bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and construction status of the Mu2e electromagnetic calorimeter mechanical structures
Authors: Atanov N. , Baranov V. , Borrel L. , Bloise C. , Budagov J. , Ceravolo S. , Cervelli F. , Colao F. , Cordelli M. , Corradi G. , Davydov Y.I. , Di Falco S. , Diociaiuti E. , Donati S. , Echenard B. , Ferrari C. , Gioiosa A. , Giovannella S. , Giusti V. , Glagolev V. , Grancagnolo F. , Hampai D. , Happacher F. , Hitlin D. , Lin D. , Martini M. , Middleton S. , Miscetti S. , Morescalchi L. , Paesani D. , Pasciuto D. , Pedreschi E. , Porter F. , Raffaelli F. , Saputi A. , Sarra I. , Spinella F. , Taffara A. , Tassielli G.F. , Tereshchenko V. , Usubov Z. , Vasilyev I.I. , Zanetti A. , Zhu R.Y. 
Published: November 2022

Abstract
The Mu2e experiment at Fermilab will search for the CLFV neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the evidence of physics beyond the Standard Model. Mu2e comprises a straw-tracker, an electromagnetic calorimeter and an external veto for cosmic rays. The calorimeter provides electron identification, a fast trigger and aids track reconstruction. It is a state-of-the-art crystal calorimeter and employs 1340 pure CsI crystals readout by UV-extended SiPM and fast electronics. The design consists of two identical annular disks positioned at the relative distance of 70 cm downstream the target.The hostile Mu2e conditions (total ionizing dose of 12 krad and a neutron fluence of 5 × 1010 n/cm2 @ 1 MeVeq (Si)/y, 1 T magnetic field and vacuum level of 10−4 Torr) posed tight constraints on the mechanical structures and materials choice. The support structure of the two crystal matrices employs two aluminum hollow rings and parts made of open-cell vacuum-compatible carbon fiber. SiPMs and front-end electronics for each crystal are assembled in one mechanical unit inserted in a machined copper holder. The units are supported by a plate made of vacuum-compatible material. The plate integrates the cooling system made of a network of copper lines flowing a low temperature fluid and placed in thermal contact with the copper holders. The DAQ is hosted in aluminum crates positioned on the lateral surface of the disks. The crates also integrate the DAQ electronics cooling system. We review the constraints on the calorimeter structures design, the development of all the structural components, including the simulations that have determined the materials and technological choices and the specifications of the cooling station, components production and quality assurance tests, the procedures for detector assembly, transportation and installation in the experimental area.
Parameterization of electron attachment rate constants for impurities in LArTPC detectors
Authors: Li Y. , Bromberg C. , Diwan M. , Kettell S. , Martynenko S. , Qian X. , Paolone V. , Stewart J. , Thorn C. , Zhang C. 
Published: November 2022

Abstract
The ability of free electrons to drift long distances at
high velocities in pure liquid argon under an applied electric field
has been exploited for the past forty years to implement detectors
with increasingly larger volumes for high energy physics research.
The attachment of free electrons to impurities in the LAr is an
important limit on the free instrumented volume of these extremely
large detectors, and impurity concentrations as small as 100 ppt can
reduce their resolution and efficiency. In this paper, we summarize
the electron attachment rate constants as a function of the applied
electric field, for common impurities in LArTPCs, obtained from data
in the literature. We further provide analytical functions to
parameterize the data, which are useful to compare with new
measurements, to model and analyze the performance of existing
detectors, and to predict the performance of new detectors.
BV quantization of dynamical fuzzy spectral triples
Authors: Gaunt James , Nguyen Hans , Schenkel Alexander 
Published: November 2022

Abstract
This paper provides a systematic study of gauge symmetries in the dynamical fuzzy spectral triple models for quantum gravity that have been proposed by Barrett and collaborators. We develop both the classical and the perturbative quantum BV formalism for these models, which in particular leads to an explicit homological construction of the perturbative quantum correlation functions. We show that the relevance of ghost and antifield contributions to such correlation functions depends strongly on the background Dirac operator

D

0

around which one perturbs, and in particular on the amount of gauge symmetry that it breaks. This will be illustrated by studying quantum perturbations around (a) the gauge-invariant zero Dirac operator

D
0

=
0

in a general

(
p
,
q
)

-model, and (b) a simple example of a non-trivial

D

0

in the quartic

(
0
,
1
)

-model.
Reparameterized semi-empirical methods for computing anharmonic vibrational frequencies of multiply-bonded hydrocarbons
Authors: Westbrook Brent R , Layfield Joshua P , Lee Timothy J , Fortenberry Ryan C 
Published: November 2022

Abstract
Reparameterized semi-empirical methods can reproduce gas-phase experimental vibrational frequencies to within 24 cm−1 or better for a 100-fold decrease in computational cost in the anharmonic fundamental vibrational frequencies. To achieve such accuracy and efficiency, the default parameters in the PM6 semi-empirical model are herein optimized to reproduce the experimental and high-level theoretical vibrational spectra of three small hydrocarbon molecules, C2H2, c-C3H2, and C2H4, with the hope that these same parameters will be applicable to large polycyclic aromatic hydrocarbons (PAHs). This massive cost reduction allows for the computation of explicit anharmonic frequencies and the inclusion of resonance corrections that have been shown to be essential for accurate predictions of anharmonic frequencies. Such accurate predictions are necessary to help to disentangle the heretofore unidentified infrared spectral features observed around diverse astronomical bodies and hypothesized to be caused by PAHs, especially with the upcoming influx of observational data from the James Webb Space Telescope. The optimized PM6 parameters presented herein represent a substantial step in this direction with those obtained for ethylene (C2H4) yielding a 37% reduction in the mean absolute error of the fundamental frequencies compared to the default PM6 parameters.
Emotional Management in Catastrophic Times
Authors: Lunbeck Elizabeth 
Published: November 2022

Abstract
How can we feel safe in a world riven by conflict and in the grip of “the crazy”? What emotional strategies are available to make unbearable realities bearable? Should we side with liveliness and engagement over despair and resignation? The books under review converge on these questions. Sally Weintrobe focuses on responses to the ongoing climate emergency, offering a bracing indictment of neoliberalism’s failures in fomenting it and making a case for the role understanding the psyche—split between caring and uncaring parts—can play in countering it. Arguing that all of us harbor desires for omnipotence and entitled dominion over nature and over others, Weintrobe calls on us to mobilize the caring parts of our selves to counter indifference and resignation. Heather Murray focuses on the twentieth century’s shifting emotional regimes, using the asylum and its records to chart the displacement of passivity and resignation as culturally virtuous modes of engagement by a valorization of activity, intensity, and struggle. Yet, she asks, should we not pause to consider resignation as a sensible psychic strategy offering refuge from the clamors of a world out of control? Is opting out a viable strategy for survival or a fantasy doomed to fail?
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability
Authors: Díaz-Seoane Sandra , Rey Barreiro Xabier , Villaverde Alejandro F 
Published: November 2022

Abstract

Motivation
STRIKE-GOLDD is a toolbox that analyses the structural identifiability and observability of possibly non-linear, non-rational ODE models that may have known and unknown inputs. Its broad applicability comes at the expense of a lower computational efficiency than other tools.

Results
STRIKE-GOLDD 4.0 includes a new algorithm, ProbObsTest, specifically designed for the analysis of rational models. ProbObsTest is significantly faster than the previously available FISPO algorithm when applied to computationally expensive models. Providing both algorithms in the same toolbox allows combining generality and computational efficiency. STRIKE-GOLDD 4.0 is implemented as a Matlab toolbox with a user-friendly graphical interface.

Availability and implementation
STRIKE-GOLDD 4.0 is a free and open-source tool available under a GPLv3 license. It can be downloaded from GitHub at https://github.com/afvillaverde/strike-goldd.

Supplementary information
Supplementary data are available at Bioinformatics online.
The architecture of the European Union’s pandemic preparedness and response policy framework
Authors: Eerens Dimitri , Hrzic Rok , Clemens Timo 
Published: November 2022

Abstract

Background
COVID-19 has highlighted the importance of preparedness and response systems when faced with a pandemic. The rapid spread of the disease throughout Europe raised questions about the capacity of the European Union (EU) and its Member States to combat serious cross-border threats to health. This article provides an overview of institutional arrangements for pandemic preparedness before the COVID-19 pandemic and outlines the changes proposed by the European Health Union (EHU) framework.

Methods
A systematic review of relevant EU law, EU policy documents and the scientific literature was conducted. EUR-lex, PubMed, Web of Science core collection and Google Scholar databases were searched for relevant records published after the year 2000. The proposed new regulatory framework was extracted from the EHU legislative package. The results were organized according to the Public Health Emergency Preparedness Logic Model.

Results
The main EU bodies involved in preparedness and response are the European Centre for Disease Prevention and Control (ECDC), the European Commission and the Health Security Committee (HSC). The proposed changes of the EHU focus on strengthening the auditing capabilities of the ECDC, increasing the scope of EU action in managing medical countermeasures, and further formalizing the HSC.

Conclusions
The proposal takes bold steps to address technical and political issues of preparedness and response; whereas, on the latter point, it is likely that amendments to the proposal will not address long-standing challenges in preparing for and coordinating national responses to a future EU-wide pandemic.
learnMSA: learning and aligning large protein families
Authors: Becker Felix , Stanke Mario 
Published: November 2022

Abstract

Background
The alignment of large numbers of protein sequences is a challenging task and its importance grows rapidly along with the size of biological datasets. State-of-the-art algorithms have a tendency to produce less accurate alignments with an increasing number of sequences. This is a fundamental problem since many downstream tasks rely on accurate alignments.

Results
We present learnMSA, a novel statistical learning approach of profile hidden Markov models (pHMMs) based on batch gradient descent. Fundamentally different from popular aligners, we fit a custom recurrent neural network architecture for (p)HMMs to potentially millions of sequences with respect to a maximum a posteriori objective and decode an alignment. We rely on automatic differentiation of the log-likelihood, and thus, our approach is different from existing HMM training algorithms like Baum–Welch. Our method does not involve progressive, regressive, or divide-and-conquer heuristics. We use uniform batch sampling to adapt to large datasets in linear time without the requirement of a tree. When tested on ultra-large protein families with up to 3.5 million sequences, learnMSA is both more accurate and faster than state-of-the-art tools. On the established benchmarks HomFam and BaliFam with smaller sequence sets, it matches state-of-the-art performance. All experiments were done on a standard workstation with a GPU.

Conclusions
Our results show that learnMSA does not share the counterintuitive drawback of many popular heuristic aligners, which can substantially lose accuracy when many additional homologs are input. LearnMSA is a future-proof framework for large alignments with many opportunities for further improvements.
Frictional properties of Opalinus Clay: influence of humidity, normal stress and grain size on frictional stability
Authors: Bigaroni Nico , Scuderi Marco Maria , Cappa Frédéric , Guglielmi Yves , Nussbaum Christophe , Aldega Luca , Pozzi Giacomo , Collettini Cristiano 
Published: November 2022

SUMMARYThe Opalinus Clay (OPA) is a clay-rich formation considered as a potential host rock for radioactive waste repositories and as a caprock for carbon storage in Switzerland. Its very low permeability (10−19 to 10−21 m2) makes it a potential sealing horizon, however the presence of faults that may be activated during the lifetime of a repository project can compromise the long-term hydrological confinement, and lead to mechanical instability. Here, we have performed laboratory experiments to test the effect of relative humidity (RH), grain size (g.s.) and normal stress on rate-and-state frictional properties and stability of fault laboratory analogues corresponding to powders of OPA shaly facies. The sifted host rock powders at different grain size fractions (&lt;63 μm and 63 &lt; g.s. &lt; 125 μm), at room (∼25 per cent) and 100 per cent humidity, were slid in double-direct shear configuration, under different normal stresses (5–70 MPa). We observe that peak friction, μpeak and steady-state friction, μss, depend on water vapour content and applied normal stress. Increasing relative humidity from ∼25 per cent RH (room humidity) to 100 per cent RH causes a decrease of frictional coefficient from 0.41 to 0.35. The analysis of velocity-steps in the light of rate-and-state friction framework shows that the stability parameter (a–b) is always positive (velocity-strengthening), and it increases with increasing sliding velocity and humidity. The dependence of (a–b) on slip rate is lost as normal stress increases, for each humidity condition. By monitoring the variations of the layer thickness during the velocity steps, we observe that dilation (Δh) is directly proportional to the sliding velocity, decreases with normal stress and is unaffected by humidity. Microstructural analysis shows that most of the deformation is accommodated within B-shear zones, and the increase of normal stress (σn) promotes the transition from strain localization and grain size reduction to distributed deformation on a well-developed phyllosilicate network. These results suggest that: (1) the progressive loss of velocity dependence of frictional stability parameter (a–b) at σn &gt; 35 MPa is dictated by a transition from localized to distributed deformation and (2) water vapour content does not affect the deformation mechanisms and dilation, whereas it decreases steady-state friction (μss), and enhances fault stability.
Cultural Viewpoint Metaphors Resignification to Teach Programming
Authors: Corrêa Joseline Melo , Pereira Mota Marcelle 
Published: November 2022

Abstract
Technologies permeate contemporary society, and the ability to use computer science concepts in problem-solving is essential to everyone. This paper presents an epistemic tool of semiotic engineering whose meaning is resignified to the context of teaching programming to initial learners. Aiming to help these students absorb programming concepts, we structured a gradual form of presentation using the interaction with a new system as a journey through a new culture, based on the Cultural Viewpoint Metaphors theory. After that, we applied this resignification in an introductory programming workshop using visual programming and the BBC Micro:bit embedded device. Results from the workshop revealed that this gradual introduction could help novices in the programming concepts learning process, showing the potential of this approach in teaching programming.
Safety and Efficacy of Pure and a Nanosuspension of D-limonene for Controlling Pigeon Lice
Authors: Gadelhaq Sahar M , Aboelhadid Shawky M , Abdel-Baki Abdel-Azeem S , Hassan Khaled M , Arafa Waleed M , Ibrahium Samar M , Al-Quraishy Saleh , Hassan Ahmed O , Abd El-Kareem Shams G 
Published: November 2022

Abstract
This study investigated the safety and efficacy of two forms of D-limonene (DL) against Columbicola columbae (pigeon feather lice); pure and a nanoemulsion formulation (DLN). The cell cytotoxicity of the prepared forms of DL/DLN was investigated using skin cell lines. In vitro and ex vivo bioassays were applied on lice. The ex vivo bioassay was done on cut feathers containing lice eggs. The in vivo experiment was conducted on pigeons naturally infested by lice. The infested pigeons were treated with DL, DLN, or deltamethrin (D) as a positive control. Both forms of D-limonene were found to be safe when applied to the normal human skin fibroblast cell line, but DLN was toxic to skin cell carcinoma. The in vitro and ex vivo results of both DL and DLN forms were similar. All eggs treated with DL, DLN, and D failed to hatch (100%). The in vivo results showed complete elimination of lice 24 h post-treatment (PT), and biochemical analysis showed that the treated birds retained normal kidney and liver functions. Treated groups also showed improved productivity in the 4 months PT. In conclusion, DL and DLN are safe and effective in controlling feather lice infestation in pigeons and successful treatment encourages bird productivity.
Phytohormones in plant responses to boron deficiency and toxicity
Authors: Chen Xi , Smith Steven M , Shabala Sergey , Yu Min 
Published: November 2022

AbstractBoron (B) is an essential element for plant growth. Many agricultural soils around the globe have either insufficient or excessive amounts of available B, with major implications for crop production. Understanding major limitations imposed by B nutritional disorders may allow breeding crops for improved B use efficiency as well as make them more resilient to excessive B, thus reducing yield penalties. It has become apparent that B-related physiological disorders are mediated in large part by their impact on plant hormone production and signaling. The aim of this review is to summarize current knowledge of the roles of hormones in plant responses to B and their impact on plant growth and development. The most significant effect of B deficiency is the inhibition of root elongation. Boron deficiency promotes the redistribution of auxin in the root elongation zone. Together with cytokinin signals and ethylene, this redistribution and modulation of auxin content triggers inhibition of the root cell elongation. Under B deficiency, root development is also regulated by brassinosteroids and jasmonic acid. Excess B can induce the production of reactive oxygen species (ROS). Abscisic acid and salicylic acid are both produced in response to B toxicity, and both can induce the antioxidant defense system to detoxify ROS. Another adaptation to B toxicity involves changes in the expression levels and activity of aquaporins in roots, thus reducing the uptake of water and delivery of B into the transpiration stream. In addition, abscisic acid mediates stomatal closure to further limit transpiration and the consequent accumulation of B in leaves.
Mediastinal Mass Discovered in the Second Trimester, a Rare Presentation of Hodgkin’s Lymphoma in Pregnancy
Authors: Purmalek Monica M , Kopelman Zachary A , Griffis Jeffery D , Mehlhaff Krista M , Gonzalez-Brown Veronica M 
Published: November 2022

ABSTRACT
Newly diagnosed malignancy during pregnancy is rare affecting approximately 1 in 1,000 pregnancies. Breast followed by hematologic malignancies are most common. Hodgkin’s lymphoma (HL) is a lymphoid neoplasm which can present with lymphadenopathy or mediastinal mass and represents 6% of all malignancies diagnosed during pregnancy. Treatment involves a combination of chemotherapy with or without adjuvant radiation which poses significant challenges when diagnosed antepartum. We highlight a 28-year-old primigravida at 26 weeks gestation who presented to the emergency department in Japan with cough, dyspnea, and sore throat for 3-5 days. Initial chest radiography demonstrated a large perihilar mass with mediastinal shift. Follow-up CT chest revealed an anterior mediastinal mass measuring 8 cm × 19 cm × 16 cm with features concerning for aggressive lymphoma. The patient was subsequently transferred to a stateside tertiary care center for expedited workup. She underwent two core needle biopsies, both of which were non-diagnostic. Cardiothoracic surgery performed a cervical mediastinoscopy with excision of the enlarged right supraclavicular lymph node. Pathologic analysis revealed classical HL, nodular sclerosis subtype. Treatment was initiated with adriamycin, bleomycin, vinblastine, and dacarbazine with two cycles planned antepartum followed by additional cycles postpartum. The patient had an uncomplicated vaginal delivery at 38 weeks gestation. Diagnosis of HL in pregnancy is rare, and expedited diagnosis can be challenging as multiple diagnostic and treatment modalities may impact pregnancy. Management in pregnancy requires a multidisciplinary approach, and decisions regarding treatment and delivery timing should be weighed against risk to the fetus.
Long-term efficacy and safety of canakinumab in the treatment of systemic juvenile idiopathic arthritis in Japanese patients: Results from an open-label Phase III study
Authors: Iwata Naomi , Nishimura Kenichi , Hara Ryoki , Imagawa Tomoyuki , Shimizu Masaki , Tomiita Minako , Umebayashi Hiroaki , Takei Syuji , Seko Noriko , Wakabayashi Ryota , Yokota Shumpei 
Published: November 2022

ABSTRACT

Objectives
The objective of the study was to report the efficacy and safety of canakinumab treatment in Japanese patients with systemic juvenile idiopathic arthritis (sJIA) over a 48-week study period.

Methods
Patients were administered canakinumab 4 mg/kg (maximum dose 300 mg) every 4 weeks, with no dose adjustments. The key outcome measures included adapted American College of Rheumatology paediatric (aACR pedi) 30/50/70/90/100 response, proportion of patients with inactive disease, and corticosteroid (CS) tapering.

Results
In total, 16/19 (84.2%) patients received canakinumab for ≥96 weeks reaching end-of-study (EOS) visit without premature discontinuation. Regardless of the level of joint involvement at baseline, high aACR pedi responses were observed throughout the study; at the EOS, aACR pedi 90/100 response rates were 84.2%/63.2%, respectively. The proportion of patients who successfully tapered CSs at EOS was 66.7% (12/18), of which 10 patients were steroid-free. The most common adverse events were infections (238.3 events/100 patient-years). Serious adverse events were observed in 52.6%. The event (n=1) adjudicated as possible macrophage activation syndrome was preceded by sJIA flare. No deaths were reported.

Conclusions
Canakinumab treatment resulted in a sustained treatment response in sJIA patients over 48 weeks and was associated with CS tapering in majority of patients. No new safety findings were reported.