bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of new reference genes for accurate quantitative reverse transcriptase-PCR normalization in the Antarctic plant Colobanthus quitensis under abiotic stress conditions
Authors: Bertini Laura , Proietti Silvia , Focaracci Francesca , Canini Fabiana , Bravo Leon A. , Rabert Claudia , Caruso Carla 
Published: February 2021

AbstractThe Antarctic ecotype of Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Maritime Antarctica which is now facing with the rapid local warming experienced in the Antarctic Peninsula during the last decades. Thus, the identification of the molecular mechanisms leading to the adaptation to this warming trend is a new target for modern cell physiology. The selection of suitable reference genes for quantification of key stress-responsive genes through quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) is important to ensure accurate and reliable results. In this study, we evaluated the expression stability of eleven candidate genes in C. quitensis under different abiotic stress conditions using geNorm and RefFinder tools. The statistical analysis showed that the appropriate reference genes varied depending on the experimental conditions, even if EF1α and PP2Acs ranked as the most stable reference genes when all stress conditions were considered. To further validate the stability of the selected reference genes, the expression patterns of C. quitensis catalase gene (CqCAT) was analyzed. The reference genes validated in this study will be useful for improving the accuracy of qRT-PCR analysis for gene expression studies of the Antarctic ecotype of C. quitensis and could be extended to other ecotypes adapted to low temperatures.
The development of a faecal incontinence core outcome set: an international Delphi study protocol
Authors: Assmann Sadé , Keszthelyi Daniel , Kleijnen Jos , Kimman Merel , Anastasiou Foteini , Bradshaw Elissa , Carrington Emma , Chiarioni Giuseppe , Maeda Yasuko , Muris Jean , Pohl Daniel , Rydningen Mona , Vaizey Carolynne , Breukink Stephanie 
Published: February 2021

Abstract
Purpose
Faecal incontinence (FI) is estimated to affect around 7.7% of people. There is a lack of uniformity in outcome definitions, measurement and reporting in FI studies. Until now, there is no general consensus on which outcomes should be assessed and reported in FI research. This complicates comparison between studies and evidence synthesis, potentially leading to recommendations not evidence-based enough to guide physicians in selecting an FI therapy. A solution for this lack of uniformity in reporting of outcomes is the development of a Core Outcome Set (COS) for FI. This paper describes the protocol for the development of a European COS for FI.

Methods
Patient interviews and a systematic review of the literature will be performed to identify patient-, physician- and researcher-oriented outcomes. The outcomes will be categorised using the COMET taxonomy and put forward to a group of patients, physicians (i.e. colorectal surgeons, gastroenterologists and general practitioners) and researchers in a Delphi consensus exercise. This exercise will consist of up to three web-based rounds in which participants will prioritise and condense the list of outcomes, which is expected to result in consensus. A consensus meeting with participants from all stakeholder groups will take place to reach a final agreement on the COS.

Discussion
This study protocol describes the development of a European COS to improve reliability and consistency of outcome reporting in FI studies, thereby improving evidence synthesis and patient care.

Trial registration
This project has been registered in the COMET database on the 1st of April 2020, available at http://www.comet-initiative.org/Studies/Details/1554. The systematic review has been registered on the PROSPERO database on the 31st of August 2020, available at https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=202020&VersionID=1381336.
Wide distribution of prion infectivity in the peripheral tissues of vCJD and sCJD patients
Authors: Douet Jean-Yves , Huor Alvina , Cassard Hervé , Lugan Séverine , Aron Naima , Arnold Mark , Vilette Didier , Torres Juan-Maria , Ironside James W. , Andreoletti Olivier 
Published: February 2021

AbstractSporadic Creutzfeldt-Jakob disease (sCJD) is the commonest human prion disease, occurring most likely as the consequence of spontaneous formation of abnormal prion protein in the central nervous system (CNS). Variant Creutzfeldt–Jakob disease (vCJD) is an acquired prion disease that was first identified in 1996. In marked contrast to vCJD, previous investigations in sCJD revealed either inconsistent levels or an absence of PrPSc in peripheral tissues. These findings contributed to the consensus that risks of transmitting sCJD as a consequence of non-CNS invasive clinical procedures were low. In this study, we systematically measured prion infectivity levels in CNS and peripheral tissues collected from vCJD and sCJD patients. Unexpectedly, prion infectivity was detected in a wide variety of peripheral tissues in sCJD cases. Although the sCJD infectivity levels varied unpredictably in the tissues sampled and between patients, these findings could impact on our perception of the possible transmission risks associated with sCJD.
Distress severity in perceptual anomalies moderates the relationship between prefrontal brain structure and psychosis proneness in nonclinical individuals
Authors: Evermann Ulrika , Schmitt Simon , Meller Tina , Pfarr Julia-Katharina , Grezellschak Sarah , Nenadić Igor 
Published: February 2021

AbstractIn the general population, psychosis risk phenotypes occur independently of attenuated prodromal syndromes. Neurobiological correlates of vulnerability could help to understand their meaningfulness. Interactions between the occurrence of psychotic-like experiences (PLE) and other psychological factors e.g., distress related to PLE, may distinguish psychosis-prone individuals from those without risk of future psychotic disorder. We aimed to investigate whether (a) correlates of total PLE and distress, and (b) symptom dimension-specific moderation effects exist at the brain structural level in non-help-seeking adults reporting PLE below and above the screening criterion for clinical high-risk (CHR). We obtained T1-weighted whole-brain MRI scans from 104 healthy adults from the community without psychosis CHR states for voxel-based morphometry (VBM). Brain structural associations with PLE and PLE distress were analysed with multiple linear regression models. Moderation of PLE by distress severity of two types of positive symptoms from the Prodromal Questionnaire (PQ-16) screening inventory was explored in regions-of-interest after VBM. Total PQ-16 score was positively associated with grey matter volume (GMV) in prefrontal regions, occipital fusiform and lingual gyri (p < 0.05, FDR peak-level corrected). Overall distress severity and GMV were not associated. Examination of distress severity on the positive symptom dimensions as moderators showed reduced strength of the association between PLE and rSFG volume with increased distress severity for perceptual PLE. In this study, brain structural variation was related to PLE level, but not distress severity, suggesting specificity. In healthy individuals, positive relationships between PLE and prefrontal volumes may indicate protective features, which supports the insufficiency of PLE for the prediction of CHR. Additional indicators of vulnerability, such as distress associated with perceptual PLE, change the positive brain structure relationship. Brain structural findings may strengthen clinical objectives through disentanglement of innocuous and risk-related PLE.
Boundedness for a Fully Parabolic Keller–Segel Model with Sublinear Segregation and Superlinear Aggregation
Authors: Frassu Silvia , Viglialoro Giuseppe 
Published: February 2021

AbstractThis work deals with a fully parabolic chemotaxis model with nonlinear production and chemoattractant. The problem is formulated on a bounded domain and, depending on a specific interplay between the coefficients associated to such production and chemoattractant, we establish that the related initial-boundary value problem has a unique classical solution which is uniformly bounded in time. To be precise, we study this zero-flux problem
$$ \textstyle\begin{cases} u_{t}= \Delta u - \nabla \cdot (f(u) \nabla v) & \text{ in } \Omega \times (0,T_{max}), \\ v_{t}=\Delta v-v+g(u) & \text{ in } \Omega \times (0,T_{max}), \end{cases} $$

{

u
t

=
Δ
u
−
∇
⋅
(
f
(
u
)
∇
v
)

in
Ω
×
(
0
,

T

m
a
x

)
,

v
t

=
Δ
v
−
v
+
g
(
u
)

in
Ω
×
(
0
,

T

m
a
x

)
,

where $\Omega $
Ω
is a bounded and smooth domain of $\mathbb{R}^{n}$

R
n

, for $n\geq 2$
n
≥
2
, and $f(u)$
f
(
u
)
and $g(u)$
g
(
u
)
are reasonably regular functions generalizing, respectively, the prototypes $f(u)=u^{\alpha }$
f
(
u
)
=

u
α

and $g(u)=u^{l}$
g
(
u
)
=

u
l

, with proper $\alpha , l>0$
α
,
l
>
0
. After having shown that any sufficiently smooth $u(x,0)=u_{0}(x)\geq 0$
u
(
x
,
0
)
=

u
0

(
x
)
≥
0
and $v(x,0)=v_{0}(x)\geq 0$
v
(
x
,
0
)
=

v
0

(
x
)
≥
0
produce a unique classical and nonnegative solution $(u,v)$
(
u
,
v
)
to problem (◊), which is defined on $\Omega \times (0,T_{max})$
Ω
×
(
0
,

T

m
a
x

)
with $T_{max}$

T

m
a
x

denoting the maximum time of existence, we establish that for any $l\in (0,\frac{2}{n})$
l
∈
(
0
,

2
n

)
and $\frac{2}{n}\leq \alpha <1+\frac{1}{n}-\frac{l}{2}$

2
n

≤
α
<
1
+

1
n

−

l
2

, $T_{max}=\infty $

T

m
a
x

=
∞
and $u$
u
and $v$
v
are actually uniformly bounded in time.The paper is in line with the contribution by Horstmann and Winkler (J. Differ. Equ. 215(1):52–107, 2005) and, moreover, extends the result by Liu and Tao (Appl. Math. J. Chin. Univ. Ser. B 31(4):379–388, 2016). Indeed, in the first work it is proved that for $g(u)=u$
g
(
u
)
=
u
the value $\alpha =\frac{2}{n}$
α
=

2
n

represents the critical blow-up exponent to the model, whereas in the second, for $f(u)=u$
f
(
u
)
=
u
, corresponding to $\alpha =1$
α
=
1
, boundedness of solutions is shown under the assumption $0< l<\frac{2}{n}$
0
<
l
<

2
n

.
Dynamics studied by Quasielastic Neutron Scattering (QENS)
Authors: Kruteva Margarita 
Published: February 2021

AbstractQuasielastic neutron scattering (QENS) allows measurement of the molecular displacements in time and space, from pico- to tens of nanoseconds and from Ångstroms to nanometers, respectively. The method probes dynamics from fast vibrational modes down to slow diffusive motion. Every scattering experiment leads to a dynamic structure factor $$S\left( {\vec Q,\omega } \right)$$

S

Q
→

,
ω

or its spatial and temporal Fourier transform (van Hove correlation function $$G\left( {\vec r,t} \right)$$

G

r
→

,
t

). This shows exactly where the atoms are and how they move. In this manuscript the basics of the QENS method are presented and a few examples highlighting the potentials of QENS are given: (i) diffusion of liquids and gases in nano- and mesoporous materials; (ii) hydrogen dynamics in a high temperature polymer electrolyte fuel cell (HT-PEFC) and (iii) influence of the surface interactions on polymer dynamics in nanopores.
How to determine the consensus threshold in group decision making: a method based on efficiency benchmark using benefit and cost insight
Authors: Chao Xiangrui , Dong Yucheng , Kou Gang , Peng Yi 
Published: February 2021

AbstractIn the past 10 years, a large number of consensus-reaching approaches for group decision making (GDM) have been proposed. While these methods either focus on the cost of the consensus reaching or the convergency of the consensus process, the consensus efficiency has long been ignored. Meanwhile, the measurements of consensus threshold are often determined by some subjective and intuitive judgements, such as management experience and estimations for the degree of satisfaction, which lack a theoretical foundation. In management applications, how to measure consensus and how to evaluate a consensus reaching method are also ambiguous. To tackle these questions, we introduce efficiency measures into the consensus reaching process of GDM and achieve a comprehensive evaluation of current consensus methods through an efficiency analysis of consensus costs and consensus improvement. From the perspective of efficiency, we propose a benchmark in consensus reaching by data envelopment analysis without explicit input benchmark models, and then present an objective method for consensus threshold determination in GDM. Finally, we use numerical examples to illustrate the usability of our method.
Design and development of a new ambr250® bioreactor vessel for improved cell and gene therapy applications
Authors: Rotondi Marco , Grace Ned , Betts John , Bargh Neil , Costariol Elena , Zoro Barney , Hewitt Christopher J. , Nienow Alvin W. , Rafiq Qasim A. 
Published: February 2021

AbstractThe emergence of cell and gene therapies has generated significant interest in their clinical and commercial potential. However, these therapies are prohibitively expensive to manufacture and can require extensive time for development due to our limited process knowledge and understanding. The automated ambr250® stirred-tank bioreactor platform provides an effective platform for high-throughput process development. However, the original dual pitched-blade 20 mm impeller and baffles proved sub-optimal for cell therapy candidates that require suspension of microcarriers (e.g. for the culture of adherent human mesenchymal stem cells) or other particles such as activating Dynabeads® (e.g. for the culture of human T-cells). We demonstrate the development of a new ambr250® stirred-tank bioreactor vessel which has been designed specifically to improve the suspension of microcarriers/beads and thereby improve the culture of such cellular systems. The new design is unbaffled and has a single, larger elephant ear impeller. We undertook a range of engineering and physical characterizations to determine which vessel and impeller configuration would be most suitable for suspension based on the minimum agitation speed (NJS) and associated specific power input (P/V)JS. A vessel (diameter, T, = 60 mm) without baffles and incorporating a single elephant ear impeller (diameter 30 mm and 45° pitch-blade angle) was selected as it had the lowest (P/V)JS and therefore potentially, based on Kolmogorov concepts, was the most flexible system. These experimentally-based conclusions were further validated firstly with computational fluid dynamic (CFD) simulations and secondly experimental studies involving the culture of both T-cells with Dynabeads® and hMSCs on microcarriers. The new ambr250® stirred-tank bioreactor successfully supported the culture of both cell types, with the T-cell culture demonstrating significant improvements compared to the original ambr250® and the hMSC-microcarrier culture gave significantly higher yields compared with spinner flask cultures. The new ambr250® bioreactor vessel design is an effective process development tool for cell and gene therapy candidates and potentially for autologous manufacture too.
Soil organic carbon fractions in the Great Plains of the United States: an application of mid-infrared spectroscopy
Authors: Sanderman Jonathan , Baldock Jeffrey A. , Dangal Shree R. S. , Ludwig Sarah , Potter Stefano , Rivard Charlotte , Savage Kathleen 
Published: February 2021

AbstractSpectroscopy is a powerful means of increasing the availability of soil data necessary for understanding carbon cycling in a changing world. Here, we develop a calibration transfer methodology to appropriately apply an existing mid infrared (MIR) spectral library with analyte data on the distribution of soil organic carbon (SOC) into particulate (POC), mineral-associated (MAOC), and pyrogenic (PyC) forms to nearly 8000 soil samples collected in the Great Plains ecoregion of the United States. We then use this SOC fraction database in combination with a machine learning-based predictive soil mapping approach to explore the controls on the distribution of fractions through soil profiles and across the region. The relative abundance of each fraction had unique depth distribution profiles with POC fraction dropping exponentially with depth, the MAOC fraction having a broad distribution with a maxima at 35–50 cm, and the PyC fraction showed a slight subsurface maxima (10–20 cm) and then a steady decline with increasing depth. Within the Great Plains ecoregion, clay content was a strong control on the total amount and relative proportion of each fraction in both the surface and subsoil horizons. Sandy soils and soils in cool semi-arid regions contained significantly more POC relative to the MAOC and PyC fractions. Cultivated soils had significantly less SOC than grassland soils with losses following a predictable pattern: POC > MAOC ≫ PyC. This SOC fraction database and resulting maps can now form the basis for improved representation of SOC dynamics in biogeochemical models.
Gray-box monitoring of hyperproperties with an application to privacy
Authors: Stucki Sandro , Sánchez César , Schneider Gerardo , Bonakdarpour Borzoo 
Published: February 2021

AbstractRuntime verification is a complementary approach to testing, model checking and other static verification techniques to verify software properties. Monitorability characterizes what can be verified (monitored) at run time. Different definitions of monitorability have been given both for trace properties and for hyperproperties (properties defined over sets of traces), but these definitions usually cover only some aspects of what is important when characterizing the notion of monitorability. The first contribution of this paper is a refinement of classic notions of monitorability both for trace properties and hyperproperties, taking into account, among other things, the computability of the monitor. A second contribution of our work is to show that black-box monitoring of HyperLTL (a logic for hyperproperties) is in general unfeasible, and to suggest a gray-box approach in which we combine static and runtime verification. The main idea is to call a static verifier as an oracle at run time allowing, in some cases, to give a final verdict for properties that are considered to be non-monitorable under a black-box approach. Our third contribution is the instantiation of this solution to a privacy property called distributed data minimization which cannot be verified using black-box runtime verification. We use an SMT-based static verifier as an oracle at run time. We have implemented our gray-box approach for monitoring data minimization into the proof-of-concept tool Minion. We describe the tool and apply it to a few case studies to show its feasibility.
The J-integral for mixed-mode loaded cracks with cohesive zones
Authors: Scheel Johannes , Schlosser Alexander , Ricoeur Andreas 
Published: February 2021

AbstractThe J-integral quantifies the loading of a crack tip, just as the crack tip opening displacement (CTOD) emanating from the cohesive zone model. Both quantities, being based on fundamentally different interpretations of cracks in fracture mechanics of brittle or ductile materials, have been proven to be equivalent in the late 60s of the previous century, however, just for the simple mode-I loading case. The relation of J and CTOD turned out to be uniquely determined by the constitutive law of the cohesive zone in front of the physical crack tip. In this paper, a J-integral vector is derived for a mixed-mode loaded crack based on the cohesive zone approach, accounting for the most general case of a mode-coupled cohesive law. While the$$J_1$$J1-coordinate, as energy release rate of a straight crack extension, is uniquely related to the cohesive potential at the physical crack tip and thus to the CTOD, the$$J_2$$J2-coordinate depends on the solution of the specific boundary value problem in terms of stresses and displacement gradients at the cohesive zone faces. The generalized relation is verified for the Griffith crack, employing solutions of the Dugdale crack based on improved holomorphic functions.
Coupling a discrete twin model with cohesive elements to understand twin-induced fracture
Authors: Grilli Nicolò , Tarleton Edmund , Cocks Alan C. F. 
Published: February 2021

Abstract
The interplay between twinning and fracture in metals under deformation is an open question. The plastic strain concentration created by twin bands can induce large stresses on the grain boundaries. We present simulations in which a continuum model describing discrete twins is coupled with a crystal plasticity finite element model and a cohesive zone model for intergranular fracture. The discrete twin model can predict twin nucleation, propagation, growth and the correct twin thickness. Therefore, the plastic strain concentration in the twin band can be modelled. The cohesive zone model is based on a bilinear traction-separation law in which the damage is caused by the normal stress on the grain boundary. An algorithm is developed to generate interface elements at the grain boundaries that satisfy the traction-separation law. The model is calibrated by comparing polycrystal simulations with the experimentally observed strain to failure and maximum stress. The dynamics of twin and crack nucleation have been investigated. First, twins nucleate and propagate in a grain, then, microcracks form near the intersection between twin tips and grain boundaries. Microcracks appear at multiple locations before merging. A propagating crack can nucleate additional twins starting from the grain boundary, a few micrometres away from the original crack nucleation site. This model can be used to understand which type of texture is more resistant against crack nucleation and propagation in cast metals in which twinning is a deformation mechanism. The code is available online at https://github.com/TarletonGroup/CrystalPlasticity.

Graphic Abstract
A thermo-mechanical machining method for improving the accuracy and stability of the geometric shape of long low-rigidity shafts
Authors: Świć Antoni , Gola Arkadiusz , Sobaszek Łukasz , Šmidová Natalia 
Published: February 2021

AbstractThe article presents a new thermo-mechanical machining method for the manufacture of long low-rigidity shafts which combines straightening and heat treatment operations. A fixture for thermo-mechanical treatment of long low-rigidity shafts was designed and used in tests which involved axial straightening of shafts combined with a quenching operation (performed to increase the corrosion resistance of the steel used as stock material). The study showed that an analysis of the initial deflections of semi-finished shafts of different dimensions and determination of the maximum corrective deflection in the device could be used as a basis for performing axial straightening of shaft workpieces with simultaneous heat treatment and correction of the initial deflection of the workpiece. The deflection is corrected by stretching the fibers of the stock material, at any cross-section of the shaft, up to the yield point and generating residual stresses symmetrical to the axis of the workpiece. These processes allow to increase the accuracy and stability of the geometric shape of the shaft.