bluuebunny/crossref_metadata_2025 huggingface dataset:
Key Pathogenic Factors in Coronavirus Disease 2019–Associated Coagulopathy and Acute Lung Injury Highlighted in a Patient With Copresentation of Acute Myelocytic Leukemia: A Case Report
Authors: Olson Lyra B. , Naqvi Ibtehaj A. , Turner Daniel J. , Morrison Sarah A. , Kraft Bryan D. , Chen Lingye , Sullenger Bruce A. , Nair Smita K. , Que Loretta G. , Levy Jerrold H.
Published: March 2021

The role of concurrent illness in coronavirus disease 2019 (COVID-19) is unknown. Patients with leukemia may display altered thromboinflammatory responses. We report a 53-year-old man presenting with acute leukemia and COVID-19 who developed thrombotic complications and acute respiratory distress syndrome. Multiple analyses, including rotational thromboelastometry and flow cytometry on blood and bronchoalveolar lavage, are reported to characterize coagulation and immune profiles. The patient developed chemotherapy-induced neutropenia that may have protected his lungs from granulocyte-driven hyperinflammatory acute lung injury. However, neutropenia also alters viral clearing, potentially enabling ongoing viral propagation. This case depicts a precarious equilibrium between leukemia and COVID-19.
Delayed Obstructive Hydrocephalus After Cardiac Surgery With Cardiopulmonary Bypass in a Patient With Cerebellar Infarction: A Case Report
Authors: Hoshino Shun , Kido Koji , Maeda Keisuke , Ichiba Toshihisa , Takatori Makoto
Published: March 2021

Obstructive hydrocephalus caused by brainstem compression is a life-threatening complication and usually occurs within 6 days, with peak on day 3 after onset of cerebellar infarction. We present a case of obstructive hydrocephalus that developed on day 8 in a patient with cerebellar infarction. A 39-year-old man with cerebellar infarction caused by myocardial infarction–related intraventricular thrombus underwent left ventricular thrombectomy under cardiopulmonary bypass. He was lucid postoperatively, but his consciousness was diminished on day 8 because of obstructive hydrocephalus. Cerebral edema due to cardiopulmonary bypass may contribute to delayed onset of obstructive hydrocephalus, especially in patients with large-sized cerebellar infarction.
The Trade-Comovement Puzzle
Authors: Drozd Lukasz A. , Kolbin Sergey , Nosal Jaromir B.
Published: March 2021

Standard international transmission mechanism of productivity shocks predicts a weak endogenous linkage between trade and business cycle synchronization: a problem known as the trade-comovement puzzle. We provide the foundational analysis of the puzzle, pointing to three natural candidate resolutions: (i) financial market frictions, (ii) Greenwood-Hercowitz-Huffman preferences, and (iii) dynamic trade elasticity that is low in the short run but high in the long run. We show the effects of each of these candidate resolutions analytically and evaluate them quantitatively. We find that while (i) and (ii) fall short of the data, (iii) goes a long way toward resolving the puzzle. (JEL E32, F14, F44)
History Dependence in the Housing Market
Authors: Bracke Philippe , Tenreyro Silvana
Published: March 2021

Using data on the universe of housing transactions in England and Wales over a 20-year period, we document that sale prices and selling propensities are affected by house prices prevailing in the period in which properties were previously bought. Using administrative data on mortgages, we show that cognitive frictions explain most of the history dependence in sale prices, whereas credit frictions are more relevant for selling propensities. We corroborate our analysis with data on online house listings, and we estimate the impact of history dependence on the collapse and slow recovery of housing market activity in the postcrisis period. (JEL E32, R21, R31)
Evaluating the Economic Cost of Coastal Flooding
Authors: Desmet Klaus , Kopp Robert E. , Kulp Scott A. , Nagy Dávid Krisztián , Oppenheimer Michael , Rossi-Hansberg Esteban , Strauss Benjamin H.
Published: March 2021

Sea level rise will cause spatial shifts in economic activity over the next 200 years. Using a spatially disaggregated, dynamic model of the world economy, this paper estimates the consequences of probabilistic projections of local sea level changes. Under an intermediate scenario of greenhouse gas emissions, permanent flooding is projected to reduce global real GDP by 0.19 percent in present value terms. By the year 2200, a projected 1.46 percent of the population will be displaced. Losses in coastal localities are much larger. When ignoring the dynamic response of investment and migration, the loss in real GDP in 2200 increases from 0.11 percent to 4.5 percent. (JEL E23, F01, Q54, Q56)
Transmission of Monetary Policy with Heterogeneity in Household Portfolios
Authors: Luetticke Ralph
Published: March 2021

This paper assesses the importance of heterogeneity in household portfolios for the transmission of monetary policy in a New Keynesian business cycle model with uninsurable income risk and assets with different liquidity. In this environment, monetary transmission works through investment, but redistribution lowers the elasticity of investment via two channels: (i) heterogeneity in marginal propensities to invest, and (ii) time variation in the liquidity premium. Monetary contractions redistribute to wealthy households who have high propensities to invest and a low marginal value of liquidity, thereby stabilizing investment. I provide empirical evidence for countercyclical liquidity premia and heterogeneity in household portfolio responses. (JEL E12, E32, E52, G11, G51)
Sovereign Debt Restructurings
Authors: Dvorkin Maximiliano , Sánchez Juan M. , Sapriza Horacio , Yurdagul Emircan
Published: March 2021

Sovereign debt crises involve debt restructurings characterized by a mix of face value haircuts and maturity extensions. The prevalence of maturity extensions has been hard to reconcile with economic theory. We develop a model of endogenous debt restructuring that captures key facts of sovereign debt and restructuring episodes. While debt dilution pushes for negative maturity extensions, three factors are important in overcoming the effects of dilution and generating maturity extensions upon restructurings: income recovery after default, credit exclusion after restructuring, and regulatory costs of book value haircuts. We employ dynamic discrete choice methods that allow for smoother decision rules, rendering the problem tractable. (JEL E44, F34, F41, H63)
Viewing Injury in Dancers from a Psychological Perspective - A Literature Review
Authors: Pollitt Erin E. , Hutt Kim
Published: March 2021

It has been reported that injury among dancers has a lifetime incidence of 90%, and recent research suggests that up to 60% of those dancers injured will meet the requirements for clinical referral to a psychologist. This study aims to review the existing literature in the field of
dance psychology that focuses on psychological antecedents and responses to injury. Several relevant theories in dance psychology are reviewed. From this literature, it is suggested that psychological techniques can be taught in educational settings to equip dance students with the necessary
tools to look after their bodies and minds, reduce the risk of injury, and aid in healing existing injuries. Greater emphasis should also be placed on combining physical and psychological support to improve holistic care and treatment of dancers' injuries.
Από το Βυζάντιο στην Ινδία και Άπω Ανατολή
Authors: Κορδώσης Αλέξανδρος
Published: March 2021

Η περιοχή της Ερυθράς και η προέκτασή της προς Ινδία, μέσω των θαλασσινών δρόμων, παρουσίαζε πάντα ενδιαφέρον. Σώζονται κείμενα Βυζαντινών συγγραφέων, που παρέχουν πολύτιμες πληροφορίες για τις χώρες της Ερυθράς και του κόλπου του Άντεν, για ορισμένες περιοχές του ινδικού κόσμου, καθώς και για τον δρόμο που οδηγούσε προς Ινδία και Κίνα, μέσα από πολυσύχναστα λιμάνια, στα οποία, κατά τους πρώτους χριστιανικούς αιώνες, η ελληνική γλώσσα αποτελούσε τη lingua franca της εποχής, ενώ δεν έλειπαν και οι χριστιανικές κοινότητες, τουλάχιστον ως την Κεϋλάνη. Ελληνική γλώσσα και χριστιανικές κοινότητες διευκόλυναν την κινητικότητα και το εμπόριο. Κατά την πρώτη βυζαντινή περίοδο τμήματα του παλιού θαλασσινού δρόμου, που περνούσε από τον Ανατολικό Ινδικό, ξεχνιούνται και παίρνουν σπουδαιότητα άλλοι δευτερεύοντες δρόμοι, μέσω Γάγγη και Ασσάμ. Η βυζαντινή ναυτική παρουσία στον Ινδικό μειώθηκε, αλλά δεν κατέστη ανύπαρκτη κατά τον 4ο αι. μ. Χ. (ιδίως από τον Μ. Κωνσταντίνο ως τον Ιουλιανό) και ίσως και στον 5ο αιώνα, οι κερδισμένοι όμως από το εμπόριο ήταν οι ενδιάμεσοι λαοί Αιθίοπες, Άραβες, Ινδοί κλπ., με τη νήσο Κεϋλάνη (Ταπροβάνη ή Σιελεδίβα) να αποτελεί το κέντρο του παγκόσμιου εμπορίου και τη νήσο Διβούς (μάλλον Λακκαδίβες) ένα από τα πιο πολυσύχναστα σημεία. Οι Βυζαντινοί προσπαθούσαν να ελέγχουν το εμπόριο ακόμη και με πολεμικές αναμετρήσεις, μέσω συμμαχικών ενδιάμεσων λαών, όπως ο πόλεμος μεταξύ Αιθιοπίας και Ευδαίμονος Αραβίας (Υεμένης), στον οποίο επικράτησε η σύμμαχός τους Αιθιοπία, και ουσιαστικά εναντίον της αντιζήλου Περσίας. Φαίνεται ότι πέτυχαν, εν μέρει τον σκοπό τους, οι Πέρσες όμως κατόρθωσαν να μπλοκάρουν τον θαλασσινό δρόμο, κυριεύοντας την Υεμένη και στερώντας από τους Βυζαντινούς τις βάσεις τους στην Ερυθρά και τον Ινδικό και απομονώνοντάς τους από τους συμμάχους τους, Αιθίοπες.
Η σχέση του λεξιλογικού επιπέδου παιδιών προσχολικής ηλικίας με το ψυχοκοινωνικό τους προφίλ
Authors: Μοκαΐτη Φανή , Καρούσου Αλεξάνδρα
Published: March 2021

Language is a powerful tool for interpersonal communication and social interaction but also a critical tool for self-regulation of emotions, behavior, and thought. Although limited in number, studies that investigate the relationship between language development and preschool children’s psychosocial skills have shown that children with language difficulties often experience behavioral and social difficulties as well. The samples of these studies, however, usually include children who have already been referred for language disorders –not, therefore, representing the full range of language difficulties– and often lack comparative data from typically developing children. This study aims to explore the relationship between preschool children’s psychosocial profile and their language competence, as reflected in their expressive vocabulary size. Data were collected from 118 Greek-speaking children who course their first year in Kindergarten (4-5 years old). They were given the standardized Greek version of the Word Finding Vocabulary Test. Their psychosocial profile was assessed with a sociometric test as well as the Emotional Well-being Scale for Preschool Children and the Greek standardized version of the Preschool Behavior Checklist given to their teachers. Results reveal interesting relationships between children’s linguistic competence and their social, emotional, and behavioral profiles.
Γλωσσικά και γνωστικά ελλείμματα στο σύνδρομο Sotos: μια μελέτη περίπτωσης
Authors: Μπερμπερίδου Δέσποινα
Published: March 2021

Sotos syndrome is a genetic disorder of mental retardation characterized by specific facial characteristics, overgrowth in childhood, cognitive impairment and speech and language difficulties. In this paper, we report on a single case study of a female adolescent, TK, aged 15;9 diagnosed with Sotos syndrome. The main goal was to investigate her phonological short-term memory abilities as well as her visuospatial memory abilities and language abilities. We employed the following tests: (a) Raven’s Progressive Matrices and Vocabulary Scales (Greek edition) (Raven et al., 2003/2004), (b) Renfrew Word Finding Vocabulary Test – Greek edition (Vogindroukas et al., 2009), (c) Peabody Picture Vocabulary Test –Special Edition (Greek edition) (Simos et al., 2012), (d) Action Picture Test – Greek edition (Vogindroukas et al., 2011), and (e) Bezevegis et al.’s (2008) memory test. The most profound deficiencies were observed in expressive vocabulary and pragmatic/communicative skills, while difficulties were also found in verbal short-term memory. Deficiencies were also observed in verbal and non-verbal IQ in agreement with previous findings (Cole & Hughes, 1994. de Boer et al., 2004. Finegan et al., 1994). TK’s performance on visuospatial sketchpad was slightly better compared to the results obtained through the other tests. We discuss the clinical implications of our findings.
Die spätantike Gräbergruppe Basel-Waisenhaus
Authors: Baumann Michael , Asal Markus , Allemann Martin
Published: March 2021

Im Jahr 2010 wurde bei Bauarbeiten im Areal des Basler Waisenhauses eine kleinere Gruppe von Gräbern entdeckt, die anhand von wenigen Beigaben mit einiger Wahrscheinlichkeit in das zweite Viertel des 5. Jahrhunderts datiert. Mit dem Fund dieser Gräber liegt für die Epoche der Spätantike in Basel erstmals eine Gruppe von Bestattungen vor, die eine zivile rechtsrheinische Siedlungstätigkeit ausserhalb der bekannten Befestigungsanlagen in der ersten Hälfte des 5. Jahrhunderts anzeigt.
The network structure of depressive symptomatology in Peruvian adults with arterial hypertension
Authors: Ramos-Vera Cristian , Banos-Chaparro Jonatan , Ogundokun Roseline Oluwaseun
Published: March 2021

Background: Globally, arterial hypertension (AH) has increased by 90% over the last four decades, and has increased by 1.6% in Peru over the previous four years. Scientific evidence indicates the prevalence of depressive symptoms in patients with AH and its importance in the comprehensive evaluation of the adult for adherence to clinical treatment. Previous studies carried out in the Peruvian population with AH mostly report the prevalence and associations, but do not indicate which depressive symptoms are more relevant in patients with AH. This study involved a network analysis of depressive symptomatology in Peruvian patients with AH using network estimation. Network analysis is used in this study for analysis, control, and monitoring purposes.

Method: A representative cross-sectional study at the national level, using secondary data from 2019 Demographic and Family Health Survey (ENDES) was performed. The sample used included men and women of age over 17 years diagnosed with AH and was able to respond to Patient Health Questionnaire-9 (PHQ-9).

Results: The symptoms of depressive mood (bridging force and centrality) and energy fatigue or loss (bridge centrality) play an essential role in the network structure, as does the feeling of uselessness in terms of closeness and intermediation.

Conclusion: The study highlighted the symptoms related to depressive mood and energy fatigue or loss as bridging symptoms, which could trigger a depressive episode in patients diagnosed with AH. The results will contribute to developing personalized treatments aimed at patients with specific depressive symptoms who have also been diagnosed with AH. The study analysis presents statistical coefficients of effect size (≤ 0,1 = small; > 0,1 to < 0,5 = moderate; ≥ 0,5 = large) to determine network connections.
MGMT promoter gene methylation and neurological scale improvement in glioma: a cohort study
Authors: Gunawan Pricilla Yani , Islam Andi Asadul , July Julius , Patelongi Ilhamjaya , Bukhari Agussalim , Massi Muhammad Nasrum
Published: March 2021

Background: Glioma is one of the most common primary brain tumours and conveys a dismal prognosis despite aggressive treatment. Several biomarkers have been studied in the hope of yielding better diagnostic accuracy and improving patient management. Besides survival, functional and neurological disability are concerns that have no lesser importance. In 2017, a disease-specific assessment tool – the Neurologic Assessment in Neuro-Oncology (NANO) scale – was developed to measure neurologic function in neuro-oncology cases. We sought to determine biomarkers that might be associated with neurological scale improvement in glioma patients. 

Methods: Glioma grade II-IV patients were recruited from three major hospitals in Jakarta-Tangerang. Isocitrate dehydrogenase (IDH) mutation and O6-methylguanine-DNA methyltransferase (MGMT) promoter gene methylation were tested, as well as patients’ neurological function before surgery and three months after. Improvement in neurological scale (NANO scale) was considered positive if there was a decrement of ≥1 of the scale. 

Results: There were 54 patients included in the study. Mean age was 43.63 (14.723) years old, and 61.1% were male. As much as 16 (29.6%) carried a mutation in codon 132 of the IDH1 gene, and 33 (61.1%) were MGMT methylated. Median NANO scale score before and three months after surgery was 4 (0-12) and 3 (0-12), respectively. Neurological improvement was found in 44 (81.5%) of the patients. Among patients with MGMT promoter gene methylation, 90.9% showed neurological improvement (p=0.035; OR=5; 95%CI 1.122-22.272). 

Conclusions: Gliomas with MGMT promoter gene methylation are more likely to show neurological improvement three months after surgery.
The in vitro direct mycobacterial growth inhibition assay (MGIA) for the early evaluation of TB vaccine candidates and assessment of protective immunity: a protocol for non-human primate cells
Authors: Tanner Rachel , Hoogkamer Emily , Bitencourt Julia , White Andrew , Boot Charelle , Sombroek Claudia C. , Harris Stephanie A. , O'Shea Matthew K. , Wright Daniel , Wittenberg Rachel , Sarfas Charlotte , Satti Iman , Verreck Frank A.W. , Sharpe Sally A. , Fletcher Helen A. , McShane Helen
Published: March 2021

The only currently available approach to early efficacy testing of tuberculosis (TB) vaccine candidates isin vivopreclinical challenge models. These typically include mice, guinea pigs and non-human primates (NHPs), which must be exposed to virulentM.tbin a ‘challenge’ experiment following vaccination in order to evaluate protective efficacy. This procedure results in disease development and is classified as ‘Moderate’ in severity under EU legislation and UK ASPA licensure. Furthermore, experiments are relatively long and animals must be maintained in high containment level facilities, making them relatively costly. We describe anin vitroprotocol for the direct mycobacterial growth inhibition assay (MGIA) for use in the macaque model of TB vaccine development with the aim of overcoming some of these limitations. Importantly, using anin vitroassay in place ofin vivo M.tbchallenge represents a significant refinement to the existing procedure for early vaccine efficacy testing. Peripheral blood mononuclear cell and autologous serum samples collected from vaccinated and unvaccinated control animals are co-cultured with mycobacteria in a 48-well plate format for 96 hours. Adherent monocytes are then lysed to release intracellular mycobacteria which is quantified using the BACTEC MGIT system and colony-forming units determined relative to an inoculum control and stock standard curve. We discuss related optimisation and characterisation experiments, and review evidence that the direct NHP MGIA provides a biologically relevant model of vaccine-induced protection. The potential end-users of the NHP MGIA are academic and industry organisations that conduct the assessment of TB vaccine candidates and associated protective immunity using the NHP model. This approach aims to provide a method for high-throughput down-selection of vaccine candidates going forward toin vivoefficacy testing, thus expediting the development of a more efficacious TB vaccine and offering potential refinement and reduction to the use of NHPs for this purpose.
A deep learning segmentation strategy that minimizes the amount of manually annotated images
Authors: Pécot Thierry , Alekseyenko Alexander , Wallace Kristin
Published: March 2021

Deep learning has revolutionized the automatic processing of images. While deep convolutional neural networks have demonstrated astonishing segmentation results for many biological objects acquired with microscopy, this technology's good performance relies on large training datasets. In this paper, we present a strategy to minimize the amount of time spent in manually annotating images for segmentation. It involves using an efficient and open source annotation tool, the artificial increase of the training data set with data augmentation, the creation of an artificial data set with a conditional generative adversarial network and the combination of semantic and instance segmentations. We evaluate the impact of each of these approaches for the segmentation of nuclei in 2D widefield images of human precancerous polyp biopsies in order to define an optimal strategy.
Time-Varying Risk Aversion and Dynamic Portfolio Allocation
Authors: Li Haitao , Wu Chongfeng , Zhou Chunyang
Published: March 2021

Despite the overwhelming evidence of time-varying risk aversion documented in recent literature, standard dynamic portfolio theories often adopt an assumption of constant (relative) risk aversion due to analytical tractability. In “Time Varying Risk Aversion and Dynamic Portfolio Allocation,” Li et al. explicitly consider the implications of time-varying risk aversion for dynamic portfolio allocation under the framework of regime-switching models. An investor with regime-dependent utility exhibits a decreasing relative risk aversion (DRRA) and has higher risk aversion when a bear market regime is more likely in the future. They develop an efficient dynamic programming algorithm that overcomes the challenges imposed by regime-dependent preference in obtaining time-consistent portfolio policies. The empirical results show that VIX is an important predictor of regime shifts and that investors with regime-dependent risk aversion achieve better investment performance than those with constant risk aversion.
Regional Frequency Analysis of Maximum Monthly Rainfall in Haryana State of India Using L-Moments
Authors: Nain Mohit , Hooda B. K.
Published: March 2021

The paper aims to select the appropriate regional frequency distribution for the maximum monthly rainfall and estimation of quantiles using L-moments for the 27 rain gauge stations in Haryana. These 27 rain gauge stations were grouped into three homogeneous regions (Region-1, Region-2, and Region-3) using Ward’s method of cluster analysis. To confirm the homogeneity of each region, L-moments based measure of heterogeneity was used. For each homogeneous region, a regional distribution was selected with the help of the L-moments ratio diagram and goodness-of-fit test. Results of the goodness-of-fit test and L-moments ratio diagram indicated that Generalized Logistic and Generalized Extreme Value distributions were best- fitted regional frequency distributions for the Region-1 and Region-2 respectively while for Region-3, Pearson Type-3) was best-fitted distribution. The quantiles for each region were calculated and the regional growth curves were developed. The accuracy measurements were determined using Monte Carlo simulations for the regional quantiles. Results of simulations showed that uncertainty in regional quantiles measured by Root Mean Square Error value and 90 percent error limits were small when the return period was low but uncertainty in quantiles increases as the return period increases.
Honeybee (Apis mellifera) Maternal Effect Causes Alternation of DNA Methylation Regulating Queen Development
Authors: He Xu Jiang , Wei Hao , Jiang Wu Jun , Liu Yi Bo , Wu Xiao Bo , Zeng Zhijiang
Published: March 2021

Queen-worker caste dimorphism is a typical trait for honeybees (Apis mellifera). We previously showed a maternal effect on caste differentiation and queen development, where queens emerged from queen-cell eggs (QE) had higher quality than queens developed from worker cell eggs (WE). In this study, newly-emerged queens were reared from QE, WE, and 2-day worker larvae (2L). The thorax size and DNA methylation levels of queens were measured. We found that queens emerging from QE had significantly larger thorax length and width than WE and 2L. Epigenetic analysis showed that QE/2L comparison had the most different methylated genes (DMGs, 612) followed by WE/2L (473), and QE/WE (371). Interestingly, a great number of DMGs (42) were in genes belonging to mTOR, MAPK, Wnt, Notch, Hedgehog, FoxO, and Hippo signaling pathways that are involved in regulating caste differentiation, reproduction and longevity. This study proved that honeybee maternal effect causes epigenetic alteration regulating caste differentiation and queen development.
Variational scaling law for atmospheric propagation
Authors: Potoczak Bragdon Sophia , Cargill Daniel , Grosek Jacob
Published: March 2021

A new scaling law model for propagation of optical beams through
atmospheric turbulence is presented and compared to a common scalar
stochastic waveoptics technique. This methodology tracks the evolution
of the important beam wavefront and phasefront parameters of a
propagating Gaussian-shaped laser field as it moves through
atmospheric turbulence, assuming a conservation of power. As with
other scaling laws, this variational technique makes multiple
simplifying assumptions about the optical beam to capture the
essential features of interest, while significantly reducing the
computational cost of calculation. This variational scaling law is
shown to work reliably with moderately high turbulence strengths.
Individual design of aberration-free intraocular lenses
Authors: Chassagne Bruno , Canioni Lionel
Published: March 2021

An analytical tool capable of easily calculating a new aspheric intraocular lens (IOL) (shape factor, aspherization) chosen to be designed as “aberration free” in terms of spherical aberration and/or coma is reported. In terms of retinal image quality, the theoretical performances given by the new proposed IOLs compare well with commercial IOLs.
Single-shot measurement of the nonlinear refractive index of air at 9.2 µm with a picosecond terawatt CO2 laser
Authors: Polyanskiy Mikhail N. , Babzien Marcus , Pogorelsky Igor V. , Kupfer Rotem , Vodopyanov Konstantin L. , Palmer Mark A.
Published: March 2021

We developed a simple, accurate single-shot method to determine the nonlinear refractive index of air by measuring the evolution of the spatial shape of a laser beam propagating through the atmosphere. A distinctive feature of this new method, which relies on a modified Fresnel propagation model for data analysis, is the use of a hard aperture for producing a well-defined, high-quality beam from a comparatively non-uniform quasi-flat-top beam, which is typical for high-peak-power lasers. The nonlinear refractive index of air for a very short (2 ps) long-wave infrared (LWIR) laser pulse was measured for the first time, to the best of our knowledge, yielding

n
2

=
3.0
×

10

−
23

m

2

/

W

at 9.2 µm. This result is 40% lower than a corresponding measurement with longer (200 ps) LWIR pulses at a similar wavelength.
Inflection point: a perspective on photonic nanojets
Authors: Gu Guoqiang , Zhang Pengcheng , Chen Sihui , Zhang Yi , Yang Hui
Published: March 2021

When light propagates through the edge or middle part of a microparticle’s incoming interface, there is a basic rule that light converges and diverges rapidly or slowly at the output port. These two parts are referred to as the region of rapid change (RRC) and region of slow change (RSC), respectively. Finding the boundary point between RRC and RSC is the key to reveal and expound upon this rule scientifically. Based on the correlation between light convergence–divergence and the slope of emergent light, combined with the relationship between a natural logarithm and growth in physical reality and the second derivative of a function in practical significance, we determine the boundary point between RRC and RSC, namely, the inflection point. From such a perspective, a photonic nanojet (PNJ) and near-field focusing by light irradiation on RSC and RRC, as well as the position of the inflection point under different refractive index contrasts and the field distribution of light focusing, are studied with finite-element-method-based numerical simulation and ray-optics-based theoretical analysis. By illuminating light of different field intensity ratios to the regions divided by the inflection point, we demonstrate the generation of a photonic hook (PH) and the modulation of PNJ/PH in a new manner.
Super-resolution imaging by optical incoherent synthetic aperture with one channel at a time
Authors: Bulbul Angika , Rosen Joseph
Published: March 2021

Imaging with an optical incoherent synthetic aperture (SA) means that the incoherent light from observed objects is processed over time from various points of view to obtain a resolution equivalent to single-shot imaging by the SA larger than the actual physical aperture. The operation of such systems has always been based on two-wave interference where the beams propagate through two separate channels. This limitation of two channels at a time is removed in the present study with the proposed SA where the two beams pass through the same single channel at any given time. The system is based on a newly developed self-interference technique named coded aperture correlation holography. At any given time, the recorded intensity is obtained from interference between two waves co-propagating through the same physical channel. One wave oriented in a particular polarization is modulated by a pseudorandom coded phase mask and the other one oriented orthogonally passes through an open subaperture. Both subapertures are multiplexed at the same physical window. The system is calibrated by a point spread hologram synthesized from the responses of a guide star. All the measurements are digitally processed to achieve a final image with a resolution higher than that obtained by the limited physical aperture. This unique configuration can offer alternatives for the current cumbersome systems composed of far apart optical channels in the large optical astronomical interferometers. Furthermore, the proposed concept paves the way to an SA system with a single less-expensive compact light collector in an incoherent optical regime that may be utilized for future ground-based or space telescopes.
Androgens regulate ovarian gene expression by balancing Ezh2-Jmjd3 mediated H3K27me3 dynamics
Authors: Roy Sambit , Huang Binbin , Sinha Niharika , Wang Jianrong , Sen Aritro
Published: March 2021

Conventionally viewed as male hormone, androgens play a critical role in female fertility. Although androgen receptors (AR) are transcription factors, to date very few direct transcriptional targets of ARs have been identified in the ovary. Using mouse models, this study provides three critical insights about androgen-induced gene regulation in the ovary and its impact on female fertility. First, RNA-sequencing reveals a number of genes and biological processes that were previously not known to be directly regulated by androgens in the ovary. Second, androgens can also influence gene expression by decreasing the tri-methyl mark on lysine 27 of histone3 (H3K27me3), a gene silencing epigenetic mark. ChIP-seq analyses highlight that androgen-induced modulation of H3K27me3 mark within gene bodies, promoters or distal enhancers have a much broader impact on ovarian function than the direct genomic effects of androgens. Third, androgen-induced decrease of H3K27me3 is mediated through (a) inhibiting the expression and activity of Enhancer of Zeste Homologue 2 (EZH2), a histone methyltransferase that promotes tri-methylation of K27 and (b) by inducing the expression of a histone demethylase called Jumonji domain containing protein-3 (JMJD3/KDM6B), responsible for removing the H3K27me3 mark. Androgens through the PI3K/Akt pathway, in a transcription-independent fashion, increase hypoxia-inducible factor 1 alpha (HIF1α) protein levels, which in turn induce JMJD3 expression. Furthermore, proof of concept studies involving in vivo knockdown of Ar in the ovary and ovarian (granulosa) cell-specific Ar knockout mouse model show that ARs regulate the expression of key ovarian genes through modulation of H3K27me3.
Density responses of lesser-studied carnivores to habitat and management strategies in southern Tanzania’s Ruaha-Rungwa landscape
Authors: Hardouin Marie , Searle Charlotte E. , Strampelli Paolo , Smit Josephine , Dickman Amy , Lobora Alex L. , Rowcliffe J. Marcus
Published: March 2021

Compared to emblematic large carnivores, most species of the order Carnivora receive little conservation attention despite increasing anthropogenic pressure and poor understanding of their status across much of their range. We employed systematic camera trapping and spatially explicit capture-recapture modelling to estimate variation in population density of serval, striped hyaena and aardwolf across the mixed-use Ruaha-Rungwa landscape in southern Tanzania. We selected three sites representative of different habitat types, management strategies, and levels of anthropogenic pressure: Ruaha National Park’s core tourist area, dominated by Acacia-Commiphora bushlands and thickets; the Park’s miombo woodland; and the neighbouring community-run MBOMIPA Wildlife Management Area, also covered in Acacia-Commiphora. The Park’s miombo woodlands supported a higher serval density (5.56 [Standard Error = ±2.45] individuals per 100 km2) than either the core tourist area (3.45 [±1.04] individuals per 100 km2) or the Wildlife Management Area (2.08 [±0.74] individuals per 100 km2). Taken together, precipitation, the abundance of apex predators, and the level of anthropogenic pressure likely drive such variation. Striped hyaena were detected only in the Wildlife Management Area and at low density (1.36 [±0.50] individuals per 100 km2), potentially due to the location of the surveyed sites at the edge of the species’ global range, high densities of sympatric competitors, and anthropogenic edge effects. Finally, aardwolf were captured in both the Park’s core tourist area and the Wildlife Management Area, with a higher density in the Wildlife Management Area (13.25 [±2.48] versus 9.19 [±1.66] individuals per 100 km2), possibly as a result of lower intraguild predation and late fire outbreaks in the area surveyed. By shedding light on three understudied African carnivore species, this study highlights the importance of miombo woodland conservation and community-managed conservation, as well as the value of by-catch camera trap data to improve ecological knowledge of lesser-studied carnivores.
Bioleaching of iron from laterite soil using an isolated Acidithiobacillus ferrooxidans strain and application of leached laterite iron as Fenton’s catalyst in selective herbicide degradation
Authors: S Bhaskar , Manu Basavaraju , M Y Sreenivasa
Published: March 2021

A novel isolated strain Acidithiobacillus ferrooxidans BMSNITK17 has been investigated for its bioleaching potential from lateritic soil and the results are presented. System conditions like pH, feed mineral particle size, pulp density, temperature, rotor speed influences bioleaching potential of Acidithiobcillus ferrooxidans BMSNITK17 in leaching out iron from laterite soil. Effect of sulfate addition on bioleaching efficiency is studied. The bioleached laterite iron (BLFe’s) on evaluation for its catalytic role in Fenton’s oxidation for the degradation of ametryn and dicamba exhibits 94.24% of ametryn degradation and 92.45% of dicamba degradation efficiency. Fenton’s oxidation performed well with the acidic pH 3. The study confirms the role of Acidithiobacillus ferrooxidans in leaching iron from lateritic ore and the usage of bioleached lateritic iron as catalyst in the Fenton’s Oxidation.
How array design creates SNP ascertainment bias
Authors: Geibel Johannes , Reimer Christian , Weigend Steffen , Weigend Annett , Pook Torsten , Simianer Henner
Published: March 2021

Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™Genome-Wide Chicken Arrayin silicoand evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
Light chain skewing in autoantibodies and B-cell receptors of the citrullinated antigen-binding B-cell response in rheumatoid arthritis
Authors: Slot Linda M. , Vergroesen Rochelle D. , Kerkman Priscilla F. , Staudinger Ellen , Reijm Sanne , van Dooren Hugo J. , van der Voort Ellen I. H. , Huizinga Tom W. J. , Toes René E. M. , Scherer Hans U.
Published: March 2021

Rheumatoid arthritis (RA) is a chronic autoimmune disease affecting 1% of the world population. RA is associated with the presence of autoantibodies, of which anti-citrullinated protein antibodies (ACPA) are most prominent. ACPA are produced by citrullinated antigen-binding B cells that have presumably survived tolerance checkpoints. So far, it is unclear how and when such autoreactive B cells emerge. Light chain (LC) rearrangement and mutation rates can be informative with regard to selection steps during B-cell development. Therefore, we studied LC characteristics of ACPA-expressing B cells and secreted ACPA with the aim to better understand the development of this disease-specific, autoreactive B-cell response. Paired ACPA-IgG and ACPA-depleted IgG were isolated from serum (n = 87) and synovial fluid (SF, n = 21) of patients with established RA. We determined the LC composition for each fraction by ELISA using kappa(Igκ)- and lambda(Igλ) LC-specific antibodies. Cellular LC expression was determined using flow cytometry. In addition, we used a B-cell receptor (BCR)-specific PCR to obtain LC variable region sequences of citrullinated antigen- and tetanus toxoid (TT)-binding B cells. In serum, we observed an increased frequency of lambda LC in ACPA-IgG (1.64:1) compared to control IgG (2.03:1) and to the κ/λ ratio reported for healthy individuals (2:1). A similar trend towards higher frequencies of lambda LCs was observed for ACPA-IgG in SF (1.84:1). Additionally, the percentage of Igλ-expressing B cells was higher for citrullinated antigen-binding B cells (51%) compared to TT-specific (43%) and total CD19+CD20+B cells (36%). Moreover, an increased Igλ percentage was observed in BCR-sequences derived from ACPA-expressing (49%) compared to TT-specific B cells (34%). Taken together, we report an enhanced frequency of lambda LCs in the secreted ACPA-IgG repertoire and, on the cellular level, in BCR sequences of ACPA-expressing B cells compared to control. This skewing in the autoreactive B-cell repertoire could reflect a process of active selection.
Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus
Authors: Giddings Lesley-Ann , Lountos George T. , Kim Kang Woo , Brockley Matthew , Needle Danielle , Cherry Scott , Tropea Joseph E. , Waugh David S.
Published: March 2021

N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent kcat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s-1 and 0.24 ± 0.01 s-1, respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent kcat for NADPH (0.034 ± 0.008 s-1) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH KM was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent kcat and KM for cadaverine in Csaky assays were 0.048 ± 0.004 s-1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.
Evaluation of the basic assay performance of the GeneSoc® rapid PCR testing system for detection of severe acute respiratory syndrome coronavirus 2
Authors: Watanabe Ryosuke , Asai Satomi , Kakizoe Hidehumi , Saeki Hirofumi , Masukawa Atsuko , Miyazawa Miki , Ohtagawa Kazumi , Ravzanaaadii Mend-Amar , Doi Mika , Atsumi Haruyo , Umezawa Kazuo , Miyachi Hayato
Published: March 2021

In the ongoing coronavirus disease 2019 (COVID-19) pandemic, PCR has been widely used for screening patients displaying relevant symptoms. The rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enables prompt diagnosis and the implementation of proper precautionary and isolation measures for the patient. In the present study, we aimed to evaluate the basic assay performance of an innovative PCR system, GeneSoC® (Kyorin Pharmaceutical Co. Ltd., Tokyo, Japan). A total of 1,445 clinical samples were submitted to the clinical laboratory, including confirmed or suspected cases of COVID-19, from February 13 to August 31. Specimen types included nasopharyngeal swabs. The sampling was performed several times for each patient every 2–7 days. Using this system, sequences specific for SARS-CoV-2 RNA could be detected in a sample within 10–15 min using the microfluidic thermal cycling technology. Analytical sensitivity studies showed that GeneSoC® could detect the target sequence of the viral envelope and RNA-dependent RNA-polymerase (RdRp) genes at 5 and 10 copies/μL, respectively. The precision of the GeneSoC® measurements using clinical isolates of the virus at a concentration of 103 copies/μL was favorable for both the genes; within-run repeatability and between-run reproducibility coefficient of variation values were less than 3% and 2%, respectively; and the reproducibility of inter-detection units was less than 5%. Method comparison by LightCycler® 480 showed the positive and negative agreement to be 100% [(174/174) and (1271/1271), respectively]. GeneSoC® proved to be a rapid and reliable detection system for the prompt diagnosis of symptomatic COVID-19 patients and could help reduce the spread of infections and facilitate more rapid treatment of infected patients.
KG2Vec: A node2vec-based vectorization model for knowledge graph
Authors: Wang YueQun , Dong LiYan , Jiang XiaoQuan , Ma XinTao , Li YongLi , Zhang Hao
Published: March 2021

Since the word2vec model was proposed, many researchers have vectorized the data in the research field based on it. In the field of social network, the Node2Vec model improved on the basis of word2vec can vectorize nodes and edges in social networks, so as to carry out relevant research on social networks, such as link prediction, and community division. However, social network is a network with homogeneous structure. When dealing with heterogeneous networks such as knowledge graph, Node2Vec will lead to inaccurate prediction and unreasonable vector quantization data. Specifically, in the Node2Vec model, the walk strategy for homogeneous networks is not suitable for heterogeneous networks, because the latter has distinguishing features for nodes and edges. In this paper, a Heterogeneous Network vector representation method is proposed based on random walks and Node2Vec, called KG2vec (Heterogeneous Network to Vector) that solves problems related to the inadequate consideration of the full-text semantics and the contextual relations that are encountered by the traditional vector representation of the knowledge graph. First, the knowledge graph is reconstructed and a new random walk strategy is applied. Then, two training models and optimizing strategies are proposed, so that the contextual environment between entities and relations is obtained, semantically providing a full vector representation of the Heterogeneous Network. The experimental results show that the KG2VEC model solves the problem of insufficient context consideration and unsatisfactory results of one-to-many relationship in the vectorization process of the traditional knowledge graph. Our experiments show that KG2vec achieves better performance with higher accuracy than traditional methods.