bluuebunny/crossref_metadata_2025 huggingface dataset:
MAD‐UNet: A deep U‐shaped network combined with an attention mechanism for pancreas segmentation in CT images
Authors: Li Weisheng , Qin Sheng , Li Feiyan , Wang Linhong
Published: November 2020

Purpose

Pancreas segmentation is a difficult task because of the high intrapatient variability in the shape, size, and location of the organ, as well as the low contrast and small footprint of the CT scan. At present, the U‐Net model is likely to lead to the problems of intraclass inconsistency and interclass indistinction in pancreas segmentation. To solve this problem, we improved the contextual and semantic feature information acquisition method of the biomedical image segmentation model (U‐Net) based on a convolutional network and proposed an improved segmentation model called the multiscale attention dense residual U‐shaped network (MAD‐UNet).

Methods

There are two aspects considered in this method. First, we adopted dense residual blocks and weighted binary cross‐entropy to enhance the semantic features to learn the details of the pancreas. Using such an approach can reduce the effects of intraclass inconsistency. Second, we used an attention mechanism and multiscale convolution to enrich the contextual information and suppress learning in unrelated areas. We let the model be more sensitive to pancreatic marginal information and reduced the impact of interclass indistinction.

Results

We evaluated our model using fourfold cross‐validation on 82 abdominal enhanced three‐dimensional (3D) CT scans from the National Institutes of Health (NIH‐82) and 281 3D CT scans from the 2018 MICCAI segmentation decathlon challenge (MSD). The experimental results showed that our method achieved state‐of‐the‐art performance on the two pancreatic datasets. The mean Dice coefficients were 86.10% ± 3.52% and 88.50% ± 3.70%.

Conclusions

Our model can effectively solve the problems of intraclass inconsistency and interclass indistinction in the segmentation of the pancreas, and it has value in clinical application. Code is available at https://github.com/Mrqins/pancreas‐segmentation.
Multi‐technical study of copper oxide on graphitic carbon nitride and its role in the photocatalytic reactions
Authors: Wojtyła Szymon , Baran Tomasz
Published: November 2020

Based on a facile three‐step preparation method, CuO/g‐C3N4 photocatalysts have been successfully synthesized by exfoliation of a bulk graphitic carbon nitride and subsequent hydrothermal decoration with CuO nanoparticles. Several advanced scientific tools were used to characterize crucial features of the prepared materials, in particular, to understand the role of copper oxide in photocatalytic reactions. CuO/g‐C3N4 reached a remarkably increased light‐induced photocatalytic reduction of water to hydrogen as well as oxidation of formaldehyde to CO2, in comparison with a neat g‐C3N4. The presence of CuO co‐catalyst resulted in more than 10 times higher H2 production rate. The increase of photocatalytic efficiency was observed also in the case of HCHO oxidation, but the effect of CuO addition was less impressive. Moreover, it has been evidenced that the durability of photocatalyst raised with an increasing amount of copper oxide. Simultaneously, the copper modified composites exhibited an improved photoelectrocatalytic (PEC) performance, confirmed by the photocurrent density measurements. In the following paper we described our findings concerning the role of copper oxide in CuO/g‐C3N4 composites.
Conversion of explicit microplane model with boundaries to a constitutive subroutine for implicit finite element programs
Authors: Nguyen Hoang T. , Caner Ferhun C. , Bažant Zdeněk P.
Published: November 2020

Whereas various simplistic microplane models of limited applicability, defined by stress–strain curves on the microplane, can function as either explicit or implicit, the explicit‐to‐implicit conversion of realistic versatile microplane models for plain or fiber‐reinforced concrete, shale and composites has remained a challenge for quarter century. The reason is that these realistic models use microplane stress–strain boundaries defined by inequalities. Here, we show how the conversion can be easily achieved on the microplane level and then transferred to a tangent stiffness tensor or an inelastic stiffness tensor to be used in Newton–Raphson iterations within a loading step. To ensure convergence, a minor adjustment in the M7 algorithm is introduced to achieve continuity. Power‐law convergence, almost quadratic in most cases, is also demonstrated. Seven examples of crack‐band finite element simulations of challenging laboratory tests document nearly identical implicit and explicit results, as well as good match of test data. Three of them, including the vertex effect in compression‐torsion tests, pure Mode II shear fracture, and the “gap test” of the crack‐parallel compression effect on Mode I load‐deflection curve, have not been reproduced by other models before. The coding of implicit M7 subroutine, usable in, for example, UMAT of ABAQUS, is posted for a free download.
Coupling hydrogeophysics with hydrodynamic modelling to infer subsurface hydraulic architecture of an alluvial floodplain
Authors: Martin J. Michael , Everett Mark E. , Knappett Peter S.K.
Published: November 2020

This paper underscores the importance of spatially dense geophysical data sets for making informed decisions in water management strategies. Such decisions may require understanding how site‐specific subsurface architecture – especially hydraulic connectivity – impacts the response of a shallow aquifer to anthropogenic hydrologic disturbances (e.g. over‐pumping of a shallow aquifer). At a 0.2‐km2 alluvial floodplain site characterized by thick clay over fine sand to gravel and shale bedrock in the subtropical, sub‐humid belt of the Gulf Coast of the United States, we image an asymmetrically shaped, compartmentalized, sand‐dominated channel‐belt using electrical resistivity tomography and 31 time‐domain electromagnetic soundings probing to depths of ∼40 m and ∼90 m, respectively. Lithological interpretation and a hydrological model are developed based on the geophysical data and nearby sediment cores, where the resistivity of the groundwater is 9.1 Ωm. In a modelling scenario wherein the compartmentalized sand channel‐belt starts out dry (i.e. an over‐pumped shallow aquifer), we simulate 26 weeks of infiltration due to flooding of the surface. Preferential filling of the channel‐belt occurs through its sides rather than from above, generating a new understanding of the hydraulic connectivity around and into asymmetrically shaped, sand‐dominated channel‐belts. This insight can inform decisions about the optimal placement of shallow water wells in a heterogeneous alluvial floodplain aquifer system and also highlights the dangers of over‐pumping.
Drought activates MYB41 orthologs and induces suberization of grapevine fine roots
Authors: Zhang Li , Merlin Isabelle , Pascal Stéphanie , Bert Pierre‐François , Domergue Frédéric , Gambetta Gregory A.
Published: November 2020

The permeability of roots to water and nutrients is controlled through a variety of mechanisms and one of the most conspicuous is the presence of the Casparian strips and suberin lamellae. Roots actively regulate the creation of these structures developmentally, along the length of the root, and in response to the environment, including drought. In the current study, we characterized the suberin composition along the length of grapevine fine roots during development and in response to water deficit, and in the same root systems we quantified changes in expression of suberin biosynthesis‐ and deposition‐related gene families (via RNAseq) allowing the identification of drought‐responsive suberin‐related genes. Grapevine suberin composition did not differ between primary and lateral roots, and was similar to that of other species. Under water deficit there was a global upregulation of suberin biosynthesis which resulted in an increase of suberin specific monomers, but without changes in their relative abundances, and this upregulation took place across all the developmental stages of fine roots. These changes corresponded to the upregulation of numerous suberin biosynthesis‐ and export‐related genes which included orthologs of the previously characterized AtMYB41 transcriptional factor. Functional validation of two grapevine MYB41 orthologs, VriMYB41 and VriMYB41‐like, confirmed their ability to globally upregulate suberin biosynthesis, export, and deposition. This study provides a detailed characterization of the developmental and water deficit induced suberization of grapevine fine roots and identifies important orthologs responsible for suberin biosynthesis, export, and its regulation in grape.
Halide Vapor Phase Epitaxy of In2O3 and (In1−xGax)2O3 on Sapphire Substrates and GaN/Al2O3 Templates
Authors: Stepanov Sergey , Nikolaev Vladimir , Pechnikov Alexei , Scheglov Mikhail , Chikiryaka Andrei , Chernykh Alexey , Odnobludov Maxim , Andreeva Valentina , Polyakov Alexander Y.
Published: November 2020

The growth of cubic and rhombohedral In2O3 and (InGa)2O3 epitaxial films by halide vapor phase epitaxy (HVPE) is reported. The deposition is carried out at 625 °C using indium trichloride (InCl3), gallium monochloride (GaCl), and O2 precursors on (0001) sapphire substrates, HVPE‐grown Ga2O3/Al2O3 and metal‐organic chemical vapor deposition (MOCVD)‐grown GaN/Al2O3 templates. The HVPE growth of phase pure In2O3 and (InGa)2O3 with corundum structure is reported for the first time.
Full‐length genome sequencing of RNA viruses—How the approach can enlighten us on hepatitis C and hepatitis E viruses
Authors: Laugel Elodie , Hartard Cédric , Jeulin Hélène , Berger Sibel , Venard Véronique , Bronowicki Jean‐Pierre , Schvoerer Evelyne
Published: November 2020

Among the five main viruses responsible for human hepatitis, hepatitis C virus (HCV) and hepatitis E virus (HEV) are different while sharing similarities. Both viruses can be transmitted by blood or derivatives whereas HEV can also follow environmental or zoonotic routes. These highly variable RNA viruses can cause chronic hepatitis potentially leading to hepatocarcinoma. HCV and HEV can develop new structures and functions under selective pressure to adapt to host immunity, human tissues, treatments or even various animal reservoirs. Elsewhere, with directly acting antiviral treatments, HCV can be eradicated whereas HEV is an emerging pathogen against which specific treatments have to be improved. As a unique molecular tool able to explore viral genomic plasticity, full‐length genome (FLG) sequencing has become easier, faster and cheaper. The present review will show how FLG sequencing can explore these RNA viruses with the aim to investigate key genomics data to improve basic knowledge, patients' healthcare and preventive tools.
Visible Light–Induced Degradation of Inverted Polymer:Nonfullerene Acceptor Solar Cells: Initiated by the Light Absorption of ZnO Layer
Authors: Liu Bowen , Han Yunfei , Li Zerui , Gu Huimin , Yan Lingpeng , Lin Yi , Luo Qun , Yang Shangfeng , Ma Chang-Qi
Published: November 2020

Power conversion efficiencies (PCEs) of polymer solar cells (PSCs) have exceeded 18% in the last few years. Stability has therefore become the next most important issue before commercialization. Herein, the degradation behaviors of the inverted PM6:IT‐4F (PBDB‐T‐2F:3,9‐bis(2‐methylene‐((3‐(1,1‐dicyanomethylene)‐6,7‐difluoro)‐indanone))‐5,5,11,11‐tetrakis(4‐hexylphenyl)‐dithieno[2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene) solar cells with different ZnO layers are systematically investigated. The PCE decay rates of the cells and the photobleaching process of the IT‐4F containing organic films on ZnO surface are directly correlated with the light‐absorption ability of the ZnO layer in the visible light range, indicating that photochemical decomposition of IT‐4F is initiated by the light absorption of ZnO layer. By analyzing the products of the aged ZnO/IT‐4F films with matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS), it is confirmed that photochemical reactions at the IT‐4F/ZnO interface include de‐electron‐withdrawing units and dealkylation on the side‐phenyl ring. Hydroxyl radicals generated by the photo‐oxidation of dangling hydroxide by ZnO are confirmed by electron spin resonance (ESR) spectroscopy measurements, which is attributed as the main reason causing the decomposition of IT‐4F. Surface treatment of ZnO with hydroxide and/or hydroxyl radical scavenger is found to be able to improve the stability of the PSCs, which further supports the proposed degradation mechanism.
Fire resistance of integral composite beams with superposed slabs
Authors: Lyu Junli , Chen Qichao , Lyu Jingjing , Cai Yongyuan , Zhou Shengnan
Published: November 2020

The uniform‐load fire behaviors of four full‐scale integral composite beams with superposed slabs were tested, considering the post‐cast‐slab thickness, shear‐connector spacing, and precast‐slab overlap length on the steel‐beam upper flange. The concrete temperature distribution along the slab thickness, the temperature of the rebar inside the slab, the temperature distribution along the steel‐beam height, the bending stiffness, and the overall integrity of the superposed slabs and steel beam were studied. ABAQUS simulations of the temperature‐field and deformation behaviors of the composite beams with superposed slabs under coupled thermal and mechanical loading were performed. No damage to the post‐cast and precast slab bonding interface during the heating process was apparent. The post‐cast joint had no obvious influence on the structure, which could still bear loads. The composite‐beam temperature field and bending stiffness were not significantly affected by the bonding interface of the new and old concrete and the post‐cast joint. Overall, the post‐cast slab thickness and shear‐connector spacing predominantly influenced the composite‐beam fire resistance. The experiment and numerical results agree well, verifying the numerical‐model validity and feasibility.
Extensive hepatic portal venous gas and gastric pneumatosis in a cat
Authors: Spiller Karin T. , Eisenberg Beth W.
Published: November 2020

A 15‐year‐old female neutered Domestic Long Hair cat was presented for acute hematemesis. Initial diagnostic workup, including serum biochemistry panel, complete blood count and coagulation profile, was unremarkable. Abdominal ultrasound showed gastric mural thickening and non‐obstructive gastric foreign material. Endoscopy was performed to remove the foreign matter and obtain biopsies. Significant abnormalities of the upper gastrointestinal (GI) tract were not noted endoscopically. Overnight, the patient required a packed red blood cell transfusion following two episodes of severe hematemesis, hypotension and collapse. Serial radiographs and ultrasound revealed hepatic portal venous gas (HPVG). Computed tomography (CT) scan confirmed massive gas accumulation within the liver and emphysematous gastritis. The patient became increasingly unstable and, given her rapid decline, humane euthanasia was elected. Gastric and duodenal histopathology showed inflammatory changes, spirochetosis and mucosal epithelial degeneration. HPVG is a rarely described finding and prognosis varies drastically depending on aetiology. To the best of our knowledge, this is the first description of portal vein gas documented on multiple imaging modalities, including CT, in a cat. The patient in this report had several potential risk factors including prior endoscopy, compromise of the intestinal barrier and evidence of gastric mural bacterial invasion.
A vanishing dynamic capillarity limit equation with discontinuous flux
Authors: Graf M. , Kunzinger M. , Mitrovic D. , Vujadinovic D.
Published: November 2020

We prove existence and uniqueness of a solution to the Cauchy problem corresponding to the dynamics capillarity equation $$\begin{aligned} {\left\{ \begin{array}{ll} \partial _t u_{\varepsilon ,\delta } +\mathrm {div} {\mathfrak f}_{\varepsilon ,\delta }(\mathbf{x}, u_{\varepsilon ,\delta })=\varepsilon \Delta u_{\varepsilon ,\delta }+\delta (\varepsilon ) \partial _t \Delta u_{\varepsilon ,\delta }, \ \ \mathbf{x} \in M, \ \ t\ge 0\\ u|_{t=0}=u_0(\mathbf{x}). \end{array}\right. } \end{aligned}$$

∂
t

u

ε
,
δ

+
div

f

ε
,
δ

(
x
,

u

ε
,
δ

)

=
ε
Δ

u

ε
,
δ

+
δ

(
ε
)

∂
t

Δ

u

ε
,
δ

,

x
∈
M
,

t
≥
0

u
|

t
=
0

=

u
0

(
x
)

.

Here, $${{\mathfrak {f}}}_{\varepsilon ,\delta }$$

f

ε
,
δ

and $$u_0$$

u
0

are smooth functions while $$\varepsilon $$
ε
and $$\delta =\delta (\varepsilon )$$

δ
=
δ
(
ε
)

are fixed constants. Assuming $${{\mathfrak {f}}}_{\varepsilon ,\delta } \rightarrow {{\mathfrak {f}}}\in L^p( {\mathbb {R}}^d\times {\mathbb {R}};{\mathbb {R}}^d)$$

f

ε
,
δ

→
f
∈

L
p

(

R

d

×
R
;

R

d

)

for some $$1<p<\infty $$

1
<
p
<
∞

, strongly as $$\varepsilon \rightarrow 0$$

ε
→
0

, we prove that, under an appropriate relationship between $$\varepsilon $$
ε
and $$\delta (\varepsilon )$$

δ
(
ε
)

depending on the regularity of the flux $${{\mathfrak {f}}}$$
f
, the sequence of solutions $$(u_{\varepsilon ,\delta })$$

(

u

ε
,
δ

)

strongly converges in $$L^1_{loc}({\mathbb {R}}^+\times {\mathbb {R}}^d)$$

L

loc

1

(

R

+

×

R

d

)

toward a solution to the conservation law $$\begin{aligned} \partial _t u +\mathrm {div} {{\mathfrak {f}}}(\mathbf{x}, u)=0. \end{aligned}$$

∂
t

u
+
div
f

(
x
,
u
)

=
0
.

The main tools employed in the proof are the Leray–Schauder fixed point theorem for the first part and reduction to the kinetic formulation combined with recent results in the velocity averaging theory for the second. These results have the potential to generate a stable semigroup of solutions to the underlying scalar conservation laws different from the Kruzhkov entropy solutions concept.
Synthesis and biological evaluation of novel N-substituted nipecotic acid derivatives with tricyclic cage structures in the lipophilic domain as GABA uptake inhibitors
Authors: Rudy Heinrich-Karl A. , Höfner Georg , Wanner Klaus T.
Published: November 2020

A new class of GABA reuptake inhibitors with sterically demanding, highly rigid tricyclic cage structures as the lipophilic domain was synthesized and investigated in regard to their biological activity at the murine GABA transporters (mGAT1–mGAT4). The construction of these compounds, consisting of nipecotic acid, a symmetric tricyclic amine, and a plain hydrocarbon linker connecting the two subunits via their amino nitrogens, was accomplished via reductive amination of a nipecotic acid derivative with an N-alkyl substituent displaying a terminal aldehyde function with tricyclic secondary amines. The target compounds varied with regard to spacer length, the bridge size of one of the bridges, and the substituents of the tricyclic skeleton to study the impact of these changes on their potency. Among the tested compounds nipecotic acid ethyl ester derivates with phenyl residues attached to the cage subunit showed reasonable inhibitory potency and subtype selectivity in favor of mGAT3 and mGAT4, respectively.
Self-organization of organoids from endoderm-derived cells
Authors: Lewis Allison , Keshara Rashmiparvathi , Kim Yung Hae , Grapin-Botton Anne
Published: November 2020

Organoids constitute biological systems which are used to model organ development, homeostasis, regeneration, and disease in vitro and hold promise for use in therapy. Reflecting in vivo development, organoids form from tissue cells or pluripotent stem cells. Cues provided from the media and individual cells promote self-organization of these uniform starting cells into a structure, with emergent differentiated cells, morphology, and often functionality that resemble the tissue of origin. Therefore, organoids provide a complement to two-dimensional in vitro culture and in vivo animal models of development, providing the experimental control and flexibility of in vitro methods with the three-dimensional context of in vivo models, with fewer ethical restraints than human or animal work. However, using organoids, we are only just beginning to understand on the cellular level how the external conditions and signaling between individual cells promote the emergence of cells and structures. In this review, we focus specifically on organoids derived from endodermal tissues: the starting conditions of the cells, signaling mechanisms, and external media that allow the emergence of higher order self-organization.
Snow mold of winter cereals: a complex disease and a challenge for resistance breeding
Authors: Ponomareva Mira L. , Gorshkov Vladimir Yu. , Ponomarev Sergey N. , Korzun Viktor , Miedaner Thomas
Published: November 2020

Key message

Snow mold resistance is a complex quantitative trait highly affected by environmental conditions during winter that must be addressed by resistance breeding.

Snow mold resistance in winter cereals is an important trait for many countries in the Northern Hemisphere. The disease is caused by at least four complexes of soilborne fungi and oomycetes of whichMicrodochium nivaleandM. majusare among the most common pathogens. They have a broad host range covering all winter and spring cereals and can basically affect all plant growth stages and organs. Their attack leads to a low germination rate, and/or pre- and post-emergence death of seedlings after winter and, depending on largely unknown environmental conditions, also to foot rot, leaf blight, and head blight. Resistance in winter wheat and triticale is governed by a multitude of quantitative trait loci (QTL) with mainly additive effects highly affected by genotype × environment interaction. Snow mold resistance interacts with winter hardiness in a complex way leading to a co-localization of resistance QTLs with QTLs/genes for freezing tolerance. In practical breeding, a multistep procedure is necessary with (1) freezing tolerance tests, (2) climate chamber tests for snow mold resistance, and (3) field tests in locations with and without regularly occurring snow cover. In the future, resistance sources should be genetically characterized also in rye by QTL mapping or genome-wide association studies. The development of genomic selection procedures should be prioritized in breeding research.
Optimal Control of the Principal Coefficient in a Scalar Wave Equation
Authors: Clason Christian , Kunisch Karl , Trautmann Philip
Published: November 2020

We consider optimal control of the scalar wave equation where the control enters as a coefficient in the principal part. Adding a total variation penalty allows showing existence of optimal controls, which requires continuity results for the coefficient-to-solution mapping for discontinuous coefficients. We additionally consider a so-called multi-bang penalty that promotes controls taking on values pointwise almost everywhere from a specified discrete set. Under additional assumptions on the data, we derive an improved regularity result for the state, leading to optimality conditions that can be interpreted in an appropriate pointwise fashion. The numerical solution makes use of a stabilized finite element method and a nonlinear primal–dual proximal splitting algorithm.
Indications and Outcomes for Non‐Trauma Emergency Laparotomy: A Comparison of Rwanda, South Africa, and the USA
Authors: Rickard Jennifer , Pohl Linda , Abahuje Egide , Kariem Nazmie , Englbrecht Surita , Kloppers Christo , Malatji Sekoaere , Sibomana Isaie , Robbins Alexandria J. , Chu Kathryn
Published: November 2020

Background

Emergency conditions requiring exploratory laparotomy (EL) can be challenging. The objective of this study is to describe indications, outcomes, and risk factors for perioperative mortality (POMR) after non‐trauma EL.

Methods

This was a prospective study of patients undergoing non‐trauma EL at four hospitals in Rwanda, South Africa, and the USA. Multivariate logistic regression was used to determine factors associated with POMR.

Results

Over one year, there were 632 EL with the most common indications appendicitis (n = 133, 21%), peptic ulcer disease (PUD) (n = 101, 16%), and hernia (n = 74, 12%). In Rwanda, the most common indications were appendicitis (n = 41, 19%) and hernia (n = 37, 17%); in South Africa appendicitis (n = 91, 28%) and PUD (n = 60, 19%); and in the USA, PUD (n = 16, 19%) and adhesions from small bowel obstruction (n = 16, 19%).

POMR was 11%, with no difference between countries (Rwanda 7%, South Africa 12%, US 16%, p = 0.173). Risk factors associated with increased odds of POMR included typhoid intestinal perforation (adjusted odds ratio (aOR): 16.48; 95% confidence interval (CI): 4.31, 62.98; p value < 0.001), mesenteric ischemia (aOR: 13.77, 95% CI: 4.21, 45.08, p value < 0.001), cancer (aOR: 5.84, 95% CI: 2.43, 14.05, p value < 0.001), other diagnoses (aOR: 3.97, 95% CI: 3.03, 5.20, p value < 0.001), high ASA score (score ≥ 3) (aOR: 3.95, 95% CI: 3.03, 5.15, p value < 0.001), peptic ulcer disease (aOR: 2.82, 95% CI: 1.64, 4.85, p value < 0.001), age > 60 years (aOR: 2.32, 95% CI: 1.41, 3.83, p value = 0.001), and ICU admission (aOR: 2.23, 95% CI: 1.24, 3.99, p value = 0.007). Surgery in the US was associated with decreased odds of POMR (aOR: 0.41, 95% CI: 0.21, 0.80, p value = 0.009).

Conclusions

Indications for EL vary between countries and POMR is high. Differences in mortality were associated with patient and disease characteristics with certain diagnoses associated with increased risk of mortality. Understanding the risk factors and outcomes for patients with EL can assist providers in judicious patient selection, both for patient counselling and resource allocation.
Glucocorticoid maintenance therapy and severe infectious complications in ANCA-associated vasculitis: a retrospective analysis
Authors: Speer Claudius , Altenmüller-Walther Christine , Splitthoff Jan , Nusshag Christian , Kälble Florian , Reichel Paula , Morath Christian , Zeier Martin , Bergner Raoul , Schaier Matthias
Published: November 2020

To study the impact of glucocorticoid maintenance dose and treatment duration on outcomes in patients with AAV (ANCA-associated vasculitis) with emphasis on infectious complications. A total of 130 AAV patients from two German vasculitis centers diagnosed between August 2004 and January 2019 treated with cyclophosphamide and glucocorticoids for induction therapy and glucocorticoids for maintenance therapy were retrospectively enrolled. We investigated the influence of glucocorticoid maintenance therapy on patient survival, time to relapse, kidney function, infectious complications and irreversible physical damage. The patients were divided into the following groups: patients treated according to the predefined reduction scheme (< 7.5 mg) or patients treated with glucocorticoids ≥ 7.5 mg after 6 months. Compared to patients receiving < 7.5 mg glucocorticoids after 6 months, patients receiving $$\ge $$
≥
7.5 mg had an increased rate of infectious episodes per patient (1.7 vs. 0.6; p < 0.001), including urinary tract infection (p = 0.007), pneumonia (p = 0.003), opportunistic pneumonia (p = 0.022) and sepsis (p = 0.008). Especially pneumonia during the first 24 months after disease onset [hazard ratio, 3.0 (95% CI 1.5 − 6.1)] led to more deaths from infection (p = 0.034). Glucocorticoid maintenance therapy after 6 months had no impact on relapse rate or patient survival and decline in kidney function was comparable. Glucocorticoid maintenance therapy with $$\ge $$
≥
7.5 mg after 6 months is associated with more severe infectious complications leading to an increased frequency of deaths from infection. Glucocorticoid maintenance therapy has no effect on time to relapse or patient survival and should therefore be critically revised throughout the aftercare of AAV patients.
Modeling low-dose radiation-induced acute myeloid leukemia in male CBA/H mice
Authors: Stouten Sjors , Verduyn Lunel Sjoerd , Finnon Rosemary , Badie Christophe , Dekkers Fieke
Published: November 2020

The effect of low-dose ionizing radiation exposure on leukemia incidence remains poorly understood. Possible dose-response curves for various forms of leukemia are largely based on cohorts of atomic bomb survivors. Animal studies can contribute to an improved understanding of radiation-induced acute myeloid leukemia (rAML) in humans. In male CBA/H mice, incidence of rAML can be described by a two-hit model involving a radiation-induced deletion with Sfpi1 gene copy loss and a point mutation in the remaining Sfpi1 allele. In the present study (historical) mouse data were used and these processes were translated into a mathematical model to study photon-induced low-dose AML incidence in male CBA/H mice following acute exposure. Numerical model solutions for low-dose rAML incidence and diagnosis times could respectively be approximated with a model linear-quadratic in radiation dose and a normal cumulative distribution function. Interestingly, the low-dose incidence was found to be proportional to the modeled number of cells carrying the Sfpi1 deletion present per mouse following exposure. After making only model-derived high-dose rAML estimates available to extrapolate from, the linear-quadratic model could be used to approximate low-dose rAML incidence calculated with our mouse model. The accuracy in estimating low-dose rAML incidence when extrapolating from a linear model using a low-dose effectiveness factor was found to depend on whether a data transformation was used in the curve fitting procedure.
The relationship between the gut microbiome and host gene expression: a review
Authors: Nichols Robert G. , Davenport Emily R.
Published: November 2020

Despite the growing knowledge surrounding host–microbiome interactions, we are just beginning to understand how the gut microbiome influences—and is influenced by—host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
In-season weather data provide reliable yield estimates of maize and soybean in the US central Corn Belt
Authors: Joshi Vijaya R. , Kazula Maciej J. , Coulter Jeffrey A. , Naeve Seth L. , Garcia y Garcia Axel
Published: November 2020

Weather conditions regulate the growth and yield of crops, especially in rain-fed agricultural systems. This study evaluated the use and relative importance of readily available weather data to develop yield estimation models for maize and soybean in the US central Corn Belt. Total rainfall (Rain), average air temperature (Tavg), and the difference between maximum and minimum air temperature (Tdiff) at weekly, biweekly, and monthly timescales from May to August were used to estimate county-level maize and soybean grain yields for Iowa, Illinois, Indiana, and Minnesota. Step-wise multiple linear regression (MLR), general additive (GAM), and support vector machine (SVM) models were trained with Rain, Tavg, and with/without Tdiff. For the total study area and at individual state level, SVM outperformed other models at all temporal levels for both maize and soybean. For maize, Tavg and Tdiff during July and August, and Rain during June and July, were relatively more important whereas for soybean, Tavg in June and Tdiff and Rain during August were more important. The SVM model with weekly Rain and Tavg estimated the overall maize yield with a root mean square error (RMSE) of 591 kg ha−1(4.9%nRMSE) and soybean yield with a RMSE of 205 kg ha−1(5.5%nRMSE). Inclusion of Tdiff in the model considerably improved yield estimation for both crops; however, the magnitude of improvement varied with the model and temporal level of weather data. This study shows the relative importance of weather variables and reliable yield estimation of maize and soybean from readily available weather data to develop a decision support tool in the US central Corn Belt.
Intraoperative mapping of executive function using electrocorticography for patients with low-grade gliomas
Authors: Erez Yaara , Assem Moataz , Coelho Pedro , Romero-Garcia Rafael , Owen Mallory , McDonald Alexa , Woodberry Emma , Morris Robert C. , Price Stephen J. , Suckling John , Duncan John , Hart Michael G. , Santarius Thomas
Published: November 2020

Background

Intraoperative functional mapping with direct electrical stimulation during awake surgery for patients with diffuse low-grade glioma has been used in recent years to optimize the balance between surgical resection and quality of life following surgery. Mapping of executive functions is particularly challenging because of their complex nature, with only a handful of reports published so far. Here, we propose the recording of neural activity directly from the surface of the brain using electrocorticography to map executive functions and demonstrate its feasibility and potential utility.

Methods

To track a neural signature of executive function, we recorded neural activity using electrocorticography during awake surgery from the frontal cortex of three patients judged to have an appearance of diffuse low-grade glioma. Based on existing functional magnetic resonance imaging (fMRI) evidence from healthy participants for the recruitment of areas associated with executive function with increased task demands, we employed a task difficulty manipulation in two counting tasks performed intraoperatively. Following surgery, the data were extracted and analyzed offline to identify increases in broadband high-gamma power with increased task difficulty, equivalent to fMRI findings, as a signature of activity related to executive function.

Results

All three patients performed the tasks well. Data were recorded from five electrode strips, resulting in data from 15 channels overall. Eleven out of the 15 channels (73.3%) showed significant increases in high-gamma power with increased task difficulty, 26.6% of the channels (4/15) showed no change in power, and none of the channels showed power decrease. High-gamma power increases with increased task difficulty were more likely in areas that are within the canonical frontoparietal network template.

Conclusions

These results are the first step toward developing electrocorticography as a tool for mapping of executive function complementarily to direct electrical stimulation to guide resection. Further studies are required to establish this approach for clinical use.
The network boundary specification problem in the global and world city research: investigation of the reliability of empirical results from sampled networks
Authors: Pažitka Vladimír , Wójcik Dariusz
Published: November 2020

Despite the well-known dependence of vertex and network structural parameters on network boundary specification employed by researchers, there has so far been effectively no discussion of this methodological caveat in the global and world city literature. Given the reliance of empirical studies of urban networks on the sampling of underlying actors that form these networks by their interactions, we consider it of key importance to examine the dependence of network centralities of cities on network boundary specification. We consider three distinctive modelling approaches based on: (a) office networks, (b) ownership ties and (c) inter-organisational projects. Our results indicate that city network centralities obtained from sampled networks are highly consistent with those obtained from whole network analysis for samples featuring as little as 4% (office networks), 10% (ownership ties) and 25% (inter-organisational projects) of the underlying actors.
Numerical modelling of intra-wave sediment transport on sandy beaches using a non-hydrostatic, wave-resolving model
Authors: Mancini Giulia , Briganti Riccardo , McCall Robert , Dodd Nicholas , Zhu Fangfang
Published: November 2020

The mutual feedback between the swash zone and the surf zone is known to affect large-scale morphodynamic processes such as breaker bar migration on sandy beaches. To fully resolve this feedback in a process-based manner, the morphodynamics in the swash zone and due to swash-swash interactions must be explicitly solved, e.g., by means of a wave-resolving numerical model. Currently, few existing models are able to fully resolve the complex morphodynamics in the swash zone, and none is practically applicable for engineering purposes. This work aims at improving the numerical modelling of the intra-wave sediment transport on sandy beaches in an open-source wave-resolving hydro-morphodynamic framework (e.g., non-hydrostatic XBeach). A transport equation for the intra-wave suspended sediment concentration, including an erosion and a deposition rate, is newly implemented in the model. Two laboratory experiments involving isolated waves and wave trains are simulated to analyse the performance of the model. Numerical results show overall better performance in simulating single waves rather than wave trains. For the latter, the modelling of the morphodynamic response improves in the swash zone compared with the existing sediment transport modelling approach within non-hydrostatic XBeach, while the need of including additional physical processes to better capture sediment transport and bed evolution in the surf zone is highlighted in the paper.
Recent advances in carbon capture storage and utilisation technologies: a review
Authors: Osman Ahmed I. , Hefny Mahmoud , Abdel Maksoud M. I. A. , Elgarahy Ahmed M. , Rooney David W.
Published: November 2020

Human activities have led to a massive increase in $$\hbox {CO}_{2}$$

CO
2

emissions as a primary greenhouse gas that is contributing to climate change with higher than $$1\,^{\circ }\hbox {C}$$

1

∘

C

global warming than that of the pre-industrial level. We evaluate the three major technologies that are utilised for carbon capture: pre-combustion, post-combustion and oxyfuel combustion. We review the advances in carbon capture, storage and utilisation. We compare carbon uptake technologies with techniques of carbon dioxide separation. Monoethanolamine is the most common carbon sorbent; yet it requires a high regeneration energy of 3.5 GJ per tonne of $$\hbox {CO}_{2}$$

CO
2

. Alternatively, recent advances in sorbent technology reveal novel solvents such as a modulated amine blend with lower regeneration energy of 2.17 GJ per tonne of $$\hbox {CO}_{2}$$

CO
2

. Graphene-type materials show $$\hbox {CO}_{2}$$

CO
2

adsorption capacity of 0.07 mol/g, which is 10 times higher than that of specific types of activated carbon, zeolites and metal–organic frameworks. $$\hbox {CO}_{2}$$

CO
2

geosequestration provides an efficient and long-term strategy for storing the captured $$\hbox {CO}_{2}$$

CO
2

in geological formations with a global storage capacity factor at a Gt-scale within operational timescales. Regarding the utilisation route, currently, the gross global utilisation of $$\hbox {CO}_{2}$$

CO
2

is lower than 200 million tonnes per year, which is roughly negligible compared with the extent of global anthropogenic $$\hbox {CO}_{2}$$

CO
2

emissions, which is higher than 32,000 million tonnes per year. Herein, we review different $$\hbox {CO}_{2}$$

CO
2

utilisation methods such as direct routes, i.e. beverage carbonation, food packaging and oil recovery, chemical industries and fuels. Moreover, we investigated additional $$\hbox {CO}_{2}$$

CO
2

utilisation for base-load power generation, seasonal energy storage, and district cooling and cryogenic direct air $$\hbox {CO}_{2}$$

CO
2

capture using geothermal energy. Through bibliometric mapping, we identified the research gap in the literature within this field which requires future investigations, for instance, designing new and stable ionic liquids, pore size and selectivity of metal–organic frameworks and enhancing the adsorption capacity of novel solvents. Moreover, areas such as techno-economic evaluation of novel solvents, process design and dynamic simulation require further effort as well as research and development before pilot- and commercial-scale trials.
Different environmental variables predict distribution and cover of the introduced red seaweed Eucheuma denticulatum in two geographical locations
Authors: Eggertsen M. , Tano S. A. , Chacin D. H. , Eklöf J. S. , Larsson J. , Berkström C. , Buriyo A. S. , Halling C.
Published: November 2020

In this study we examined abiotic and biotic factors that could potentially influence the presence of a non-indigenous seaweed, Eucheuma denticulatum, in two locations, one outside (Kane’ohe Bay, Hawai’i, USA) and one within (Mafia Island, Tanzania) its natural geographical range. We hypothesized that the availability of hard substrate and the amount of wave exposure would explain distribution patterns, and that higher abundance of herbivorous fishes in Tanzania would exert stronger top–down control than in Hawai’i. To address these hypotheses, we surveyed E. denticulatum in sites subjected to different environmental conditions and used generalized linear mixed models (GLMM) to identify predictors of E. denticulatum presence. We also estimated grazing intensity on E. denticulatum by surveying the type and the amount of grazing scars. Finally, we used molecular tools to distinguish between indigenous and non-indigenous strains of E. denticulatum on Mafia Island. In Kane’ohe Bay, the likelihood of finding E. denticulatum increased with wave exposure, whereas on Mafia Island, the likelihood increased with cover of coral rubble, and decreased with distance from areas of introduction (AOI), but this decrease was less pronounced in the presence of coral rubble. Grazing intensity was higher in Kane’ohe Bay than on Mafia Island. However, we still suggest that efforts to reduce non-indigenous E. denticulatum should include protection of important herbivores in both sites because of the high levels of grazing close to AOI. Moreover, we recommend that areas with hard substrate and high structural complexity should be avoided when farming non-indigenous strains of E. denticulatum.
Manure recycling from urban livestock farms for closing the urban–rural nutrient loops
Authors: Tadesse Solomon Tulu , Oenema Oene , van Beek Christy , Ocho Fikre Lemessa
Published: November 2020

Rapid urbanization in developing countries is attracting urban livestock farming, which is associated with feed nutrient imports and manure nutrient accumulations. Here, we report on manure nutrients (N, P and K) production on urban livestock farms in Addis Ababa and Jimma in Ethiopia, and estimate manure recovery on these farms and its recycling in urban, peri-urban and rural crop farms. Estimates were based on data from farm surveys, statistics, literature and model calculations. Urban livestock farms had on average 13 tropical livestock units and positive N, P and K balances. Urban crop farms had negative N and K balances, and did not use manure from urban livestock farms. We estimated that 0.5–2.6 Gg N, 0.2–0.8 Gg P and 0.9–3.7 Gg K can be collected in manure from the 5,200 urban livestock farms in Addis Ababa year−1, and can be recycled in crop land. Two manure allocation strategies were explored: balanced P fertilization and balanced N fertilization. The former allowed greater precision in matching nutrient supply to demand, and was associated with greater manure transport and distribution, up to rural areas. Manure recycling has several benefits: synthetic fertilizer savings (75–300 million Ethiopian Birr year−1 for Addis Ababa), soil fertility replenishment, and reductions in water pollution. However, there are various cultural, educational and institutional barriers for manure recycling. We argue that more quantitative data and scenario analyses are needed for deliberative decision making and for exploring more sustainable development pathways of urban livestock farms, re-connected to crop farms via manure recycling.
Learning environments preferred by university students: a shift toward informal and flexible learning environments
Authors: Valtonen Teemu , Leppänen Ulla , Hyypiä Mareena , Kokko Anna , Manninen Jyri , Vartiainen Henriikka , Sointu Erkko , Hirsto Laura
Published: November 2020

Universities are facing new challenges that pose various demands for developing learning environments. These challenges are related to different pedagogical approaches, the use of information and communications technology (ICT), the diversification of student populations, and new expectations related to working life. This study focused on university students’ perceptions of preferred learning environments and their thoughts about the best learning environments for the higher-education level. The main data consisted of answers to open questions from 230 students. Additionally, a questionnaire was used to gain an overall picture of students’ experiences in the current learning environment. Five main themes emerged: characteristics of the campus; available resources; flexibility of learning opportunities; pedagogy; and implementation of ICT in education. Further, two larger perspectives were highlighted. One was the need for informal learning environments (where students can study alone or with peers or just hang out). The second perspective pertains to the flexibility of learning, demonstrating the need for learning environments that allow participation without the need to come to the campus for face-to-face meetings. The need for resources (particularly ICT and the support and availability of teaching personnel) was also highlighted. The study provides important perspectives for developing appropriate learning environments for higher education.
The Role of Future Time Perspective, Body Awareness, and Social Connectedness in the Relationship Between Self-efficacy and Resilience
Authors: O’Neill Ellsy , Clarke Philip , Fido Dean , Vione Katia Correa
Published: November 2020

Defined as the successful adaptation to dynamic environments, resilience is considered a cornerstone of mental health. However, with the underpinnings of resilience not yet fully understood, this manuscript tests the potential contribution of self-efficacy and embeddedness on resilience (explored through validated measures of future time perspective, body awareness, and social connectedness). The convenience sample of 18-to-77-year-old adults included 297 individuals, of which 36 were men and 171 were female. Participants completed online surveys composed of fifty-two questions in total, measuring self-efficacy, resilience, social connectedness, FTP, and body awareness. Resilience was positively related to self-efficacy, future time perspective, and social connectedness—but not to body awareness—and self-efficacy was positively associated with indices of embeddedness. Considering these correlations, and that only self-efficacy significantly predicted resilience, an exploratory model was proposed to test whether embeddedness directly predicted self-efficacy, and whether self-efficacy directly predicted resilience. Structural Equation Modelling suggested a good fit of this model, elucidating the interplay of psychological mechanisms underlying resilience. Thus, we identify potential variables of interest for clinical interventions aimed at increasing resilience and self-efficacy. Theoretical implications and future research are suggested based on these findings.