bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High speed data link optimization for digitalized transfer to processing FPGA
Authors: Collado J. , Gonzalez V. , Gadea A. 
Published: November 2021

State-of-the-art arrays of detectors, that require digital processing, may have a sizeable number of digitalized signal links. This is the case in several experimental nuclear physics instruments. Moreover, the data rate of the sampled signals, defined primary by the signal bandwidth of the individual detectors, may not exhaust the capabilities of a single FPGA transceiver input.
The preprocessing is usually carried out in a modern FPGA with transceiver data rate capabilities over 10Gbps. Moreover, cost effective FPGA have a limited number of transceivers for given FPGA processing capabilities. The investigation of a cost-effective and efficient solution to the mismatch between both data rates, optimizing simultaneously the use of the FPGA resources, is the topic of the present work.
We have developed a solution based on the Time Domain Multiplexing link aggregation, in the form of a Mezzanine board. This mezzanine combines four channels from an optical or copper input up to 2.5 Gbps to one up to 10Gbps, and serves them to the FPGA via the mezzanine connector. The board itself is controlled by a small FPGA by the Two Wire Interface (TWI) protocol as a standalone intelligent device, so minimum slow control is needed. The solution has been also developed for a motherboard housing a SoM module and FMC connector as an alternative implementation. An associated firmware has been developed to de-aggregate the data in the FPGA and recover the original sampled data, based on JESD204 communication protocol, inside the FPGA. The method has been validated and applications, beyond the development of the AGATA electronics, may be envisioned.
Jules Horowitz Reactor Irradiation Devices: Inspection Methods proposal
Authors: Hillberg Seppo , Baque François , Gaillot Stéphane 
Published: November 2021

Jules Horowitz Reactor (JHR) irradiation test devices (so called ADELINE and MADISON) must undergo a periodic inspection every 40 months (French ESP(N) Regulation). The first step of inspection proposal was performed from October 2019 to March 2020 and concerns application of non-destructive methods for electron beam welds, while examining the possible methods and locations that could be utilized.
This study has been performed in collaboration between VTT Technical Research Centre of Finland Ltd and French CEA with VTT employee secondment at CEA Cadarache. The initial conclusions of this work are the following:
• Two inspection methods are likely needed.
• Eddy current is likely suitable for surface examination while volumetric ultrasonic inspection can be used for tube bodies.
• Inspection under-water in a storage pool (EPI) is likely the best option for location in the JHR.
• Some automation and remote controls will be needed during the inspection process. The inspection area is quite large as the whole tube bodies will be inspected.
• Internal surfaces located between the nested tubes likely cannot be inspected for corrosion and therefore, sealing the space from oxygen and water will be likely be the best option.
• Experimental reference is a critical next step of the work to assess and qualify the inspection methods.
As the next step, CEA will continue discussions on requirements of the mock-ups: for eddy current inspection, a Zircaloy-4 planar specimen with artificial reflectors is needed. For ultrasonic reference, a representative mock-up of the cylinder with a weld and artificial defect(s) is needed. The mock-up testing will provide an experimental reference to CIVA calculations as simulations of this work have been performed with CIVA software, which is extensively used in the industry and research organizations in simulation of non-destructive control.
This study will allow further steps in the future, up to the qualification of inspection methods for JHR test devices.
Neutron Coincidence Measurements and Monte Carlo Modelling of Waste Drums Containing Reference Nuclear Material
Authors: Borella A. , Rossa R. , Boden S. , Bruggeman C. , Rogiers B. , Smets S. , Valcke E. 
Published: November 2021

Within the EC-funded CHANCE project several non-destructive techniques are being considered for the assay of waste bearing drums. Such techniques include calorimetry, gamma-ray spectrometry and neutron coincidence counting. The aim is to quantify uncertainties on the inventory of radionuclides, and how these are potentially reduced by combining the signatures from different techniques in the data analysis.
In this framework, neutron coincidence measurements were carried out with two slab counters based on 3He detectors coupled to shift register electronics. Such a system consists of two identical slabs with 6 detectors each, and is transportable, rather compact and flexible in terms of sizes and geometries that can be measured. With this system three 200 L drums containing certified reference nuclear material and different filling materials were measured. The certified nuclear material was in the form of 21 pellets of mixed oxide of U and Pu with a total mass of about 10.5 g; in addition, a single pellet of about 10.05 g was also available. The pellets could be placed in predefined positions within the drum in a reproducible way. The geometry and composition of the three drums was well characterized and consisted of Ethafoam, a mixture of Ethafoam, stainless steel and PVC, and mortar with an inner core of extruded polystyrene. The measurement setup was arranged such that the drum was placed between the two slab counters. The positions of the slab counters relative to the drum were accurately measured before each measurement, and a dedicated system was used to minimize the uncertainty on the detector positioning.
The measurement data were first analysed by applying the point model of Hage and the mass of nuclear material in the drum was determined from the rate of totals and reals and the radionuclide composition. Due to the fact that not all the point model conditions were met, we found that the point model overestimates the mass up to about 50%. In addition, a Monte Carlo model of the measurement geometry was developed using the MCNP code. The model was used to determine a calibration factor between the reals rate and the mass of the sample. Measurements with a calibrated 252Cf source were used to verify the model. With a Monte Carlo based approach the mass of the mixed oxide pellets is within a few percent from the nominal values, except for strongly asymmetrical configurations where the deviation is up to about 20%. The results reveal the importance of an accurate background correction and of accounting for surrounding materials of the building such as walls, floor and ceiling in the Monte Carlo model.
Rare Tumors in Children and Adolescents – the STEP Working
Groupʼs Evolution to a Prospective Registry
Authors: Hippert Felicitas , Desing Lena , Diez Sonja , Witowski Andrea , Bernbeck Benedikt , Abele Michael , Seitz Christian , Erdmann Friederike , Brecht Ines , Schneider Dominik T. 
Published: November 2021

AbstractBackground Very rare tumors (VRT) in children and adolescents have such a low
incidence that until recently, they have not been integrated into the clinical
and scientific network of pediatric oncology. Data is very limited and
consistent treatment strategies are missing. Thus, VRTs are classic orphan
diseases. To counteract this problem, the Arbeitsgemeinschaft für
Seltene Tumorerkrankungen in der Pädiatrie (STEP) was founded. Here we
report on patient recruitment during the first 10 years. Patients Patients aged
up to 18 years and not included in any other clinical trial or GPOH registry
were included in this analysis. Methods Data was collected from 2008 to 2018 by
means of a standardized form. The recorded diagnoses were descriptively analyzed
focusing on histology, localization, and year of report. Results A total of 623
patients with VRTs were registered. During 2008–2014, the annual number
of registrations was around 40 and is around 90 since 2015. Most frequent
diagnoses included tumors of the skin (n=150), tumors of the
gastrointestinal tract (n=102), tumors of the gonads (n=77), the
ENT region (n=68), and miscellaneous tumors (n=107).
Discussion With the establishment of central structures for clinical
consultation and documentation of VRTs, the number of registrations increased.
Comprehensively, VRTs are as common as other classic pediatric oncology tumors,
but extremely heterogeneous in terms of localization, histology, and prognosis.
By a centralized and complete registration and analysis of VRTs, also in
collaboration with international partners, it is possible to develop treatment
strategies and thus greatly increase treatment quality.
Physiological and proteomic analyses of Tunisian local grapevine (
Authors: Azri Wassim , Jardak Rahma , Cosette Pascal , Guillou Clément , Riahi Jawaher , Mliki Ahmed 
Published: November 2021

Drought is one of the major environmental constraints threatening viticulture worldwide. Therefore, it is critical to reveal the molecular mechanisms underlying grapevine (Vitis vinifera L.) drought stress tolerance useful to select new species with higher tolerance/resilience potentials. Drought-tolerant Tunisian local grapevine cultivar Razegui was exposed to water deficit for 16 days. Subsequent proteomic analysis revealed 49 differentially accumulated proteins in leaves harvested on the drought-stressed vines. These proteins were mainly involved in photosynthesis, stress defence, energy and carbohydrate metabolism, protein synthesis/turnover and amino acid metabolism. Physiological analysis revealed that reduction of photosynthesis under drought stress was attributed to the downregulation of the light-dependent reactions, Calvin cycle and key enzymes of the photorespiration pathway. The accumulation of proteins involved in energy and carbohydrate metabolism indicate enhanced need of energy during active stress acclimation. Accumulation of protein amino acids seems to play a protective role under drought stress due to their osmoprotectant and ROS scavenging potential. Reduced protein synthesis and turnover help plants preserving energy to fight drought stress. Proteins related to stress defence might scavenge ROS and transmit the ROS signal as an oxidative signal transducer in drought-stress signalling. All of these original results represent valuable information towards improving drought tolerance of grapevine and promoting sustainable viticulture under climate change conditions.
Melatonin improves the photosynthesis in
Authors: Vafadar Farinaz , Amooaghaie Rayhaneh , Ehsanzadeh Parviz , Ghanati Faezeh 
Published: November 2021

This study investigated: (1) the effects of various concentrations of melatonin (MT) and Ca2+; and (2) the impact of crosstalk between these signal molecules on photosynthesis and salt tolerance of Dracocephalum kotschyi Boiss. Results indicated that 5 mM CaCl2, as well as 100 μM MT were the best concentrations for increasing shoot dry weight, leaf area, SPAD index, maximum quantum efficiency of photosystem II (Fv/Fm), and decreasing malondialdehyde content under salinity stress. The impact of MT on growth and photosynthesis was closely linked to its effect on enhancing antioxidant enzyme activities in leaves. Application of p-chlorophenylalanine, as an inhibitor of MT biosynthesis, negated the impacts of MT on the aforementioned attributes. Salinity and MT boosted cytosolic Ca2+ concentration. Exogenous MT, as well as Ca2+, enhanced tolerance index, membrane stability, leaf area, the content of chlorophyll (Chl) a, Chl b, and carotenoids (Car), Fv/Fm, and stomatal conductance under salinity stress. These impacts of MT were eliminated by applying a calmodulin antagonist, a Ca2+ chelator and a Ca2+ channel blocker. These novel findings indicate that the MT-induced effects on photosynthetic parameters and salt-evoked oxidative stress were mediated through calcium/calmodulin (Ca2+/CaM) signalling.
Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes
Authors: Ma Shiyang , Dalgleish James , Lee Justin , Wang Chen , Liu Linxi , Gill Richard , Buxbaum Joseph D. , Chung Wendy K. , Aschard Hugues , Silverman Edwin K. , Cho Michael H. , He Zihuai , Ionita-Laza Iuliana 
Published: November 2021

SignificanceGene-based tests are important tools for elucidating the genetic basis of complex traits. Despite substantial recent efforts in this direction, the existing tests are still limited, owing to low power and detection of false-positive signals due to the confounding effects of linkage disequilibrium. In this paper, we describe a gene-based test that attempts to address these limitations by incorporating data on long-range chromatin interactions, several recent technical advances for region-based testing, and the knockoff framework for synthetic genotype generation. Through extensive simulations and applications to multiple diseases and traits, we show that the proposed test increases the power over state-of-the-art gene-based tests and provides a narrower focus on the possible causal genes involved at a locus.
Opening of a cryptic pocket in β-lactamase increases penicillinase activity
Authors: Knoverek Catherine R. , Mallimadugula Upasana L. , Singh Sukrit , Rennella Enrico , Frederick Thomas E. , Yuwen Tairan , Raavicharla Shreya , Kay Lewis E. , Bowman Gregory R. 
Published: November 2021

Significance
A protein is a shape-shifter, but it is currently unclear which of the many structures a protein can adopt are relevant for its function. Here, we examine conformations that contain a “cryptic” pocket (i.e., a pocket absent in ligand-free structures). Cryptic pockets have potential utility in drug discovery efforts because they provide a means to target “undruggable” proteins (i.e., proteins lacking known pockets) or enhance rather than inhibit protein function. In this study, we use a combination of thiol-labeling and kinetic assays, NMR, and molecular dynamic simulations to identify the function of the Ω-loop cryptic pocket in β-lactamase enzymes. We find that an open pocket population is beneficial for hydrolysis of the substrate benzylpenicillin.
The use of smallwords in the speech of German learners of English
Authors: Rosen Anna 
Published: November 2021

Abstract
Based on data from the German component of LINDSEI and two native speaker corpora, this study investigates the consequences of language learning in an instructional setting versus additional natural exposure for the use of 18 fluency-enhancing smallwords. It thus complements previous studies of selected discourse markers in German learner English and offers a more in-depth analysis of individual differences in advanced learners’ speech in terms of frequency and appropriateness of use. Adding to earlier research, which has found that exposure to natural input is clearly beneficial to a more native-like use of discourse markers, the results of the present study also suggest that smallwords are teachable and that teaching in this area needs to be made more efficient.
Integrating corpus literacy into language teacher education
Authors: Callies Marcus 
Published: November 2021

Abstract
Despite the increasing popularization and availability of corpus tools and resources, the practice of English language teaching still seems to be only marginally affected by the corpus-linguistic turn, because comparatively few teachers were trained in corpus linguistics and use corpora or corpus software regularly themselves (Mukherjee 2004; Römer 2011). This chapter first reports on a recent survey that updates and largely confirms Mukherjee’s (2004) findings. It is argued that while university students of modern languages are increasingly familiarized with the research-based use of corpora in linguistic content classes, this research perspective is not sufficiently translated into a teaching perspective for corpora to be considered a useful addition to the toolbox of language teachers. The chapter then reports on the integration of corpus linguistics into the curriculum for English language teacher students by exposing them to the use of corpora and corpus methods from a researcher’s, teacher’s and learner’s perspective.
Fabrication and calibration of nanostructured vanadium-doped ZnO-based micromachined sensor with superior sensitive for underwater acoustic measurement
Authors: Gao Wei , Zhang Yu , Ma Binghe , Luo Jian , Deng Jinjun 
Published: November 2021

Abstract
A high-performance micromachined piezoelectric sensor based nanostructured vanadium-doped zinc oxide (ZnO) film with air-backing has been developed and characterized for underwater acoustic application. The sensing cell with a low foot-print of 2.0 mm × 2.0 mm is fabricated by Micro electro mechanical systems (MEMS) technology using a ZnO-on-silicon-on-insulator process platform. An optimal ratio of piezoelectric coefficient to the relative permittivity is obtained about 6.3 in the Zn0.98V0.02O sensing cell, improving by an order of magnitude compared with other notable piezoelectric films, plays a mainly dominant role in the enhanced piezoelectric response. Calibrations in the standard underwater instrument have demonstrated that the presented sensor could achieve an acoustic pressure sensitivity of −165 ± 2 dB (1 V μPa−1) over a bandwidth 10 Hz–10 kHz, outperforming the same kind of reported devices. The maximum non-linearity is no more than 0.3%, the sensitivity variation is no more than ±0.7 dB in the temperature range from 10 °C to 50 °C, indicating a better stability and higher reliability. The proposed sensor with a superior acoustic sensitivity gives a great application potential in underwater acoustic measurements.
Limit theorems for sums of products of consecutive partial quotients of continued fractions
Authors: Hu Hui , Hussain Mumtaz , Yu Yueli 
Published: November 2021

Abstract
Let [a
1(x), a
2(x), …, a

n
(x), …] be the continued fraction expansion of an irrational number x ∈ (0, 1). The study of the growth rate of the product of consecutive partial quotients a

n
(x)a

n+1(x) is associated with the improvements to Dirichlet’s theorem (1842). We establish both the weak and strong laws of large numbers for the partial sums

S

n

(

x

)

=

∑

i
=
1

n

a

i

(

x

)

a

i
+
1

(

x

)

as well as, from a multifractal analysis point of view, investigate its increasing rate. Specifically, we prove the following results:
• For any ϵ > 0, the Lebesgue measure of the set

x
∈

(

0
,
1

)

:

S

n

(

x

)

n

log

2

n

−

1

2

log

2

⩾
ϵ

tends to zero as n to infinity.
• For Lebesgue almost all x ∈ (0, 1),

lim

n
→
∞

S

n

(

x

)

−

max

1
⩽
i
⩽
n

a

i

(

x

)

a

i
+
1

(

x

)

n

log

2

n

=

1

2

log

2

.

• The Hausdorff dimension of the set

E

(

ϕ

)

≔

x
∈

(

0
,
1

)

:

lim

n
→
∞

S

n

(

x

)

ϕ

(

n

)

=
1

is determined for a range of increasing functions

ϕ
:
N
→

R

+

.
An adaptive spot placement method on Cartesian grid for pencil beam scanning proton therapy
Authors: Lin Bowen , Fu Shujun , Lin Yuting , Rotondo Ronny L , Huang Weizhang , Li Harold H , Chen Ronald C , Gao Hao 
Published: November 2021

Abstract
Pencil beam scanning proton radiotherapy (RT) offers flexible proton spot placement near treatment targets for delivering tumoricidal radiation dose to tumor targets while sparing organs-at-risk. Currently the spot placement is mostly based on a non-adaptive sampling (NS) strategy on a Cartesian grid. However, the spot density or spacing during NS is a constant for the Cartesian grid that is independent of the geometry of tumor targets, and thus can be suboptimal in terms of plan quality (e.g. target dose conformality) and delivery efficiency (e.g. number of spots). This work develops an adaptive sampling (AS) spot placement method on the Cartesian grid that fully accounts for the geometry of tumor targets. Compared with NS, AS places (1) a relatively fine grid of spots at the boundary of tumor targets to account for the geometry of tumor targets and treatment uncertainties (setup and range uncertainty) for improving dose conformality, and (2) a relatively coarse grid of spots in the interior of tumor targets to reduce the number of spots for improving delivery efficiency and robustness to the minimum-minitor-unit (MMU) constraint. The results demonstrate that (1) AS achieved comparable plan quality with NS for regular MMU and substantially improved plan quality from NS for large MMU, using merely about 10% of spots from NS, where AS was derived from the same Cartesian grid as NS; (2) on the other hand, with similar number of spots, AS had better plan quality than NS consistently for regular and large MMU.
Deep learning-based 3D in vivo dose reconstruction with an electronic portal imaging device for magnetic resonance-linear accelerators: a proof of concept study
Authors: Li Yongbao , Xiao Fan , Liu Biaoshui , Qi Mengke , Lu Xingyu , Cai Jiajun , Zhou Linghong , Song Ting 
Published: November 2021

Abstract

Objective. To develop a novel deep learning-based 3D in vivo dose reconstruction framework with an electronic portal imaging device (EPID) for magnetic resonance-linear accelerators (MR-LINACs). Approach. The proposed method directly back-projected 2D portal dose into 3D patient coarse dose, which bypassed the complicated patient-to-EPID scatter estimation step used in conventional methods. A pre-trained convolutional neural network (CNN) was then employed to map the coarse dose to the final accurate dose. The electron return effect caused by the magnetic field was captured with the CNN model. Patient dose and portal dose datasets were synchronously generated with Monte Carlo simulation for 96 patients (78 cases for training and validation and 18 cases for testing) treated with fixed-beam intensity-modulated radiotherapy in four different tumor sites, including the brain, nasopharynx, lung, and rectum. Beam angles from the training dataset were further rotated 2–3 times, and doses were recalculated to augment the datasets. Results. The comparison between reconstructed doses and MC ground truth doses showed mean absolute errors <0.88% for all tumor sites. The averaged 3D γ-passing rates (3%, 2 mm) were 97.42%±2.66% (brain), 98.53%±0.95% (nasopharynx), 99.41%±0.46% (lung), and 98.63%±1.01% (rectum). The dose volume histograms and indices also showed good consistency. The average dose reconstruction time, including back projection and CNN dose mapping, was less than 3 s for each individual beam. Significance. The proposed method can be potentially used for accurate and fast 3D dosimetric verification for online adaptive radiotherapy using MR-LINACs.
Effect of voltage polarity and supply frequency on the properties of plasma contacting liquid electrodes and gold nanoparticle synthesis
Authors: Thai Van-Phuoc , Saito Nobuo , Nakamura Tsubasa , Takahashi Kazumasa , Sasaki Toru , Kikuchi Takashi 
Published: November 2021

Abstract
Plasma contacting with liquid (PCL) provides many charged particles and reactive species into the liquid. The difficulty in controlling or selecting each specific species has significantly limited its applications in industry. Here, we present a study on using voltage polarity to regulate the type of charged particles absorbing from the plasma into the liquid. A detailed understanding of the processes at the plasma–liquid interface and electrolysis due to switching in voltage polarity was determined via a visual pH observation, measuring the concentration of H2O2 and solvated electrons. The results indicated that changes in voltage polarity strongly affect the plasma properties, chemical properties and electrolysis process in liquid, and also in the types of reducing species for gold nanoparticle (GNP) synthesis. The results also showed that using a suitable frequency could improve the efficiency of absorption of H2O2 from plasma into the bulk liquid as well as the yield in the production of GNPs. The results provide a way to select desired species from the plasma to be transferred into the liquid for a distinct purpose and to accompany other properties in the system of PCL.