bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field output correction factors and electron fluence perturbation of the microSilicon and microSilicon X detectors
Authors: Delbaere Alexia , Younes Tony , Simon Luc , Khamphan Catherine , Vieillevigne Laure 
Published: March 2022

Abstract

Objective. The aim of this study was to determine field output correction factors

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and electron fluence perturbation for new PTW unshielded microSilicon and shielded microSilicon X detectors. Approach.

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factors were calculated for 6 and 10 MV with and without flattening filter beams delivered by a TrueBeam STx. Correction factors were determined for field sizes ranging from 0.5 × 0.5 cm2 to 3 × 3 cm2 using both experimental and numerical methods. To better understand the underlying physics of their response, total electron (+positron) fluence spectra were scored in the sensitive volume considering the various component-dependent perturbations. Main results. The microSilicon and microSilicon X detectors can be used down to the smallest studied field size by applying corrections factors fulfilling the tolerance of 5% recommended by the IAEA TRS483. Electron fluence perturbation in both microSilicon detectors was greater than that in water but to a lesser extent than their predecessors. The main contribution of the overall perturbation of the detectors comes from the materials surrounding their sensitive volume, especially the epoxy in the case of unshielded diodes and the shielding for shielded diodes. This work demonstrated that the decrease in the density of the epoxy for the microSilicon led to a decrease in the electron fluence perturbation. Significance. A real improvement was observed regarding the design of the microSilicon and microSilicon X detectors compared to their predecessors.
Effect of inclusion of pitch-angle dependence on a simplified model of RF deposition in tokamak plasma
Authors: Taylor D M A , Mantsinen M J , Gallart D , Manyer J , Sirén P 
Published: March 2022

Abstract
Using the PION ICRH modelling code and comparisons against JET tokamak experiments, the effect of including pitch angle dependence within the RF diffusion operator on the fast ion particle distribution functions is quantified. It is found to be of greatest importance in cases of higher harmonic heating and lower heating ion mass, resulting in faster drop-off of the distribution’s high energy tail. We see differences of several orders of magnitude in the high-energy range and significant non-linear alterations by several tens of percent to ion species power partition. ITER scenario operational parameters are also considered, and this improved treatment is shown to benefit anticipated ITER scenarios with second harmonic hydrogen heating, according to our predictions. PION’s combination of benchmarked simplified wave physics and Fokker-Planck treatment offers modelling advantages. Since including the pitch angle dependence in the RF diffusion operator has not led to a significant increase in the required computing time when modelling different ICRF schemes in JET discharges, it has been made available within the production code.
Comment on ‘Single particle nonlocality with completely independent reference states’
Authors: Das Tamoghna , Karczewski Marcin , Mandarino Antonio , Markiewicz Marcin , Woloncewicz Bianka , Żukowski Marek 
Published: March 2022

Abstract
We comment on the purported violation of local realism, by a single photon induced correlations between homodyne detectors, which one can find in: (2008) New J. Phys.
10 113024 [arXiv:0807.0109]. The claim is erroneous, due to a calculational mistake. As the result is the basis of other claims in the paper, they are unsubstantiated.
Local tensor-network codes
Authors: Farrelly Terry , Tuckett David K , Stace Thomas M 
Published: March 2022

Abstract
Tensor-network codes enable the construction of large stabilizer codes out of tensors describing smaller stabilizer codes. An application of tensor-network codes was an efficient and exact decoder for holographic codes. Here, we show how to write some topological codes, including the surface code and colour code, as simple tensor-network codes. We also show how to calculate distances of stabilizer codes by contracting a tensor network. The algorithm actually gives more information, including a histogram of all logical coset weights. We prove that this method is efficient in the case of stabilizer codes encoded via local log-depth circuits in one dimension and holographic codes. Using our tensor-network distance calculator, we find a modification of the rotated surface code that has the same distance but fewer minimum-weight logical operators by ‘doping’ the tensor network, i.e., we break the homogeneity of the tensor network by locally replacing tensors. For this example, this corresponds to an improvement in successful error correction of almost 2% against depolarizing noise (in the perfect-measurement setting), but comes at the cost of introducing three higher-weight stabilizers. Our general construction lets us pick a network geometry (e.g., a Euclidean lattice in the case of the surface code), and, using only a small set of seed codes (constituent tensors), build extensive codes with the potential for optimisation.
Long-range surface plasmon resonance biosensors with cytop/Al/Perovskite and cytop/Al/MoS2 configurations
Authors: Kumar Mohit , Thapa Khem B. , Singh Pawan 
Published: March 2022

Abstract
In this paper, long range surface plasmon resonance (LRSPR) biosensors with cytop/Al/Perovskite and cytop/Al/MoS2 configurations have been theoretically investigated and compared with standard LRSPR biosensor with cytop/Al/graphene configuration. To calculate the optical properties of considered configurations for the desired application, transfer matrix method for TM mode has been used to obtain reflectance. The sensitivity of the considered configurations for designed biosensors has been investigated with variation of optical parameters of the structure. A new configuration of LRSPR biosensors based on Al- MoS2 or Al-Perovskite has been proposed to enhance sensitivity, detection accuracy, and efficiency. The maximum value of sensitivity of the proposed Al-Perovskite based LRSPR biosensor is found to be 4847 RIU−1. Moreover, the sensitivity of Al-MoS2 and Al-Peroskite based LRSPR biosensors show nearly 10% and nearly 30% more optical responses respectively than the Al-graphene based LRSPR biosensor.
Some experimental studies on the UV spark pin-array pre-ionization in TEA CO2 laser
Authors: Torabi Reza , Salmani Nejhad Hamid , Kazemi Babak , Sarshogh Mohammad Hossein 
Published: March 2022

Abstract
The output characteristics of a UV pin array pre-ionized transversely excited atmospheric CO2 laser have been experimentally studied in detail. The effects of the applied voltage and capacitance of the main capacitors on the laser performance was investigated. By increasing the voltage at a constant capacitance, not only the laser output energy increases, but also the pulse build-up time, width and tail length decrease. Also, the stability conditions of the discharge were investigated and the cross section of the laser output beam at different input energies was compared.
Spectrum1k — integrated circuit for medical imaging designed in CMOS 40 nm
Authors: Kmon P. , Szczygieł R. , Kłeczek R. , Górni D. , Węgrzyn G. , Niedzielska A. , Sitko K. , Drwal P. 
Published: March 2022

Abstract
We present a multichannel integrated circuit of pixel architecture designed in CMOS 40 nm technology. The chip is composed of 40 × 24 pixels of 75 µm pitch working in the single photon counting mode, each built of front-end amplifier, peak and hold detector, 6-bit analog to digital converter, and memory composed of 64 × 12-bit counters. Thanks to the proposed functionality it is possible to store in each pixel separately information of incoming particles energy spectrum. The chip is dedicated to operating with both electrons and holes of 2.2 ke−–35 ke− energy range. The IC occupies an area of 2 × 4.5 mm2, is already back from fabrication, and is under preliminary measurements.
The Octopus processor for the CMS L1 muon trigger for High Luminosity LHC
Authors: Bachtis M. , Campos D. , Jones J. , Tepper M. 
Published: March 2022

Abstract
The upgraded L1 muon trigger system of the CMS experiment in the High Luminosity Large Hadron Collider is based on custom processors featuring large Field Programmable Gate Arrays (FPGAs) connected by large numbers of optical links. These provide the I/O bandwidth and power necessary to process the complex algorithms used during the collection of physics data. The design and performance requirements of these processors creates significant challenges in signal integrity, power delivery, and thermal management. In this paper we describe the Octopus processor, featuring a large Xilinx Virtex Ultrascale+ FPGA and up to 128 links interfaced to optics through high quality twin-ax copper cables. Results on signal integrity at 25 Gb/s and the first demonstration of 50+ Gb/s links with pluggable optics in CMS are also shown, demonstrating bit error rates below 10−15 at a 95% confidence level. The thermal performance is measured inside an Advanced-TCA crate with acceptable thermal margins up to 200 W of chip power. Future improvements are mentioned, potentially allowing operation at up to 300 W.
The isolated USB programmer board for lpGBT configuration in ATLAS-HGTD upgrade
Authors: Han L. , Zhang J. , Liang Z. , Zhang L. , Qi M. , Chen S. 
Published: March 2022

Abstract
To configure the lpGBT chips that will be used on the peripheral electronics boards of the ATLAS-HGTD upgrade for the HL-LHC, a miniature and isolated USB programmer board for lpGBT (UPL) was developed based on an USB-protocol converter. Compared with the currently-used lpGBT programmer piGBT, the UPL has the advantages of compact profile, electrical isolation and cross-platform compatibility. In addition, it has a 14-pin header connector with one I2C port and six GPIOs available, and a dedicated GUI for lpGBT configuration. In particular, its isolation performance is completely determined by its I2C isolator and power isolator, both of which have the high isolation voltages of more than 1000 V AC RMS and 2000 V DC. The UPL was extensively tested by configuring a lpGBT-based board, and the lpGBT can always be successfully configured, and the bit error rate of the data transmission is always less than 1 × 10−13.
Adsorption performance of magnetic Mg0.5Ni0.5Fe2O4 nanoparticles for reactive red 2BF
Authors: Ouyang Hezhong , Liu Shuyan , Wang Zhou , Liu Aihua , Liu Dandan , Xu Shuping 
Published: March 2022

Abstract
A novel nitrate solution combustion process for formation of magnetic Mg0.5Ni0.5Fe2O4 nanoparticles was introduced, and XRD, VSM, SEM, TEM, and BET techniques were employed to characterize the nanoparticles. For Mg0.5Ni0.5Fe2O4 nanoparticles prepared at 400 °C for 2 h with 20 ml absolute ethanol, the average size and the saturation magnetization were approximately 22 nm and 8.1 A·m2 kg−1, respectively. Mg0.5Ni0.5Fe2O4 nanomaterials were subjected to reactive red 2BF adsorption, and the adsorption performances were investigated. The results revealed that the experimental data fit the Temkin isotherm model and the pseudo-second-order kinetics model, suggesting that the RR-2BF adsorption process was a monolayer-multilayer-associated chemisorption mechanism. The effects of pH on the adsorption capacity and cycle capacity of the magnetic Mg0.5Ni0.5Fe2O4 nanoparticles for the adsorption of reactive red 2BF were revealed.
Understanding the Psychology of Social Order
Authors: Tyler Tom 
Published: March 2022

Abstract
Looking across different societies it is clear that there have been many viable systems for managing social order. Each system has particular strengths and weaknesses and its utility depends upon its compatibility to the features of the society within which it exists. This suggestion is supported by empirical research showing that rewards and punishments, social norms, moral values, and legitimacy-based legal orders are all successful in some societies, under some conditions. Social science theories and research findings provide a guide for predicting those situations within with a particular form of authority is most likely to lead to a viable and sustainable social order.
Failed Performance on the Test of Memory Malingering and Misdiagnosis in Individuals with Early-Onset Dysexecutive Alzheimer’s Disease
Authors: Corriveau-Lecavalier Nick , Alden Eva C , Stricker Nikki H , Machulda Mary M , Jones David T 
Published: March 2022

Abstract

Objective
Individuals with early-onset dysexecutive Alzheimer’s disease (dAD) have high rates of failed performance validity testing (PVT), which can lead to symptom misinterpretation and misdiagnosis.

Method
The aim of this retrospective study is to evaluate rates of failure on a common PVT, the test of memory malingering (TOMM), in a sample of clinical patients with biomarker-confirmed early-onset dAD who completed neuropsychological testing.

Results
We identified seventeen patients with an average age of symptom onset at 52.25 years old. Nearly fifty percent of patients performed below recommended cut-offs on Trials 1 and 2 of the TOMM. Four of six patients who completed outside neuropsychological testing were misdiagnosed with alternative etiologies to explain their symptomatology, with two of these patients’ performances deemed unreliable based on the TOMM.

Conclusions
Low scores on the TOMM should be interpreted in light of contextual and optimally biological information and do not necessarily rule out a neurodegenerative etiology.
Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction
Authors: Xuan Ping , Wang Meng , Liu Yong , Wang Dong , Zhang Tiangang , Nakaguchi Toshiya 
Published: March 2022

AbstractMotivationComputerized methods for drug-related side effect identification can help reduce costs and speed up drug development. Multisource data about drug and side effects are widely used to predict potential drug-related side effects. Heterogeneous graphs are commonly used to associate multisourced data of drugs and side effects which can reflect similarities of the drugs from different perspectives. Effective integration and formulation of diverse similarities, however, are challenging. In addition, the specific topology of each heterogeneous graph and the common topology of multiple graphs are neglected.ResultsWe propose a drug-side effect association prediction model, GCRS, to encode and integrate specific topologies, common topologies and pairwise attributes of drugs and side effects. First, multiple drug-side effect heterogeneous graphs are constructed using various kinds of similarities and associations related to drugs and side effects. As each heterogeneous graph has its specific topology, we establish separate module based on graph convolutional autoencoder (GCA) to learn the particular topology representation of each drug node and each side effect node, respectively. Since multiple graphs reflect the complex relationships among the drug and side effect nodes and contain common topologies, we construct a module based on GCA with sharing parameters to learn the common topology representations of each node. Afterwards, we design an attention mechanism to obtain more informative topology representations at the representation level. Finally, multi-layer convolutional neural networks with attribute-level attention are constructed to deeply integrate the similarity and association attributes of a pair of drug-side effect nodes. Comprehensive experiments show that GCRS’s prediction performance is superior to other comparing state-of-the-art methods for predicting drug-side effect associations. The recall rates in top-ranked candidates and case studies on five drugs further demonstrate GCRS’s ability in discovering potential drug-related side effects.Contactzhang@hlju.edu.cn
LOCAN: a python library for analyzing single-molecule localization microscopy data
Authors: Doose Sören 
Published: March 2022

AbstractSummarySingle-molecule localization microscopy has become an important part of the super-resolution microscopy toolbox in biomedical research. Software platforms for applying analytical methods to the point-based data structures are needed that offer both routine application and flexible customization of analysis procedures. We present a python library called LOCAN that consists of well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook.Availability and implementationThe package source code is released open-source under a BSD-3 license at https://github.com/super-resolution/Locan. It can be installed from the Python Package Index at https://pypi.org/project/locan. Documentation is available at https://locan.readthedocs.io.
Placental structure, function, and mitochondrial phenotype relate to fetal size in each fetal sex in mice
Authors: Salazar-Petres Esteban , Pereira-Carvalho Daniela , Lopez-Tello Jorge , Sferruzzi-Perri Amanda Nancy 
Published: March 2022

Abstract
Fetal growth depends on placental function, which requires energy from mitochondria. Here we investigated whether mitochondrial function in the placenta relates to the growth of the lightest and heaviest fetuses of each sex within the litter of mice. Placentas from the lightest and heaviest fetuses were taken to evaluate placenta morphology (stereology), mitochondrial energetics (high-resolution respirometry), mitochondrial regulators, nutrient transporters, hormone handling, and signaling pathways (qPCR and Western blotting). We found that mitochondrial complex I and II oxygen consumption rate was greater for placentas supporting the lightest female fetuses, although placental complex I abundance of the lightest females and complexes III and V of the lightest males were decreased compared to their heaviest counterparts. Expression of mitochondrial biogenesis (Nrf1) and fission (Drp1 and Fis1) genes was lower in the placenta from the lightest females, whilst biogenesis-related gene Tfam was greater in the placenta of the lightest male fetuses. In addition, placental morphology and steroidogenic gene (Cyp17a1 and Cyp11a1) expression were aberrant for the lightest females, but glucose transporter (Slc2a1) expression was lower in only the lightest males versus their heaviest counterparts. Differences in intra-litter placental phenotype were related to changes in the expression of hormone-responsive (androgen receptor) and metabolic signaling (AMPK, AKT, and PPARγ) pathways. Thus, in normal mouse pregnancy, placental structure, function, and mitochondrial phenotype are differentially responsive to the growth of the female and male fetus. This study may inform the design of sex-specific therapies for placental insufficiency and fetal growth abnormalities with life-long benefits for the offspring.
Unbiased metabolome screen leads to personalized medicine strategy for amyotrophic lateral sclerosis
Authors: Boddy Sarah , Islam Mahjabin , Moll Tobias , Kurz Julian , Burrows David , McGown Alexander , Bhargava Anushka , Julian Thomas H , Harvey Calum , Marshall Jack NG , Hall Benjamin PC , Allen Scott P , Kenna Kevin P , Sanderson Eleanor , Zhang Sai , Ramesh Tennore , Snyder Michael P , Shaw Pamela J , McDermott Christopher , Cooper-Knock Johnathan 
Published: March 2022

Abstract
Amyotrophic lateral sclerosis is a rapidly progressive neurodegenerative disease that affects 1/350 individuals in the United Kingdom. The cause of amyotrophic lateral sclerosis is unknown in the majority of cases. Two-sample Mendelian randomization enables causal inference between an exposure, such as the serum concentration of a specific metabolite, and disease risk. We obtained genome-wide association study summary statistics for serum concentrations of 566 metabolites which were population matched with a genome-wide association study of amyotrophic lateral sclerosis. For each metabolite, we performed Mendelian randomization using an inverse variance weighted estimate for significance testing. After stringent Bonferroni multiple testing correction, our unbiased screen revealed three metabolites that were significantly linked to the risk of amyotrophic lateral sclerosis: Estrone-3-sulphate and bradykinin were protective, which is consistent with literature describing a male preponderance of amyotrophic lateral sclerosis and a preventive effect of angiotensin-converting enzyme inhibitors which inhibit the breakdown of bradykinin. Serum isoleucine was positively associated with amyotrophic lateral sclerosis risk. All three metabolites were supported by robust Mendelian randomization measures and sensitivity analyses; estrone-3-sulphate and isoleucine were confirmed in a validation amyotrophic lateral sclerosis genome-wide association study. Estrone-3-sulphate is metabolized to the more active estradiol by the enzyme 17β-hydroxysteroid dehydrogenase 1; further, Mendelian randomization demonstrated a protective effect of estradiol and rare variant analysis showed that missense variants within HSD17B1, the gene encoding 17β-hydroxysteroid dehydrogenase 1, modify risk for amyotrophic lateral sclerosis. Finally, in a zebrafish model of C9ORF72-amyotrophic lateral sclerosis, we present evidence that estradiol is neuroprotective. Isoleucine is metabolized via methylmalonyl-CoA mutase encoded by the gene MMUT in a reaction that consumes vitamin B12. Multivariable Mendelian randomization revealed that the toxic effect of isoleucine is dependent on the depletion of vitamin B12; consistent with this, rare variants which reduce the function of MMUT are protective against amyotrophic lateral sclerosis. We propose that amyotrophic lateral sclerosis patients and family members with high serum isoleucine levels should be offered supplementation with vitamin B12.
Neurochemical and cognitive changes precede structural abnormalities in the TgF344-AD rat model
Authors: Fowler Caitlin F. , Goerzen Dana , Devenyi Gabriel A. , Madularu Dan , Chakravarty M. Mallar , Near Jamie 
Published: March 2022

AbstractAlzheimer’s disease is a progressive neurodegenerative disorder with a decades-long pre-symptomatic phase, substantiating the need for prodromal biomarker development and early intervention. To deconstruct the processes underlying disease progression and identify potential biomarkers, we used neuroimaging techniques with high translational potential to human clinical studies in the TgF344-AD rat model which recapitulates the full spectrum of Alzheimer’s neuropathology (progressive amyloid deposition, tauopathy, frank neuronal loss, gliosis, and cognitive dysfunction). We employed longitudinal MRI and magnetic resonance spectroscopy in conjunction with behavioural testing to characterize multiple facets of disease pathology in male and female TgF344-AD rats (n = 26, 14M/12F) relative to wildtype littermates (n = 24, 12M/12F). Testing was performed at 4, 10, 16, and 18 months, covering much of the adult rat lifespan and multiple stages of disease progression. The TgF344-AD model demonstrated impaired spatial reference memory in the Barnes Maze by 4 months of age, followed by neurochemical abnormalities in the hippocampus by 10 months and major structural changes by 16 months. Specifically, TgF344-AD rats displayed increased total choline and lactate, and decreased total creatine, taurine, and N-acetylaspartate to myo-inositol ratio, dentate gyrus hypertrophy, and atrophy in the hippocampus, hypothalamus, and nucleus accumbens. Overall, these findings support the use of MRI and magnetic resonance spectroscopy for the development of non-invasive biomarkers of disease progression, clarify the timing of pathological feature presentation in this model, and contribute to the validation of the TgF344-AD rat as a highly relevant model for pre-clinical Alzheimer’s disease research.