bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic phenotype of B cells from young and elderly HIV individuals
Authors: Frasca Daniela , Pallikkuth Suresh , Pahwa Savita 
Published: August 2021

Abstract
Background
HIV infection induces inflammaging and chronic immune activation (IA), which are negatively associated with protective humoral immunity. Similar to HIV, aging is also associated with increased inflammaging and IA. The metabolic requirements of B cell responses in HIV infected (HIV+) individuals are not known, although metabolic abnormalities have been reported in these individuals. How these metabolic abnormalities are exacerbated by aging is also not known.

Methods
B cells were isolated by magnetic sorting from the blood of young and elderly HIV + individuals, as well as from the blood of age-matched healthy controls. We evaluated the composition of the B cell pool by flow cytometry, the expression of RNA for pro-inflammatory and metabolic markers by qPCR and their metabolic status using a Seahorse XFp extracellular flux analyzer.

Results
In this study we have evaluated for the first time the metabolic phenotype of B cells from young and elderly HIV + individuals as compared to those obtained from age-matched healthy controls. Results show that the B cell pool of HIV + individuals is enriched in pro-inflammatory B cell subsets, expresses higher levels of RNA for pro-inflammatory markers and is hyper-metabolic, as compared to healthy controls, and more in elderly versus young HIV + individuals, suggesting that this higher metabolic phenotype of B cells is needed to support B cell IA. We have identified the subset of Double Negative (DN) B cells as the subset mainly responsible for this hyper-inflammatory and hyper-metabolic profile.

Conclusions
Our results identify a relationship between intrinsic B cell inflammation and metabolism in HIV + individuals and suggest that metabolic pathways in B cells from HIV + individuals may be targeted to reduce inflammaging and IA and improve B cell function and antibody responses.
The impact of visuospatial perception on distance judgment and depth perception in an Augmented Reality environment in patients after stroke: an exploratory study
Authors: Höhler Chiara , Rasamoel Nils David , Rohrbach Nina , Hansen John Paulin , Jahn Klaus , Hermsdörfer Joachim , Krewer Carmen 
Published: August 2021

AbstractBackgroundAugmented Reality (AR)-based interventions are applied in neurorehabilitation with increasing frequency. Depth perception is required for the intended interaction within AR environments. Until now, however, it is unclear whether patients after stroke with impaired visuospatial perception (VSP) are able to perceive depth in the AR environment.MethodsDifferent aspects of VSP (stereovision and spatial localization/visuoconstruction) were assessed in 20 patients after stroke (mean age: 64 ± 14 years) and 20 healthy subjects (HS, mean age: 28 ± 8 years) using clinical tests. The group of HS was recruited to assess the validity of the developed AR tasks in testing stereovision. To measure perception of holographic objects, three distance judgment tasks and one three-dimensionality task were designed. The effect of impaired stereovision on performance in each AR task was analyzed. AR task performance was modeled by aspects of VSP using separate regression analyses for HS and for patients.ResultsIn HS, stereovision had a significant effect on the performance in all AR distance judgment tasks (p = 0.021,p = 0.002,p = 0.046) and in the three-dimensionality task (p = 0.003). Individual quality of stereovision significantly predicted the accuracy in each distance judgment task and was highly related to the ability to perceive holograms as three-dimensional (p = 0.001). In stroke-survivors, impaired stereovision had a specific deterioration effect on only one distance judgment task (p = 0.042), whereas the three-dimensionality task was unaffected (p = 0.317). Regression analyses confirmed a lacking impact of patients’ quality of stereovision on AR task performance, while spatial localization/visuoconstruction significantly prognosticated the accuracy in distance estimation of geometric objects in two AR tasks.ConclusionImpairments in VSP reduce the ability to estimate distance and to perceive three-dimensionality in an AR environment. While stereovision is key for task performance in HS, spatial localization/visuoconstruction is predominant in patients. Since impairments in VSP are present after stroke, these findings might be crucial when AR is applied for neurorehabilitative treatment. In order to maximize the therapy outcome, the design of AR games should be adapted to patients’ impaired VSP. Trial registration: The trial was not registered, as it was an observational study.
Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population
Authors: Lu Wenqian , Luo Mingjuan , Fang Xiangnan , Zhang Rong , Li Shanshan , Tang Mengyang , Yu Xiangtian , Hu Cheng 
Published: August 2021

Abstract
Background
Gestational diabetes mellitus (GDM), one of the most common pregnancy complications, can lead to morbidity and mortality in both the mother and the infant. Metabolomics has provided new insights into the pathology of GDM and systemic analysis of GDM with metabolites is required for providing more clues for GDM diagnosis and mechanism research. This study aims to reveal metabolic differences between normal pregnant women and GDM patients in the second- and third-trimester stages and to confirm the clinical relevance of these new findings.

Methods
Metabolites were quantitated with the serum samples of 200 healthy pregnant women and 200 GDM women in the second trimester, 199 normal controls, and 199 GDM patients in the third trimester. Both function and pathway analyses were applied to explore biological roles involved in the two sets of metabolites. Then the trimester stage-specific GDM metabolite biomarkers were identified by combining machine learning approaches, and the logistic regression models were constructed to evaluate predictive efficiency. Finally, the weighted gene co-expression network analysis method was used to further capture the associations between metabolite modules with biomarkers and clinical indices.

Results
This study revealed that 57 differentially expressed metabolites (DEMs) were discovered in the second-trimester group, among which the most significant one was 3-methyl-2-oxovaleric acid. Similarly, 72 DEMs were found in the third-trimester group, and the most significant metabolites were ketoleucine and alpha-ketoisovaleric acid. These DEMs were mainly involved in the metabolism pathway of amino acids, fatty acids and bile acids. The logistic regression models for selected metabolite biomarkers achieved the area under the curve values of 0.807 and 0.81 for the second- and third-trimester groups. Furthermore, significant associations were found between DEMs/biomarkers and GDM-related indices.

Conclusions
Metabolic differences between healthy pregnant women and GDM patients were found. Associations between biomarkers and clinical indices were also investigated, which may provide insights into pathology of GDM.
In-flight transmission of wild-type SARS-CoV-2 and the outbreak potential of imported clusters of COVID-19: a review of published evidence
Authors: Kelly David , Bambury Niamh , Boland Mairin 
Published: August 2021

Abstract
International air travel has been highlighted as a concern since the beginning of the COVID-19 pandemic with respect to importation of cases. We summarise the available evidence for in-flight transmission of wild type SARS-CoV-2 during 2020, and for imported COVID-19 clusters to cause outbreaks. This paper provides a data baseline prior to the emergence of new mutations causing SARS-CoV-2 variants of concern, whose characteristics may increase the potential risk of in-flight transmission and imported outbreaks. The evidence on in-flight transmission of wild-type SARS-CoV-2 is limited, and is described in a small number of published reports. Most of the available evidence pertains to the early phase of the COVID-19 pandemic, during a period without non-pharmaceutical interventions such as distancing and in-flight mask wearing. There is considerable potential for outbreaks of COVID-19 from imported cases or clusters when public health guidance around quarantine of travellers and self-isolation of cases is not adhered to. Risks can be mitigated by measures such as: avoiding non-essential travel, targeted testing and quarantine of travellers from high incidence regions or regions of concern, managed quarantine processes, and protocols for rapid investigation and control of transmission from a possible variant of concern. Measures should be dynamically assessed and proportionate to the level of risk.

Graphical abstract
WHO/ISUP grading of clear cell renal cell carcinoma and papillary renal cell carcinoma; validation of grading on the digital pathology platform and perspectives on reproducibility of grade
Authors: Browning Lisa , Colling Richard , Verrill Clare 
Published: August 2021

Abstract
Background
There are recognised potential pitfalls in digital diagnosis in urological pathology, including the grading of dysplasia. The World Health Organisation/International Society of Urological Pathology (WHO/ISUP) grading system for renal cell carcinoma (RCC) is prognostically important in clear cell RCC (CCRCC) and papillary RCC (PRCC), and is included in risk stratification scores for CCRCC, thus impacting on patient management. To date there are no systematic studies examining the concordance of WHO/ISUP grading between digital pathology (DP) and glass slide (GS) images. We present a validation study examining intraobserver agreement in WHO/ISUP grade of CCRCC and PRCC.

Methods
Fifty CCRCCs and 10 PRCCs were graded (WHO/ISUP system) by three specialist uropathologists on three separate occasions (DP once then two GS assessments; GS1 and GS2) separated by wash-out periods of at least two-weeks. The grade was recorded for each assessment, and compared using Cohen’s and Fleiss’s kappa.

Results
There was 65 to 78% concordance of WHO/ISUP grading on DP and GS1. Furthermore, for the individual pathologists, the comparative kappa scores for DP versus GS1, and GS1 versus GS2, were 0.70 and 0.70, 0.57 and 0.73, and 0.71 and 0.74, and with no apparent tendency to upgrade or downgrade on DP versus GS. The interobserver kappa agreement was less, at 0.58 on DP and 0.45 on GS.

Conclusion
Our results demonstrate that the assessment of WHO/ISUP grade on DP is noninferior to that on GS. There is an apparent slight improvement in agreement between pathologists on RCC grade when assessed on DP, which may warrant further study.
Naloxone availability in independent community pharmacies in Georgia, 2019
Authors: Gilbert Lauren , Elliott Jennifer , Beasley Lauren , Oranu Ekene , Roth Kimberly , Nguyễn Jennifer 
Published: August 2021

Abstract
Background
Increasing the availability of naloxone among people who use opioids, and friends and family of past and present people who use opioids is a vitally important mission to reduce the occurrence of opioid-related overdose deaths. The purpose of this study was to determine the availability of naloxone in independent community pharmacies in Georgia. Secondary objectives include determining pharmacists’ knowledge regarding the standing order and ability to counsel regarding naloxone.

Methods
A cross-sectional study using a secret shopper approach with phone contact was conducted over a period of 10 months. The study was population based and was conducted at all independent pharmacies in the state of Georgia. All independent community pharmacies in the state of Georgia were contacted and asked the naloxone questions with a 96% response rate (n = 520).

Results
Five hundred fifty-eight independent community pharmacies were called, with a 96% response rate (n = 520 pharmacies). Two hundred-twenty pharmacies reported having naloxone in stock. Of the 335 pharmacists asked, 174 (51.9%) incorrectly said that a prescription was required. The mean (SD) cash price was $148.02 (27.40), with a range of $0 to $300. Of 237 pharmacists asked who had naloxone in stock or who stated they could get naloxone in stock, 212 stated that they could demonstrate how to use it, 8 stated they could not, and 17 said that they possibly could or were unsure how to use it.

Conclusions
This study provided insight into the limited availability of naloxone at independent community pharmacies in Georgia after the standing order was issued. The majority of pharmacists at independent pharmacies in Georgia were not using the publicly available state naloxone standing order. Additionally, the low availability of naloxone and its high cost for uninsured individuals are significant structural barriers for reducing opioid-related mortality.
Nomogram to predict collapse-free survival after core decompression of nontraumatic osteonecrosis of the femoral head
Authors: Zhao En-Ze , Liu Zun-Han , Zeng Wei-Nan , Ding Zi-Chuan , Luo Zhen-Yu , Zhou Zong-Ke 
Published: August 2021

AbstractBackgroundNontraumatic osteonecrosis of the femoral head (NONFH) is a devastating disease, and the risk factors associated with progression into collapse after core decompression (CD) remain poorly defined. Therefore, we aim to define risk factors associated with collapse-free survival (CFS) after CD of precollapse NONFH and to propose a nomogram for individual risk prediction.MethodsAccording to the baseline characteristics, clinical information, radiographic evaluations, and laboratory examination, a nomogram was developed using a single institutional cohort of patients who received multiple drilling for precollapse NONFH between January 2007 and December 2019 to predict CFS after CD of precollapse NONFH. Furthermore, we usedCstatistics, calibration plot, and Kaplan-Meier curve to test the discriminative ability and calibration of the nomogram to predict CFS.ResultsOne hundred and seventy-three patients who underwent CD for precollapse NONFH were retrospectively screened and included in the present study. Using a multiple Cox regression to identify relevant risk factors, the following risk factors were incorporated in the prediction of CFS: acute onset of symptom (HR, 2.78; 95% CI, 1.03–7.48;P= 0.043), necrotic location of Japanese Investigation Committee (JIC) C1 and C2 (HR, 3.67; 95% CI, 1.20–11.27;P= 0.023), necrotic angle in the range of 250–299°(HR, 5.08; 95% CI, 1.73–14.93;P= 0.003) and > 299° (HR, 9.96; 95% CI, 3.23–30.70;P< 0.001), and bone marrow edema (BME) before CD (HR, 2.03; 95% CI, 1.02-4.02;P= 0.042). TheCstatistics was 0.82 for CFS which revealed good discriminative ability and calibration of the nomogram.ConclusionsIndependent predictors of progression into collapse after CD for precollapse NONFH were identified to develop a nomogram predicting CFS. In addition, the nomogram could divide precollapse NONFH patients into prognosis groups and performed well in internal validation.
Atypical and rare cause of myocardial infarction: coronary subclavian steal syndrome (CSSS) treated by a carotid-subclavian bypass in a 71-year-old female patient
Authors: Walensi Mikolaj , Bernheim Johannes , Ulatowski Nikodemus , Piotrowski Michal , Karaindros Konstantinos , Juntermanns Benjamin , Mikat Christian , Heesen Roland , Hoffmann Johannes N. 
Published: August 2021

Abstract
Background
The coronary subclavian steal syndrome (CSSS) is a rare complication after coronary arterial bypass graft operations (CABG) using the left or right internal mammary artery ((L/R)IMA). It results from a retrograde blood flow from the IMA into the subclavian artery (SA) due to a stenosis or occlusion of the SA proximal to the IMA origin. This “steal phenomenon” leads to a decreased blood flow in the IMA and may result in myocardial ischemia (MIS) and even myocardial infarction (MIN). Treatment options include interventional and surgical therapy.

Case presentation
We report the case of a 71-year old woman, who suffered from an acute non-ST elevation myocardial infarction (NSTEMI) 11 years after LIMA-CABG surgery and who was treated successfully with a carotid-subclavian bypass (CSB) after failed interventional therapy.

Conclusion
CSB may be regarded as a viable treatment option for patients suffering CSSS in the case of MIS and even an acute MIN/NSTEMI, especially in the case of missing or failed interventional therapy attempts. Specialists in cardiothoracic and vascular surgery should be aware of possible CSSS conditions and know about appropriate diagnostic and therapeutic options.
Two large-scale forest scenario modelling approaches for reporting CO2 removal: a comparison for the Romanian forests
Authors: Blujdea Viorel N. B. , Sikkema Richard , Dutca Ioan , Nabuurs Gert-Jan 
Published: August 2021

AbstractBackgroundForest carbon models are recognized as suitable tools for the reporting and verification of forest carbon stock and stock change, as well as for evaluating the forest management options to enhance the carbon sink provided by sustainable forestry. However, given their increased complexity and data availability, different models may simulate different estimates. Here, we compare carbon estimates for Romanian forests as simulated by two models (CBM and EFISCEN) that are often used for evaluating the mitigation options given the forest-management choices.ResultsThe models, calibrated and parameterized with identical or harmonized data, derived from two successive national forest inventories, produced similar estimates of carbon accumulation in tree biomass. According to CBM simulations of carbon stocks in Romanian forests, by 2060, the merchantable standing stock volume will reach an average of 377 m3 ha−1, while the carbon stock in tree biomass will reach 76.5 tC ha−1. The EFISCEN simulations produced estimates that are about 5% and 10%, respectively, lower. In addition, 10% stronger biomass sink was simulated by CBM, whereby the difference reduced over time, amounting to only 3% toward 2060.ConclusionsThis model comparison provided valuable insights on both the conceptual and modelling algorithms, as well as how the quality of the input data may affect calibration and projections of the stock and stock change in the living biomass pool. In our judgement, both models performed well, providing internally consistent results. Therefore, we underline the importance of the input data quality and the need for further data sampling and model improvements, while the preference for one model or the other should be based on the availability and suitability of the required data, on preferred output variables and ease of use.
The impact of a community based rehabilitation program in Afghanistan: a longitudinal analysis using propensity score matching and difference in difference analysis
Authors: Trani Jean-Francois , Vasquez-Escallon Juanita , Bakhshi Parul 
Published: August 2021

Abstract
Background
The 2006 United Nations Convention on the Rights of Persons with Disabilities states that the achievement of equal rights, empowerment and social inclusion of people with disabilities requires comprehensive rehabilitation services encompassing all components of the World Health Organization Community based rehabilitation (CBR) matrix: health, education, livelihood, social and empowerment. CBR programs specifically aim to deliver such comprehensive interventions. In the present study, we investigate the impact of a CBR program in Afghanistan on all these components.

Methods
We enrolled 1861 newly recruited CBR participants with disabilities in the study, from 169 villages between July 2012 and December 2013 as well as 1132 controls with disabilities randomly selected through a two-stage process within 6000 households from 100 villages in the same provinces but outside the catchment area of the CBR program. We interviewed them again after one (midline) and two (end-line) years in the study. Using propensity score matching and difference in difference analysis, we estimated the impact of the CBR on outcomes of interest, namely mobility, activities of daily living, communication, participation in social and community life, emotional well-being and employment.

Results
Three years on average into the CBR program, participants showed a significant and close to medium effect size reduction in emotional (Cohen’s d = − 0.48, 95%CI[− 0.58--0.38]), and social participation challenges (Cohen’s d = − 0.45, 95%CI[− 0.53−− 0.36]); small to medium effect size reduction in unemployment (Cohen’s d = − 0.21, 95%CI[− 0.33--0.10]), activities of daily living (Cohen’s d = − 0.26, 95%CI[− 0.35--0.18]), mobility (Cohen’s d = − 0.36, 95%CI[− 0.44--.29]) and communication challenges (Cohen’s d = − 0.38, 95%CI[− 0.46--0.3]).

Conclusions
Our study indicates that a CBR program may provide positive rehabilitation outcomes for persons with disabilities even in a conflict context, and improve overall well-being of all participants with disabilities, whatever their impairment, individual characteristics and the CBR matrix components considered.

Trial registration
ISRCTN, ISRCTN50214054. Registered August 5th 2020 - retrospectively registered
Comparison of 16S and whole genome dog microbiomes using machine learning
Authors: Lewis Scott , Nash Andrea , Li Qinghong , Ahn Tae-Hyuk 
Published: August 2021

Abstract
Background
Recent advances in sequencing technologies have driven studies identifying the microbiome as a key regulator of overall health and disease in the host. Both 16S amplicon and whole genome shotgun sequencing technologies are currently being used to investigate this relationship, however, the choice of sequencing technology often depends on the nature and experimental design of the study. In principle, the outputs rendered by analysis pipelines are heavily influenced by the data used as input; it is then important to consider that the genomic features produced by different sequencing technologies may emphasize different results.

Results
In this work, we use public 16S amplicon and whole genome shotgun sequencing (WGS) data from the same dogs to investigate the relationship between sequencing technology and the captured gut metagenomic landscape in dogs. In our analyses, we compare the taxonomic resolution at the species and phyla levels and benchmark 12 classification algorithms in their ability to accurately identify host phenotype using only taxonomic relative abundance information from 16S and WGS datasets with identical study designs. Our best performing model, a random forest trained by the WGS dataset, identified a species (Bacteroides coprocola) that predominantly contributes to the abundance of leuB, a gene involved in branched chain amino acid biosynthesis; a risk factor for glucose intolerance, insulin resistance, and type 2 diabetes. This trend was not conserved when we trained the model using 16S sequencing profiles from the same dogs.

Conclusions
Our results indicate that WGS sequencing of dog microbiomes detects a greater taxonomic diversity than 16S sequencing of the same dogs at the species level and with respect to four gut-enriched phyla levels. This difference in detection does not significantly impact the performance metrics of machine learning algorithms after down-sampling. Although the important features extracted from our best performing model are not conserved between the two technologies, the important features extracted from either instance indicate the utility of machine learning algorithms in identifying biologically meaningful relationships between the host and microbiome community members. In conclusion, this work provides the first systematic machine learning comparison of dog 16S and WGS microbiomes derived from identical study designs.