bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing bleb mass dynamics in single cells using quantitative phase microscopy
Authors: Steelman Zachary A. , Sedelnikova Anna , Coker Zachary N. , Kiester Allen , Noojin Gary , Ibey Bennett L. , Bixler Joel N.
Published: May 2021

Understanding biological responses to directed energy (DE) is critical
to ensure the safety of personnel within the Department of Defense. At
the Air Force Research Laboratory, we have developed or adapted
advanced optical imaging systems that quantify biophysical responses
to DE. One notable cellular response to DE exposure is the formation
of blebs, or semi-spherical protrusions of the plasma membrane in
living cells. In this work, we demonstrate the capacity of
quantitative phase imaging (QPI) to both visualize and quantify the
formation of membrane blebs following DE exposure. QPI is an
interferometric imaging tool that uses optical path length as a
label-free contrast mechanism and is sensitive to the non-aqueous mass
density, or dry mass, of living cells. Blebs from both CHO-K1 and U937
cells were generated after exposure to a series of 600 ns, 21.2 kV/cm
electric pulses. These blebs were visualized in real time, and their
dry mass relative to the rest of the cell body was quantified as a
function of time. It is our hope that this system will lead to an
improved understanding of both DE-induced and apoptotic blebbing.
Unified k-space theory of optical coherence tomography
Authors: Zhou Kevin C. , Qian Ruobing , Dhalla Al-Hafeez , Farsiu Sina , Izatt Joseph A.
Published: May 2021

We present a general theory of optical coherence tomography (OCT), which synthesizes the fundamental concepts and implementations of OCT under a common 3Dk-space framework. At the heart of this analysis is the Fourier diffraction theorem, which relates the coherent interaction between a sample and plane wave to the Ewald sphere in the 3Dk-space representation of the sample. While only the axial dimension of OCT is typically analyzed ink-space, we show that embracing a fully 3Dk-space formalism allows explanation of nearly every fundamental physical phenomenon or property of OCT, including contrast mechanism, resolution, dispersion, aberration, limited depth of focus, and speckle. The theory also unifies diffraction tomography, confocal microscopy, point-scanning OCT, line-field OCT, full-field OCT, Bessel beam OCT, transillumination OCT, interferometric synthetic aperture microscopy (ISAM), and optical coherence refraction tomography (OCRT), among others. Our unified theory not only enables clear understanding of existing techniques but also suggests new research directions to continue advancing the field of OCT.
Extraction and control of permittivity of hyperbolic metamaterials with optical nonlocality
Authors: Xin Jian , Zong Jie , Gao Junhua , Wang Yuxiao , Song Yinglin , Zhang Xueru
Published: May 2021

Metal nanorod arrays exhibit hyperbolic dispersion and optical nonlocality under certain conditions. Therefore, their optical behaviors can hardly be expressed by incident-angle-independent effective permittivity. Here we extract effective permittivity of silver nanorod arrays with diameters of 4 nm, 12 nm, and 20 nm by polarized transmission method in the visible range. The incident angles are chosen from 20° to 60° to study the influence of optical nonlocality on permittivity. We demonstrate how the diameter of the nanorods can control the effective permittivity beyond the effective medium theory. The results suggest that the effective permittivity gradually loses its accuracy as the diameter increases due to the optical nonlocality. Our experiment verifies that ultrathin nanorod arrays can resist the fluctuations caused by changes in incident angle. We also extract k-dependent effective permittivity of nanorods with larger diameters.
Anisotropic luminescence and third-order electric susceptibility of Mg-doped gallium oxide under the half-bandgap edge
Authors: Zhang Naiji , Kislyakov Ivan M. , Xia Changtai , Qi Hongji , Wang Jun , Mohamed H. F.
Published: May 2021

Strong anisotropy of photoluminescence of a (100)-cut β-Ga2O3 and a Mg-doped β-Ga2O3 single crystals was found in UV and visible spectral range, the bands of which were attributed to different types of transitions in the samples. Green photoluminescence in the Mg-doped sample was enhanced approximately twice. A remarkable enhancement of two-photon absorption and self-focusing in β-Ga2O3 after doping was revealed by 340-fs laser Z-scanning at 515 nm. The absolute value of complex third order susceptibility χ(3) determined from the study increases by 19 times in [001] lattice direction. Saturable absorption and associated self-defocusing were found in the undoped crystal in the [010] direction, which was explained by the anisotropic excitation of F-centers on intrinsic oxygen defects. This effect falls out of resonance in the Mg-doped crystal. The χ(3) values which are provided by a decrease of bandgap in Mg-doped β-Ga2O3 are χ(3) [001] = 1.85·10−12 esu and χ(3) [010]=χ(3)
yyyy
 = 0.92·10−12 esu. Our result is only one order of magnitude lower than the best characteristic in green demonstrated by a Mg-doped GaN, which encourages subsequent development of Mg-doped β-Ga2O3 as an effective nonlinear optical material in this region.
Multifunctional metalens generation using bilayer all-dielectric metasurfaces: erratum
Authors: Chen Li , Hao Yuan , Zhao Lin , Wu Ruihuan , Liu Yue , Wei Zhongchao , Xu Ning , Li Zhaotang , Liu Hongzhan
Published: May 2021

We provide corrected equations for our previous publication [Opt. Express 29, 9332(2021)10.1364/OE.420003].
Inverse Anderson transition in photonic cages
Authors: Longhi Stefano
Published: May 2021

Transport inhibition via Anderson localization is ubiquitous in disordered periodic lattices. However, in crystals displaying only flatbands, disorder can lift macroscopic band flattening, removing geometric localization and enabling transport in certain conditions. Such a striking phenomenon, dubbed inverse Anderson transition and predicted for three-dimensional flatband systems, has thus far not been directly observed. Here we suggest a simple quasi one-dimensional photonic flatband system, namely, an Aharonov–Bohm photonic cage, in which correlated binary disorder induces an inverse Anderson transition and ballistic transport.
The impact of the COVID-19 pandemic on rabies reemergence in Latin America: The case of Arequipa, Peru
Authors: Raynor Brinkley , Díaz Elvis W. , Shinnick Julianna , Zegarra Edith , Monroy Ynes , Mena Claudia , De la Puente-León Micaela , Levy Michael Z. , Castillo-Neyra Ricardo
Published: May 2021

In Latin America, there has been tremendous progress towards eliminating canine rabies. Major components of rabies elimination programs leading to these successes have been constant and regular surveillance for rabid dogs and uninterrupted yearly mass dog vaccination campaigns. Unfortunately, vital measures to control COVID-19 have had the negative trade-off of jeopardizing these rabies elimination and prevention activities. We aimed to assess the effect of interrupting canine rabies surveillance and mass dog vaccination campaigns on rabies trends. We built a deterministic compartment model of dog rabies dynamics to create a conceptual framework for how different disruptions may affect rabies virus transmission. We parameterized the model for conditions found in Arequipa, Peru, a city with active rabies virus transmission. We examined our results over a range of plausible values for R0 (1.36–2.0). Also, we prospectively evaluated surveillance data during the pandemic to detect temporal changes. Our model suggests that a decrease in canine vaccination coverage as well as decreased surveillance could lead to a sharp rise in canine rabies within months. These results were consistent over all plausible values of R0. Surveillance data from late 2020 and early 2021 confirms that in Arequipa, Peru, rabies cases are on an increasing trajectory. The rising rabies trends in Arequipa, if indicative to the region as whole, suggest that the achievements made in Latin America towards the elimination of dog-mediated human rabies may be in jeopardy.
Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images
Authors: Lin Ye , Andersson Sean B.
Published: May 2021

Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the location of the emitter inside each frame of a sequence of camera images is estimated using, for example, Gaussian fitting (GF), and these locations are linked to provide an estimate of the trajectory. Trajectories are then analyzed by using Mean Square Displacement (MSD) or Maximum Likelihood Estimation (MLE) techniques to determine motion parameters such as diffusion coefficients. However, the problems of localization and parameter estimation are clearly coupled. Motivated by this, we have created an Expectation Maximization (EM) based framework for simultaneous localization and parameter estimation. We demonstrate this framework through two representative methods, namely, Sequential Monte Carlo combined with Expectation Maximization (SMC-EM) and Unscented Kalman Filter combined with Expectation Maximization (U-EM). Using diffusion in two-dimensions as a prototypical example, we conduct quantitative investigations on localization and parameter estimation performance across a wide range of signal to background ratios and diffusion coefficients and compare our methods to the standard techniques based on GF-MSD/MLE. To demonstrate the flexibility of the EM based framework, we do comparisons using two different camera models, an ideal camera with Poisson distributed shot noise but no readout noise, and a camera with both shot noise and the pixel-dependent readout noise that is common to scientific complementary metal-oxide semiconductor (sCMOS) camera. Our results indicate our EM based methods outperform the standard techniques, especially at low signal levels. While U-EM and SMC-EM have similar accuracy, U-EM is significantly more computationally efficient, though the use of the Unscented Kalman Filter limits U-EM to lower diffusion rates.
Fertilization and seasonality influence on the photochemical performance of tree legumes in forest plantation for area recovery in the Amazon
Authors: Jaquetti Roberto Kirmayr , Gonçalves José Francisco de Carvalho , Nascimento Henrique Eduardo Mendonça , da Costa Karen Cristina Pires , Maia Jair Max Furtunato , Schimpl Flávia Camila
Published: May 2021

N-fixing leguminous species can reach atmospheric dinitrogen gas (N2), having an advantage under N-limited degraded environments. These N-fixers are constantly used as facilitative species. Chlorophyllafluorescence (ChF) acknowledges how different species take up and use light energy during photosynthesis. These techniques assess stress and performance responses to photosynthesis and are used for the selection of species with potential for reforestation. Six Fabaceae species were selected for this study: three nonfixing species (Cenostigma tocantinum,Senna reticulataandDipteryx odorata) and three N-fixing species (Clitoria fairchildiana,Inga edulisandAcaciaspp.). Variations in chlorophyll fluorescence under high vs. low water and nutrient conditions were studied. Multivariate analysis was performed to detect the effects of seasonality and fertilization on dark-adapted ChF two years after the experiment was established. The correlation among ChF variables and growth, photosynthesis and foliar nutrient concentrations was evaluated. Under high water- and nutrient-availability conditions, plants exhibited an enhanced performance index on absorption basis values correlated with electron transport fluxes. Under drought and nutrient-poor conditions, most species exhibit increased energy dissipation as photoprotection. High interspecific variation was found; therefore, species-specific responses should be considered in future ChF studies. Corroborating the ability to colonize high-light environments, N-fixers showed an increased performance index correlated with electron transport and Zn and N foliar concentrations. Negative correlations were found between photosynthesis and trapped fluxes. Diameter growth was positively correlated with electron transport fluxes. Given the different responses among species, ChF is an effective technique to screen for seasonality, fertilization and species effects and should be considered for use during forest restoration. Finally, the addition of fertilization treatments may facilitate tropical forest restoration due to the importance of nutrients in physiological processes. N-fixers showed high photochemical performance and tolerance to abiotic stress in degraded areas and therefore should be included to support ecosystem biomass restoration.
Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p
Authors: Stewart Taylor , Wolfe Benjamin E. , Fuchs Stephen M.
Published: May 2021

Across eukaryotes, homopolymeric repeats of amino acids are enriched in regulatory proteins such as transcription factors and chromatin remodelers. These domains play important roles in signaling, binding, prion formation, and functional phase separation. Azf1p is a prion-forming yeast transcription factor that contains two homorepeat domains, a polyglutamine and a polyasparagine domain. In this work, we report a new phenotype for Azf1p and identify a large set of genes that are regulated by Azf1p during growth in glucose. We show that the polyasparagine (polyN) domain plays a subtle role in transcription but is dispensable for Azf1p localization and prion formation. Genes upregulated upon deletion of the polyN domain are enriched in functions related to carbon metabolism and storage. This domain may therefore be a useful target for engineering yeast strains for fermentation applications and small molecule production. We also report that both the polyasparagine and polyglutamine domains vary in length across strains of S. cerevisiae and propose a model for how this variation may impact protein function.
Prognosis and transition of multi-site pain during the course of 5 years: Results of knee pain and function from a prospective cohort study among 756 adolescents
Authors: Holden Sinead , Roos Ewa M. , Straszek Christian Lund , Olesen Jens Lykkegaard , Jensen Martin Bach , Graven-Nielsen Thomas , Rathleff Michael Skovdal
Published: May 2021

Introduction

Multi-site pain has not been investigated among adolescents suffering from knee pain. This study aimed to examine the trajectory of pain in adolescents with knee-pain, to determine if multi-site pain in adolescents together with other established prognostic factors (frequency of pain, sex, sports participation, Health Related Quality of Life (HRQoL)) was associated with five-year prognosis of knee-pain and function.

Methods

This prospective cohort study included 504 adolescents with knee pain and 252 controls. At five-year follow-up, participants responded to an questionnaire which documented prescence and severity of knee pain and co-occurring pain.

Results

At follow-up, 358 (71.0%) of those with knee-pain at baseline, and 182 (72.2%) controls responded. Female sex, low HRQoL, daily pain, and multi-site pain were associated with an increased odds of knee pain after 5 years (odds ratio: 1.41–3.37). Baseline multi-site pain was not associated with problems running at follow-up, whereas higher sports participation at baseline was associated with less problems running at follow-up (odd ratio 0.49). Among those with knee-pain at inclusion, the number of pain sites increased from a median of 2 (IQR 1–3) to 4 (IQR 2–6) at follow-up (P<0.05). Those with multi-site pain at follow-up score significantly worse in self-reported knee function, compared to those with one pain site only.

Conclusion

This study identified a set of factors that appeared to be associated with an increased risk of knee pain at five years follow up. Research is needed to understand and help direct treatment of adolescents with multi-site pain.
The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand
Authors: Winkworth Richard C. , Bellgard Stanley E. , McLenachan Patricia A. , Lockhart Peter J.
Published: May 2021

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0–304.4 years and 95% HPDs of 206.9–414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.
Hourly fetal urine production rate in isolated oligohydramnios at term
Authors: Seol Hyun-Joo , Kim Ho Yeon , Cho Geum-Joon , Oh Min-Jeong
Published: May 2021

Objective

The aim of this study was to evaluate the hourly fetal urine production rate (HFUPR) via three-dimensional ultrasonography in women with isolated oligohydramnios and compare with normal pregnant women at term.

Materials and methods

This was a prospective observational cohort study of 112 women from 34 to 40 6/7 weeks’ gestation. They were classified into three groups according to the amniotic fluid index (AFI) and ultrasonographic estimated fetal weight (EFW) as isolated oligohydramnios (defined as AFI below 5% and appropriate EFW corresponding to gestational age) (n = 34) and IUGR (defined as EFW below 5% corresponding to gestational age irrespective amniotic fluid) (n = 17), and normal pregnancy (n = 61). HFUPR was measured using three-dimensional virtual organ computer-aided analysis. Adverse perinatal outcomes in all participants were examined.

Results

There was no significant difference in HFUPR between patients with isolated oligohydramnios and women with normal pregnancies (median, 40.0 mL/h [interquartile range [IQR] 31.0–66.5] vs. 48.6 [31.5–81.2], p = 0.224). HFUPR was significantly decreased in the IUGR group (13.8 mL/h [IQR 10.1–24.8]), compared to the normal pregnancy group (p<0.001) and the isolated oligohydramnios group (p<0.001). HFUPR was significantly decreased in neonates with adverse perinatal outcomes compared to the control (24.7 mL/h [IQR 13.4–47.4] vs. 43.6 [29.8–79.0], p = 0.016).

Conclusion

HFUPR was not decreased in patients with isolated oligohydramnios but was decreased in patients with IUGR when compared to normal controls at term.
Longitudinal stability of a multimodal visco-elastic polyacrylamide gel phantom for magnetic resonance and ultrasound shear-wave elastography
Authors: Usumura Masashi , Kishimoto Riwa , Ishii Koki , Hotta Eika , Kershaw Jeff , Higashi Tatsuya , Obata Takayuki , Suga Mikio
Published: May 2021

We evaluated the long-term stability of a newly developed viscoelastic phantom made of polyacrylamide (PAAm) gel for magnetic resonance elastography (MRE) and ultrasound-based shear-wave elastography (US SWE). The stiffness of the cylindrical phantom was measured at 0, 13 and 18 months. Storage and loss moduli were measured with MRE, and shear-wave speed (SWS) was measured with US SWE. Long-term stability was evaluated in accordance with the Quantitative Imaging Biomarker Alliance (QIBA) profiles for each modality. The initial storage and loss moduli of the phantom were 5.01±0.22 and 1.11±0.15 respectively, and SWS was 2.57±0.04 m/s. The weight of the phantom decreased by 0.6% over the 18 months. When measured with MRE, the stiffness of the phantom decreased and changes to the storage and loss moduli were -3.0% and -4.6% between 0 and 13 months, and -4.3% and 0.0% between 0 and 18 months. The US measurements found that SWS decreased by 2.4% over the first 13 months and 3.6% at 18 months. These changes were smaller than the tolerances specified in the QIBA profiles, so the viscoelastic PAAm gel phantom fulfilled the condition for long-term stability. This new phantom has the potential to be used as a quality assurance and quality control phantom for MRE and US SWE.
Patterns of mobility and its impact on retention in care among people living with HIV in the Manhiça District, Mozambique
Authors: Bernardo Edson L. , Nhampossa Tacilta , Clouse Kate , Carlucci James G. , Fernández-Luis Sheila , Fuente-Soro Laura , Nhacolo Ariel , Sidat Mohsin , Naniche Denise , Moon Troy D.
Published: May 2021

Introduction

Retention in HIV care is a challenge in Mozambique. Mozambique´s southern provinces have the highest mobility levels of the country. Mobility may result in poorer response to HIV care and treatment initiatives.

Methods

We conducted a cross-sectional survey to explore the impact of mobility on retention for HIV-positive adults on ART presenting to the clinic in December 2017 and January 2018. Survey data were linked to participant clinical records from the HIV care and treatment program. This study took place in Manhiça District, southern Mozambique. We enrolled self-identified migrants (moved outside of Manhiça District ≤12 months prior to survey) and non-migrants, matched by age and sex.

Results

390 HIV-positive adults were included. We found frequent movement: 45% of migrants reported leaving the district 3–5 times over the past 12 months, usually for extended stays. South Africa was the most common destination (71%). Overall, 30% of participants had at least one delay (15–60 days) in ART pick-up and 11% were delayed >60 days, though no significant difference was seen between mobile and non-mobile cohorts. Few migrants accessed care while traveling.

Conclusion

Our population of mobile and non-mobile participants showed frequent lapses in ART pick-up. Mobility could be for extended time periods and HIV care frequently did not continue at the destination. Studies are needed to evaluate the impact of Mozambique´s approach of providing 3-months ART among mobile populations and barriers to care while traveling, as is better education on how and where to access care when traveling.
Poor retention and care-related sex disparities among youth living with HIV in rural Mozambique
Authors: Ahonkhai Aima A. , Aliyu Muktar H. , Audet Carolyn M. , Bravo Magdalena , Simmons Melynda , Claquin Gael , Memiah Peter , Fernando Anibal N. , Carlucci James G. , Shepherd Bryan E. , Van Rompaey Sara , Yu Zhihong , Gong Wu , Vermund Sten H. , Wester C. William
Published: May 2021

Background

There are few studies that characterize sex-related differences in HIV outcomes among adolescents and young adults (AYA) 15–24 years of age.

Methods

We conducted a retrospective cohort study among AYA who enrolled in a comprehensive HIV program in Mozambique between 2012–2016. We assessed patients by sex and pregnancy/lactation status, comparing time to combination antiretroviral therapy (ART) initiation using Cox proportional hazard models. We employed multivariable logistic regression to investigate pre- and post-ART retention. Patients were defined as ‘retained pre-ART’ if they attended at least 3 of 4 required visits or started ART in the 6 months after enrollment, and ‘retained post-ART’ if they had any ART pickup or clinical visit during the last 90 days of the one-year follow-up period.

Results

Of 47,702 patients in the cohort, 81% (n = 38,511) were female and 19% (n = 9,191) were male. Of the females, 57% (n = 21,770) were non-pregnant and non-lactating (NPNL) and 43% (n = 16,741) were pregnant or lactating (PL). PL (aHR 2.64, 95%CI:2.47–2.81) and NPNL females (aHR 1.36, 95%CI:1.30–1.42) were more likely to initiate ART than males. PL females had higher odds of pre-ART retention in care (aOR 3.56, 95%CI: 3.30–3.84), as did NPNL females (aOR 1.71, 95%CI: 1.62–1.81), compared to males. This was also true for retention post-ART initiation, with higher odds for both PL (aOR 1.78, 95%CI:1.63–1.94) and NPNL females (aOR 1.50, 95%CI:1.35–1.65) compared to males.

Conclusions

PL females were most likely to initiate ART and remain in care post-ART in this AYA cohort, likely reflecting expansion of Option B+. Despite pregnancy and policy driven factors, we observed important sex-related disparities in this cohort. NPNL females were more likely to initiate ART and be retained in care before and after ART initiation than males. These data suggest that young males need targeted interventions to improve these important care continuum outcomes.
Restoring trust in truth-seekers: Effects of op/eds defending journalism and justice
Authors: Pingree Raymond J. , Santia Martina , Bryanov Kirill , Watson Brian K.
Published: May 2021

A healthy democracy requires trust that people can be impartial in important truth-seeking institutions including journalism, justice, and science. Recently some U.S. elites have adopted alarmingly extreme rhetoric against truth-seekers, denouncing mainstream journalism as fake news, criminal investigations as partisan witch-hunts, climate science as a hoax, and career civil servants as a deep state conspiracy. In response, some news organizations have taken the unusual step of publishing op/eds defending these institutions. Two experiments tested effects of such op/eds. In study 1, participants spent twelve days using a purpose-built news portal containing real, timely news with random assignment to the availability of real, timely op/eds defending impartiality of truth-seekers. These op/eds increased trust in truth-seeking institutions and increased the belief that people can serve as impartial professionals. Study 2 replicated this with a laboratory experiment assigning video op/ed exposure instead of text op/ed availability while adding several outcomes.
eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression
Authors: Stone Joshua K. , Vukadin Lana , Ahn Eun-Young Erin
Published: May 2021

Emerging evidence has shown that active enhancers are abundantly transcribed, generating long non-coding RNAs, called enhancer RNAs (eRNAs). While putative eRNAs are often observed from RNA sequencing, the roles of most eRNAs remain largely unknown. Previously, we identified putative enhancer regions at the MALAT1 locus that form chromatin-chromatin interactions under hypoxia, and one of these enhancers is located about 30 kb downstream of the NEAT1 gene and -20 kb upstream of the MALAT1 gene (MALAT1–20 kb enhancer). Here, we report that a novel eRNA, named eRNA of the NEAT1-MALAT1-Locus (eNEMAL), is transcribed from the MALAT1–20 kb enhancer and conserved in primates. We found that eNEMAL is upregulated in response to hypoxia in multiple breast cancer cell lines, but not in non-tumorigenic MCF10A cells. Overexpression and knockdown of eNEMAL revealed that alteration of eNEMAL level does not affect MALAT1 expression. Instead, we found that eNEMAL upregulates the long isoform of NEAT1 (NEAT1_2) without increasing the total NEAT1 transcript level in MCF7 breast cancer cells, suggesting that eNEMAL has a repressive effect on the 3’-end polyadenylation process required for generating the short isoform of NEAT1 (NEAT1_1). Altogether, we demonstrated that an eRNA transcribed from a MALAT1 enhancer regulates NEAT1 isoform expression, implicating the MALAT1–20 kb enhancer and its transcript eNEMAL in co-regulation of MALAT1 and NEAT1 in response to hypoxia in breast cancer cells.
Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)
Authors: Cui Chengqi , Liu Yanyang , Liu Yan , Cui Xianghua , Sun Zhiyu , Du Zhenwei , Wu Ke , Jiang Xiaolin , Mei Hongxian , Zheng Yongzhan
Published: May 2021

Sesame (Sesamum indicumL.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elucidate the factors affecting the genetic architecture of seed coat color, 366 sesame germplasm lines were evaluated for seed coat color in 12 environments. The genome-wide association studies (GWAS) for three seed coat color space values, best linear unbiased prediction (BLUP) values from a multi-environment trial analysis and principal component scores (PCs) of three seed coat color space values were conducted. GWAS for three seed coat color space values identified a total of 224 significant single nucleotide polymorphisms (SNPs,P< 2.34×10−7), with phenotypic variation explained (PVE) ranging from 1.01% to 22.10%, and 35 significant SNPs were detected in more than 6 environments. Based on BLUP values, 119 significant SNPs were identified, with PVE ranging from 8.83 to 31.98%. Comparing the results of the GWAS using phenotypic data from different environments and the BLUP values, all significant SNPs detected in more than 6 environments were also detected using the BLUP values. GWAS for PCs identified 197 significant SNPs, and 30 were detected in more than 6 environments. GWAS results for PCs were consistent with those for three color space values. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). Finally, 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.
Improving production and quality of life for smallholder farmers through a climate resilience program: An experience in the Brazilian Sertão
Authors: Gori Maia Alexandre , Burney Jennifer Anne , Morales Martínez José Daniel , Cesano Daniele
Published: May 2021

We use a combination of economic and wellbeing metrics to evaluate the impacts of a climate resilience program designed for family farmers in the semiarid region of Brazil. Most family farmers in the region are on the verge of income and food insufficiency, both of which are exacerbated in prolonged periods of droughts. The program assisted farmers in their milk and sheepmeat production, implementing a set of climate-smart production practices and locally-adapted technologies. We find that the program under evaluation had substantive and significant impacts on production practices, land management, and quality of life in general, using several different quasi-experimental strategies to estimate the average treatment effect on the treated farmers. We highlight the strengths and limitations of each evaluation strategy and how the set of analyses and outcome indicators complement each other. The evaluation provides valuable insights into the economic and environmental sustainability of family farming in semiarid regions, which are under growing pressure from climate change and environmental degradation worldwide.
Farm diversification as a potential success factor for small-scale farmers constrained by COVID-related lockdown. Contributions from a survey conducted in four European countries during the first wave of COVID-19
Authors: Benedek Zsófia , Fertő Imre , Galamba Marreiros Cristina , Aguiar Pâmela Mossmann de , Pocol Cristina Bianca , Čechura Lukáš , Põder Anne , Pääso Piia , Bakucs Zoltán
Published: May 2021

This paper explores to what extent product and marketing channel diversification contributed to the economic success of small-scale agricultural producers involved in short food supply chains after the outbreak of the COVID-19 pandemic. A survey was conducted between April and July 2020 in four countries of the European Union–Estonia, Hungary, Portugal and Romania,–resulting in a relatively large sample of farmers (N = 421). The analysis was built on a semi-nonparametric approach. Approximately 19 percent of small-scale producers were able to increase sales during the first wave of the pandemic, although country-level variation was significant. Fruits and vegetables were by far the most popular products. The importance of specific channels varied across countries, but farm gate sales were among the most important marketing channels both before and during the first wave. The importance of channels that were based on digital resources and home delivery increased. Our evidence indicates that diversification was a strategy that paid off, both in terms of marketing channels and different product categories. However, the impact appears to be nonlinear; the initial advantage generated by diversification rapidly tapered off, either temporarily (in the case of products), or permanently (in the case of marketing channels). Later research may clarify whether these findings are generalizable in other socio-economic contexts, as well as in a non-COVID situation.
Measuring implicit sequence learning and dual task ability in mild to moderate Parkinson´s disease: A feasibility study
Authors: Freidle Malin , Johansson Hanna , Lebedev Alexander V. , Ekman Urban , Lövdén Martin , Franzén Erika
Published: May 2021

We investigated the feasibility aspects of two choice reaction time tasks designed to assess implicit sequence learning and dual task ability in individuals with mild to moderate Parkinson’s disease in comparison to healthy individuals. Twelve individuals with mild to moderate Parkinson’s disease and 12 healthy individuals, all ≥ 60 years of age, were included. A serial reaction time task was used as a measure of implicit sequence learning and a similar task but with the addition of a simple counting task, was used as a measure of dual task ability. We have present thorough descriptive statistics of the data but we have refrained from any inferential statistics due to the small sample size. All participants understood the task instructions and the difficulty level of both tasks was deemed acceptable. There were indications of task fatigue that demand careful choices for how best to analyse the data from such tasks in future trials. Ceiling effects were present in several accuracy outcomes, but not in the reaction time outcomes. Overall, we found both tasks to be feasible to use in samples of individuals with mild to moderate Parkinson’s disease and healthy older individuals.
Designing a hybrid dimension reduction for improving the performance of Amharic news document classification
Authors: Endalie Demeke , Tegegne Tesfa
Published: May 2021

The volume of Amharic digital documents has grown rapidly in recent years. As a result, automatic document categorization is highly essential. In this paper, we present a novel dimension reduction approach for improving classification accuracy by combining feature selection and feature extraction. The new dimension reduction method utilizes Information Gain (IG), Chi-square test (CHI), and Document Frequency (DF) to select important features and Principal Component Analysis (PCA) to refine the features that have been selected. We evaluate the proposed dimension reduction method with a dataset containing 9 news categories. Our experimental results verified that the proposed dimension reduction method outperforms other methods. Classification accuracy with the new dimension reduction is 92.60%, which is 13.48%, 16.51% and 10.19% higher than with IG, CHI, and DF respectively. Further work is required since classification accuracy still decreases as we reduce the feature size to save computational time.
Variability of Rayleigh and Moreland test results using anomaloscope in young adults without color vision disorders
Authors: Zabel Jacek , Przekoracka-Krawczyk Anna , Olszewski Jan , Michalak Krzysztof Piotr
Published: May 2021

Aim

To validate the reference ranges proposed by the manufacturer of the Oculus HMC Anomaloscope MR for Rayleigh and Moreland tests in healthy young adults.

Method

The manual Rayleigh (red-green) and the Moreland (blue-green) anomaloscope tests were performed on 90 healthy subjects (54 female, 36 male, 178 eyes) residing in Poland, aged between 18–45 years, and without color vision disorders (assessed with HRR test). The analyzed parameters for both the Rayleigh and the Moreland tests were as follows: the lower (R1/M1) and the upper (R2/M2) limits; the center (RC/MC) and the width (RW/MW) of the matching ranges.

Results

The results of the Rayleigh test were similar to the values proposed in the anomaloscope user’s manual, however, with a small shift of RC and R2 towards the red color. The double-peak distribution of R2 with a small second peak (approximately at R2 = 52) was mainly due to the measurements in male subjects (nmale = 8, nfemale = 2), which suggests that this group might be diagnosed with subtle protanomaly. The results of the Moreland test showed a high MW which did not correspond to the reference range described in the anomaloscope user’s manual. The observed significant correlations between R1 and M1 suggest that the M1 parameter seems to be the best indicator of blue vision quality.

Conclusions

Oculus HMC Anomaloscope MR is a sensitive tool for detection of prot-deuteranomalies but the reference ranges for young adults require a certain adjustment towards the red color. The parameters obtained for the Moreland test varied significantly between the subjects and therefore the test should not be used as is to diagnose color vision deficits in the green-blue area (tritanomaly).
Computational tools for inversion and uncertainty estimation in respirometry
Authors: Cho Taewon , Pendar Hodjat , Chung Julianne
Published: May 2021

In many physiological systems, real-time endogeneous and exogenous signals in living organisms provide critical information and interpretations of physiological functions; however, these signals or variables of interest are not directly accessible and must be estimated from noisy, measured signals. In this paper, we study an inverse problem of recovering gas exchange signals of animals placed in a flow-through respirometry chamber from measured gas concentrations. For large-scale experiments (e.g., long scans with high sampling rate) that have many uncertainties (e.g., noise in the observations or an unknown impulse response function), this is a computationally challenging inverse problem. We first describe various computational tools that can be used for respirometry reconstruction and uncertainty quantification when the impulse response function is known. Then, we address the more challenging problem where the impulse response function is not known or only partially known. We describe nonlinear optimization methods for reconstruction, where both the unknown model parameters and the unknown signal are reconstructed simultaneously. Numerical experiments show the benefits and potential impacts of these methods in respirometry.
Dynamical SPQEIR model assesses the effectiveness of non-pharmaceutical interventions against COVID-19 epidemic outbreaks
Authors: Proverbio Daniele , Kemp Françoise , Magni Stefano , Husch Andreas , Aalto Atte , Mombaerts Laurent , Skupin Alexander , Gonçalves Jorge , Ameijeiras-Alonso Jose , Ley Christophe
Published: May 2021

Against the current COVID-19 pandemic, governments worldwide have devised a variety of non-pharmaceutical interventions to mitigate it. However, it is generally difficult to estimate the joint impact of different control strategies. In this paper, we tackle this question with an extended epidemic SEIR model, informed by a socio-political classification of different interventions. First, we inquire the conceptual effect of mitigation parameters on the infection curve. Then, we illustrate the potential of our model to reproduce and explain empirical data from a number of countries, to perform cross-country comparisons. This gives information on the best synergies of interventions to control epidemic outbreaks while minimising impact on socio-economic needs. For instance, our results suggest that, while rapid and strong lockdown is an effective pandemic mitigation measure, a combination of social distancing and early contact tracing can achieve similar mitigation synergistically, while keeping lower isolation rates. This quantitative understanding can support the establishment of mid- and long-term interventions, to prepare containment strategies against further outbreaks. This paper also provides an online tool that allows researchers and decision makers to interactively simulate diverse scenarios with our model.
Gender differences in suicide-related communication of young suicide victims
Authors: Balt Elias , Mérelle Saskia , van Bergen Diana , Gilissen Renske , van der Post Pommeline , Looijmans Milou , Creemers Daan , Rasing Sanne , Mulder Wico , van Domburgh Lieke , Popma Arne
Published: May 2021

Objectives

There is limited insight into gender differences in suicide-related communication (SRC) in youths. SRC is defined as“the act of conveying one’s own suicide ideation,intent or behaviours to another person”. Increasing our understanding of SRC in youths will enable us to recognize and specify needs of female versus male youths. The current study explores SRC in a sample of Dutch suicide victims aged under 20 and examines gender differences.

Methods

Interview data from a psychological autopsy study of 35 youths who died by suicide in the Netherlands in 2017 were analysed. Qualitative analyses were performed to examineexplicitSRC throughout the youths’ lives andimplicitSRC during the last months prior to suicide. We employed the Constant Comparative Method to explore patterns in the debut, form, frequency, medium, content, type of recipient, and SRC in the last months prior to suicide death.

Results

We identified commonalities in the SRC of youths, including the content of suicide notes and an emphasis on suicide method and preparation in the last months. Girls, however, had an earlier debut of SRC, a higher frequency ofexplicitSRC, and more often directed SRC towards varied types of recipients compared to boys. Moreover, SRC of girls seemed focused on coping and achieving support from others more than SRC of boys. The SRC of boys in comparison to girls was often ambiguous or diluted by “humorous” connotations.

Conclusion

Unique patterns in SRC of boys and girls posed corresponding challenges for next of kin to interpret communications and respond adequately to SRC. The early debut of girls’ SRC highlights the importance of early screening and prevention efforts in girls, while the late debut and ambiguity in boys’ SRC implores professionals and next of kin to encourage young males to be unequivocal about suicide ideation or intent.
Non-Indigenous Canadians’ and Americans’ moral expectations of Indigenous peoples in light of the negative impacts of the Indian Residential Schools
Authors: Doiron Mackenzie J. , Branscombe Nyla , Matheson Kimberly
Published: May 2021

The historical trauma associated with the Indian Residential School (IRS) system was recently brought to the awareness of the Canadian public. Two studies investigated how the salience of this collective victimization impacted non-Indigenous Canadians’ expectations that Indigenous peoples ought to derive psychological benefits (e.g., learned to appreciate life) and be morally obligated to help others. Study 1 found that modern racism was related to perceptions that Indigenous peoples psychologically benefitted from the IRS experience, which in turn, predicted greater expectations of moral obligation. Study 2 replicated the relations among racism, benefit finding, and moral obligation among non-Indigenous Canadians (historical perpetrators of the harm done) and Americans (third-party observers). Americans were uniquely responsive to a portrayal of Indigenous peoples in Canada as strong versus vulnerable. Factors that distance observers from the victim (such as racism or third-party status) appear to influence perceptions of finding benefit in victimization experiences and expectations of moral obligation.
Impact of COL6A4P2 gene polymorphisms on the risk of lung cancer: A case-control study
Authors: Dang Xiaodong , Zhao Wenhui , Li Chen , Yang Hua , Li Dianzhen , Zhang Shanshan , Jin Tianbo
Published: May 2021

Lung cancer (LC) is a malignant tumor that poses the greatest threat to human health and life. Most studies suggested that the occurrence of LC is associated with environmental and genetic factors. We aimed to explore the association betweenCOL6A4P2single nucleotide polymorphisms (SNPs) and CHD risk in the Chinese Southern Han population. Based on the ‘case-control’ experimental design (510 cases and 495 controls), we conducted an association study between five candidateCOL6A4P2SNPs and the corresponding LC risk. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated by logistic regression to analyze the LC susceptibility under different genetic models. The results showed thatCOL6A4P2rs34445363 was significantly associated with LC risk under alleles model (OR = 1.26, 95%CI: 1.01–1.58,p= 0.038). In addition, rs34445363 was also significantly associated with LC risk under the log-additive model (OR = 1.26, 95%CI: 1.01–1.58,p= 0.041). The results of subgroup analysis showed that rs34445363 (OR = 1.42, 95%CI: 1.03–1.95, p = 0.033) and rs61733464 (OR = 0.72, 95%CI: 0.52–0.99,p= 0.048) were both significantly associated with LC risk in the log-additive model among participants who were ≤ 61 years old. We also found that the variation of rs34445363 (GA vs. GG, OR = 1.73, 95%CI: 1.04–2.86,p= 0.034) and rs77941834 (TA vs. TT, OR = 1.88, 95%CI: 1.06–3.34,p= 0.032) were associated with LC risk in the codominant model among female participants. Our study is the first to find thatCOL6A4P2gene polymorphism is associated with LC risk in the Chinese Han population. Our study provides a basic reference for individualized LC prevention.