bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-messenger high-energy signatures of decaying dark matter and the effect of background light
Authors: Skrzypek B. , Chianese M. , Argüelles C.A.
Published: January 2023

The IceCube Neutrino Observatory at the South Pole has measured astrophysical neutrinos
using through-going and starting events in the TeV to PeV energy range. The origin of these
astrophysical neutrinos is still largely unresolved, and among their potential sources could be
dark matter decay. Measurements of the astrophysical flux using muon neutrinos are in slight
tension with starting event measurements. This tension is driven by an excess observed in the
energy range of 40–200 TeV with respect to the through-going expectation. Previous works have
considered the possibility that this excess may be due to heavy dark matter decay and have placed
constraints using gamma-ray and neutrino data. However, these constraints are not without
caveats, since they rely on the modeling of the astrophysical neutrino flux and the sources of
gamma-ray emission. In this work, we derive background-agnostic galactic and extragalactic
constraints on decaying dark matter by considering Tibet-ASγ data, Fermi-LAT diffuse data,
and the IceCube high-energy starting event sample. For the gamma-ray limits, we investigate the
uncertainties on secondary emission from electromagnetic cascades during propagation arising from
the unknown intensity of the extragalactic background light. We find that such uncertainties
amount to a variation of up to ∼ 55% in the gamma-ray limits derived with extragalactic
data. Our results imply that a significant fraction of the astrophysical neutrino flux could be
due to dark matter and that ruling it out depends on the assumptions on the gamma-ray and neutrino
background. The latter depends on the yet unidentified sources.
Validation of 2D
Te
and
ne
measurements made with Helium imaging spectroscopy in the volume of the TCV divertor
Authors: Linehan B.L. , Perek A. , Duval B.P. , Bagnato F. , Blanchard P. , Colandrea C. , De Oliveira H. , Février O. , Flom E. , Gorno S. , Goto M. , Marmar E. , Martinelli L. , Mathews A. , Muñoz-Burgos J. , Mykytchuk D. , Offeddu N. , Oliveira D.S. , Reimerdes H. , Reiter D. , Schmitz O. , Terry J.L. , Theiler C. , Tsui C.K. , Vincent B. , Wijkamp T. , Wüthrich C. , Zholobenko W. ,   the TCV Team
Published: January 2023

Multi-spectral imaging of helium atomic emission (HeMSI) has been used to create 2D poloidal maps of

T

e

and

n

e

in TCV’s divertor. To achieve these measurements, TCV’s MANTIS multispectral cameras (Perek et al 2019 Rev. Sci. Instrum.
90 123514) simultaneously imaged four He I lines (two singlet and two triplet) and a He II line (468 nm) from passively present He and He+. The images, which were absolutely calibrated and covered the whole divertor region, were inverted through the assumption of toroidal symmetry to create emissivity profiles and, consequently, line-ratio profiles. A collisional-radiative model (CRM) was applied to the line-ratio profiles to produce 2D poloidal maps of

T

e

and

n

e

. The collisional-radiative modeling was accomplished with the Goto helium CRM code (Zholobenko et al 2018 Nucl. Fusion
58 126006, Zholobenko et al 2018 Technical Report, Goto 2003 J. Quant. Spectrosc. Radiat. Transfer
76 331–44) which accounts for electron-impact excitation (EIE) and deexcitation, and electron–ion recombination (EIR) with

He

+

. The HeMSI

T

e

and

n

e

measurements were compared with co-local Thomson scattering measurements. The two sets of measurements exhibited good agreement for ionizing plasmas:

(

5

eV

⩽

T

e

⩽
60

eV

, and

2
×

10

18

m

−
3

⩽

n

e

⩽
3
×

10

19

m

−
3

)

in the case of majority helium plasmas, and

(

10

eV

⩽

T

e

⩽
40

eV

,

2
×

10

18

m

−
3

⩽

n

e

⩽
3
×

10

19

m

−
3

)

in the case of majority deuterium plasmas. However, there were instances where HeMSI measurements diverged from Thomson scattering. When

T

e

⩽
10

eV

in majority deuterium plasmas, HeMSI deduced inaccurately high values of

T

e

. This disagreement cannot be rectified within the CRM’s EIE and EIR framework. Second, on sporadic occasions within the private flux region, HeMSI produced erroneously high measurements of

n

e

. Multi-spectral imaging of Helium emission has been demonstrated to produce accurate 2D poloidal maps of

T

e

and

n

e

within the divertor of a tokamak for plasma conditions relevant to contemporary divertor studies.
Modeling of crowd groups with an extended social field model
Authors: Yu Bin
Published: January 2023

A social field model is extended by adding supports of simulations of crowd group related dynamics such as group cohesion, back-tracking, etc. A computational implementation combining heterogeneous computing and multi-threading technologies is developed to integrate the proposed extension into a heterogeneous computing framework. Hence modeling of group related dynamics can be accomplished in a very efficient manner. In the section of numerical experiments, the extended model is firstly validated with a set of practical data. Results show that the simulated evacuation time matches the practical one quite well. Then a study of fundamental diagrams is expanded with considerations of crowd groups. It is shown that the impact of crowd groups mainly happens in the regime of low densities and would become insignificant in the regime of high densities.
Replica analysis of the lattice-gas restricted Boltzmann machine partition function
Authors: Hoyle David C
Published: January 2023

We study the expectation value of the logarithm of the partition function of large binary-to-binary lattice-gas restricted Boltzmann machines (RBMs) within a replica-symmetric ansatz, averaging over the disorder represented by the parameters of the RBM Hamiltonian. Averaging over the Hamiltonian parameters is done with a diagonal covariance matrix. Due to the diagonal form of the parameter covariance matrix not being preserved under the isomorphism between the Ising and lattice-gas forms of the RBM, we find differences in the behaviour of the quenched log partition function of the lattice-gas RBM compared to that of the Ising RBM form usually studied. We obtain explicit expressions for the expectation and variance of the lattice-gas RBM log partition function per node in the thermodynamic limit. We also obtain explicit expressions for the leading order finite size correction to the expected log partition function per node, and the threshold for the stability of the replica-symmetric approximation. We show that the stability threshold of the replica-symmetric approximation is equivalent, in the thermodynamic limit, to the stability threshold of a recent message-passing algorithm used to construct a mean-field Bethe approximation to the RBM free energy. Given the replica-symmetry assumption breaks down as the level of disorder in the spin-spin couplings increases, we obtain asymptotic expansions, in terms of the variance controlling this disorder, for the replica-symmetric log partition function and the replica-symmetric stability threshold. We confirm the various results derived using simulation.
Performance of neutron-irradiated 4H-silicon carbide diodes subjected to alpha radiation
Authors: Gaggl P. , Gsponer A. , Thalmeier R. , Waid S. , Pellegrini G. , Godignon P. , Rafí J.M. , Bergauer T.
Published: January 2023

The unique electrical and material properties of 4H-silicon-carbide (4H-SiC) make it a promising candidate material for high rate particle detectors. In contrast to the ubiquitously used silicon (Si), 4H-SiC offers a higher carrier saturation velocity and larger breakdown voltage, enabling a high intrinsic time resolution and mitigating pile-up effects. Additionally, as radiation hardness requirements grow more demanding in the context of future high luminosity high energy physics experiments, wide-bandgap materials such as 4H-SiC could offer better performance due to low dark currents and higher atomic displacement thresholds. In this work, the detector performance of 50 µm thick 4H-SiC p-in-n planar pad sensors was investigated at room temperature, using an 241Am alpha source at reverse biases of up to 1100 V. Samples subjected to neutron irradiation with fluences of up to 1 × 1016 neq/cm2 were included in the study in order to quantify the radiation hardness properties of 4H-SiC. A calibration of the absolute number of collected charges was performed using a GATE simulation. The obtained results are compared to previously performed UV transient current technique (TCT) studies. Samples exhibit a drop in charge collection efficiency (CCE) with increasing irradiation fluence, partially compensated at high reverse bias voltages far above full depletion voltage. At fluences of 5 × 1014 neq/cm2 and 1 × 1015 neq/cm2, CCEs of 64 % and 51 % are obtained, decreasing to 15 % at 5 × 1015 neq/cm2. A plateau of the collected charges is observed in accordance with the depletion of the volume the alpha particles penetrate for an unirradiated reference detector. For the neutron-irradiated samples, such a plateau only becomes apparent at higher reverse bias, roughly 600 V and 900 V for neutron fluences of 5 × 1014 neq/cm2 and 1 × 1015 neq/cm2. For the highest investigated fluence, CCE behaves almost linearly with increasing reverse bias. Compared to UV-TCT measurements, the reverse bias required to deplete a sensitive volume covering full energy deposition is lower, due to the small penetration depth of the alpha particles. At the highest reverse bias, the measured CCE values agree well with earlier UV-TCT studies, with discrepancies between 1% and 5%.
Production and testing of the powerboard for ATLAS ITk Strip barrel modules
Authors: Haber C. , Heim T. , Kelly S. , Krizka K. , Zhang Z.
Published: January 2023

The upgrade of the ATLAS ITk strips detector for HL-LHC will employ a custom PCB (powerboard) for on-module DC-DC conversion, HV switching, and monitoring. Production of about 14100 of such PCBs with high reliability is a big challenge. This paper will present the production procedure and quality control (QC) testing system for the powerboards to be installed on ITk Strip barrel modules. During production, about 150 powerboards will be produced every week. Each powerboard will need to pass QC tests before they are assembled to module. The QC tests include thermal cycling between −35 °C and 40 °C, soak test (continuous running of DC-DC converter at high load at 20 °C), and basic functionality and characterization electrical tests of the low voltage (LV), high voltage (HV), and monitoring functions of the powerboard. A custom QC test system is described, which is based on a reusable PCB (active board) with all testing circuits, a one-time powerboard carrier card, and a Z-turn SoC board which hosts and runs the testing program. The production procedure and QC test system has been tested with 400 powerboards during pre-production, and the system has been proven ready for production with the desired testing program, speed, safety, and cost. Performance and typical failures of powerboards observed during the QC test of pre-production powerboards is also presented.
Development of a Stitched Monolithic Pixel Sensor prototype (MOSS chip) towards the ITS3 upgrade of the ALICE Inner Tracking system
Authors: Vicente Leitao P. , Aglieri Rinella G. , Bugiel S. , Cecconi L. , de Melo J.L.A. , De Robertis G. , Deng W. , Dorda Martin A. , Dorosz P. , Fang X. , Gajanana D. , Gromov V. , Hodges A. , Hong G.H. , Kremastiotis I. , Kugathasan T. , Loddo F. , Marras D. , Matthew S. , Morel F. , Piro F. , Pulli A. , Sedgwick I. , Snoeys W. , Soudier J. , Valin I. , Yelkenci A.
Published: January 2023

The MOnolithic Stitched Sensor (MOSS) is a development prototype chip towards the ITS3 vertexing detector for the ALICE experiment at the LHC. Designed using a 65 nm CMOS Imaging technology, it aims at profiting from the stitching technique to construct a single-die monolithic pixel detector of 1.4 cm × 26 cm. The MOSS prototype is one of the prototypes developed within the CERN-EP R&D framework to learn how to make stitched wafer-scale sensors with satisfactory yield. This contribution will describe some of the design challenges of a stitched pixel sensor and the techniques adopted during the development of this prototype.
Software tools for hybrid quality control for the CMS Outer Tracker Phase-2 Upgrade
Authors: Mateos Domínguez I. , Blanchot G. , Chatagnon P. , Cooperstein S. , Di Mattia A. , Honma A. , Klein K. , Kovacs M. , La Rosa A. , Makarenko I. , Otarid Y. , Pauls A. , Pissaki Z. , Schleidweiler K. , Seif El Nasr S. , Zografos A.
Published: January 2023

Fifty thousand hybrid circuits of five different types will be manufactured for the Phase-2 Upgrade of the CMS Outer Tracker. These circuits must undergo a strict quality control process, composed of functional testing and visual inspection, before they can be assembled into modules. The hybrids will be functionally tested first at the manufacturing site. Afterwards, they will be visually inspected and functionally tested again at CERN or at collaborating institutes. Results from these processes will be stored in the CMS production database. This paper presents the software tools developed to carry out these tasks.
A radiation hard bandgap voltage reference for the ARCADIA project
Authors: Traversi G. , Falchieri D. , Gaioni L. , Manghisoni M. , Pezzoli M. , Ratti L. , Re V.
Published: January 2023

This work presents the design and characterization results of a radiation hard bandgap reference circuit fabricated in a 110 nm CMOS technology for the Main Demonstrator chip of the ARCADIA project. The design, based on a current-mode approach in order to be able to output a smaller than 1.2 V reference voltage, employs diode-connected MOSFETs instead of BJTs to enhance the radiation hardness and a second amplifier to improve the current mirror of the output branch and therefore the line regulation of the circuit. This paper describes the features of the circuit and its measured results.
Studies of event burst phenomenon with SiPMs in liquid nitrogen
Authors: Tsang T. , Chen H. , Gao S. , Giacomini G. , Radeka V. , Rescia S.
Published: January 2023

Silicon photomultiplier (SiPM) are used to collect scintillation photons in many cryogenic noble liquid detectors deployed around the world, such as DarkSide, nEXO, MEGII, ProtoDUNE and DUNE. An event burst phenomenon was observed during routine characterization on many models of SiPMs operated in liquid nitrogen. These bursts of consecutive pulses are initiated by an intense dark photoelectron pulse with an event rate much lower than the time-uncorrelated thermal dark pulse. Although the rate of these burst events is very low, it can potentially compromise some dedicated rare physics event searches which are also anticipated to be of extremely low rate. Here, we systematically studied the behavior of the event burst phenomenon and identified the probable cause of the phenomenon. This investigation is important for the selection of SiPMs for use in noble liquid detectors, high energy physics experiments, and industrial applications where SiPMs are used in cryogenic environment.
A dedicated and versatile system for testing the radiation hardness of various integrated circuits
Authors: Placinta V.M. , Cojocariu L.N. , Maciuc F.
Published: January 2023

This work describes the architecture of a versatile system that is dedicated to the testing of various integrated circuits in radiation (e.g., ASICs, FPGAs). The system powers the device under test remotely. It monitors and reads out in real time various parameters, like: power consumption, voltage and current (with resolution of 100 µV and 100 µA, respectively), specific operational parameters of the device under test and its package temperature. A key feature of this system is its multi-channel and remote power supply capabilities, used to power the device under test. It embeds built-in features to detect and record single-event latch-ups, single event upsets and to monitor total ionizing dose cumulative effects. A graphical user interface allows the user to connect and to control the entire system through a dedicated ethernet interface from a safe location zone, and record to disk measurements data.
Unified Modulation Pattern Analysis (UMPA) algorithm for 1D sensitive X-ray phase contrast imaging techniques
Authors: Di Trapani V. , Brombal L. , De Marco F. , Dreossi D. , Thibault P.
Published: January 2023

X-ray phase contrast imaging (XPCI) techniques are sensitive to refraction (differential-phase) and small-angle X-ray scattering (dark-field) signals, not measurable with conventional absorption imaging techniques. Among XPCI techniques, edge illumination (EI), grating interferometry (GI), and speckle-based imaging (SBI) make use of wavefront markers, such as absorbing masks with periodical apertures or random diffusers, to encode refraction and dark-field signals induced by the sample. The Unified Modulated Pattern Analysis (UMPA) provides an algorithmic solution to extract the transmission, refraction, and dark-field images from EI, GI, and SBI datasets where the wavefront marker is directly resolved by the employed detection system. In its original implementation, UMPA has been designed for XPCI techniques sensitive to refractions along two axes. This work presents a modified version of the algorithm to extend its applicability to all the existing XPCI techniques that use wavefront markers with sensitivity to refraction limited along one direction (UMPA-1D). The algorithm, written in C++ and Cython and parallelized with OpenMP, enables fast reconstruction times that are particularly convenient for large tomographic datasets. The validity of the UMPA-1D has been demonstrated using both simulated images and real acquisitions with an EI setup in beam-tracking mode.
Radiation-tolerant all-digital clock generators for HEP applications
Authors: Biereigel S. , Kulis S. , Mendes E. , Hazell P. , Moreira P. , Prinzie J.
Published: January 2023

The emergence of high-precision timing systems in High Energy Physics motivates new developments in the domain of clock generation and distribution. Particularly, when considering the challenges arising from adopting advanced deep-submicron CMOS technology nodes, all-digital PLL and clock and data recovery (CDR) architectures constitute a promising option for future high energy physics (HEP) experiments. Both LC oscillator and ring oscillator-based all-digital PLL/CDR blocks for front-end ASICs were studied, designed, manufactured and characterized. Their design, the hardening considerations, as well as the performance obtained with these circuits are presented in this article.
The upgraded quench protection system for main quadrupoles in the LHC
Authors: Skoczeń Andrzej , Steckert Jens , Spasic Jelena , Blasco Serrano Daniel , Mundra Surbhi , Pridii Tetiana
Published: January 2023

The protection of superconducting magnets is a very important issue and demanding challenge in the LHC and other superconducting accelerating facilities. The quench phenomenon can destroy components of the accelerator, and therefore this digital system was designed, implemented, tested, and installed near each superconducting magnet in the LHC tunnel. The quench detection principle relies on the extraction of resistive voltage by compensation of the inductive part of the voltage. This article presents briefly the architecture applied to the design and the validation of the FPGA-based quench detector for the main quadrupoles of the LHC. The article focusses on digital design with the use of FPGA by VHDL coding and on the verification by simulation. The design is a replacement for the old detection system.
Automated real-space lattice extraction for atomic force microscopy images
Authors: Corrias Marco , Papa Lorenzo , Sokolović Igor , Birschitzky Viktor , Gorfer Alexander , Setvin Martin , Schmid Michael , Diebold Ulrike , Reticcioli Michele , Franchini Cesare
Published: January 2023

Analyzing atomically resolved images is a time-consuming process requiring solid experience and substantial human intervention. In addition, the acquired images contain a large amount of information such as crystal structure, presence and distribution of defects, and formation of domains, which need to be resolved to understand a material’s surface structure. Therefore, machine learning techniques have been applied in scanning probe and electron microscopies during the last years, aiming for automatized and efficient image analysis. This work introduces a free and open source tool (AiSurf: Automated Identification of Surface Images) developed to inspect atomically resolved images via scale-invariant feature transform and clustering algorithms. AiSurf extracts primitive lattice vectors, unit cells, and structural distortions from the original image, with no pre-assumption on the lattice and minimal user intervention. The method is applied to various atomically resolved non-contact atomic force microscopy images of selected surfaces with different levels of complexity: anatase TiO2(101), oxygen deficient rutile TiO2(110) with and without CO adsorbates, SrTiO3(001) with Sr vacancies and graphene with C vacancies. The code delivers excellent results and is tested against atom misclassification and artifacts, thereby facilitating the interpretation of scanning probe microscopy images.
Variability analysis of monthly precipitation vector time series in Australia by a new spatiotemporal entropy statistic
Authors: Hines Benjamin , Qian Guoqi , Chu Tingjin , Tordesillas Antoinette
Published: January 2023

Changing climate in Australia has significant impacts on the country’s economy, environment and social well-being. Addressing such impacts, particularly that of precipitation change, entails immediate action due to the more frequent occurrence of extreme dry or wet events in Australia in recent decades. In this paper we investigate the intra-annual Australian precipitation variability and how it changes over space and time. We quantify this variability using information entropy—a statistical tool for measuring the uncertainty of a random variable over its sample space, and propose a compositional data model to compute optimal spatiotemporal estimators of this entropy using 1/1979-to-3/2022 monthly satellite precipitation estimates from the National Oceanic and Atmospheric Administration. The results enable us to identify those locations/times where/when extreme intra-annual precipitation variation or unevenness occurred. We find this variability has been changing over time in large regions of southeastern Queensland and on the coast of South Australia, which would be difficult to find without using the proposed approach. We uncover the development of extreme entropy in the months leading up to, and in the location of, four extreme precipitation events in Australia where inter-annual precipitation amounts and/or trends proved insignificant. In marked contrast to annual precipitation, we found entropy has a weak association with the El Niño Southern Oscillation cycle.
How does increasing temperature affect the sub-annual distribution of monthly rainfall?
Authors: Tie Jiahao , Kim Seokhyeon , Sharma Ashish
Published: January 2023

This paper investigates the relationship between temperature and sub-annual rainfall patterns using long-term monthly rainfall and temperature data from 1920 to 2018 in Australia. A parameter (τ) is used to measure the evenness of temporal rainfall distribution within each year, with τ = 0 indicating a uniform pattern. The study examines the relationship between τ and temperature for each year, considering whether it was warmer or cooler than average across five climate zones (CZs) in Australia, including tropical, arid, and three temperate climate classes. This study discovered a considerable association between annual maximum temperature and the distribution of monthly rainfall, with high temperatures resulting in greater variation (as represented by larger τ values) in the sub-annual distribution of monthly rainfall throughout all CZs, particularly in arid regions with τ values ranging from 0.27 to 0.52. In contrast, regions with temperate climates without dry seasons had a lower and narrower range of τ, from 0.15 to 0.26. This variability in rainfall distribution makes managing water resources more challenging in arid regions in Australia.
The 𝒫(𝜑)₂ Model on de Sitter Space
Authors: Barata João , Jäkel Christian , Mund Jens
Published: January 2023

In 1975 Figari, Høegh-Krohn and Nappi constructed theP(φ)2{\mathscr P}(\varphi )_2model on the de Sitter space. Here we complement their work with new results, which connect this model to various areas of mathematics. In particular, i.) we discuss the causal structure of de Sitter space and the induces representations of the Lorentz group. We show that the UIRs ofSO0(1,2)SO_0(1,2)for both the principal and the complementary series can be formulated on Hilbert spaces whose functions are supported on a Cauchy surface. We describe the free classical dynamical system in both its covariant and canonical form, and present the associated quantum one-particle KMS structures in the sense of Kay (1985). Furthermore, we discuss the localisation properties of one-particle wave functions and how these properties are inherited by the algebras of local observables.

ii.) we describe the relations between the modular objects (in the sense of Tomita-Takesaki theory) associated to wedge algebras and the representations of the Lorentz group. We connect the representations of SO(1,2) to unitary representations ofSO(3)SO(3)on the Euclidean sphere, and discuss how theP(φ)2{\mathscr P}(\varphi )_2interaction can be represented by a rotation invariant vector in the Euclidean Fock space. We present a novel Osterwalder-Schrader reconstruction theorem, which shows that physicalinfrared problemsare absent on de Sitter space. As shown in Figari, Høegh-Krohn, and Nappi (1975), the ultraviolet problems are resolved just like on flat Minkowski space. We state the Haag–Kastler axioms for theP(φ)2{\mathscr P}(\varphi )_2model and we explain how thegeneratorsof the boosts and the rotations for the interacting quantum field theory arise from thestress-energy tensor. Finally, we show that the interacting quantum fields satisfy theequations of motionin their covariant form. In summary, we argue that the de SitterP(φ)2{\mathscr P}(\varphi )_2model is the simplest and most explicit relativistic quantum field theory, which satisfies basic expectations, like covariance, particle creation, stability and finite speed of propagation.
The Second Moment Theory of Families of 𝐿-Functions–The Case of Twisted Hecke 𝐿-Functions
Authors: Blomer Valentin , Fouvry Étienne , Kowalski Emmanuel , Michel Philippe , Milićević Djordje , Sawin Will
Published: January 2023

For a fairly general family of

L
L

-functions, we survey the known consequences of the existence of asymptotic formulas with power-saving error term for the (twisted) first and second moments of the central values in the family.

We then consider in detail the important special case of the family of twists of a fixed cusp form by primitive Dirichlet characters modulo a prime

q
q

, and prove that it satisfies such formulas. We derive arithmetic consequences: a positive proportion of central values

L
(
f
⊗
χ
,
1

/

2
)

L(f\otimes \chi ,1/2)

are non-zero, and indeed bounded from below; there exist many characters

χ
\chi

for which the central

L
L

-value is very large; the probability of a large analytic rank decays exponentially fast. We finally show how the second moment estimate establishes a special case of a conjecture of Mazur and Rubin concerning the distribution of modular symbols.
NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration
Authors: Abid Dhoha , Brent Michael R
Published: January 2023

Motivation

Many methods have been proposed for mapping the targets of transcription factors (TFs) from gene expression data. It is known that combining outputs from multiple methods can improve performance. To date, outputs have been combined by using either simplistic formulae, such as geometric mean, or carefully hand-tuned formulae that may not generalize well to new inputs. Finally, the evaluation of accuracy has been challenging due to the lack of genome-scale, ground-truth networks.

Results

We developed NetProphet3, which combines scores from multiple analyses automatically, using a tree boosting algorithm trained on TF binding location data. We also developed three independent, genome-scale evaluation metrics. By these metrics, NetProphet3 is more accurate than other commonly used packages, including NetProphet 2.0, when gene expression data from direct TF perturbations are available. Furthermore, its integration mode can forge a consensus network from gene expression data and TF binding location data.

Availability and implementation

All data and code are available at https://zenodo.org/record/7504131#.Y7Wu3i-B2x8.

Supplementary information

Supplementary data are available at Bioinformatics online.
How to optimally sample a sequence for rapid analysis
Authors: Frith Martin C , Shaw Jim , Spouge John L
Published: January 2023

Motivation

We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimizers, syncmers and minimally overlapping words, were developed by heuristic intuition, and are not optimal.

Results

We present a sequence-sampling approach that provably optimizes sensitivity for a whole class of sequence comparison methods, for randomly evolving sequences. It is likely near-optimal for a wide range of alignment-based and alignment-free analyses. For real biological DNA, it increases specificity by avoiding simple repeats. Our approach generalizes universal hitting sets (which guarantee to sample a sequence at least once) and polar sets (which guarantee to sample a sequence at most once). This helps us understand how to do rapid sequence analysis as accurately as possible.

Availability and implementation

Source code is freely available at https://gitlab.com/mcfrith/noverlap.

Supplementary information

Supplementary data are available at Bioinformatics online.
Third-generation computational approaches for genetic variant interpretation
Authors: Costain Gregory , Andrade Danielle M
Published: January 2023

This scientific commentary refers to ‘Delineation of functionally essential protein regions for 242 neurodevelopmental genes’ by Iqbal et al. (https://doi.org/10.1093/brain/awac381).
Android Malware Detection in Bytecode Level Using TF-IDF and XGBoost
Authors: Ozogur Gokhan , Erturk Mehmet Ali , Gurkas Aydin Zeynep , Aydin Muhammed Ali
Published: January 2023

Android is the dominant operating system in the smartphone market and there exists millions of applications in various application stores. The increase in the number of applications has necessitated the detection of malicious applications in a short time. As opposed to dynamic analysis, it is possible to obtain results in a shorter time in static analysis as there is no need to run the applications. However, obtaining various information from application packages using reverse engineering techniques still requires a substantial amount of processing power. Although some attempts have been made to solve this problem by analyzing binary files without decoding the source code, there is still more work to be done in this area. In this study, we analyzed the applications in bytecode level without decoding the binary source files. We proposed a model using Term Frequency - Inverse Document Frequency (TF-IDF) word representation for feature extraction and Extreme Gradient Boosting (XGBoost) method for classification. The experimental results show that our model classifies a given application package as a malware or benign in 2.75 s with 99.05% F1-score on a balanced dataset, and in 3.30 s with 99.35% F1-score on an imbalanced dataset containing obfuscated malwares.
Connecting the Young: High School Graduates’ Matching to First Jobs in Booms and Great Recessions
Authors: Hensvik Lena , Müller Dagmar , Skans Oskar Nordström
Published: January 2023

Using Swedish economy-wide data, we examine the relationship between business-cycle conditions and the use of social contacts in the process where young workers are matched to their first real jobs. We measure social contacts acquired during paid work during high school, and we rely on interacted class-establishment fixed-effect models to isolate the effects of interest. One-third of post-graduation matches are formed at establishments where youths worked during their studies. Graduates are much more likely to match with sites to which adult co-workers from these jobs have relocated. The importance of these job-finding channels is strongly counter-cyclical for young labour market entrants.
Routine use of percutaneous femoral cannulation in minimally invasive cardiac surgery
Authors: Ma Kristina , Kastengren Mikael , Svenarud Peter , Green Ram , Dalén Magnus
Published: January 2023

OBJECTIVES

Large series of percutaneous femoral access for extracorporeal circulation in minimally invasive cardiac surgery (MICS) are scarcely reported.

METHODS

This is a single-centre study describing the use of percutaneous femoral access in patients undergoing MICS via minithoracotomy. Femoral artery closure was performed with a plug-based closure device. To reduce the risk for vascular complications, intraoperative ultrasound assessment of correct deployment of the arterial closure device was done during the later period of the study.

RESULTS

During a 5-year period, 650 patients underwent percutaneous femoral cannulation and decannulation with device closure of the femoral artery puncture. Two hundred and seven patients (31.8%) were operated in the early phase of the experience (August 2017–August 2019), without the use of intraoperative ultrasound assessment of closure device deployment. During the later period of our experience (August 2019–September 2022), 443 patients (68.2%) were operated, of whom all underwent intraoperative ultrasound assessment of closure device deployment. Of the patients operated without intraoperative ultrasound assessment, 6 patients (2.9%) experienced vascular complications compared with none of the patients in whom intraoperative ultrasound-assessment was used (P < 0.001). In total, 15 patients (2.3%) underwent conversion to surgical cutdown owing to incomplete haemostasis or femoral artery stenosis/occlusion and the mechanism was intravascular deployment of the closure device in all 15 cases.

CONCLUSIONS

Percutaneous femoral access in MICS is safe and the need for surgical cutdown was infrequent. The risk for vascular complications is minimized with the use of intraoperative ultrasound assessment of the correct positioning of the vascular closure device.

CLINICAL TRIAL REGISTRATION NUMBER

http://www.clinicaltrials.gov; Unique identifier: NCT05462769.
Outcomes of the modified Yacoub aortocoronary flap technique for ‘non-separable’ single sinus coronary arteries with intramural course in the neonatal arterial switch operation
Authors: Van den Eynde Jef , van der Palen Roel L F , Knobbe Ingmar , Straver Bart , Stöger Lauran , Ricciardi Gabriella , Konings Thelma C , Jongbloed Monique R M , Hazekamp Mark G
Published: January 2023

OBJECTIVES

Coronary transfer remains the most crucial part of the arterial switch operation (ASO); yet, certain coronary anatomies prohibit the use of button or trap-door transfer techniques. In the rare setting of ‘non-separable’ single sinus coronary arteries with intramural course, the modified Yacoub aortocoronary flap technique is a viable option. The aim of this study is to describe this operative technique and review its early- and mid-term outcomes.

METHODS

This retrospective analysis included all cases with ‘non-separable’ single sinus coronary arteries with intramural course where the modified Yacoub aortocoronary flap technique served as a bail-out option.

RESULTS

Of 516 patients who underwent ASO at our institution between January 1977 and April 2022, 14 underwent the modified Yacoub aortocoronary flap technique. The median age at ASO was 10 (interquartile range 7–19) days. Hospital mortality occurred in 3 patients (21.4%), all being related to coronary complications. All hospital survivors were still alive at a median of 9.1 (interquartile range 4.2–18.3) years after the ASO. None of them developed complaints of ischaemia, ventricular arrhythmias, ventricular dysfunction or exercise intolerance. Surveillance computed tomography angiography showed stable aortocoronary relationships free from stenosis, compression and kinking. No reoperations for coronary artery problems and/or neoaortic valve or root problems were needed.

CONCLUSIONS

Although close monitoring of early coronary events seems crucial to prevent perioperative mortality, the modified Yacoub aortocoronary flap technique may serve as a viable bail-out option in patients with ‘non-separable’ single sinus coronary anatomy with intramural course, with excellent results among hospital survivors.
Temporal trends in the incidence of malignancy in heart failure: a nationwide Danish study
Authors: Bruhn Jonas , Malmborg Morten , Garred Caroline H , Ravn Pauline , Zahir Deewa , Andersson Charlotte , Gislason Gunnar , Torp-Pedersen Christian , Kragholm Kristian , Fosbol Emil , Butt Jawad H , Lang Ninian N , Petrie Mark C , McMurray John , Kober Lars , Schou Morten
Published: January 2023

Aims

Cancer and heart failure (HF) share risk factors, pathophysiological mechanisms, and possibly genetics. Improved HF survival may increase the risk of cancer due to a competing risk. Whether the incidence of cancer has increased over time in patients with HF as survival has improved is unclear. Therefore, temporal trends of new onset cancer in HF patients between 1997 and 2016 were investigated.

Methods and results

Using Danish nationwide registers, 103 711 individuals alive, free of cancer, and aged 30–80 years 1 year after HF diagnosis (index date) were included between 1 January 1997 and 31 December 2016. A five-year incidence rate of cancer for each year after index date was calculated. The median age and proportion of women at the index date decreased with advancing calendar time [1997–2001: 70.3 interquartile range (Q1–Q3 62.5–75.7), 60.9% men; 2012–16: 67.6 (59.2–73.8), 67.5% men]. The five-year incidence rate of cancer was 20.9 and 20.2 per 1,000 person-years in 1997 and 2016, respectively. In a multivariable Cox regression model, the hazard rates between index years 1997 (reference) and 2016 were not significantly different [hazard ratio 1.09 (0.97–1.23)]. The five-year absolute risk of cancer did not change with advancing calendar year, going from 9.0% (1997–2001) to 9.0% (2012–16). Five-year cumulative incidence of survival for HF patients increased with advancing calendar year, going from 55.9% (1997–2001) to 74.3% (2012–2016).

Conclusion

Although cancer rates during 1997–2016 have remained stable within 1–6 years after the HF diagnosis, long-term survival following a HF diagnosis has increased significantly.
Combination of current and new electrocardiographic-based criteria: a novel score for the discrimination of left bundle branch capture
Authors: Briongos-Figuero Sem , Estévez-Paniagua Álvaro , Sánchez-Hernández Ana , Muñoz-Aguilera Roberto
Published: January 2023

Aims

Most of the criteria used to diagnose direct capture of the left bundle branch (LBB) have never been validated in an external sample. We hypothesized that lead aVL might add relevant information, and the combination of several electrocardiograph (ECG)-based criteria might discriminate better LBB capture from left ventricular septal (LVS) capture, than each criterion separately.

Methods and results

Single-centre study involving all consecutive patients who received LBB area pacing. LBB capture was defined according to QRS morphology transition criteria during decremental pacing. Multivariate logistic regression analysis was performed to develop a predictive score for LBB capture. A total of 71 patients with confirmed LBB capture were analysed. The optimal cut-off values of R wave peak time (RWPT) in lead V6 (V6-RWPT) and V6-V1 interpeak interval for the discrimination of LBB capture were <83 ms and ≥33 ms, respectively. The RWPT in lead aVL (aVL-RWPT) showed a good discrimination power for the differential diagnosis of LBB capture and LVS capture. The optimal value for aVL-RWPT was 79 ms [sensitivity (SN) and specificity (SP) of 71.2% and 88.4%, respectively]. A new score, with a good diagnostic performance (area under the curve of 0.976), was constructed gathering the information from V6-RWPT, aVL-RWPT, and V6-V1 interpeak interval. The optimal score of 3 points showed a SN and SP of 89.2% and 100%, respectively for the differentiation of LBB capture.

Conclusions

ECG-based criteria are useful to confirm the capture of the LBB. The combination of V6-RWPT, aVL-RWPT, and V6-V1 interpeak interval values demonstrated better diagnostic performance than isolated measurements.
Cost-effectiveness analysis of cardiac implantable electronic devices with reactive atrial-based antitachycardia pacing
Authors: Noda Takashi , Ueda Nobuhiko , Tanaka Yuji , Ishiguro Yoko , Matsumoto Tomoko , Uenishi Tatsuhiro , Yamaguchi Hiroko , Shoji Ayako , Myung Jae-Eun , Kusano Kengo
Published: January 2023

Aims

Reactive atrial-based anti-tachycardia pacing (rATP) in pacemakers (PMs) and cardiac resynchronization therapy defibrillators (CRT-Ds) has been reported to prevent progression of atrial fibrillation, and this reduced progression is expected to decrease the risk of complications such as stroke and heart failure (HF). This study aimed to assess the cost-effectiveness of rATP in PMs and CRT-Ds in the Japanese public health insurance system.

Methods and results

We developed a Markov model comprising five states: bradycardia, post-stroke, mild HF, severe HF, and death. For devices with rATP and control devices without rATP, we compared the incremental cost-effectiveness ratio (ICER) from the payer's perspective. Costs were estimated from healthcare resource utilisation data in a Japanese claims database. We evaluated model uncertainty by analysing two scenarios for each device. The ICER was 763 729 JPY/QALY (5616 EUR/QALY) for PMs and 1,393 280 JPY/QALY (10 245 EUR/QALY) for CRT-Ds. In all scenarios, ICERs were below 5 million JPY/QALY (36 765 EUR/QALY), supporting robustness of the results.

Conclusion

According to a willingness to pay threshold of 5 million JPY/QALY, the devices with rATP were cost-effective compared with control devices without rATP, showing that the higher reimbursement price of the functional categories with rATP is justified from a healthcare economic perspective.
Induction and sustenance of antibacterial activities distinguishes response of mice toSalmonellaTyphi from response toSalmonellaTyphimurium
Authors: Yadav Jitender , Qadri Ayub
Published: January 2023

Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid in humans, shares a high degree of homology with a closely related serovar, S. Typhimurium. Yet, unlike S. Typhimurium, S. Typhi does not establish infection in mice, the reasons for which are not well understood. Here, we present evidence that the response of mice to infection with S. Typhi is marked by early antibacterial activities. Cell-free peritoneal fluids from S. Typhi but not S. Typhimurium—infected mice inhibited the replication of Salmonella ex vivo. The production of this activity was reduced in the presence of the serine protease inhibitor, phenylmethylsulfonlyl fluoride (PMSF). PMSF also inhibited the generation of antibacterial activity released from in vitro S. Typhi—infected peritoneal macrophages in a cell death—dependent manner. Infection with S. Typhimurium but not S. Typhi was associated with reduction in the mRNA levels of iron-regulating molecules, ferroportin and lipocalin. These results suggest that early induction and sustenance of antibacterial activities may contribute to the nonestablishment of infection with S. Typhi in mice.
A functional spectrum of PROKR2 mutations identified in isolated hypogonadotropic hypogonadism
Authors: Wang Xinying , Chen Danna , Zhao Yaguang , Men Meichao , Chen Zhiheng , Jiang Fang , Zheng Ruizhi , Stamou Maria I , Plummer Lacey , Balasubramanian Ravikumar , Li Jia-Da
Published: January 2023

Isolated hypogonadotropic hypogonadism (IHH) is a rare disease with hypogonadism and infertility caused by the defects in embryonic migration of hypothalamic gonadotropin-releasing hormone (GnRH) neurons, hypothalamic GnRH secretion or GnRH signal transduction. PROKR2 gene, encoding a G-protein coupled receptor PROKR2, is one of the most frequently mutated genes identified in IHH patients. However, the functional consequences of several PROKR2 mutants remain elusive. In this study, we systematically analyzed the Gαq, Gαs and ERK1/2 signaling of 23 IHH-associated PROKR2 mutations which are yet to be functionally characterized. We demonstrate that blockage of Gαq, instead of MAPK/ERK pathway, inhibited PROK2-induced migration of PROKR2-expressing cells, implying that PROKR2-related IHH results primarily due to Gαq signaling pathway disruption. Combined with previous reports, we categorized a total of 63 IHH-associated PROKR2 mutations into four distinct groups according Gαq pathway functionality: (i) neutral (N, >80% activity); (ii) low pathogenicity (L, 50–80% activity); (iii) medium pathogenicity (M, 20–50% activity) and (iv) high pathogenicity (H, <20% activity). We further compared the cell-based functional results with in silico mutational prediction programs. Our results indicated that while Sorting Intolerant from Tolerant predictions were accurate for transmembrane region mutations, mutations localized in the intracellular and extracellular domains were accurately predicted by the Combined Annotation Dependent Depletion prediction tool. Our results thus provide a functional database that can be used to guide diagnosis and appropriate genetic counseling in IHH patients with PROKR2 mutations.
Routine double-ovarian-stimulation (DuoStim) in poor responders lacks rationale, evidence, and follow-up
Authors: Tocci Angelo , Barad David , Łukaszuk Krzysztof , Orvieto Raoul
Published: January 2023

Double ovarian stimulation (DuoStim), initially only suggested for fertility preservation in cancer patients, is now increasingly also used in routine clinical IVF, especially in poor responders. The claimed rational for this is the alleged existence of multiple follicular waves in a single intermenstrual interval, allowing for retrieval of more oocytes in a single IVF cycle. This commentary argues that this expansion of purpose lacks rationale, evidence, and follow-up. Consequently, we suggest that, unless valid clinical indications have been established, DuoStim be only subject of controlled clinical trials with appropriate experimental consents.