bluuebunny/crossref_metadata_2025 huggingface dataset:
Noninvasive Hemoglobin Monitoring for Postoperative Pediatric Orthopaedic Patients: A Preliminary Study
Authors: Mathew Smitha E. , Pulido Natalie , Larson A. Noelle , Stans Anthony A. , Milbrandt Todd A. , Shaughnessy William J.
Published: July 2022

Background:

Hemoglobin (Hgb) levels are frequently checked through venipuncture [invasive hemoglobin (iHgb)] in pediatric orthopaedic patients after high blood loss procedures. This needlestick may causes further anxiety and fear in hospitalized children. Noninvasive hemoglobin (nHgb) monitoring has been effectively utilized in the adult intensive care and postoperative total joint arthroplasty setting. nHgb monitoring has not yet been validated in children for routine postoperative Hgb assessment in pediatric orthopaedics.

Methods:

In this prospective study, 46 pediatric orthopaedic patients were enrolled who were undergoing surgery and postoperative standard of care iHgb testing. On postoperative day 1, Hgb levels were obtained through venipuncture and nHgb monitor (Pronto-7; Masimo) within a 2-hour period. Patient preferences, iHgb and nHgb values, time to result, and provider preferences were recorded. Cost data were estimated based on the standard Medicare payment rates for lab services versus the cost of nHgb probe.

Results:

nHgb results were obtained after 1 attempt in 38 patients (83%), after multiple attempts in 7 patients (15%), and could not be obtained in 1 patient. The mean time to obtain nHgb value was significantly shorter than that to obtain iHgb results (1.3±1.5 vs. 40±18.1 min; P<0.0001). The mean nHgb value was significantly higher than the mean iHgb value (11.7±1.5 vs. 10.6±1.1 g/dL, P<0.0001). nHgb exceeded iHgb by 2 g/dL or more in 12 (26%) patients (2.64±0.9 vs. 0.54±0.84 g/dL; P<0.0001). The concordance correlation coefficient between the 2 Hgb methods was 0.59, indicating moderate agreement. Forty-three (93%) of our patients and 34 (74%) of the care providers preferred nHgb over iHgb if results were equivalent. At our institution, the cost per iHgb monitoring is approximately $28 per blood draw as compared with $5 for nHgb monitoring. Interestingly, no patients required postoperative transfusion during the study period, as asymptomatic patients with no cardiac disease are typically observed unless the Hgb is <6.

Conclusions:

nHgb monitoring in postoperative pediatric patients overestimated Hgb levels compared with the standard of care methods; however, nHgb had high patient and provider satisfaction and had moderate agreement with iHgb. As no patients required transfusion, postoperative Hgb checks could likely be discontinued in some portion of our population.

Level of Evidence:

Level Ib—Diagnostic study.
Safety, Tolerability, and Effects of a Single Subcutaneous Administration of SP16 – a SERPIN-like, Small Peptide Agonist of the Low-Density Lipoprotein–like Receptor 1– on the Acute Inflammatory Response in Patients With ST-Segment Elevation Myocardial Infarction
Authors: Van Tassell Benjamin W. , Wohlford George F. , Del Buono Marco Giuseppe , Damonte Juan Ignacio , Markley Roshanak , Turlington Jeremy , Kadariya Dinesh , Talasaz Azita , Ho Jane , Marawan Amr , Thomas Georgia K. , Austin Dana , Gineste Cyrille , Gelber Cohava , Abbate Antonio
Published: July 2022

Background:

Modulation of the inflammatory response is a promising therapeutic strategy in acute myocardial infarction. The novel approach is based on the anti-inflammatory and cytoprotective properties mediated by the engagement of the low-density lipoprotein‒related protein 1 (LRP1) receptor. SERPIN peptide 16 (SP16) is a synthetic, selective LRP1 agonist. We herein present the results of a study with a single subcutaneous administration of SP16 in 10 patients with STEMI, to appraise its safety and tolerability and explore the effects on the acute inflammatory response, infarct size, and cardiac function.

Methods:

Ten patients with ST-segment elevation myocardial infarction (STEMI) were enrolled within 12 hours of symptoms onset and 6 hours of percutaneous coronary intervention in a single-center, single-arm, open-label study of a single subcutaneous administration of SP16 (0.2 mg/kg). Serial clinical biomarkers and echocardiography data were collected up to 12 months. The data are presented separately for the treatment group and compared with historical controls from a placebo-treated arm in a recently completed clinical trial (N = 28) with similar enrollment criteria.

Results:

All ten patients with STEMI received subcutaneous administration of SP16, 381 [272–478] minutes after percutaneous coronary intervention, without any treatment-related adverse events. The area under the curve for C-reactive protein was 133 [46–528] mg·d/L in the SP16-treated group versus 286 [141–581] mg·d/L in the historical placebo-treated group (P = 0.161). The area under the curve for creatine kinase–myocardial band was 1432 [675–3089] ng·d/mL in the SP16-treated group versus 2367 [830–4750] ng·d/mL in the historical placebo-treated patients (P = 0.428). Left ventricular ejection fraction was 46% [39–54] at baseline and 51% [46–58] at 1 year follow-up in SP16-treated patients (interval change 5% [−0.3% to +9%] P = 0.05) and 44% [38%–56%] at baseline and 53% [43%–59%] at 1 year follow-up in historical placebo-treated patients (interval change 3% [−5% to 10%], P = 0.305).

Conclusion:

A single subcutaneous administration of SP16, a synthetic targeted LRP1 agonist, was safe and well-tolerated in patients with STEMI. A trend toward reduction in the inflammatory response and infarct size with SP16 was noted; however, the sample size for this study was not based on formal statistical criteria. More extensive studies are planned to determine the clinical efficacy of SP16 in STEMI.

NCT: NCT04225533.
Lipoprotein subfractions and subclinical vascular health in middle aged women: does menopause status matter?
Authors: Qi Meiyuzhen , Chen Xirun , Krauss Ronald M. , Matthews Karen , Janssen Imke , Brooks Maria M. , McConnell Dan , Crawford Sybil L. , El Khoudary Samar R.
Published: July 2022

Objective

During midlife, women experience changes in lipoprotein profiles and deterioration in vascular health measures. We analyzed the associations of groups of lipoprotein subfractions as determined by principal component analysis (PCA) with subclinical vascular health measures in midlife women and tested if these associations were modified by menopause status.

Methods

PCA was used to generate principal components (PCs) from 12 lipoprotein subfractions quantified among 545 midlife women. The associations of the identified PCs and concurrent vascular health measures were assessed using linear or logistic regressions among participants with carotid intima-media thickness (cIMT; n = 259), coronary artery calcium (n = 249), or aortic calcium (n = 248) scores.

Results

PCA generated four PCs representing groups of (1) small, medium, and large very low-density lipoproteins subclasses—very low-density lipoprotein PC; (2) very small, small, and medium low-density lipoprotein (LDL) subclasses—small-medium LDL-PC; (3) large and small high-density lipoproteins subclasses and midzone particles—high-density lipoprotein PC; and (4) large LDL and small intermediate-density lipoproteins—large LDL-PC. Small-medium LDL-PC was positively associated with cIMT, coronary artery calcium, and aortic calcium in unadjusted but not in adjusted models. Menopause status modified the positive association of the small-medium LDL-PC with cIMT (interaction P = 0.02) such that this association was stronger after versus before menopause (P = 0.01).

Conclusions

Carotid intimal medial thickening is positively and independently associated with small- and medium-sized LDL particles after menopause. Monitoring levels of specific lipoprotein fractions may have value in identifying midlife women at risk for developing atherosclerotic vascular disease.
Association between spine injury and opioid misuse in a prospective cohort of Level I trauma patients
Authors: Tilhou Alyssa Shell , Glass Joseph E. , Hetzel Scott J. , Shana Ola Elizabeth , Borza Tudor , Baltes Amelia , Deyo Bri M.F. , Agarwal Suresh , O’Rourke Ann , Brown Randall T.
Published: July 2022

Objective:

To explore patient and treatment factors explaining the association between spine injury and opioid misuse.

Design:

Prospective cohort study.

Setting:

Level I trauma center in a Midwestern city.

Participants:

English speaking patients aged 18 to 75 on Trauma and Orthopedic Surgical Services receiving opioids during hospitalization and prescribed at discharge.

Exposure:

Spine injury on the Abbreviated Injury Scale.

Main outcome measures:

Opioid misuse was defined by using opioids: in a larger dose, more often, or longer than prescribed; via a non-prescribed route; from someone other than a prescriber; and/or use of heroin or opium. Exploratory factor groups included demographic, psychiatric, pain, and treatment factors. Multivariable logistic regression estimated the association between spine injury and opioid misuse when adjusting for each factor group.

Results:

Two hundred eighty-five eligible participants consented of which 258 had baseline injury location data and 224 had follow up opioid misuse data. Most participants were male (67.8%), white (85.3%) and on average 43.1 years old. One-quarter had a spine injury (25.2%). Of those completing follow-up measures, 14 (6.3%) developed misuse. Treatment factors (injury severity, intubation, and hospital length of stay) were significantly associated with spine injury. Spine injury significantly predicted opioid misuse [odds ratio [OR] 3.20, 95% confidence interval [CI] (1.05, 9.78)]. In multivariable models, adjusting for treatment factors attenuated the association between spine injury and opioid misuse, primarily explained by length of stay.

Conclusion:

Spine injury exhibits a complex association with opioid misuse that predominantly operates through treatment factors. Spine injury patients may represent a subpopulation requiring early intervention to prevent opioid misuse.
The prevention of hospital-acquired pressure injuries among adult immobilized patients in a mental health department: a best practice implementation project
Authors: Dobre Claudia E. , Gagiu Corina , Jitianu Dorinela A. , Zazu Mariana , Mazilu Doina C. , Jiménez Marina Gallego
Published: July 2022

Objectives:

The aim of this implementation project was to promote evidence-based practices regarding hospital-acquired pressure injuries prevention practices among immobilized adult patients in a mental health department and to measure the level of compliance with the best practice in this field.

Introduction:

Pressure injuries can have significant restrictions on the patient's quality of life; affect the patient physically, psychologically, and socially; lead to increased costs and length of hospital stay; and are closely linked to increased mortality. Thus, the best evidence practice implementation project was conducted in the mental health ward of a large teaching hospital in Bucharest.

Method:

The current evidence implementation project used the JBI Practical Application of Clinical Evidence System and Getting Research into Practice. The best practices project was carried out in a mental health department with 70 beds at Bucharest's largest mental health hospital. This analysis of nursing practice included all immobile patients who were hospitalized in the ward.

Results:

Through the project to implement best practices for the prevention of pressure injuries, the activity of nurses was improved. If initially, the prevention of pressure injuries was a deficient activity in the hospital (compliance between 0 and 82%), after the implementation of the project, compliance with the recommendations of evidence-based practices was radically improved, obtaining a maximum percentage of 100% for all these activities: patient assessment, use of assessment tools, use of necessary devices, provision of high protein diet and patient education.

Conclusion:

The current project contributed to the standardization and improvement of nurses’ practice of pressure injuries prevention in patients with mental illness and immobility hospitalized in a psychiatric ward. The development of future audits will help identify the sustainability of the implemented prevention measures.
Residual characteristics of buprofezin during rice
processing
Authors: Cho Mihyun , Im Moo-Hyeog
Published: July 2022

In this study, we aimed to analyze changes in the residual levels of buprofezin
during milling, washing, cooking, and processing of rice to make porridge, rice
cakes, and cookies. The pesticide residue levels in rice were analyzed using
high-performance liquid chromatograph with UV detector. The residual buprofezin
level in brown rice was 21.8 mg/kg, and after milling, that in polished rice was
1.73 mg/kg, with elimination of 92.1% of the pesticide residue. The rate of
reduction in buprofezin levels during brown rice washing was 21.6-57.3%, and the
residual level of buprofezin during polished rice washing decreased by
27.4-67.2%. When brown rice was cooked using an electric cooker and pressure
cooker, buprofezin levels reduced by 51.7 and 55.5%, respectively. When washed
polished rice was cooked using an electric cooker and pressure cooker,
buprofezin levels reduced by 83.6 and 82.3%, respectively. When washed polished
rice was soaked for 30 min and then cooked using an electric cooker and pressure
cooker, buprofezin levels reduced by 87.1 and 88.0%, respectively. After
processing polished rice into porridge, rice cakes, and cookies, the residue
level of buprofezin decreased by 89.7, 82.0, and 79.4%, respectively, compared
to the residual level in polished rice. In conclusion, various rice processing
methods decrease the residue levels of buprofezin.
Preparation of large biological samples for high-resolution, hierarchical, multi-modal imaging
Authors: Brunet J. , Walsh C. L. , Wagner W. L. , Bellier A. , Werlein C. , Marussi S. , Jonigk D. D. , Verleden S. E. , Ackermann M. , Lee Peter D. , Tafforeau Paul
Published: July 2022

Imaging the different scales of biological tissue is essential for understanding healthy organ behavior and pathophysiological changes. X-ray micro-tomography using both laboratory (µCT) and synchrotron sources (sCT) is a promising tool to image the 3D morphology at the macro- and micro-scale of large samples, including intact human organs. Preparation of large samples for high resolution imaging techniques remains a challenge due to limitations with current methods, such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe a protocol to prepare, stabilize, and image large soft-tissue samples with X-ray microtomography. We demonstrate the protocol using intact human organs and Hierarchical Phase-Contrast Tomography (HiP-CT) imaging at the European Synchrotron Radiation Facility, but the protocol is equally applicable to a range of biological samples, including complete organisms, for both laboratory and synchrotron source tomography. Our protocol enhances the contrast of the sample, while preventing sample motion during the scan, even in case of different sample orientations. Bubbles trapped during mounting and those formed during scanning (in case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging (MRI), CT, and histological observation. We describe a protocol for sample preparation and mounting which requires 25 to 34 days for a large organ such as an intact human brain or heart. This preparation time varies depending on the composition, size, and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local pixel size of one micron using HiP-CT.
COVID-19 Causes Ciliary Dysfunction as Demonstrated by Human Intranasal Micro-Optical Coherence Tomography Imaging
Authors: Vijaykumar Kadambari , Leung Hui Min , Barrios Amilcar , Fernandez-Petty Courtney M. , Solomon George M. , Hathorne Heather Y. , Wade Justin D. , Monroe Kathryn , Slaten Katie Brand , Li Qian , Leal Sixto M. , Moates Derek B. , Pierce Hannah M. , Olson Kristian R. , Currier Paul , Foster Sam , Marsden Doug , Tearney Guillermo J. , Rowe Steven M.
Published: July 2022

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), causative agent of coronavirus disease 2019 (COVID-19), binds via ACE2 receptors, highly expressed in ciliated cells of the nasal epithelium. Micro-optical coherence tomography (μOCT) is a minimally invasive intranasal imaging technique that can determine cellular and functional dynamics of respiratory epithelia at 1-μm resolution, enabling real time visualization and quantification of epithelial anatomy, ciliary motion, and mucus transport. We hypothesized that respiratory epithelial cell dysfunction in COVID-19 will manifest as reduced ciliated cell function and mucociliary abnormalities, features readily visualized by μOCT. Symptomatic outpatients with SARS-CoV-2 aged ≥ 18 years were recruited within 14 days of symptom onset. Data was interpreted for subjects with COVID-19 (n=13) in comparison to healthy controls (n=8). Significant reduction in functional cilia, diminished ciliary beat frequency, and abnormal ciliary activity were evident. Other abnormalities included denuded epithelium, presence of mucus rafts, and increased inflammatory cells. Our results indicate that subjects with mild but symptomatic COVID-19 exhibit functional abnormalities of the respiratory mucosa underscoring the importance of mucociliary health in viral illness and disease transmission. Ciliary imaging enables investigation of early pathogenic mechanisms of COVID-19 and may be useful for evaluating disease progression and therapeutic response.

Graphical abstract
Compression-enabled interpretability of voxelwise encoding models
Authors: Kamali Fatemeh , Suratgar Amir Abolfazl , Menhaj Mohammadbagher , Abbasi-Asl Reza
Published: July 2022

Voxelwise encoding models based on convolutional neural networks (CNNs) have emerged as state-of-the-art predictive models of brain activity evoked by natural movies. Despite their superior predictive performance, the huge number of parameters in CNN-based models have made them difficult to interpret. Here, we investigate whether model compression can build more interpretable and more stable CNN-based voxelwise models while maintaining accuracy. We used multiple compression techniques to prune less important CNN filters and connections, a receptive field compression method to select receptive fields with optimal center and size, and principal component analysis to reduce dimensionality. We demonstrate that the model compression improves the accuracy of identifying visual stimuli in a hold-out test set. Additionally, compressed models offer a more stable interpretation of voxelwise pattern selectivity than uncompressed models. Finally, the receptive field-compressed models reveal that the optimal model-based population receptive fields become larger and more centralized along the ventral visual pathway. Overall, our findings support using model compression to build more interpretable voxelwise models.
Imputing the parental origin of the sibling’s haplotype from parental phenotypes
Authors: Liang Yanyu
Published: July 2022

To recruit cases for late-onset disease study is challenging since these diseases occur in elder people. Moreover, typically we have a very limited number of late-onset disease cases in Biobank data. But, on the other hand, the parental disease status may be available by questionnaire. Because of this, methods have been developed to utilize parental disease status instead Liu et al. (2017); Hujoel et al. (2020). In these approaches, the late-onset phenotype of the participant is imputed from parental statuses. And, downstream, a genome-wide association study (GWAS) is performed using the participant’s genotype and imputed phenotype. In this paper, we take another view on utilizing parental phenotypes. We treat this problem as missing parental genotype rather than missing participant’s phenotype. First, we propose an imputation scheme to infer the parental origin of the participant’s genotype from a collection of extra parental phenotypes (non-focal phenotypes) and the participant’s genotype. Second, we propose a computationally efficient approach to incorporate the imputed parental origin information into the downstream GWAS. We explore the feasibility of the proposed two-step approach on simulated and real data. And we derive the power increase of GWAS as a function of imputation quality. These results indicate that the imputation scheme needs about 100 non-focal phenotypes to achieve enough accuracy to facilitate the GWAS downstream.
Multimodal wearable sensors inform cycles of seizure risk
Authors: Gregg Nicholas M. , Pal Attia Tal , Nasseri Mona , Joseph Boney , Karoly Philippa J. , Cui Jie , Stirling Rachel E. , Viana Pedro F. , Richner Thomas J. , Nurse Ewan S. , Schulze-Bonhage Andreas , Cook Mark J. , Worrell Gregory A. , Richardson Mark P. , Freestone Dean R. , Brinkmann Benjamin H.
Published: July 2022

Objective

Seizure unpredictability is a major source of disability for people with epilepsy. Recent work using chronic brain recordings has established that for many individuals with epilepsy seizure risk is not random, but corresponds to circadian and multiday (multidien) cycles in brain excitability. Here, we aimed to evaluate whether multimodal wearable device recordings can characterize cycles of seizure risk, and compare wearables performance with concurrent chronic brain recordings.

Methods

Fourteen subjects underwent long-term ambulatory monitoring with a multimodal wrist worn device (measuring heart rate, heart rate variability, accelerometry, tonic and phasic electrodermal activity, temperature) and an implanted responsive neurostimulation system (measuring interictal epileptiform abnormalities (IEA) and electrographic seizures). Wavelet time-frequency analyses identified circadian and multiday cycles in wearable and brain recordings. Circular statistics assessed seizure phase locking to cycles in physiology.

Results

Ten subjects met inclusion criteria. The mean recording duration was 232 days. Seven subjects had reliable electrographic seizure detections (mean 76 seizures). Seizure phase locking to multiday cycles occurred in six (IEA), five (temperature), four (heart rate, phasic electrodermal activity), and three (accelerometry, heart rate variability, tonic electrodermal activity) subjects. Seizure phase locking to residual HR multiday cycles (HR after regression of correlated physical activity (ACC)) increased to six subjects.

Interpretation

Long timescale cyclical changes in wearable recordings are common in epilepsy, and seizures occur at preferred phases of these cycles for many individuals. Broadly accessible wearable technology can provide new insights into the chronobiology of epilepsy with implications for seizure forecasting.
Individual tree-based vs pixel-based approaches to mapping forest functional traits and diversity by remote sensing
Authors: Zheng Zhaoju , Zeng Yuan , Schuman Meredith C. , Jiang Hailan , Schmid Bernhard , Schaepman Michael E. , Morsdorf Felix
Published: July 2022

Trait-based approaches, focusing on the functional characteristics of vascular plants in a community, have been increasingly used in plant ecology and biodiversity research. Compared with traditional field survey (which typically samples individual trees), remote sensing enables quantifying functional traits over large contiguous areas, but assigning trait values to biological units such as species and individuals is difficult with pixel-based approaches. We used a subtropical forest landscape in China to compare an approach based on LiDAR-delineated individual tree crowns (ITCs) with a pixel-based approach for assessing functional traits from remote sensing data. We compared trait distributions, trait–trait relationships and functional diversity metrics obtained by the two approaches at changing grain and extent. We found that morphological traits derived from airborne laser scanning showed more differences between ITC- and pixel-based approaches than physiological traits estimated by imaging spectroscopy data. Pixel sizes approximating average tree crowns yielded similar results as ITCs, but 95th quantile height and foliage height diversity tended to be overestimated and leaf area index underestimated relative to ITC-based values. With increasing pixel size, the differences to ITC- based trait values became larger and less trait variance was captured, indicating information loss. The consistency of ITC- and pixel-based functional richness measures also decreased with increasing pixel grain, and changed with the observed extent for functional diversity monitoring. We conclude that whereas ITC-based approaches in principle allow partitioning of variation between individuals, genotypes and species, at high resolution, pixel-based approaches come close to this and can be suitable for assessing ecosystem-scale trait variation by weighting individuals and species according to coverage.
Reliability metrics of outcome measures during the single and double leg drop jump tests
Authors: Celik Huseyin , Yildirim Ahmet , Unver Evrim , Mavili Caner , Yilmaz Ekrem , Ozturk Ferhat , Arpinar-Avsar Pinar , Cinemre Sukru Alpan
Published: July 2022

Although a number of previous studies have studied reliability metrics of outcome measures during single and double leg drop jump tests, none of them presented detailed reliability information for both tests with a group of collegiate athletes of both genders. The aim of this study was therefore to assess the reliability of outcome measures during the single and double leg drop jump tests with proper reliability metrics. Seventeen handball players (11 male and 6 female) participated in the experiments. Each player performed three double leg and three single drop jumps from a 30 cm height box onto a portable force plate in two sessions a week apart. Sixteen outcome measures, including jump height (JH), ground contact time (GCT), reactive strength index (RSI), were calculated. Four groups of reliability metrics like absolute agreement and consistency intraclass correlation coefficients (inter-day and intra-day), standard error of measurement, coefficient of variation, and minimal metrically detectable change were estimated for reliability assessment. The outcome measures as RSI and its individual components JH and GCT together with normalized vertical stiffness (Kvert) yielded high inter-day and intra-day intraclass correlation coefficients and low standard error of measurement and coefficient of variation levels for the double leg drop jump test. The more challenging single leg drop jump test could also be considered reproducible with some other highly reliable outcome measure set by keeping JH, GCT, and normalized Kvert and replacing vertical jump impulse with RSI. The results of the current study therefore suggested the drop jump tests could be deemed reliable to be used for short-term and long-term monitoring needs for a group of collegiate athletes of both genders.
Genetic drift shapes the evolution of a highly dynamic metapopulation
Authors: Angst Pascal , Ameline Camille , Ebert Dieter , Fields Peter D.
Published: July 2022

The dynamics of extinction and (re)colonization in habitat patches are common features of metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogenDaphnia magna. For comparison, we characterized diversity in a single, large, stableD. magnapopulation. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared to the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in more isolated, younger subpopulations. Our study sheds light on the genomic consequences of extinction–(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that the evolutionary process is largely driven by genetic drift.
A scalable assay for chemical preference of small freshwater fish
Authors: Gallois Benjamin , Pontani Léa-lætitia , Debrégeas Georges , Candelier Raphaël
Published: July 2022

Sensing the chemical world is of primary importance for aquatic organisms, and small freshwater fish are increasingly used in toxicology, ethology, and neuroscience by virtue of their ease of manipulation, tissue imaging amenability, and genetic tractability. However, precise behavioral analyses are generally challenging to perform due to the lack of knowledge of what chemical the fish are exposed to at any given moment. Here we developed a behavioral assay and a specific infrared dye to probe the preference of young zebrafish for virtually any compound. We found that the innate aversion of zebrafish to citric acid is not mediated by modulation of the swim but rather by immediate avoidance reactions when the product is sensed and that the preference of juvenile zebrafish for ATP changes from repulsion to attraction during successive exposures. We propose an information-based behavioral model for which an exploration index emerges as a relevant behavioral descriptor, complementary to the standard preference index. Our setup features a high versatility in protocols and is automatic and scalable, which paves the way for high-throughput preference compound screening at different ages.
Accurate delineation of individual tree crowns in tropical forests from aerial RGB imagery using Mask R-CNN
Authors: Ball James G. C. , Hickman Sebastian H. M. , Jackson Tobias D. , Koay Xian Jing , Hirst James , Jay William , Archer Matthew , Aubry-Kientz Mélaine , Vincent Grégoire , Coomes David A.
Published: July 2022

Tropical forests are a major component of the global carbon cycle and home to two-thirds of terrestrial species. Upper-canopy trees store the majority of forest carbon and can be vulnerable to drought events and storms. Monitoring their growth and mortality is essential to understanding forest resilience to climate change, but in the context of forest carbon storage, large trees are underrepresented in traditional field surveys, so estimates are poorly constrained. Aerial photographs provide spectral and textural information to discriminate between tree crowns in diverse, complex tropical canopies, potentially opening the door to landscape monitoring of large trees. Here we describe a new deep convolutional neural network method,Detectree2, which builds on the Mask R-CNN computer vision framework to recognise the irregular edges of individual tree crowns from airborne RGB imagery. We trained and evaluated this model with 3,797 manually delineated tree crowns at three sites in Malaysian Borneo and one site in French Guiana. As an example application, we combined the delineations with repeat lidar surveys (taken between 3 and 6 years apart) of the four sites to estimate the growth and mortality of upper-canopy trees.Detectree2delineated 65,000 upper-canopy trees across 14 km2of aerial images. The skill of the automatic method in delineating unseen test trees was good (F1score = 0.64) and for the tallest category of trees was excellent (F1score = 0.74). As predicted from previous field studies, we found that growth rate declined with tree height and tall trees had higher mortality rates than intermediate-size trees. Our approach demonstrates that deep learning methods can automatically segment trees in widely accessible RGB imagery. This tool (provided as an open-source Python package) has many potential applications in forest ecology and conservation, from estimating carbon stocks to monitoring forest phenology and restoration.

Python package available to install athttps://github.com/PatBall1/Detectree2
Frameshifts may carry oncogenic potential beyond loss of function and categorize genes’ role in tumor development
Authors: Kirov Stefan
Published: July 2022

In this work I present evidence that frameshift mutations represent substantial oncogenic potential across multiple tumor types and may change our understanding of the function of some genes with well established tumor suppressor. I analyzed data deposited in Cbio portal and show that frameshifts, even when they result in the removal of a substantial part of a protein have the potential to create recurring large domains with unknown function. Based on this analysis I propose a novel categorization of genes according to their association with cancer that is more reflective of a complex nature that goes beyond the simple division to tumor suppressors and oncogenes.
Measurement of Cervical Neuronal Activity during Stress Challenge Using Novel Flexible Adhesive Surface Electrodes
Authors: Bu Yifeng , Kurniawa Jonas F. , Prince Jacob , Nguyen Andrew K. L. , Ho Brandon , Sit Nathan L. J. , Pham Timothy , Wu Vincent M. , Tjhia Boris , Shin Andrew J. , Wu Tsung-Chin , Tu Xin M. , Rao Ramesh , Coleman Todd P. , Lerman Imanuel
Published: July 2022

This study introduces a flexible, adhesive-integrated electrode array that was developed to enable non-invasive monitoring of cervical nerve activity. The device uses silver-silver chloride as the electrode material of choice and combines it with a novel electrode array consisting of a customized biopotential data acquisition unit and integrated graphical user interface (GUI) for visualization of real-time monitoring. Preliminary testing demonstrated this novel electrode design can achieve a high signal to noise ratio during cervical neural recordings. To demonstrate the capability of the surface electrodes to detect changes in cervical neuronal activity, the cold-pressor test (CPT) and a timed respiratory challenge were employed as stressors to the autonomic nervous system. This sensor system recording, a new novel technique, was termed Cervical Electroneurography (CEN). By applying a custom spike sorting algorithm to the novel electrode measurements, neural activity was classified in two ways: 1) pre-to-post CPT, and 2) during a timed respiratory challenge. Unique to this work: 1) rostral to caudal channel position-specific (cephalad to caudal) firing patterns and 2) cross challenge biotype-specific change in average CEN firing, were observed with both CPT and the timed respiratory challenge. Future work is planned to develop an ambulatory CEN recording device that could provide immediate notification of autonomic nervous system activity changes that might indicate autonomic dysregulation in healthy subjects and clinical disease states.
ribosomal DNA instability as a potential cause of karyotype evolution
Authors: Li Duojia , Gandhi Dhyey , Kumon Tomohiro , Yamashita Yukiko M.
Published: July 2022

Karyotype refers to the configuration of the genome into a set of chromosomes. The karyotype difference between species is expected to impede various biological processes, such as chromosome segregation or meiotic chromosome pairing, potentially contributing to incompatibility. Karyotypes can rapidly change between closely related species and even among populations of the same species. However, the forces driving karyotype evolution are poorly understood. Here we describe a unique karyotype of a D. melanogaster strain isolated from the Seychelles archipelago. This strain has lost the ribosomal DNA (rDNA) locus on the X chromosome. Because the Y chromosome is the only other rDNA-bearing chromosome, all females carry at least one Y chromosome as the source of rDNA. Interestingly, we found that the strain also carries a truncated Y chromosome (YS) that is stably maintained in the population despite its inability to support male fertility. Our modeling and cytological analysis suggest that the Y chromosome has a larger negative impact on female fitness than the YS chromosome. Moreover, we generated an independent strain that lacks X rDNA and has a karyotype of XXY females and XY males. This strain quickly evolved multiple karyotypes: two new truncated Y chromosomes (similar to YS), as well as two independent X chromosome fusions that contain the Y-derived rDNA fragment, eliminating females’ dependence on the Y chromosome. Considering that Robertsonian fusions frequently occur at rDNA loci in humans, we propose that rDNA loci instability is a driving force of karyotype evolution.
Age-stratified seroprevalence of antibodies against SARS-CoV-2 in the pre- and post-vaccination era, February 2020–March 2022, Japan
Authors: Yamayoshi Seiya , Iwatsuki-Horimoto Kiyoko , Okuda Moe , Ujie Michiko , Yasuhara Atsuhiro , Murakami Jurika , Duong Calvin , Hamabata Taiki , Ito Mutsumi , Chiba Shiho , Kobayashi Ryo , Takahashi Satoshi , Mitamura Keiko , Hagihara Masao , Shibata Akimichi , Uwamino Yoshifumi , Hasegawa Naoki , Ebina Toshiaki , Izumi Akihiko , Kato Hideaki , Nakajima Hideaki , Sugaya Norio , Seki Yuki , Iqbal Asef , Kamimaki Isamu , Yamazaki Masahiko , Kawaoka Yoshihiro , Furuse Yuki
Published: July 2022

Japan has reported a small number of COVID-19 cases relative to other countries. Because not all infected people receive diagnostic tests for COVID-19, the reported number of COVID-19 cases must be lower than the actual number of infections. Assessments of the presence of antibodies against the spike protein of SARS-CoV-2 can retrospectively determine the history of natural infection and vaccination. In this study, we assessed SARS-CoV-2 seroprevalence by analyzing over 60,000 samples collected in Japan from February 2020 to March 2022. The results showed that about 5% of the Japanese population had been infected with the virus by January 2021. The seroprevalence increased with the administration of vaccinations to adults; however, among the elderly, it was not as high as the vaccination rate, probably due to poor immune responses to the vaccines and waning immunity. The infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants among children who were not eligible for vaccination. Nevertheless, their seroprevalence was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.
Impact of non-pharmaceutical interventions on COVID-19 incidence and deaths: cross-national natural experiment in 32 European countries
Authors: Costa Diogo , Rohleder Sven , Bozorgmehr med Kayvan
Published: July 2022

Purpose

Non-pharmaceutical interventions (NPIs) have been the cornerstone of COVID-19 pandemic control, but evidence on their effectiveness varies according to the methods and approaches taken to empirical analysis.

We analysed the impact of NPIs on incident SARS-CoV-2 across 32 European countries (March-December 2020) using two NPI trackers: the Corona Virus Pandemic Policy Monitor – COV-PPM, and the Oxford Covid-19 Government Response Tracker – OxCGRT.

Methods

NPIs were summarized through principal component analysis into three sets, stratified by two waves (C1-C3, weeks 5-25, and C4-C6, weeks 35-52). Longitudinal, multi-level mixed-effects negative binomial regression models were fitted to estimate incidence rate ratios for cases and deaths considering different time-lags and reverse causation (i.e. changing incidence causing NPIs), stratified by waves and geographical regions (Western, Eastern, Northern, Southern, Others).

Results

During the first wave, restrictions on movement/mobility, public transport, public events, and public spaces (C1) and healthcare system improvements, border closures and restrictions to public institutions (C2) reduced SARS-CoV-2 incidence after 28 and 35-days. Mask policies (C3) reduced SARS-CoV-2 incidence (except after 35-days). During wave 1, C1 and C2 reduced deaths after 49-days and C3 after 21, 28 and 35-days. During wave 2, restrictions on movement/mobility, public transport and healthcare system improvements (C5) decreased SARS-CoV-2 cases and deaths across all countries.

Conclusion

In the absence of pre-existing immunity, vaccines or treatment options, the impact of NPIs on SARS-CoV-2 incidence and deaths varied by regions and waves but was consistent across components of NPIs derived from two policy trackers (CoV-PPM and OxCGRT).
Health impact of routine measles vaccination and supplementary immunisation activities in 14 high burden countries: a DynaMICE modelling study
Authors: Auzenbergs Megan , Fu Han , Abbas Kaja , Procter Simon R , Cutts Felicity , Jit Mark
Published: July 2022

Background

WHO recommends ≥95% population coverage with two doses of measles-containing vaccine (MCV). Most countries used routine services to offer MCV1 and later, MCV2. Many countries conducted supplementary immunisation activities (SIAs), offering vaccination to all persons in a given age range irrespective of prior vaccination history. We estimated the relative impact of each dose and delivery route in 14 high burden countries.

Methods

We used an age-structured dynamic model (DynaMICE), to estimate the health impact of different vaccination strategies on measles susceptibility and burden over 2000-2020. We estimated their incremental impact using averted cases and deaths and their efficiency using number needed to vaccinate (NNV) to avert an additional measles case.

Findings

Compared to no vaccination, MCV1 implementation averted 823 million cases and 9.5 million deaths, with a median NNV of 1.41. Adding routine MCV2 to MCV1 further averted 108 million cases and 0.4 million deaths, while adding SIAs to MCV1 led to 249 million averted cases and 4 million deaths. Despite a larger incremental impact, adding SIAs to MCV1 showed reduced efficiency compared to adding routine MCV2, with median NNVs of 6.15 and 5.41, respectively.

Interpretation

Vaccination strategies including non-selective SIAs reach a greater proportion of unvaccinated children and reduce burden more than MCV2 alone, but efficiency is somewhat lower because of the wide age groups included in SIAs. This analysis provides insight to improve health impact and efficiency of measles vaccination.

Funding

Gavi, the Vaccine Alliance, and the Bill & Melinda Gates Foundation (OPP1157270)
Prevalence of anti-DENV IgG among routine Bangladeshi blood donors, and strategies for the future
Authors: Hoque Ashraful , Basak Sushanta Kumar , Al-Mamun A.B.M. , Rahman Marufur , Islam Kashfia
Published: July 2022

Background

Dengue is the most common arthropod-borne sickness worldwide, impacting at least 50 million people each year. The dengue virus has four primary serotypes. Infection with one serotype confers homotypic immunity but not heterologous immunity, and secondary infections may be more severe. Although blood transfusions and organ donations have also been observed, the Aedes aegypti mosquito is the primary vector for the transmission of dengue. Infection causes a continuum of clinical illness, from asymptomatic infection to dengue fever, DHF, and dengue shock syndrome (DSS).

Aim

To assess the presence of anti DENV IgG and anti DENV IgM antibodies specific to the four dengue serotypes in blood donor service donors and the importance of pre-donation screening in routine blood collection procedures.

Method

3 mL of peripheral venous blood from 507 blood donors was collected in tubes with BD vacutainer gel tube for serum separation after epidemiological records were reviewed. After that, serum was separated and tests were performed by SD Bioline Dengue Duo. Participants in the study completed a social and epidemiological questionnaire that contained information such as age, gender, and dengue diagnosis.

Result

Out of the 507 blood samples that were taken, 473 (93.3%) came from male blood donors, while the remaining 34 (6.7%) belonged to female blood donors. The ratio of males to females is 13.91 to 1. The age range is 18–60 years, and the mean and standard deviation are both 27.7 and 6.5. 183 of the 507 samples produced anti DENV IgG positivity, while 324 did not. The ratio of positive to negative was 1.25:2.

Conclusion

According to the findings of this study, quantitative methods for determining the presence of anti-dengue antibodies or detecting the dengue virus in blood donors in endemic areas should be devised in order to ensure the quality of blood transfusions.
Multi-omics provide evidence for an anti-inflammatory immune signature and metabolic alterations in patients with Long COVID Syndrome – an exploratory study
Authors: Kovarik Johannes J. , Bileck Andrea , Hagn Gerhard , Meier-Menches Samuel M. , Frey Tobias , Kaempf Anna , Hollenstein Marlene , Shoumariyeh Tarik , Skos Lukas , Reiter Birgit , Gerner Marlene C. , Spannbauer Andreas , Hasimbegovic Ena , Schmidl Doreen , Garhöfer Gerhard , Gyöngyösi Mariann , Schmetterer Klaus G. , Gerner Christopher
Published: July 2022

Despite the increasing prevalence of patients with Long Covid Syndrome (LCS), to date the pathophysiology of the disease is still unclear, and therefore diagnosis and therapy are a complex effort without any standardization. To address these issues, we performed a broad exploratory screening study applying state-of-the-art post-genomic profiling methods to blood plasma derived from three groups: 1) healthy individuals vaccinated against SARS-CoV-2 without exposure to the full virus, 2) asymptomatic fully recovered patients at least three months after SARS-CoV-2 infection, 3) symptomatic patients at least 3 months after a SARS-CoV-2 infection, here designated as Long Covid Syndrome (LCS) patients. Multiplex cytokine profiling indicated slightly elevated cytokine levels in recovered individuals in contrast to LCS patients, who displayed lowest levels of cytokines. Label-free proteome profiling corroborated an anti-inflammatory status in LCS characterized by low acute phase protein levels and a uniform down-regulation of macrophage-derived secreted proteins, a pattern also characteristic for chronic fatigue syndrome (CFS). Along those lines, eicosanoid and docosanoid analysis revealed high levels of omega-3 fatty acids and a prevalence of anti-inflammatory oxylipins in LCS patients compared to the other study groups. Targeted metabolic profiling indicated low amino acid and triglyceride levels and deregulated acylcarnithines, characteristic for CFS and indicating mitochondrial stress in LCS patients. The anti-inflammatory osmolytes taurine and hypaphorine were significantly up-regulated in LCS patients. In summary, here we present evidence for a specific anti-inflammatory and highly characteristic metabolic signature in LCS which could serve for future diagnostic purposes and help to establish rational therapeutic interventions in these patients.

One sentence Summary

Multi-omics plasma analyses demonstrate anti-inflammatory and hypo-metabolic signatures in patients with Long COVID Syndrome.