bluuebunny/crossref_metadata_2025_split huggingface dataset:
System for quantitative evaluation of DAB&H-stained breast cancer biopsy digital images (CHISEL)
Authors: Roszkowiak Lukasz , Korzynska Anna , Siemion Krzysztof , Zak Jakub , Pijanowska Dorota , Bosch Ramon , Lejeune Marylene , Lopez Carlos 
Published: April 2021

AbstractThis study presents CHISEL (Computer-assisted Histopathological Image Segmentation and EvaLuation), an end-to-end system capable of quantitative evaluation of benign and malignant (breast cancer) digitized tissue samples with immunohistochemical nuclear staining of various intensity and diverse compactness. It stands out with the proposed seamless segmentation based on regions of interest cropping as well as the explicit step of nuclei cluster splitting followed by a boundary refinement. The system utilizes machine learning and recursive local processing to eliminate distorted (inaccurate) outlines. The method was validated using two labeled datasets which proved the relevance of the achieved results. The evaluation was based on the IISPV dataset of tissue from biopsy of breast cancer patients, with markers of T cells, along with Warwick Beta Cell Dataset of DAB&H-stained tissue from postmortem diabetes patients. Based on the comparison of the ground truth with the results of the detected and classified objects, we conclude that the proposed method can achieve better or similar results as the state-of-the-art methods. This system deals with the complex problem of nuclei quantification in digitalized images of immunohistochemically stained tissue sections, achieving best results for DAB&H-stained breast cancer tissue samples. Our method has been prepared with user-friendly graphical interface and was optimized to fully utilize the available computing power, while being accessible to users with fewer resources than needed by deep learning techniques.
Computational medication regimen for Parkinson’s disease using reinforcement learning
Authors: Kim Yejin , Suescun Jessika , Schiess Mya C. , Jiang Xiaoqian 
Published: April 2021

AbstractOur objective is to derive a sequential decision-making rule on the combination of medications to minimize motor symptoms using reinforcement learning (RL). Using an observational longitudinal cohort of Parkinson’s disease patients, the Parkinson’s Progression Markers Initiative database, we derived clinically relevant disease states and an optimal combination of medications for each of them by using policy iteration of the Markov decision process (MDP). We focused on 8 combinations of medications, i.e., Levodopa, a dopamine agonist, and other PD medications, as possible actions and motor symptom severity, based on the Unified Parkinson Disease Rating Scale (UPDRS) section III, as reward/penalty of decision. We analyzed a total of 5077 visits from 431 PD patients with 55.5 months follow-up. We excluded patients without UPDRS III scores or medication records. We derived a medication regimen that is comparable to a clinician’s decision. The RL model achieved a lower level of motor symptom severity scores than what clinicians did, whereas the clinicians’ medication rules were more consistent than the RL model. The RL model followed the clinician’s medication rules in most cases but also suggested some changes, which leads to the difference in lowering symptoms severity. This is the first study to investigate RL to improve the pharmacological approach of PD patients. Our results contribute to the development of an interactive machine-physician ecosystem that relies on evidence-based medicine and can potentially enhance PD management.
Nanoslot metasurface design and characterization for enhanced organic light-emitting diodes
Authors: Kang Kyungnam , Im Seongmin , Lee Changhun , Kim Jungho , Kim Donghyun 
Published: April 2021

AbstractWe investigate bottom-emitting organic light-emitting diodes (B-OLEDs) integrated with metasurface (MS) to analyze the effect of the structural parameters on the output performance. The performance of the MS-integrated B-OLED (MIB-OLED) is evaluated by out-coupling efficiency (OCE) and reflection of the ambient light, while attention is paid mainly to dielectric capping and metal structure of MS that may influence excitation of surface plasmon (SP). The results suggest that layer thicknesses affect the performance by as much as 10% for the OCE and up to 32% for reflectance. The OCE is in general weakly affected by the structural parameters of MS. In contrast, the reflectance characteristics are found to be dominated by localized SP that is largely determined by the length and the width of a unit slot of MS. An optimization factor introduced to evaluate the performance based on out-coupling power to the radiation mode and reflectance of MIB-OLEDs confirms that integration with MS improves performance by 16% over conventional planar structure. In particular, MIB-OLED is found to enhance OCE by 51% with Lambertian-like pattern. Enhanced performance is experimentally confirmed. The findings provide insights on how to optimize the MS structure to produce MIB-OLEDs with enhanced out-coupled power and contrast ratio.
A rotationally focused flow (RFF) microfluidic biosensor by density difference for early-stage detectable diagnosis
Authors: Kim Noori , Han Kyungsup , Su Pei-Chen , Kim Insup , Yoon Yong-Jin 
Published: April 2021

AbstractLabel-free optical biosensors have received tremendous attention in point-of-care testing, especially in the emerging pandemic, COVID-19, since they advance toward early-detection, rapid, real-time, ease-of-use, and low-cost paradigms. Protein biomarkers testings require less sample modification process compared to nucleic-acid biomarkers’. However, challenges always are in detecting low-concentration for early-stage diagnosis. Here we present a Rotationally Focused Flow (RFF) method to enhance sensitivity(wavelength shift) of label-free optical sensors by increasing the detection probability of protein-based molecules. The RFF is structured by adding a less-dense fluid to focus the target-fluid in a T-shaped microchannel. It is integrated with label-free silicon microring resonators interacting with biotin-streptavidin. The suggested mechanism has demonstrated 0.19 fM concentration detection along with a significant magnitudes sensitivity enhancement compared to single flow methods. Verified by both CFD simulations and fluorescent flow-experiments, this study provides a promising proof-of-concept platform for next-generation lab-on-a-chip bioanalytics such as ultrafast and early-detection of COVID-19.
Application of regularized regression to identify novel predictors of mortality in a cohort of hemodialysis patients
Authors: Werfel Stanislas , Lorenz Georg , Haller Bernhard , Günthner Roman , Matschkal Julia , Braunisch Matthias C. , Schaller Carolin , Gundel Peter , Kemmner Stephan , Hayek Salim S. , Nusshag Christian , Reiser Jochen , Moog Philipp , Heemann Uwe , Schmaderer Christoph 
Published: April 2021

AbstractCohort studies often provide a large array of data on study participants. The techniques of statistical learning can allow an efficient way to analyze large datasets in order to uncover previously unknown, clinically relevant predictors of morbidity or mortality. We applied a combination of elastic net penalized Cox regression and stability selection with the aim of identifying novel predictors of mortality in a cohort of prevalent hemodialysis patients. In our analysis we included 475 patients from the “rISk strAtification in end-stage Renal disease” (ISAR) study, who we split into derivation and confirmation cohorts. A wide array of examinations was available for study participants, resulting in over a hundred potential predictors. In the selection approach many of the well established predictors were retrieved in the derivation cohort. Additionally, the serum levels of IL-12p70 and AST were selected as mortality predictors and confirmed in the withheld subgroup. High IL-12p70 levels were specifically prognostic of infection-related mortality. In summary, we demonstrate an approach how statistical learning can be applied to a cohort study to derive novel hypotheses in a data-driven way. Our results suggest a novel role of IL-12p70 in infection-related mortality, while AST is a promising additional biomarker in patients undergoing hemodialysis.
A non-destructive sugar-feeding assay for parasite detection and estimating the extrinsic incubation period of Plasmodium falciparum in individual mosquito vectors
Authors: Guissou Edwige , Waite Jessica L. , Jones Matthew , Bell Andrew S. , Suh Eunho , Yameogo Koudraogo B. , Djègbè Nicaise , Da Dari F. , Hien Domonbabele F. D. S. , Yerbanga Rakiswende S. , Ouedraogo Anicet G. , Dabiré Kounbobr Roch. , Cohuet Anna , Thomas Matthew B. , Lefèvre Thierry 
Published: April 2021

AbstractDespite its epidemiological importance, the time Plasmodium parasites take to achieve development in the vector mosquito (the extrinsic incubation period, EIP) remains poorly characterized. A novel non-destructive assay designed to estimate EIP in single mosquitoes, and more broadly to study Plasmodium–Anopheles vectors interactions, is presented. The assay uses small pieces of cotton wool soaked in sugar solution to collect malaria sporozoites from individual mosquitoes during sugar feeding to monitor infection status over time. This technique has been tested across four natural malaria mosquito species of Africa and Asia, infected with Plasmodium falciparum (six field isolates from gametocyte-infected patients in Burkina Faso and the NF54 strain) and across a range of temperatures relevant to malaria transmission in field conditions. Monitoring individual infectious mosquitoes was feasible. The estimated median EIP of P. falciparum at 27 °C was 11 to 14 days depending on mosquito species and parasite isolate. Long-term individual tracking revealed that sporozoites transfer onto cotton wool can occur at least until day 40 post-infection. Short individual EIP were associated with short mosquito lifespan. Correlations between mosquito/parasite traits often reveal trade-offs and constraints and have important implications for understanding the evolution of parasite transmission strategies.
Functional similarity between TGF-beta type 2 and type 1 receptors in the female reproductive tract
Authors: Ni Nan , Fang Xin , Li Qinglei 
Published: April 2021

AbstractTransforming growth factor β (TGFβ) signaling plays critical roles in reproductive development and function. TGFβ ligands signal through the TGFβ receptor type 2 (TGFBR2)/TGFBR1 complex. As TGFBR2 and TGFBR1 form a signaling complex upon ligand stimulation, they are expected to be equally important for propagating TGFβ signaling that elicits cellular responses. However, several genetic studies challenge this concept and indicate that disruption of TGFBR2 or TGFBR1 may lead to contrasting phenotypic outcomes. We have shown that conditional deletion of Tgfbr1 using anti-Mullerian hormone receptor type 2 (Amhr2)-Cre causes oviductal and myometrial defects. To determine the functional requirement of TGFBR2 in the female reproductive tract and the potential phenotypic divergence/similarity resulting from conditional ablation of either receptor, we generated mice harboring Tgfbr2 deletion using the same Cre driver that was previously employed to target Tgfbr1. Herein, we found that conditional deletion of Tgfbr2 led to a similar phenotype to that of Tgfbr1 deletion in the female reproductive tract. Furthermore, genetic removal of Tgfbr1 in the Tgfbr2-deleted uterus had minimal impact on the phenotype of Tgfbr2 conditional knockout mice. In summary, our results reveal the functional similarity between TGFBR2 and TGFBR1 in maintaining the structural integrity of the female reproductive tract.
Male courtship song drives escape responses that are suppressed for successful mating
Authors: Arez Eliane , Mezzera Cecilia , Neto-Silva Ricardo M. , Aranha Márcia M. , Dias Sophie , Moita Marta A. , Vasconcelos Maria Luísa 
Published: April 2021

AbstractPersuasion is a crucial component of the courtship ritual needed to overcome contact aversion. In fruit flies, it is well established that the male courtship song prompts receptivity in female flies, in part by causing sexually mature females to slow down and pause, allowing copulation. Whether the above receptivity behaviours require the suppression of contact avoidance or escape remains unknown. Here we show, through genetic manipulation of neurons we identified as required for female receptivity, that male song induces avoidance/escape responses that are suppressed in wild type flies. First, we show that silencing 70A09 neurons leads to an increase in escape, as females increase their walking speed during courtship together with an increase in jumping and a reduction in pausing. The increase in escape response is specific to courtship, as escape to a looming threat is not intensified. Activation of 70A09 neurons leads to pausing, confirming the role of these neurons in escape modulation. Finally, we show that the escape displays by the female result from the presence of a courting male and more specifically from the song produced by a courting male. Our results suggest that courtship song has a dual role, promoting both escape and pause in females and that escape is suppressed by the activity of 70A09 neurons, allowing mating to occur.
Tracing the origin of the crayfish plague pathogen, Aphanomyces astaci, to the Southeastern United States
Authors: Martín-Torrijos Laura , Martínez-Ríos María , Casabella-Herrero Gloria , Adams Susan B. , Jackson Colin R. , Diéguez-Uribeondo Javier 
Published: April 2021

AbstractThe oomycete Aphanomyces astaci is an emerging infectious pathogen affecting freshwater crayfish worldwide and is responsible for one of the most severe wildlife pandemics ever reported. The pathogen has caused mass mortalities of freshwater crayfish species in Europe and Asia, and threatens other susceptible species in Madagascar, Oceania and South America. The pathogen naturally coexists with some North American crayfish species that are its chronic carriers. Presumptions that A. astaci originated in North America are based on disease outbreaks that followed translocations of North American crayfish and on the identification of the pathogen mainly in Europe. We studied A. astaci in the southeastern US, a center of freshwater crayfish diversity. In order to decipher the origin of the pathogen, we investigated (1) the distribution and haplotype diversity of A. astaci, and (2) whether there are crayfish species-specificities and/or geographical restrictions for A. astaci haplotypes. A total of 132 individuals, corresponding to 19 crayfish species and one shrimp species from 23 locations, tested positive for A. astaci. Mitochondrial rnnS and rnnL sequences indicated that A. astaci from the southeastern US exhibited the highest genetic diversity so far described for the pathogen (eight haplotypes, six of which we newly describe). Our findings that A. astaci is widely distributed and genetically diverse in the region supports the hypothesis that the pathogen originated in the southeastern US. In contrast to previous assumptions, however, the pathogen exhibited no clear species-specificity or geographical patterns.
Tunneling current and noise of entangled electrons in correlated double quantum dot
Authors: Maslova N. S. , Arseyev P. I. , Mantsevich V. N. 
Published: April 2021

AbstractWe developed general approach for the analysis of tunneling current and its zero frequency noise for a wide class of systems where electron transport occurs through the intermediate structure with localized electrons. Proposed approach opens the possibility to study electron transport through multi-electron correlated states and allows to reveal the influence of spatial and spin symmetry of the total system on the electron transport. This approach is based on Keldysh diagram technique in pseudo-particle representation taking into account the operator constraint on the number of pseudo-particles, which gives the possibility to exclude non-physical states. It was shown that spatial and spin symmetry of the total system can block some channels for electron transport through the correlated quantum dots. Moreover, it was demonstrated that the stationary tunneling current and zero frequency noise in correlated coupled quantum dots depend on initial state of the system. In the frame of the proposed approach it was also shown that for the parallel coupling of two correlated quantum dots to the reservoirs tunneling current and its zero frequency noise are suppressed if tunneling occurs through the entangled triplet state with zero total spin projection on the z axis or enhanced for the tunneling through the singlet state in comparison with electron transport through the uncorrelated localized single-electron state. Obtained results demonstrate that two-electron entangled states in correlated quantum dots give the possibility to tune the zero frequency noise amplitude by blocking some channels for electron transport that is very promising in the sense of two-electron entangled states application in quantum communication and logic devices. The obtained nonmonotonic behavior of Fano factor as a function of applied bias is the direct manifestation of the possibility to control the noise to signal ration in correlated quantum dots. We also provide detailed calculations of current and noise for both single type of carriers and two different types of carriers in the presence and in the absence of Coulomb interaction in Supplementary materials.
Experimental study exploring the factors that promote rib fragility in the elderly
Authors: Liebsch Christian , Hübner Shamila , Palanca Marco , Cristofolini Luca , Wilke Hans-Joachim 
Published: April 2021

AbstractRib fractures represent a common injury type due to blunt chest trauma, affecting hospital stay and mortality especially in elderly patients. Factors promoting rib fragility, however, are little investigated. The purpose of this in vitro study was to explore potential determinants of human rib fragility in the elderly. 89 ribs from 13 human donors (55–99 years) were loaded in antero-posterior compression until fracture using a material testing machine, while surface strains were captured using a digital image correlation system. The effects of age, sex, bone mineral density, rib level and side, four global morphological factors (e.g. rib length), and seven rib cross-sectional morphological factors (e.g. cortical thickness, determined by μCT), on fracture load were statistically examined using Pearson correlation coefficients, Mann–Whitney U test as well as Kruskal–Wallis test with Dunn-Bonferroni post hoc correction. Fracture load showed significant dependencies (p < 0.05) from bone mineral density, age, antero-posterior rib length, cortical thickness, bone volume/tissue volume ratio, trabecular number, trabecular separation, and both cross-sectional area moments of inertia and was significantly higher at rib levels 7 and 8 compared to level 4 (p = 0.001/0.013), whereas side had no significant effect (p = 0.989). Cortical thickness exhibited the highest correlation with fracture load (r = 0.722), followed by the high correlation of fracture load with the area moment of inertia around the longitudinal rib cross-sectional axis (r = 0.687). High correlations with maximum external rib surface strain were detected for bone volume/tissue volume ratio (r = 0.631) and trabecular number (r = 0.648), which both also showed high correlations with the minimum internal rib surface strain (r =  − 0.644/ − 0.559). Together with rib level, the determinants cortical thickness, area moment of inertia around the longitudinal rib cross-sectional axis, as well as bone mineral density exhibited the largest effects on human rib fragility with regard to the fracture load. Sex, rib cage side, and global morphology, in contrast, did not affect rib fragility in this study. When checking elderly patients for rib fractures due to blunt chest trauma, patients with low bone mineral density and the mid-thoracic area should be carefully examined.
Transcriptomic phases of periodontitis lesions using the nonhuman primate model
Authors: Ebersole Jeffrey L. , Nagarajan Radhakrishnan , Kirakodu Sreenatha , Gonzalez Octavio A. 
Published: April 2021

AbstractWe used a nonhuman primate model of ligature-induced periodontitis to identify patterns of gingival transcriptomic after changes demarcating phases of periodontitis lesions (initiation, progression, resolution). A total of 18 adult Macaca mulatta (12–22 years) had ligatures placed (premolar, 1st molar teeth) in all 4 quadrants. Gingival tissue samples were obtained (baseline, 2 weeks, 1 and 3 months during periodontitis and at 5 months resolution). Gene expression was analyzed by microarray [Rhesus Gene 1.0 ST Array (Affymetrix)]. Compared to baseline, a large array of genes were significantly altered at initiation (n = 6049), early progression (n = 4893), and late progression (n = 5078) of disease, with the preponderance being up-regulated. Additionally, 1918 genes were altered in expression with disease resolution, skewed towards down-regulation. Assessment of the genes demonstrated specific profiles of epithelial, bone/connective tissue, apoptosis/autophagy, metabolism, regulatory, immune, and inflammatory responses that were related to health, stages of disease, and tissues with resolved lesions. Unique transcriptomic profiles occured during the kinetics of the periodontitis lesion exacerbation and remission. We delineated phase specific gene expression profiles of the disease lesion. Detection of these gene products in gingival crevicular fluid samples from human disease may contribute to a better understanding of the biological dynamics of the disease to improve patient management.
Interface induced diffusion
Authors: Gurbán S. , Sulyok A. , Menyhárd Miklos , Baradács E. , Parditka B. , Cserháti C. , Langer G. A. , Erdélyi Z. 
Published: April 2021

AbstractInterface induced diffusion had been identified in a thin film system damaged by electron bombardment. This new phenomenon was observed in Al2O3 (some nm thick)/Si substrate system, which was subjected to low energy (5 keV) electron bombardment producing defects in the Al2O3 layer. The defects produced partially relaxed. The rate of relaxation is, however, was different in the vicinity of the interface and in the "bulk" parts of the Al2O3 layer. This difference creates an oxygen concentration gradient and consequently oxygen diffusion, resulting in an altered layer which grows from the Al2O3/Si substrate interface. The relative rate of the diffusion and relaxation is strongly temperature dependent, resulting in various altered layer compositions, SiO2 (at room temperature), Al2O3 + AlOx + Si (at 500 °C), Al2O3 + Si (at 700 °C), as the temperature during irradiation varies. Utilizing this finding it is possible to produce area selective interface patterning.