bluuebunny/crossref_metadata_2025 huggingface dataset:
First-principle study on monolayer and bilayer SnP3 sheets as the potential sensors for NO2, NO, and NH3 detection
Authors: Du Jiguang , Jiang Gang
Published: April 2020

Layered SnP3 sheets have recently been predicted as interesting 2D material with many potential applications. In the present work, first-principles calculations were performed to investigate the possibility of layered SnP3 sheets as a candidate for detecting pollutant gases (CO, CO2, H2S, NH3, NO, and NO2). Our results indicate that CO, CO2, H2S molecules are all physisorbed on SnP3 sheets with an adsorption energy of 0.116–0.363 eV. On the other hand, the strong interactions of NH3, NO, and NO2 and SnP3 are found based on the moderate adsorption energy (around 1 eV for NO2) and large charge transfer. The monolayer SnP3 shows a higher affinity to these molecules than bilayer one. The chemisorption of NH3, NO, and NO2 molecules on layered SnP3 sheets could efficiently evoke the electrical signal, and show short recovery time for NH3, NO, and NO2 capture. The work function calculations exhibit significant responses to the NH3 and NO2 molecules. Our results proposed that SnP3 sheets could be utilized as a gas sensor for NO, NO2, and NH3, and extend the potential applications of 2D SnP3 sheets.
A plasmonic nanoledge array sensor for detection of anti-insulin antibodies of type 1 diabetes biomarker
Authors: Bagra Bhawna , Mabe Taylor , Tukur Frank , Wei Jianjun
Published: April 2020

Here we present a plasmonic nanoledge device with high sensitivity and selectivity used to detect protein biomarkers simply by functionalizing the device, which specifically binds to particular biomolecule or biomarkers. We employ this plasmonic nanoledge device for the detection of anti-insulin antibodies of type 1 diabetes (T1D) in buffer and human serum at the range of pg ml−1 to 100 ng ml−1. The signal transduction is based on the extraordinary optical transmission (EOT) through the nanoledge array and the optical spectral changes with the biological binding reaction between the surface functionalized insulin with anti-insulin antibody. Control experiments indicate little interferences from the human serum background and addition of other proteins such as bovine serum albumin (BSA) and epidermal growth factor (EGF) at 20 ng ml−1. The high sensitivity, specificity and easy adaptability of the plasmonic device offer new opportunities in biosensing and diagnostic applications for T1D.
Simultaneous determination of the dose and linear energy transfer (LET) of carbon-ion beams using radiochromic films
Authors: Kawashima Motohiro , Matsumura Akihiko , Souda Hikaru , Tashiro Mutsumi
Published: April 2020

Radiochromic films are useful as dosimeters in high-precision radiotherapy owing to their high spatial resolution. However, when a particle beam is measured using a radiochromic film, the dose cannot be estimated accurately because the film darkness varies with variations in linear energy transfer (LET). This paper proposes a novel method for estimating the LET and the dose based on the film darkness. In this method, after a high-LET particle beam, such as a carbon-ion beam, was incident on the film, the film was digitized and its net optical density was determined. Further, the non-linearity of the film response curve between the dose and the darkness, depending on LET, was used. Then, calibration curves were created using 290 MeV u−1 mono energetic carbon-ion beams. We used LETs of 20, 50, 100, and 150 keV µm−1 and a physical dose of 2–14 Gy. The calibration curves were approximated for each LET using a quadratic function. The correlations between the coefficients of the quadratic function and the LET were also obtained. To verify the proposed method, the films were irradiated under 12 different conditions corresponding to various depths and doses. Four depths of −2, −5, −10, and −20 mm with respect to the Bragg peak, and three different preset values were used for the film measurements. The films were analyzed in four groups, where each group comprised films irradiated at the same depth. The LETs obtained from the film analysis, ordered from the upstream of the beam, were 20, 41, 56, and 97 keV µm−1, and the doses for the lowest preset value were 3.95, 4.07, 4.03, and 3.99 Gy for the four groups. The LETs obtained from the film analysis increased toward the Bragg peak, and the doses measured in the ionization chamber were almost equal to 4 Gy.
Transforming quantum states between reference frames
Authors: Ben-Benjamin J S , Scully M O , Unruh W G
Published: April 2020

In the 1970s, Fulling, Davis, and Unruh have shown that a quantum mechanical state must be described differently in different reference frames; otherwise, quantum mechanics would contain contradictions. We present a simple method for transforming any quantum state between the Minkowski and Rindler reference frames. We show that a Wigner-like distribution, commonly used in quantum optics, is useful for treating this problem. To illustrate our method, we transform the Minkowski vacuum and number states into Rindler space, and transform the Rindler vacuum into Minkowski space, as examples. Our method could be generalized to other cases as well.
3 tera-basepairs as a fundamental limit for robust DNA replication
Authors: Mamun M Al , Albergante L , J Blow J , Newman T J
Published: April 2020

In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stall errors, we uncover a fundamental constant that describes a trade-off between genome size and architectural complexity of the developing organism. This constant has the approximate value N

U
≈ 3 × 1012 basepairs, and depends only on two highly conserved molecular properties of DNA biology. We show that our theory is successful in interpreting a diverse range of data across the Eukaryota.
A synthesis of polyethylene glycol (PEG)-coated magnetite Fe3O4 nanoparticles and their characteristics for enhancement of biosensor
Authors: Antarnusa Ganesha , Suharyadi Edi
Published: April 2020

The magnetite Fe3O4 nanoparticles were synthesized by using chemical co-precipitation method and these nanoparticles were successfully coated by polyethylene glycol (PEG) with variation concentrations of PEG. The magnetite Fe3O4 nanoparticles used as a bimolecular label (nano-tags), exhibiting a soft magnetic behavior with magnetization (
M

s

) of 77.16 emu g−1 and coercivity (
H

c

) of 50 Oe respectively. The polyethylene glycol (PEG) was used as a biocompatible polymer. The x-ray diffraction (XRD) patterns of the Fe3O4 showed that Fe3O4 was well crystallized. It also confirmed the existence of invers spinel. The diffraction peak of 35.4° was used to calculate the crystallite size. The estimation of Fe3O4 average crystallite size is 12 nm, while the PEG-coated Fe3O4 nanoparticles is 8.6 nm. The transmission electron microscopy (TEM) images of Fe3O4 showed that the morphology of magnetite Fe3O4 nanoparticle is spherical in shape with uniform grain size and good dispersibility despite the agglomeration it found in some place. The addition of PEG can decrease the agglomeration and reduce the particle size. The existence of PEG layer on Fe3O4 was confirmed by Fourier transform infrared (FTIR) spectroscopy. The result of Vibrating Sample Magnetometer (VSM) showed that saturation magnetization (M

s
) of Fe3O4 nanoparticles decreased from 77.16 to 37.15 emu g−1 with the increase of PEG weight from 0% to 50%. Such Fe3O4 nanoparticles with favorable size and tunable magnetic properties are promising biosensor applications.
A modified kinetics model and softening behavior for static recrystallization of 12Cr ultra-super-critical rotor steel
Authors: Xu Yue , Zhao Yu , Liu Jiansheng
Published: April 2020

In this paper, the static recrystallization (SRX) of 12Cr ultra-super-critical (USC) rotor steel was investigated by a series of hot compression tests on a Gleeble1500D thermal simulator. Double-hit hot deformation tests were conducted at temperatures of 1223K–1323 K and strain rates of 0.001 s−1–0.1 s−1 with inter-pass times of 10s–180 s. A conventional kinetics model of SRX was established based on flow curves obtained by regression analysis under different deformation conditions. However, a significant deviation resulted between predicted and experimental values for the SRX fraction, and therefore a modified kinetics equation was proposed by analysing the SRX characteristics and possession of the capability to accurately predict SRX softening behaviour was confirmed. Effects of hot deformation parameters on SRX softening behaviour and SRX grain size were discussed. Furthermore, microstructure deforming was observed at different inter-pass times with an optical microscope (OM), electron backscatter diffraction (EBSD) and transmission electron microscope (TEM). Analysis showed that recovery was the main softening mechanism and the fundamental nucleation mechanism for SRX was bulging at the grain boundary.
Validation of a spatially variant resolution model for small animal brain PET studies
Authors: Miranda Alan , Bertoglio Daniele , Glorie Dorien , Stroobants Sigrid , Staelens Steven , Verhaeghe Jeroen
Published: April 2020

In small animal positron emission tomography (PET) studies, given the spatial resolution of preclinical PET scanners, quantification in small regions can be challenging. Moreover, in scans where animals are placed away from the center of the field of view (CFOV), e.g. in simultaneous scans of multiple animals, quantification accuracy can be compromised due to the loss of spatial resolution towards the edge of the FOV. Here, we implemented a spatially variant resolution model to improve quantification in small regions and to allow simultaneous scanning of multiple animals without compromising quantification accuracy. The scanner’s point spread function (PSF) was characterized across the FOV and modelled using a spatially variant and asymmetric Gaussian function. The spatially variant PSF (SVPSF) was then used for resolution modelling in the iterative reconstruction. To assess the image quality, a line source phantom in a cold and warm background, as well as mouse brain [18F]FDG scans, were performed. The SVPSF and the vendor’s maximum a posteriori (MAP3D) reconstructions produced uniform spatial resolution across the scanner FOV, but MAP3D resulted in lower spatial resolution. The line sources recovery coefficient using SVPSF was similar at the CFOV and at the edge of the FOV. In contrast, the other tested reconstructions produced lower recovery coefficient at the edge of the FOV. In mouse brain reconstructions, less spill-over from hot regions to cold regions, as well as more symmetric regional brain uptake was observed using SVPSF. The contrast in brain images was the highest using SVPSF, in mice scanned at the CFOV and off-center. Incorporation of a spatially variant resolution model for small animal brain PET improves quantification accuracy in small regions and produces consistent image spatial resolution across the FOV. Therefore, simultaneous scanning of multiple animals can benefit by using spatially variant resolution modelling.
On a reverse isoperimetric inequality for relative outer parallel bodies
Authors: Saorín Gómez Eugenia , Yepes Nicolás Jesús
Published: April 2020

We show a reverse isoperimetric inequality within the class of relative outer parallel bodies, with respect to a general convex body

E
E

, along with its equality condition. Based on the convexity of the sequence of quermassintegrals of Minkowski sums we also prove further inequalities.
Positive definite functions on products of metric spaces via generalized Stieltjes functions
Authors: Menegatto V.
Published: April 2020

For quasi-metric spaces

(
X
,
ρ
)

(X,\rho )

and

(
Y
,
σ
)

(Y,\sigma )

and a positive real number

λ
\lambda

, we propose a model for generating positive definite functions
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper G Subscript r Baseline colon left-brace rho left-parenthesis x comma x Superscript prime Baseline right-parenthesis colon x comma x prime element-of upper X right-brace times left-brace sigma left-parenthesis y comma y Superscript prime Baseline right-parenthesis colon y comma y prime element-of upper Y right-brace right-arrow from bar double-struck upper R">

G
r

:
{
ρ
(
x
,

x
′

)
:
x
,

x
′

∈
X
}
×
{
σ
(
y
,

y
′

)
:
y
,

y
′

∈
Y
}
↦

R

G_r: \{\rho (x,x’):x,x’\in X\} \times \{\sigma (y,y’):y,y’ \in Y\} \mapsto \mathbb {R}

having the form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper G Subscript r Baseline left-parenthesis t comma u right-parenthesis equals StartFraction 1 Over h left-parenthesis u right-parenthesis Superscript r Baseline EndFraction f left-parenthesis StartFraction g left-parenthesis t right-parenthesis Over h left-parenthesis u right-parenthesis EndFraction right-parenthesis comma">

G
r

(
t
,
u
)
=

1

h
(
u

)
r

f

(

g
(
t
)

h
(
u
)

)

,

\begin{equation*} G_r(t,u)=\frac {1}{h(u)^r} f\left (\frac {g(t)}{h(u)}\right ), \end{equation*}

where

r
≥
λ

r\geq \lambda

,

f
f

belongs to a convex cone

S

λ
b

\mathcal {S}_\lambda ^b

of bounded completely monotone functions,

g
g

is a nonnegative valued conditionally negative definite function on

(
X
,
ρ
)

(X,\rho )

, and

h
h

is a positive valued conditionally negative definite function on

(
Y
,
σ
)

(Y,\sigma )

. In the case where

(
X
,
ρ
)

(X,\rho )

and

(
Y
,
σ
)

(Y,\sigma )

are metric spaces, we determine necessary and sufficient conditions for the strict positive definiteness of the model. The cone

S

λ
b

\mathcal {S}_\lambda ^b

possesses well-established stability properties that allow alternative formulations of the model leading to many classes of positive definite and strictly positive definite functions on

X
×
Y

X\times Y

. If

X
=

R

d

X=\mathbb {R}^d

,

Y
=

R

Y=\mathbb {R}

,

ρ
\rho

is the Euclidean distance on

X
X

,

σ

1

/

2

\sigma ^{1/2}

is the Euclidean distance on

Y
Y

,

g
(
t
)
=

t
2

g(t)=t^2

,

t
≥
0

t\geq 0

,

h
h

is a positive valued function with a completely monotone derivative, and

λ
=
d

/

2

\lambda =d/2

, then

{

G
r

:
r
≥
λ
}

\{G_r:r\geq \lambda \}

is a subset of the Gneiting’s class of covariance space-time functions on

X
×
Y

X\times Y

frequently dealt with in the literature.
The module of logarithmic derivations of a generic determinantal ideal
Authors: Burity Ricardo , Miranda-Neto Cleto
Published: April 2020

An important problem in algebra and related fields (such as algebraic and complex analytic geometry) is to find an explicit, well-structured, minimal set of generators for the module of logarithmic derivations of classes of homogeneous ideals in polynomial rings. In this note we settle the case of the ideal

P
⊂
R
=
K
[
{

X

i
,
j

}
]

P\subset R=K[\{X_{i,j}\}]

generated by the maximal minors of an

(
n
+
1
)
×
n

(n+1)\times n

generic matrix

(

X

i
,
j

)

(X_{i,j})

over an arbitrary field

K
K

with

n
≥
2

n\geq 2

. We also characterize when the derivation module of

R

/

P

R/P

is Ulrich, and we investigate this property if we replace

R

/

P

R/P

by determinantal rings arising from simple degenerations of the generic case.
Collapsed manifolds with Ricci bounded covering geometry
Authors: Huang Hongzhi , Kong Lingling , Rong Xiaochun , Xu Shicheng
Published: April 2020

We study collapsed manifolds with Ricci bounded covering geometry, i.e., Ricci curvature is bounded below and the Riemannian universal cover is non-collapsed or consists of uniform Reifenberg points. Applying the techniques in the Ricci flow, we partially extend the nilpotent structural results of Cheeger-Fukaya-Gromov, on the collapsed manifolds with (sectional curvature) local bounded covering geometry, to the manifolds with (global) Ricci bounded covering geometry.
The road towards data integration in human genomics: players, steps and interactions
Authors: Bernasconi Anna , Canakoglu Arif , Masseroli Marco , Ceri Stefano
Published: April 2020

Thousands of new experimental datasets are becoming available every day; in many cases, they are produced within the scope of large cooperative efforts, involving a variety of laboratories spread all over the world, and typically open for public use. Although the potential collective amount of available information is huge, the effective combination of such public sources is hindered by data heterogeneity, as the datasets exhibit a wide variety of notations and formats, concerning both experimental values and metadata. Thus, data integration is becoming a fundamental activity, to be performed prior to data analysis and biological knowledge discovery, consisting of subsequent steps of data extraction, normalization, matching and enrichment; once applied to heterogeneous data sources, it builds multiple perspectives over the genome, leading to the identification of meaningful relationships that could not be perceived by using incompatible data formats. In this paper, we first describe a technological pipeline from data production to data integration; we then propose a taxonomy of genomic data players (based on the distinction between contributors, repository hosts, consortia, integrators and consumers) and apply the taxonomy to describe about 30 important players in genomic data management. We specifically focus on the integrator players and analyse the issues in solving the genomic data integration challenges, as well as evaluate the computational environments that they provide to follow up data integration by means of visualization and analysis tools.
Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction
Authors: Dou Jinzhuang , Wu Degang , Ding Lin , Wang Kai , Jiang Minghui , Chai Xiaoran , Reilly Dermot F , Tai E Shyong , Liu Jianjun , Sim Xueling , Cheng Shanshan , Wang Chaolong
Published: April 2020

Whole-exome sequencing (WES) has been widely used to study the role of protein-coding variants in genetic diseases. Non-coding regions, typically covered by sparse off-target data, are often discarded by conventional WES analyses. Here, we develop a genotype calling pipeline named WEScall to analyse both target and off-target data. We leverage linkage disequilibrium shared within study samples and from an external reference panel to improve genotyping accuracy. In an application to WES of 2527 Chinese and Malays, WEScall can reduce the genotype discordance rate from 0.26% (SE= 6.4 × 10−6) to 0.08% (SE = 3.6 × 10−6) across 1.1 million single nucleotide polymorphisms (SNPs) in the deeply sequenced target regions. Furthermore, we obtain genotypes at 0.70% (SE = 3.0 × 10−6) discordance rate across 5.2 million off-target SNPs, which had ~1.2× mean sequencing depth. Using this dataset, we perform genome-wide association studies of 10 metabolic traits. Despite of our small sample size, we identify 10 loci at genome-wide significance (P < 5 × 10−8), including eight well-established loci. The two novel loci, both associated with glycated haemoglobin levels, are GPATCH8-SLC4A1 (rs369762319, P = 2.56 × 10−12) and ROR2 (rs1201042, P = 3.24 × 10−8). Finally, using summary statistics from UK Biobank and Biobank Japan, we show that polygenic risk prediction can be significantly improved for six out of nine traits by incorporating off-target data (P < 0.01). These results demonstrate WEScall as a useful tool to facilitate WES studies with decent amounts of off-target data.
Fatty acid induced lipolysis influences embryo development, gene expression and lipid droplet formation in the porcine cumulus cells†
Authors: Pawlak Piotr , Malyszka Natalia , Szczerbal Izabela , Kolodziejski Pawel
Published: April 2020

The pig oocyte maturation protocol differs from other mammalian species due to dependence on follicular fluid (FF) supplementation. One of the most abundant components of the porcine follicular fluid are fatty acids (FAs). Although evidence from other mammalian models revealed a negative impact of saturated fatty acids (SFA) on developmental competence of oocytes, pig has not yet been widely analyzed. Therefore, we aimed to investigate whether supplementation of IVM medium with 150 μM of stearic acid (SA) and oleic acid (OA) affects lipid content and expression of genes related to fatty acid metabolism in porcine cumulus–oocyte complexes and parthenogenetic embryo development. We found significant influence of fatty acids on lipid metabolism in cumulus cells without affecting the oocyte proper. The expression of ACACA, SCD, PLIN2, FADS1, and FADS2 genes was upregulated (P < 0.01) in cumulus cells, while their expression in oocytes did not change. The increase in gene expression was more pronounced in the case of OA (e.g., up to 30-fold increase in PLIN2 transcript level compared to the control). The number of lipid droplets and occupied area increased significantly in the cumulus cells and did not change in oocytes after SA treatment. Oleic acid improved the blastocyst rate (48 vs 32% in control), whereas stearic acid did not affect this parameter (27%). Additionally, we have discovered a phenotypic diversity of LD in cumulus cells in response to FA supplementation, suggesting extensive lipolysis in response to SA. Stearic acid excess in maturation media led to the formation of multiple micro lipid droplets in cumulus cells.
Xpert MTB/RIF Ultra for the Diagnosis of Tuberculous Meningitis: A Small Step Forward
Authors: Donovan Joseph , Cresswell Fiona V , Thuong Nguyen Thuy Thuong , Boulware David R , Thwaites Guy E , Bahr Nathan C ,   Tuberculous Meningitis International Research Consortium, Aarnoutse Rob E , Anderson Suzanne T B , Bahr Nathan C , Bang Nguyen D , Boulware David R , Boyles Tom , te Brake Lindsey H M , Chandra Satish , Chow Felicia C , Cresswell Fiona V , van Crevel Reinout , Davis Angharad G , Dian Sofiati , Donovan Joseph , Dooley Kelly E , Figaji Anthony , Ganiem A Rizal , Garg Ravindra Kumar , Gibb Diana M , Hamers Raph L , Hiep Nguyen T T , Imran Darma , Imron Akhmad , Jain Sanjay K , Jain Sunil K , Kalita Jayantee , Kumar Rashmi , Kumar Vinod , van Laarhoven Arjan , Lai Rachel P-J , Manesh Abi , Marais Suzaan , Mave Vidya , Meintjes Graeme , Meya David B , Misra Usha K , Modi Manish , Ordonez Alvaro A , Phu Nguyen H , Pradhan Sunil , Prasad Kameshwar , Proust Alize M , Ramakrishnan Lalita , Rohlwink Ursula , Ruslami Rovina , Schoeman Johannes F , Seddon James A , Sharma Kusum , Siddiqi Omar , Solomons Regan S , Thuong Nguyen T T , Thwaites Guy E , van Toorn Ronald , Tucker Elizabeth W , Wasserman Sean A , Wilkinson Robert J , Aarnoutse Rob E , Anderson Suzanne T B , Bahr Nathan C , Bang Nguyen D , Boulware David R , Boyles Tom , te Brake Lindsey H M , Chandra Satish , Chow Felicia C , Cresswell Fiona V , van Crevel Reinout , Davis Angharad G , Dian Sofiati , Donovan Joseph , Dooley Kelly E , Figaji Anthony , Ganiem A Rizal , Garg Ravindra Kumar , Gibb Diana M , Hamers Raph L , Hiep Nguyen T T , Imran Darma , Imron Akhmad , Jain Sanjay K , Jain Sunil K , Kalita Jayantee , Kumar Rashmi , Kumar Vinod , van Laarhoven Arjan , Lai Rachel P-J , Manesh Abi , Marais Suzaan , Mave Vidya , Meintjes Graeme , Meya David B , Misra Usha K , Modi Manish , Ordonez Alvaro A , Phu Nguyen H , Pradhan Sunil , Prasad Kameshwar , Proust Alize M , Ramakrishnan Lalita , Rohlwink Ursula , Ruslami Rovina , Schoeman Johannes F , Seddon James A , Sharma Kusum , Siddiqi Omar , Solomons Regan S , Thuong Nguyen T T , Thwaites Guy E , van Toorn Ronald , Tucker Elizabeth W , Wasserman Sean A , Wilkinson Robert J
Published: April 2020

The delayed diagnosis of tuberculous meningitis (TBM) leads to poor outcomes, yet the current diagnostic methods for identifying Mycobacterium tuberculosis in cerebrospinal fluid (CSF) are inadequate. The first comparative study of the new GeneXpert MTB/RIF Ultra (Xpert Ultra) for TBM diagnosis suggested increased sensitivity of Xpert Ultra. Two subsequent studies have shown Xpert Ultra has improved sensitivity, but has insufficient negative predictive value to exclude TBM. Collecting and processing large volumes of CSF for mycobacterial testing are important for optimal diagnostic test performance. But clinical, radiological, and laboratory parameters remain essential for TBM diagnosis and empiric therapy is often needed. We therefore caution against the use of Xpert Ultra as a single diagnostic test for TBM; it cannot be used to “rule out” TBM.
Raman Analysis Reveals Biochemical Differences in Plasma of Crohn’s Disease Patients
Authors: Morasso Carlo , Truffi Marta , Vanna Renzo , Albasini Sara , Mazzucchelli Serena , Colombo Francesco , Sorrentino Luca , Sampietro Gianluca , Ardizzone Sandro , Corsi Fabio
Published: April 2020

Backgrounds and Aims

There is no accurate and reliable circulating biomarker to diagnose Crohn’s disease [CD]. Raman spectroscopy is a relatively new approach that provides information on the biochemical composition of samples in minutes and virtually without any sample preparation. We aimed to test the use of Raman spectroscopy analysis of plasma samples as a potential diagnostic tool for CD.

Methods

We analysed by Raman spectroscopy dry plasma samples obtained from 77 CD patients [CD] and 45 healthy controls [HC]. In the dataset obtained, we analysed spectra differences between CD and HC, as well as among CD patients with different disease behaviours. We also developed a method, based on principal component analysis followed by a linear discrimination analysis [PCA-LDA], for the automatic classification of individuals based on plasma spectra analysis.

Results

Compared with HC, the CD spectra were characterised by less intense peaks corresponding to carotenoids [p <10–4] and by more intense peaks corresponding to proteins with β-sheet secondary structure [p <10–4]. Differences were also found on Raman peaks relative to lipids [p = 0.0007] and aromatic amino acids [p <10–4]. The predictive model we developed was able to classify CD and HC subjects with 83.6% accuracy [sensitivity 80.0% and specificity 85.7%] and F1-score of 86.8%.

Conclusions

Our results indicate that Raman spectroscopy of blood plasma can identify metabolic variations associated with CD and it could be a rapid pre-screening tool to use before further specific evaluation.
Arthropod Granivory of Lime-Coated Cover Crop Seeds
Authors: Bredeson Michael M , Beck Dwayne , Lundgren Jonathan G
Published: April 2020

Diversifying cropland plant communities is prerequisite to restoring ecosystem functions in agricultural habitats. Cover crops are one such way to improve biodiversity, and broadcasting calcium carbonate-coated (lime) seeds can be a viable method for plant establishment. In addition to improving seed-to-soil contact, calcium carbonate may also reduce arthropod granivory. Here we examine the effect of this seed-coating technology on arthropod granivory for seven cover crop species under field conditions. Carabidae, Gryllidae, and Staphylinidae were the three most frequently collected granivorous taxa in pitfall samples, and Pterostichus permundus and Gryllus pennsylvanicus represented 60.8% of all individual granivores. Cover crop seed damaged was variable among plant species. Among all plant species, the presence of a seed coating significantly reduced granivory by nearly 40% in the 7-d field exposure. Individually, hairy vetch and sorghum × sudan seeds were especially protected by calcium carbonate. No positive correlations were observed between invertebrate groups and the number of seeds consumed. Alternative methods for assessing the functionality of granivorous arthropod communities should be pursued, as activity-density measured from pitfall traps failed to reveal important cover crop seed consumers. Protection of cover crop seeds from granivory through a calcium carbonate coating may allow producers to adjust seeding rates and save on costs, increasing the rate of adoption for this conservation practice.
Party Politics or (Supra-)National Interest? External Relations Votes in the European Parliament
Authors: Raunio Tapio , Wagner Wolfgang
Published: April 2020

Parliamentary votes on foreign and security policy have often been demonstrations of patriotism and unity. This resonates with the notion that external relations are exempted from party politics, or that politics stops at the water's edge. Its supranational character makes the European Parliament (EP) a particularly interesting laboratory for subjecting this thesis to empirical scrutiny. Analyzing roll-call votes from 1979 to 2014, this article shows that group cohesion and coalition patterns are no different in external relations votes than in other issue areas. Members of the EP (MEPs) do not rally around a European Union flag, nor do MEPs vote as national blocs in votes on foreign and security policy, trade, and development aid. Based on statistical analyses and interviews with parliamentary civil servants, it concludes that the EP stands out by having party politics dominate all business, including external relations.
A smartphone game to prevent HIV among young Kenyans: local perceptions of mechanisms of effect
Authors: Winskell K , Sabben G , Akelo V , Ondeng’e K , Odero I , Mudhune V
Published: April 2020

Electronic games delivered via smartphones have the potential to become valuable tools in HIV prevention in high-prevalence and low-resource international settings. To ground theoretical elaboration around novel mHealth interventions in contextual realities, it is important to understand the mechanisms of their effects as perceived by local populations. Such perspectives are particularly important when working cross-culturally. ‘Tumaini’ is an interactive narrative-based smartphone game that uses a ‘choose-your-own-adventure’ format. It is designed to prevent HIV among young African adolescents (aged 11–14) by increasing age and condom use at first sex. It was developed with a US-based commercial game developer and is grounded in social behavioral theory, evidence-based practice and contextually relevant scenarios. In a 2017 randomized pilot study (n = 60) in Western Kenya, ‘Tumaini’ showed promising effects on behavioral mediators of sexual debut. In subsequent focus group discussions, adolescent participants and their parents shared their perceptions of the game’s mechanisms of effect, which included motivation to play, future orientation, decision-making, relationship to a diverse range of characters and a bridging of the virtual and real worlds. These findings align with our theoretical framework, confirm its successful translation into the intervention and will inform mediation analyses in an upcoming efficacy trial.
A rare genomic duplication in 2p14 underlies autosomal dominant hearing loss DFNA58
Authors: Lezirovitz Karina , Vieira-Silva Gleiciele A , Batissoco Ana C , Levy Débora , Kitajima Joao P , Trouillet Alix , Ouyang Ellen , Zebarjadi Navid , Sampaio-Silva Juliana , Pedroso-Campos Vinicius , Nascimento Larissa R , Sonoda Cindy Y , Borges Vinícius M , Vasconcelos Laura G , Beck Roberto M O , Grasel Signe S , Jagger Daniel J , Grillet Nicolas , Bento Ricardo F , Mingroni-Netto Regina C , Oiticica Jeanne
Published: April 2020

Here we define a ~200 Kb genomic duplication in 2p14 as the genetic signature that segregates with postlingual progressive sensorineural autosomal dominant hearing loss (HL) in 20 affected individuals from the DFNA58 family, first reported in 2009. The duplication includes two entire genes, PLEK and CNRIP1, and the first exon of PPP3R1 (protein coding), in addition to four uncharacterized long non-coding (lnc) RNA genes and part of a novel protein-coding gene. Quantitative analysis of mRNA expression in blood samples revealed selective overexpression of CNRIP1 and of two lncRNA genes (LOC107985892 and LOC102724389) in all affected members tested, but not in unaffected ones. Qualitative analysis of mRNA expression identified also fusion transcripts involving parts of PPP3R1, CNRIP1 and an intergenic region between PLEK and CNRIP1, in the blood of all carriers of the duplication, but were heterogeneous in nature. By in situ hybridization and immunofluorescence, we showed that Cnrip1, Plek and Ppp3r1 genes are all expressed in the adult mouse cochlea including the spiral ganglion neurons, suggesting changes in expression levels of these genes in the hearing organ could underlie the DFNA58 form of deafness. Our study highlights the value of studying rare genomic events leading to HL, such as copy number variations. Further studies will be required to determine which of these genes, either coding proteins or non-coding RNAs, is or are responsible for DFNA58 HL.
Prescribing Centro-Affine Curvature From One Convex Body to Another
Authors: Stancu Alina
Published: April 2020

We study a curvature flow on smooth, closed, strictly convex hypersurfaces in $\mathbb{R}^n$, which commutes with the action of $SL(n)$. The flow shrinks the initial hypersurface to a point that, if rescaled to enclose a domain of constant volume, is a smooth, closed, strictly convex hypersurface in $\mathbb{R}^n$ with centro-affine curvature proportional, but not always equal, to the centro-affine curvature of a fixed hypersurface. We outline some consequences of this result for the geometry of convex bodies and the logarithmic Minkowski inequality.
Hepatitis C Among High-Risk Alabamians: Disease Burden and Screening Effectiveness
Authors: Lee Anthony B , Karumberia Sandra , Gilmore Ashley , Williams Ebony , Bruner Nichole , Overton Edgar Turner , Saag Michael S , Franco Ricardo A
Published: April 2020

Background

The effectiveness of hepatitis C testing and linkage-to-care (LTC) is poorly characterized in low-resource jurisdictions facing gaps in harm reduction, including illegality of syringe exchange services. Effectiveness of a community-based test/LTC program was evaluated in Alabama.

Methods

In 2016–2018, shelters, drug treatment centers (DTCs), AIDS organizations, and Federally Qualified Health Centers (FQHCs) engaged in screening/LTC. A coordinator navigated individuals to confirm viremia and link to substance use treatment or primary care with hepatitis C prescribers.

Results

Point-of-care (POC) tested 4293 individuals (10% [427] antibody-positive, 71% [299/419] RNA performed, 80% [241/299] viremia confirmed) and 93% linked to care (225/241). Electronic medical record (EMR)-based reflex strategy screened 4654 (15% [679] antibody positive, 99% [670/679] RNA performed, 64% [433/679] viremia confirmed) and 85% linked to care (368/433). We observed higher odds of RNA confirmation in EMR-based reflex versus POC (OR, 2.07; P < .0001) and higher odds of LTC in EMR-based reflex versus POC (OR, 1.51; P < .0001). Overall, 53% individuals tested were nonbaby boomers.

Conclusions

In Alabama, screening at high-risk settings identified significant hepatitis C burden and reflex testing outperformed point-of-care linkage indicators. Colocating testing in DTCs and treatment in FQHCs provided key LTC venues to at-risk younger groups.
Light Traps in Shipping Containers: A New Tool for the Early Detection of Insect Alien Species
Authors: Marchioro Matteo , Battisti Andrea , Faccoli Massimo
Published: April 2020

Insects are one of the most successful groups of invasive species, and the number of new introductions has been increasing in the last decades. Insect invasions are affected mainly by the increase in international trade, as most of them travel across the world inside shipping containers. The effectiveness of sticky light traps was tested for the interception of alien pests inside the containers. The tested hypotheses were that light traps have a valuable broad-spectrum attraction and their trapping performance differs between empty or loaded containers. The optimal trap density in a container was also investigated. Trapping tests were conducted on four model species: Cadra cautella Walker (Lepidoptera: Pyralidae), Drosophila melanogaster Meigen (Diptera: Drosophilidae), Sitophilus zeamais, Motschulsky and Ips typographus L. (Coleoptera: Curculionidae). Insects were released within a standard shipping container, in either empty or loaded conditions, where sticky light traps were deployed for 15 h. Traps were tested with light on (activated) or off (control). Activated traps captured more Lepidoptera and Diptera than control ones, with no differences between empty and loaded container. Instead, Coleoptera were rarely caught, probably because of their ability to escape from traps. Results show that higher trap density in the container (from 1 to 8) increases the probability of insect capture. In conclusion, positive results on C. cautella and D. melanogaster suggest a possible application of sticky light traps against some small Lepidoptera and Diptera species flying in containers and infesting seeds, grains, and fruits, while traps need improvement for application against beetles.
A Guide and Toolbox to Replicability and Open Science in Entomology
Authors: Wittman Jacob T , Aukema Brian H
Published: April 2020

The ability to replicate scientific experiments is a cornerstone of the scientific method. Sharing ideas, workflows, data, and protocols facilitates testing the generalizability of results, increases the speed that science progresses, and enhances quality control of published work. Fields of science such as medicine, the social sciences, and the physical sciences have embraced practices designed to increase replicability. Granting agencies, for example, may require data management plans and journals may require data and code availability statements along with the deposition of data and code in publicly available repositories. While many tools commonly used in replicable workflows such as distributed version control systems (e.g., ‘git’) or script programming languages for data cleaning and analysis may have a steep learning curve, their adoption can increase individual efficiency and facilitate collaborations both within entomology and across disciplines. The open science movement is developing within the discipline of entomology, but practitioners of these concepts or those desiring to work more collaboratively across disciplines may be unsure where or how to embrace these initiatives. This article is meant to introduce some of the tools entomologists can incorporate into their workflows to increase the replicability and openness of their work. We describe these tools and others, recommend additional resources for learning more about these tools, and discuss the benefits to both individuals and the scientific community and potential drawbacks associated with implementing a replicable workflow.
Landscape of genomic imprinting and its functions in the mouse mammary gland
Authors: Xu Haibo , Zhao Lina , Feng Xu , Ma Yujie , Chen Wei , Zou Li , Yang Qin , Sun Jihong , Yu Hong , Jiao Baowei
Published: April 2020

Genomic imprinting is an epigenetic modification of DNA, whereby gene expression is restricted to either maternally or paternally inherited alleles. Imprinted genes (IGs) in the placenta and embryo are essential for growth regulation and nutrient supply. However, despite being an important nutrition delivery organ, studies on mammary gland genomic imprinting remain limited. In this study, we found that both the number of IGs and their expression levels decreased during development of the mouse mammary gland. IG expression was lineage-specific and related to mammary gland development and lactation. Meta-analysis of single-cell RNA sequencing data revealed that mammary gland IGs were co-expressed in a network that regulated cell stemness and differentiation, which was confirmed by our functional studies. Accordingly, our data indicated that IGs were essential for the self-renewal of mammary gland stem cells and IG decline was correlated with mammary gland maturity. Taken together, our findings revealed the importance of IGs in a poorly studied nutrition-related organ, i.e. the mammary gland, thus providing a reference for further studies on genomic imprinting.
Membrane-associated xylanase-like protein OsXYN1 is required for normal cell wall deposition and plant development in rice
Authors: Tu Bin , Zhang Tao , Wang Yuping , Hu Li , Li Jin , Zheng Ling , Zhou Yi , Li Jialian , Xue Fengyin , Zhu Xiaobo , Yuan Hua , Chen Weilan , Qin Peng , Ma Bingtian , Li Shigui
Published: April 2020

The rice (Oryza sativa) genome encodes 37 putative β-1,4-xylanase proteins, but none of them has been characterized at the genetic level. In this work, we report the isolation of slim stem (ss) mutants with pleiotropic defects, including dwarfism, leaf tip necrosis, and withered and rolled leaves under strong sunlight. Map-based cloning of the ss1 mutant identified the candidate gene as OsXyn1 (LOC_03g47010), which encodes a xylanase-like protein belonging to the glycoside hydrolase 10 (GH10) family. OsXyn1 was found to be widely expressed, especially in young tissues. Subcellular localization analysis showed that OsXyn1 encodes a membrane-associated protein. Physiological analysis of ss1 and the allelic ss2 mutant revealed that water uptake was partially compromised in these mutants. Consistently, the plant cell wall of the mutants exhibited middle lamella abnormalities or deficiencies. Immunogold assays revealed an unconfined distribution of xylan in the mutant cell walls, which may have contributed to a slower rate of plant cell wall biosynthesis and delayed plant growth. Additionally, water deficiency caused abscisic acid accumulation and triggered drought responses in the mutants. The findings that OsXyn1 is involved in plant cell wall deposition and the regulation of plant growth and development help to shed light on the functions of the rice GH10 family.
Simulating diverse instabilities of dust in magnetized gas
Authors: Hopkins Philip F , Squire Jonathan , Seligman Darryl
Published: April 2020

Recently, Squire & Hopkins showed that charged dust grains moving through magnetized gas under the influence of a uniform external force (such as radiation pressure or gravity) are subject to a spectrum of instabilities. Qualitatively distinct instability families are associated with different Alfvén or magnetosonic waves and drift or gyro motion. We present a suite of simulations exploring these instabilities, for grains in a homogeneous medium subject to an external acceleration. We vary parameters such as the ratio of Lorentz-to-drag forces on dust, plasma β, size scale, and acceleration. All regimes studied drive turbulent motions and dust-to-gas fluctuations in the saturated state, rapidly amplify magnetic fields into equipartition with velocity fluctuations, and produce instabilities that persist indefinitely (despite random grain motions). Different parameters produce diverse morphologies and qualitatively different features in dust, but the saturated gas state can be broadly characterized as anisotropic magnetosonic or Alfvénic turbulence. Quasi-linear theory can qualitatively predict the gas turbulent properties. Turbulence grows from small to large scales, and larger scale modes usually drive more vigorous gas turbulence, but dust velocity and density fluctuations are more complicated. In many regimes, dust forms structures (clumps, filaments, sheets) that reach extreme overdensities (up to ≫109 times mean), and exhibit substantial substructure even in nearly incompressible gas. These can be even more prominent at lower dust-to-gas ratios. In other regimes, dust self-excites scattering via magnetic fluctuations that isotropize and amplify dust velocities, producing fast, diffusive dust motions.
SCUBA-2 overdensities associated with candidate protoclusters selected from Planck data
Authors: Cheng T , Clements D L , Greenslade J , Cairns J , Andreani P , Bremer M , Conversi L , Cooray A , Dannerbauer H , De Zotti G , Eales S , González-Nuevo J , Ibar E , Leeuw L , Ma J , Michałowski M J , Nayyeri H , Riechers D A , Scott D , Temi P , Vaccari M , Valtchanov I , van Kampen E , Wang L
Published: April 2020

We measure the 850-μm source densities of 46 candidate protoclusters selected from the Planck high-z catalogue (PHz) and the Planck Catalogue of Compact Sources (PCCS) that were followed up with Herschel-SPIRE and SCUBA-2. This paper aims to search for overdensities of 850-μm sources in order to select the fields that are most likely to be genuine protoclusters. Of the 46 candidate protoclusters, 25 have significant overdensities (>5 times the field counts), 11 have intermediate overdensities (3–5 times the field counts), and 10 have no overdensity (<3 times the field counts) of 850-μm sources. We find that the enhanced number densities are unlikely to be the result of sample variance. Compared with the number counts of another sample selected from Planck’s compact source catalogues, this [PHz + PCCS]-selected sample has a higher fraction of candidate protoclusters with significant overdensities, though both samples show overdensities of 850-μm sources above intermediate level. Based on the estimated star formation rate densities (SFRDs), we suggest that both samples can efficiently select protoclusters with starbursting galaxies near the redshift at which the global field SFRD peaks (2 < z < 3). Based on the confirmation of overdensities found here, future follow-up observations on other PHz targets may greatly increase the number of genuine dusty star-forming galaxy-rich clusters/protoclusters.
Optical turbulence at Ali, China – results from the first year of lunar scintillometer observations
Authors: Hickson Paul , Feng Lu , Hellemeier Joschua A , Shen Zhixia , Xue Suijian , Yao Yongqiang , Ma Bin , Chen Hualin , Yang Rui
Published: April 2020

The location of an astronomical observatory is a key factor that affects its scientific productivity. The best astronomical sites are generally those found at high altitudes. Several such sites in western China and the Tibetan plateau are presently under development for astronomy. One of these is Ali, which, at over 5000 m, is one of the highest astronomical sites in the world. In order to further investigate the astronomical potential of Ali, we have installed a lunar scintillometer, for the primary purpose of profiling atmospheric turbulence. This paper describes the instrument and technique, and reports results from the first year of observations. We find that ground layer (GL) turbulence at Ali is remarkably weak and relatively thin. The median seeing, from turbulence in the range 11–500 m above ground, is 0.34 arcsec, with seeing better than 0.26 arcsec occurring 25 per cent of the time. Under median conditions, half of the GL turbulence lies below a height of 62 m. These initial results, and the high altitude and relatively low temperatures, suggest that Ali could prove to be an outstanding site for ground-based astronomy.
A Magnetic Snapshot Survey of F-Type Stars
Authors: Seach J M , Marsden S C , Carter B D , Neiner C , Folsom C P , Mengel M W , Oksala M E , Buysschaert B
Published: April 2020

We present a spectropolarimetric magnetic snapshot survey of 55 stars which includes 53 F-type stars ranging from spectral types F0 to F9 plus 2 chemically peculiar stars β CrB, and δ Cap. We look for magnetic fields in stars spanning a range of effective temperatures where the transition from fossil to dynamo magnetic fields is believed to occur. High-resolution spectropolarimetry using circularly polarized spectra is used to look for a magnetic detection in the Stokes V profile, determine the mean longitudinal magnetic field (Bl), and to look for correlations with stellar parameters. Surface magnetic fields are detected on 14 F-stars, and present in every spectral class from F3V-F9V ranging in strength from 0.3 ± 0.1 G (36 UMa, F8V) to 8.3 ± 0.9 G (h Dra, F8V). Thus we find photospheric magnetic fields are present in stars as early as spectral type F3V with an outer convection zone thickness less than a few per cent of the stellar radius.