bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of patient specific information in the wild on fundus photography and optical coherence tomography
Authors: Munk Marion R. , Kurmann Thomas , Márquez-Neila Pablo , Zinkernagel Martin S. , Wolf Sebastian , Sznitman Raphael 
Published: April 2021

AbstractIn this paper we analyse the performance of machine learning methods in predicting patient information such as age or sex solely from retinal imaging modalities in a heterogeneous clinical population. Our dataset consists of N = 135,667 fundus images and N = 85,536 volumetric OCT scans. Deep learning models were trained to predict the patient’s age and sex from fundus images, OCT cross sections and OCT volumes. For sex prediction, a ROC AUC of 0.80 was achieved for fundus images, 0.84 for OCT cross sections and 0.90 for OCT volumes. Age prediction mean absolute errors of 6.328 years for fundus, 5.625 years for OCT cross sections and 4.541 for OCT volumes were observed. We assess the performance of OCT scans containing different biomarkers and note a peak performance of AUC = 0.88 for OCT cross sections and 0.95 for volumes when there is no pathology on scans. Performance drops in case of drusen, fibrovascular pigment epitheliuum detachment and geographic atrophy present. We conclude that deep learning based methods are capable of classifying the patient’s sex and age from color fundus photography and OCT for a broad spectrum of patients irrespective of underlying disease or image quality. Non-random sex prediction using fundus images seems only possible if the eye fovea and optic disc are visible.
Assessing the effectiveness of two intervention methods for stony coral tissue loss disease on Montastraea cavernosa
Authors: Shilling Erin N. , Combs Ian R. , Voss Joshua D. 
Published: April 2021

AbstractStony coral tissue loss disease (SCTLD) was first observed in Florida in 2014 and has since spread to multiple coral reefs across the wider Caribbean. The northern section of Florida’s Coral Reef has been heavily impacted by this outbreak, with some reefs experiencing as much as a 60% loss of living coral tissue area. We experimentally assessed the effectiveness of two intervention treatments on SCTLD-affectedMontastraea cavernosacolonies in situ. Colonies were tagged and divided into three treatment groups: (1) chlorinated epoxy, (2) amoxicillin combined with CoreRx/Ocean Alchemists Base 2B, and (3) untreated controls. The experimental colonies were monitored periodically over 11 months to assess treatment effectiveness by tracking lesion development and overall disease status. The Base 2B plus amoxicillin treatment had a 95% success rate at healing individual disease lesions but did not necessarily prevent treated colonies from developing new lesions over time. Chlorinated epoxy treatments were not significantly different from untreated control colonies, suggesting that chlorinated epoxy treatments are an ineffective intervention technique for SCTLD. The results of this experiment expand management options during coral disease outbreaks and contribute to overall knowledge regarding coral health and disease.
Occipital cortex is modulated by transsaccadic changes in spatial frequency: an fMRI study
Authors: Baltaretu Bianca R. , Dunkley Benjamin T. , Stevens W. Dale , Crawford J. Douglas 
Published: April 2021

AbstractPrevious neuroimaging studies have shown that inferior parietal and ventral occipital cortex are involved in the transsaccadic processing of visual object orientation. Here, we investigated whether the same areas are also involved in transsaccadic processing of a different feature, namely, spatial frequency. We employed a functional magnetic resonance imaging paradigm where participants briefly viewed a grating stimulus with a specific spatial frequency that later reappeared with the same or different frequency, after a saccade or continuous fixation. First, using a whole-brain Saccade > Fixation contrast, we localized two frontal (left precentral sulcus and right medial superior frontal gyrus), four parietal (bilateral superior parietal lobule and precuneus), and four occipital (bilateral cuneus and lingual gyri) regions. Whereas the frontoparietal sites showed task specificity, the occipital sites were also modulated in a saccade control task. Only occipital cortex showed transsaccadic feature modulations, with significant repetition enhancement in right cuneus. These observations (parietal task specificity, occipital enhancement, right lateralization) are consistent with previous transsaccadic studies. However, the specific regions differed (ventrolateral for orientation, dorsomedial for spatial frequency). Overall, this study supports a general role for occipital and parietal cortex in transsaccadic vision, with a specific role for cuneus in spatial frequency processing.
Optimized preoperative determination of nerve of origin in patients with vestibular schwannoma
Authors: Rahne Torsten , Plontke Stefan K. , Fröhlich Laura , Strauss Christian 
Published: April 2021

AbstractIn vestibular schwannoma (VS) patients hearing outcome and surgery related risks can vary and depend on the nerve of origin. Preoperative origin differentiation between inferior or superior vestibular nerve may influence the decision on treatment, and the selection of optimal treatment and counselling modalities. A novel scoring system based on functional tests was designed to predict the nerve of origin for VS and was applied to a large number of consecutive patients. A prospective, double blind, cohort study including 93 patients with suspected unilateral VS was conducted at a tertiary referral centre. Preoperatively before tumor resection a functional test battery [video head-impulse test (vHIT) of all semicircular canals (SCC)], air-conducted cervical/ocular vestibular evoked myogenic potential tests (cVEMP, oVEMP), pure-tone audiometry, and speech discrimination was applied. Sensitivity and specificity of prediction of intraoperative finding by a preoperative score based on vHIT gain, cVEMP and oVEMP amplitudes and asymmetry ratios was calculated. For the prediction of inferior vestibular nerve origin, sensitivity was 73% and specificity was 80%. For the prediction of superior vestibular nerve origin, sensitivity was 60% and specificity was 90%. Based on the trade-off between sensitivity and specificity, optimized cut-off values of − 0.32 for cVEMP and − 0.11 for oVEMP asymmetry ratios and vHIT gain thresholds of 0.77 (anterior SCC), 0.84 (lateral SCC) and 0.80 (posterior SCC) were identified by receiver operator characteristic curves. The scoring system based on preoperative functional tests improves prediction of nerve of origin and can be applied in clinical routine.
Identification, Shiga toxin subtypes and prevalence of minor serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle feces
Authors: Capps Kaylen M. , Ludwig Justin B. , Shridhar Pragathi B. , Shi Xiaorong , Roberts Elisabeth , DebRoy Chitrita , Cernicchiaro Natalia , Phebus Randall K. , Bai Jianfa , Nagaraja T. G. 
Published: April 2021

AbstractShiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that cause illnesses in humans ranging from mild to hemorrhagic enteritis with complications of hemolytic uremic syndrome and even death. Cattle are a major reservoir of STEC, which reside in the hindgut and are shed in the feces, a major source of food and water contaminations. Seven serogroups, O26, O45, O103, O111, O121, O145 and O157, called ‘top-7’, are responsible for the majority of human STEC infections in North America. Additionally, 151 serogroups of E. coli are known to carry Shiga toxin genes (stx). Not much is known about fecal shedding and prevalence and virulence potential of STEC other than the top-7. Our primary objectives were to identify serogroups of STEC strains, other than the top-7, isolated from cattle feces and subtype stx genes to assess their virulence potential. Additional objective was to develop and validate a novel multiplex PCR assay to detect and determine prevalence of six serogroups, O2, O74, O109, O131, O168, and O171, in cattle feces. A total of 351 strains, positive for stx gene and negative for the top-7 serogroups, isolated from feedlot cattle feces were used in the study. Of the 351 strains, 291 belonged to 16 serogroups and 60 could not be serogrouped. Among the 351 strains, 63 (17.9%) carried stx1 gene and 300 (82.1%) carried stx2, including 12 strains positive for both. The majority of the stx1 and stx2 were of stx1a (47/63; 74.6%) and stx2a subtypes (234/300; 78%), respectively, which are often associated with human infections. A novel multiplex PCR assay developed and validated to detect six serogroups, O2, O74, O109, O131, O168, and O171, which accounted for 86.9% of the STEC strains identified, was utilized to determine their prevalence in fecal samples (n = 576) collected from a commercial feedlot. Four serogroups, O2, O109, O168, and O171 were identified as the dominant serogroups prevalent in cattle feces. In conclusion, cattle shed in the feces a number of STEC serogroups, other than the top-7, and the majority of the strains isolated possessed stx2, particularly of the subtype 2a, suggesting their potential risk to cause human infections.
Introducing two types of psychological resilience with partly unique genetic and environmental sources
Authors: Hofgaard Live Skow , Nes Ragnhild Bang , Røysamb Espen 
Published: April 2021

AbstractPsychological resilience is indicated when individuals demonstrate good mental health despite exposure to significant stress or adversity. Good mental health may involve low levels of illbeing and/or high levels of wellbeing. There is still very limited knowledge about the potential differences between these outcomes in relation to stressors. We propose a distinction between type 1 and type 2 resilience, examine their underlying genetic and environmental architecture, and identify modifiable resilience factors. The data come from a population-based twin sample (N = 1987, mean age = 63) in the Norwegian Twin Registry. Type 1 and type 2 resilience are operationalised as the residual of anxiety/depression symptoms and life satisfaction, respectively, after lifetime cumulative adversity has been regressed out. We used biometric modelling and cotwin-control linear mixed models to estimate underlying factors and identify predictors while controlling for genetic confounding. The results support the notion of two separate, but partly overlapping types of resilience. We find heritabilities of 0.30 (type 1) and 0.24 (type 2) and a genetic correlation of 0.43. Potentially causal resilience factors include, but are not limited to, meaning in life, physical activity, positive affect and relationship satisfaction. Whereas some factors are associated with both resilience types, other factors are unique to each type.
Circulating short and medium chain fatty acids are associated with normoalbuminuria in type 1 diabetes of long duration
Authors: Moon Salina , Tsay John J. , Lampert Heather , Md Dom Zaipul I. , Kostic Aleksandar D. , Smiles Adam , Niewczas Monika A. 
Published: April 2021

AbstractA substantial number of subjects with Type 1 Diabetes (T1D) of long duration never develop albuminuria or renal function impairment, yet the underlying protective mechanisms remain unknown. Therefore, our study included 308 Joslin Kidney Study subjects who had T1D of long duration (median: 24 years), maintained normal renal function and had either normoalbuminuria or a broad range of albuminuria within the 2 years preceding the metabolomic determinations. Serum samples were subjected to global metabolomic profiling. 352 metabolites were detected in at least 80% of the study population. In the logistic analyses adjusted for multiple testing (Bonferroni corrected α = 0.000028), we identified 38 metabolites associated with persistent normoalbuminuria independently from clinical covariates. Protective metabolites were enriched in Medium Chain Fatty Acids (MCFAs) and in Short Chain Fatty Acids (SCFAs) and particularly involved odd-numbered and dicarboxylate Fatty Acids. One quartile change of nonanoate, the top protective MCFA, was associated with high odds of having persistent normoalbuminuria (OR (95% CI) 0.14 (0.09, 0.23); p < 10–12). Multivariable Random Forest analysis concordantly indicated to MCFAs as effective classifiers. Associations of the relevant Fatty Acids with albuminuria seemed to parallel associations with tubular biomarkers. Our findings suggest that MCFAs and SCFAs contribute to the metabolic processes underlying protection against albuminuria development in T1D that are independent from mechanisms associated with changes in renal function.
Mechanical control of tissue shape and morphogenetic flows during vertebrate body axis elongation
Authors: Banavar Samhita P. , Carn Emmet K. , Rowghanian Payam , Stooke-Vaughan Georgina , Kim Sangwoo , Campàs Otger 
Published: April 2021

AbstractShaping embryonic tissues into their functional morphologies requires cells to control the physical state of the tissue in space and time. While regional variations in cellular forces or cell proliferation have been typically assumed to be the main physical factors controlling tissue morphogenesis, recent experiments have revealed that spatial variations in the tissue physical (fluid/solid) state play a key role in shaping embryonic tissues. Here we theoretically study how the regional control of fluid and solid tissue states guides morphogenetic flows to shape the extending vertebrate body axis. Our results show that both the existence of a fluid-to-solid tissue transition along the anteroposterior axis and the tissue surface tension determine the shape of the tissue and its ability to elongate unidirectionally, with large tissue tensions preventing unidirectional elongation and promoting blob-like tissue expansions. We predict both the tissue morphogenetic flows and stresses that enable unidirectional axis elongation. Our results show the existence of a sharp transition in the structure of morphogenetic flows, from a flow with no vortices to a flow with two counter-rotating vortices, caused by a transition in the number and location of topological defects in the flow field. Finally, comparing the theoretical predictions to quantitative measurements of both tissue flows and shape during zebrafish body axis elongation, we show that the observed morphogenetic events can be explained by the existence of a fluid-to-solid tissue transition along the anteroposterior axis. These results highlight the role of spatiotemporally-controlled fluid-to-solid transitions in the tissue state as a physical mechanism of embryonic morphogenesis.
Decay radius of climate decision for solar panels in the city of Fresno, USA
Authors: Barton-Henry Kelsey , Wenz Leonie , Levermann Anders 
Published: April 2021

AbstractTo design incentives towards achieving climate mitigation targets, it is important to understand the mechanisms that affect individual climate decisions such as solar panel installation. It has been shown that peer effects are important in determining the uptake and spread of household photovoltaic installations. Due to coarse geographical data, it remains unclear whether this effect is generated through geographical proximity or within groups exhibiting similar characteristics. Here we show that geographical proximity is the most important predictor of solar panel implementation, and that peer effects diminish with distance. Using satellite imagery, we build a unique geo-located dataset for the city of Fresno to specify the importance of small distances. Employing machine learning techniques, we find the density of solar panels within the shortest measured radius of an address is the most important factor in determining the likelihood of that address having a solar panel. The importance of geographical proximity decreases with distance following an exponential curve with a decay radius of 210 meters. The dependence is slightly more pronounced in low-income groups. These findings support the model of distance-related social diffusion, and suggest priority should be given to seeding panels in areas where few exist.
Spatio-temporal characterization of fracture healing patterns and assessment of biomaterials by time-lapsed in vivo micro-computed tomography
Authors: Wehrle Esther , Tourolle né Betts Duncan C. , Kuhn Gisela A. , Floreani Erica , Nambiar Malavika H. , Schroeder Bryant J. , Hofmann Sandra , Müller Ralph 
Published: April 2021

AbstractThorough preclinical evaluation of functionalized biomaterials for treatment of large bone defects is essential prior to clinical application. Using in vivo micro-computed tomography (micro-CT) and mouse femoral defect models with different defect sizes, we were able to detect spatio-temporal healing patterns indicative of physiological and impaired healing in three defect sub-volumes and the adjacent cortex. The time-lapsed in vivo micro-CT-based approach was then applied to evaluate the bone regeneration potential of functionalized biomaterials using collagen and bone morphogenetic protein (BMP-2). Both collagen and BMP-2 treatment led to distinct changes in bone turnover in the different healing phases. Despite increased periosteal bone formation, 87.5% of the defects treated with collagen scaffolds resulted in non-unions. Additional BMP-2 application significantly accelerated the healing process and increased the union rate to 100%. This study further shows potential of time-lapsed in vivo micro-CT for capturing spatio-temporal deviations preceding non-union formation and how this can be prevented by application of functionalized biomaterials. This study therefore supports the application of longitudinal in vivo micro-CT for discrimination of normal and disturbed healing patterns and for the spatio-temporal characterization of the bone regeneration capacity of functionalized biomaterials.
A cyclic learning approach for improving pre-stack seismic processing
Authors: Borges Oliveira Dario Augusto , Szwarcman Daniela , da Silva Ferreira Rodrigo , Zaytsev Semen , Semin Daniil 
Published: April 2021

AbstractCurrent seismic processing workflows in the oil and gas industry involve several interactions between different experts to optimize the overall data quality in various tasks, such as noise attenuation, velocity analysis and horizon picking. While many machine learning-based approaches have been proposed to support each of those steps, most of them disregard expert interactions to guide the overall optimization. This paper presents geocycles, a cyclic learning approach that mimics this iterative process, which can be applied to different pre-stack seismic processing tasks. Our method refactor these processes considering training, testing, and evaluation sub-tasks, which allow the selection of samples for greedy sequential processes targeting an overall optimum quality for very large seismic datasets. We present encouraging results showing that a cyclic structure and efficient quality metrics improved overall outcomes in up to 128% for two different seismic processing tasks in comparison to a 1-cycle machine learning approach.
A social network analysis of the spread of COVID-19 in South Korea and policy implications
Authors: Jo Wonkwang , Chang Dukjin , You Myoungsoon , Ghim Ghi-Hoon 
Published: April 2021

AbstractThis study estimates the COVID-19 infection network from actual data and draws on implications for policy and research. Using contact tracing information of 3283 confirmed patients in Seoul metropolitan areas from January 20, 2020 to July 19, 2020, this study created an infection network and analyzed its structural characteristics. The main results are as follows: (i) out-degrees follow an extremely positively skewed distribution; (ii) removing the top nodes on the out-degree significantly decreases the size of the infection network, and (iii) the indicators that express the infectious power of the network change according to governmental measures. Efforts to collect network data and analyze network structures are urgently required for the efficiency of governmental responses to COVID-19. Implications for better use of a metric such as R0 to estimate infection spread are also discussed.
Bodily ownership and agency sensations in a natural state
Authors: Hidaka Souta , Sasaki Kyoshiro , Kawagoe Toshikazu , Asai Nobuko , Teramoto Wataru 
Published: April 2021

AbstractOur bodily sensation is a fundamental cue for our self-consciousness. Whereas experimental studies have uncovered characteristics of bodily sensation, these studies investigated bodily sensations through manipulating bodily sensations to be apart from one’s own body and to be assigned to external, body-like objects. In order to capture our bodily sensation as it is, this questionnaire survey study explored the characteristics of bodily sensation using a large population-based sample (N = 580, comprising 20s to 70s age groups) without experimental manipulations. We focused on the sensations of ownership, the feeling of having a body part as one’s own, and agency, the feeling of controlling a body part by oneself, in multiple body parts (the eyes, ears, hands, legs, nose, and mouth). The ownership and agency sensations were positively related to each other in each body part. Interestingly, the agency sensation of the hands and legs had a positive relationship with the ownership sensations of the other body parts. We also found the 60s age group had a unique internal configuration, assessed by the similarity of rating scores, of the body parts for each bodily sensation. Our findings revealed the existence of unique characteristics for bodily sensations in a natural state.
Deciphering molecular details of the RAC–ribosome interaction by EPR spectroscopy
Authors: Fries Sandra J. , Braun Theresa S. , Globisch Christoph , Peter Christine , Drescher Malte , Deuerling Elke 
Published: April 2021

AbstractThe eukaryotic ribosome-associated complex (RAC) plays a significant role in de novo protein folding. Its unique interaction with the ribosome, comprising contacts to both ribosomal subunits, suggests a RAC-mediated coordination between translation elongation and co-translational protein folding. Here, we apply electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) to gain deeper insights into a RAC–ribosome contact affecting translational accuracy. We identified a local contact point of RAC to the ribosome. The data provide the first experimental evidence for the existence of a four-helix bundle as well as a long α-helix in full-length RAC, in solution as well as on the ribosome. Additionally, we complemented the structural picture of the region mediating this functionally important contact on the 40S ribosomal subunit. In sum, this study constitutes the first application of SDSL-EPR spectroscopy to elucidate the molecular details of the interaction between the 3.3 MDa translation machinery and a chaperone complex.