement in ACP included a trusting relationship with a health professional and that information then be shared across services. Health professionals accounts from the ethical discussion group departed from viewing ACP as a formal document to that of an ongoing process of seeking preferences and values. They voiced similar concerns to people with MS about uncertainty and when to initiate discussions. Some shared concerns of a lack of confidence when having ACP discussions.ConclusionThese findings support the need for a whole systems strategic approach where information about the potential benefits of ACP in all its forms can be shared with people with MS. Moreover, they highlight the need for health professionals to be skilled and trained in engaging in ACP discussions and where information is contemporaneously and seamlessly shared across services.
On the normative advantages of dopamine and striatal opponency for learning and choice
Authors: Jaskir Alana , Frank Michael J 
Published: March 2022

AbstractThe basal ganglia (BG) contribute to reward-driven behavior, but it is unclear why such behavior should rely on notoriously complex circuitry involving opponent striatal pathways. Dopamine (DA) nonlinearly modulates activity and plasticity in the BG and is itself dynamically modulated across tasks. We develop the OpAL* model to assess the normative advantages of such circuitry. In OpAL*, dynamic DA modulation differentially amplifies the striatal pathway most tuned to the accumulated history of positive or negative outcomes. This efficient coding mechanism avoids a vexing explore-exploit tradeoff that plagues traditional RL models in sparse reward environments. OpAL* exhibits robust advantages over alternative models across a range of environments, particularly with sparse reward. These advantages depend on opponent and nonlinear Hebbian plasticity mechanisms previously thought to be pathological. Finally, OpAL* captures risky choice patterns arising from DA and environmental manipulations across species, suggesting that they result from a normative biological mechanism.Everybody wants the most they can possibly getFor the least they can possibly do– Todd Snider, “Easy Money”
Clinical interpretation of machine learning models for prediction of diabetic complications using electronic health records
Authors: Momenzadeh Amanda , Shamsa Ali , Meyer Jesse G. 
Published: March 2022

AbstractType 2 diabetes is a massive public health issue that continues to grow. The rate of diabetic complication progression varies across individuals. Understanding factors that alter the rate of complication onset may uncover new clinical interventions and help prioritize individuals for more aggressive management. Here, we explore how various machine learning models and types of electronic health records can predict fast versus slow diabetic complication onset using only patient data prior to diabetes diagnosis. We find that optimized random forests generally perform best among the tested models and combining all data sources yields the best predictive performance. A key differentiator of our study is our model interpretation, which identifies specific patient metrics from each dataset that play a unique role in the progression of each complication. Overall, our clinical interpretation of machine learning models can identify patients at risk for poorer outcomes years in advance of their diabetic complication.
Biomedical consequences of elevated cholesterol-containing lipoproteins and apolipoproteins
Authors: Schmidt AF , Joshi R , Gordillo-Marañón M , Drenos F , Charoen P , Giambartolomei C , Bis JC , Gaunt TR , Hughes AD , Lawlor DA , Wong A , Price JF , Chaturvedi N , Wannamethee G , Franceschini N , Kivimaki M , Hingorani AD , Finan C 
Published: March 2022

AbstractAimsTo provide a comprehensive evaluation of the biomedical effects of circulating concentrations of cholesterol-containing lipoproteins and apolipoproteins.Methods and ResultsNuclear magnetic resonance (NMR) spectroscopy was used to measure the cholesterol content of high density (HDL-C), very low-density (VLDL-C), intermediate-density (IDL-C), and low-density (LDL-C) lipoprotein fractions; apolipoproteins Apo-A1 and Apo-B; as well as total triglycerides (TG), remnant-cholesterol (Rem-chol) and total cholesterol (TC). The causal effects of these exposures were assessed against 33 cardiovascular as well as non-cardiovascular outcomes using two-sample univariable and multivariable Mendelian randomization. We observed that most cholesterol containing lipoproteins and apolipoproteins affected coronary heart disease (CHD), cIMT, carotid plaque, CRP and blood pressure. Through MVMR we showed that many of these exposures acted independently of the more commonly measured blood lipids: HDL-C, LDL-C and TG. We furthermore found that HF risk was increased by higher concentrations of TG, VLDL-C, Rem-Chol and Apo-B, often independently of LDL-C, HDL-C or TG. Finally, a smaller subset of these exposures could be robustly mapped to non-CVD traits such as Alzheimer’s disease (HDL-C, LDL-C, IDL-C, Apo-B), type 2 diabetes (VLDL-C, IDL-C, LDL-C), and inflammatory bowel disease (LDL-C, IDL-C).ConclusionThe cholesterol content of a wide range of lipoprotein and apolipoproteins affected measures of atherosclerosis and CHD, implicating subfractions beyond LDL-C. Many of the observed effects acted independently of LDL-C, HDL-C, and TG, supporting the potential for additional, non-LDL-C, avenues to disease prevention.
International travel as a risk factor for carriage of extended-spectrum β-lactamase-producing Escherichia coli in a large sample of European individuals - The AWARE Study
Authors: Rodríguez-Molina Daloha , Berglund Fanny , Blaak Hetty , Flach Carl-Fredrik , Kemper Merel , Marutescu Luminita , Gradisteanu Gratiela Pircalabioru , Popa Marcela , Spießberger Beate , Wengenroth Laura , Chifiriuc Mariana Carmen , Larsson D. G. Joakim , Nowak Dennis , Radon Katja , de Roda Husman Ana Maria , Wieser Andreas , Schmitt Heike 
Published: March 2022

AbstractAntibiotic resistance (AR) is currently a major threat to global health, calling for a One Health approach to be properly understood, monitored, tackled, and managed. Potential risk factors for AR are often studied in specific high-risk populations, but are still poorly understood in the general population. Our aim was to explore, describe, and characterize potential risk factors for carriage of Extended-Spectrum Beta-Lactamase-resistant E. coli (ESBL-EC) in a large sample of European individuals aged between 16 and 67 years recruited from the general population in Southern Germany, the Netherlands, and Romania. Questionnaire and stool sample collection for this cross-sectional study took place from September 2018 to March 2020. Selective culture of participants’ stool samples was performed for detection of ESBL-EC. A total of 1,183 participants were included in the analyses: 333 from Germany, 689 from the Netherlands, and 161 from Romania. Travels to Northern Africa (aOR 4.03, 95% CI 1.67-9.68), Sub-Saharan Africa (aOR 4.60, 95% CI 1.60-13.26), and Asia (aOR 4.08, 95% CI 1.97-8.43) were identified as independent risk factors for carriage of ESBL-EC carriage. Therefore, travel to these regions should continue to be routinely inquired risk factors in clinical practice when considering antibiotic therapy.
OncoPubMiner: A platform for oncology publication mining
Authors: Xu Quan , Liu Yueyue , Sun Dawei , Hu Jifang , Duan Xiaohong , Song Niuben , Zhou Jiale , Su Junyan , Liu Siyao , Chen Fan , Guo Zhongjia , Li Hexiang , Zhou Qiming , Niu Beifang 
Published: March 2022

ABSTRACTKnowledge bases that are up-to-date and of expert quality are fundamental in biomedical research fields. A knowledge base established with human participation and subjected to multiple inspections is crucial for supporting clinical decision-making, especially in the exponentially growing field of precision oncology. The number of original publications in the field has skyrocketed with the advancement of technology and in-depth research evolved. It has become an increasingly pressing issue that researchers need to consider how to gather and mine these articles accurately and efficiently. In this paper, we present OncoPubMiner (https://oncopubminer.chosenmedinfo.com), a free and powerful system that combines text mining, data structure customization, publication search with online reading, project-centered and team-based data collection to realize a one-stop “keyword in, knowledge out” oncology publication mining platform. It was built by integrating all the open-access abstracts from PubMed and full-text articles from PubMed Central, and is updated on a daily basis. The system makes it straightforward to obtain precision oncology knowledge from scientific articles. OncoPubMiner will assist researchers in developing professional structured knowledge base systems efficiently, and bringing the oncology community closer to achieving precision oncology goals.Graphical AbstractOncoPubMiner’s one-stop “keyword in, knowledge out” workflow (A) is built on key features such as text mining (B), publication search (C), form customization (D), and team-based curation (E).
PRState: Incorporating Genetic Ancestry in Prostate Cancer Risk scores for African American Men
Authors: Pagadala Meghana S. , Linscott Joshua A. , Talwar James , Seibert Tyler , Rose Brent , Lynch Julie , Panizzon Matthew , Hauger Richard , Hansen Moritz H. , Sammon Jesse D. , Hayn Matthew H , Kader Karim , Carter Hannah , Ryan Stephen T. 
Published: March 2022

AbstractProstate cancer (PrCa) is one of the most genetically driven solid cancers with heritability estimates as high as 57%. African American men are at an increased risk of PrCa; however, current risk prediction models are based on European ancestry groups and may not be broadly applicable. In this study, we define an African ancestry group of 4,533 individuals to develop an African ancestry-specific PrCa polygenic risk score (PRState). We identified risk loci on chromosomes 3, 8, and 11 in the African ancestry group GWAS and constructed a polygenic risk score (PRS) from 10 African ancestry-specific PrCa risk SNPs, achieving an AUC of 0.61 [0.60-0.63] and 0.65 [0.64-0.67], when combined with age and family history. Performance dropped significantly when using ancestry-mismatched PRS models but remained comparable when using trans-ancestry models. Importantly, we validated the PRState score in the Million Veteran Program, demonstrating improved prediction of PrCa and metastatic PrCa in African American individuals. This study underscores the need for inclusion of individuals of African ancestry in gene variant discovery to optimize PRS.
Integrative genomics analysis implicates decreased FGD6 expression underlying risk of intracranial aneurysm rupture
Authors: Hale Andrew T. , He Jing , Jones Jesse 
Published: March 2022

AbstractBackgroundThe genetic determinants and mechanisms underlying intracranial aneurysm rupture (rIA) are largely unknown. Given the ∼50% mortality rate of rIA, approaches to identify patients at high-risk will inform screening, diagnostic, and preventative measures.ObjectiveOur goal was to identify and characterize the genetic basis of rIA.MethodsWe perform a genome-wide association study (GWAS) use functional genomics approaches to identify and characterize rIA-associated loci and genes. We perform a meta-analysis across 24 published GWAS of rIA. Single nucleotide polymorphisms (SNP), gene-burden analysis, and functional genomics identify and characterize genetic risk factors for rIA.ResultsOur cohort contains 84,353 individuals (7,843 rIA cases and 76,510 controls). We identify 5 independent genetic loci reaching genome-wide significance (p<5.0×10−8) for rIA including rs12310399 (FGD6, OR=1.16), which to our knowledge, has not been implicated in prior GWAS of rIA. We then quantified gene-level mutation-burden across ∼20,000 genes, and only FGD6 (containing 21 rIA-associated SNPs) reached transcriptome-wide significance. Expression quantitative trait loci (eQTL) mapping indicates that rs12310399 causes decreased FGD6 gene expression in arterial tissue. Next, we utilized publicly available single-cell RNA sequencing of normal human cerebrovascular cells obtained during resection surgery and identify high expression of FGD6 in 1 of 3 arterial lineages but absent in perivascular cells. These data suggest how alterations in FGD6 may confer risk to rIA.ConclusionWe identify and characterize a previously unknown risk loci for rIA containing FGD6. Elucidation of high-risk genetic loci may instruct population-genetic screening and clinical-genetic testing strategies to identify patients predisposed to rIA.FundingNo funding sources were used for the material presented herein.
Detection of COVID-19 and age-dependent dysosmia with paired crushable odorant ampules
Authors: Wood Ronald W. , Stodgell Christopher J , Linder Mitchell A. , Pressman Eva K. 
Published: March 2022

AbstractBackgroundSigns of anosmia can help detect COVID-19 infection when testing for viral positivity is not available. Inexpensive mass-produced disposable olfactory sensitivity tests suitable for worldwide use might serve not only as a screening tool for potential infection but also to identify cases at elevated risk of severe disease as anosmic COVID-19 patients have a better prognosis.Methods and FindingsWe adopted paired crushable ampules with two concentrations of a standard test odorant (n-butanol) as standard of care in several clinics as community prevalence of COVID-19 infection waxed and waned. This was not a clinical trial; a chart review was undertaken to evaluate the operating characteristics and potential utility of the test device as RT-PCR testing became routine. The risk of anosmia was greater in COVID-19 patients. Olfactory sensitivity was concentration-dependent, decreased with aging, and was sex-dependent at the highest concentration. Hyposmia was detected across a wider age range than expected from the literature, and tests can be optimized to characterize different age groups.Conclusionsn-Butanol at 0.32 and 3.2% in crushable ampules can be used to characterize olfactory function quickly and inexpensively and thus has potential benefits in pandemic screening, epidemiology, and clinical decision-making.