bluuebunny/crossref_metadata_2025_split huggingface dataset:
A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes
Authors: Ritch Elie J. , Herberts Cameron , Warner Evan W. , Ng Sarah W. S. , Kwan Edmond M. , Bacon Jack V. W. , Bernales Cecily Q. , Schönlau Elena , Fonseca Nicolette M. , Giri Veda N. , Maurice-Dror Corinne , Vandekerkhove Gillian , Jones Steven J. M. , Chi Kim N. , Wyatt Alexander W. 
Published: March 2023

AbstractSpecific classes of DNA damage repair (DDR) defect can drive sensitivity to emerging therapies for metastatic prostate cancer. However, biomarker approaches based on DDR gene sequencing do not accurately predict DDR deficiency or treatment benefit. Somatic alteration signatures may identify DDR deficiency but historically require whole-genome sequencing of tumour tissue. We assembled whole-exome sequencing data for 155 high ctDNA fraction plasma cell-free DNA and matched leukocyte DNA samples from patients with metastatic prostate or bladder cancer. Labels for DDR gene alterations were established using deep targeted sequencing. Per sample mutation and copy number features were used to train XGBoost ensemble models. Naive somatic features and trinucleotide signatures were associated with specific DDR gene alterations but insufficient to resolve each class. Conversely, XGBoost-derived models showed strong performance including an area under the curve of 0.99, 0.99 and 1.00 for identifying BRCA2, CDK12, and mismatch repair deficiency in metastatic prostate cancer. Our machine learning approach re-classified several samples exhibiting genomic features inconsistent with original labels, identified a metastatic bladder cancer sample with a homozygous BRCA2 copy loss, and outperformed an existing exome-based classifier for BRCA2 deficiency. We present DARC Sign (DnA Repair Classification SIGNatures); a public machine learning tool leveraging clinically-practical liquid biopsy specimens for simultaneously identifying multiple types of metastatic prostate cancer DDR deficiencies. We posit that it will be useful for understanding differential responses to DDR-directed therapies in ongoing clinical trials and may ultimately enable prospective identification of prostate cancers with phenotypic evidence of DDR deficiency.
K‐Go: An executable formal semantics of Go language in K framework
Authors: Zhao Can , Liu Qin , Hu Zonghua , Yu Ze , Wang Dejun , Meng Bo 
Published: March 2023

AbstractGo is a relatively new programming language and has become one of the most important programming languages used widely in blockchain. A formal semantics plays an important role in program synthesis, analysis and verification. The existed formal semantics of Go are not executable and do not cover the core features, hence, this paper presents an executable formal semantics for Go, called K‐Go, using rewriting logic in framework to make sure the semantics is both executable and applicable. K‐Go includes syntax, configuration and rules and covers the declaration and definition of basic types, basic expression, concurrency, main statement data reading and writing based on channel. K‐Go is validated by test set with 100% semantic coverage based on the official test suite. The evaluation experiment shows that K‐Go is correct. Using formal semantics of Go language, building Go program synthesis, analysis and verification tools is easy for analyzing more characteristics of Go programs.
Optical/X-ray/radio view of Abell 1213: A galaxy cluster with anomalous diffuse radio emission
Authors: Boschin W. , Girardi M. , De Grandi S. , Riva G. , Feretti L. , Giovannini G. , Govoni F. , Vacca V. 
Published: March 2023

Context. Abell 1213, a low-richness galaxy system, is known to host an anomalous radio halo detected in data of the Very Large Array (VLA). It is an outlier with regard to the relation between the radio halo power and the X-ray luminosity of the parent clusters.
Aims. Our aim is to analyze the cluster in the optical, X-ray, and radio bands to characterize the environment of its diffuse radio emission and to shed new light on its nature.
Methods. We used optical data from the Sloan Digital Sky Survey to study the internal dynamics of the cluster. We also analyzed archival XMM-Newton X-ray data to unveil the properties of its hot intracluster medium. Finally, we used recent data from the LOw Frequency ARray (LOFAR) at 144 MHz, together with VLA data at 1.4 GHz, to study the spectral behavior of the diffuse radio source.
Results. Both our optical and X-ray analysis reveal that this low-mass cluster exhibits disturbed dynamics. In fact, it is composed of several galaxy groups in the peripheral regions and, in particular, in the core, where we find evidence of substructures oriented in the NE–SW direction, with hints of a merger nearly along the line of sight. The analysis of the X-ray emission adds further evidence that the cluster is in an unrelaxed dynamical state. At radio wavelengths, the LOFAR data show that the diffuse emission is ∼510 kpc in size. Moreover, there are hints of low-surface-brightness emission permeating the cluster center.
Conclusions. The environment of the diffuse radio emission is not what we would expect for a classical halo. The spectral index map of the radio source is compatible with a relic interpretation, possibly due to a merger in the N–S or NE–SW directions, in agreement with the substructures detected through the optical analysis. The fragmented, diffuse radio emissions at the cluster center could be attributed to the surface brightness peaks of a faint central radio halo.
Sohlenabszess (Pododermatitis purulenta superficialis) bei einem
Trampeltier – Diagnostik, Therapie und Heilungsverlauf
Authors: Eibl Cassandra , Schoiswohl Julia , Kofler Johann 
Published: March 2023

ZusammenfassungEine ca. 14 Jahre alte Trampeltierstute wurde mit einer seit 2 Wochen bestehenden
Lahmheit an der linken Hinterextremität an der Klinik vorgestellt. Die
Befunde der allgemeinen klinischen Untersuchung waren in der Norm. Bei der
orthopädischen Untersuchung wurde eine deutliche Entlastungsstellung der
linken Hinterextremität mit Schonung der lateralen Zehe im Stand und
eine Stützbeinlahmheit 2. Grades (2 aus 5) hinten links im Schritt
festgestellt. Für die anschließenden Untersuchungen wurde das
Trampeltier sediert (0,24 mg/kg KGW Xylazin
i.m.+1,92 mg/kg KGW Ketamin
i.m.+0,04 mg/kg Butorphanol i.m.) und in Seitenlage
abgelegt. Die sonografische Untersuchung des Sohlenkissens an der linken
Hinterextremität zeigte einen 11×2,3 cm großen
Abszess mit inhomogener z.T. anechoischer, z.T. hypoechoischer
Echogenität, welcher an beiden Zehen, mit stärkerer
Ausprägung im Bereich der lateralen Zehe, zwischen dem Sohlenhorn und
dem lateralen und medialen Sohlenkissen lokalisiert war. Unter lokaler
Infiltrationsanästhesie wurde der Abszess durch einen ca.
5×5 cm großen Zugang im Sohlenhorn zentral an der Sohle
eröffnet und die Abszesshöhle kürettiert und
gespült. Die freigelegte Sohlenlederhaut war nach 6 Wochen von
neugebildetem Horn vollständig bedeckt. In der postoperativen Nachsorge
waren Verbandwechsel ca. alle 3–7 Tage notwendig, wofür das
Trampeltier jeweils sediert werden musste. Die Dosierung für Xylazin
wurde dabei anfangs weiterhin wie oben angegeben beibehalten, konnte
zwischenzeitlich geringgradig reduziert werden (0,20 mg/kg KGW
i.m.) und musste für die letzten Verbandswechsel wieder erhöht
werden (0,22 mg/kg KGW i.m.). Die Dosierung für Ketamin
konnte hingegen geringgradig reduziert (1,51 mg/kg KGW i.m.)
werden. Dadurch ließ sich eine deutliche Reduktion der Dauer der
Nachschlafphase erreichen. Nach 6 Wochen Hospitalisierung konnte das Trampeltier
lahmheitsfrei entlassen werden und zudem hatte sich bereits wieder eine neue und
belastbare Sohlenhornschicht gebildet.
Contraceptives and Thrombosis: An Intertwined Revolutionary Road
Authors: Barcellona Doris , Marongiu Francesco , Grandone Elvira 
Published: March 2023

AbstractThe development of oral contraceptives (OCs) began in 1921 and continued in the following years until the first regulatory approval from the Food and Drug Administration was granted in 1960. However, it took several years to realize that OCs presented an important but not frequent risk of venous thrombosis. Several reports ignored this dangerous effect and only in 1967 the Medical Research Council clearly stated this as an important risk. Later, research led to the formulation of second-generation OCs containing progestins, which nevertheless presented an increased thrombotic risk. In early 1980s, OCs containing third-generation progestins were introduced into the market. Only in 1995, it became clear that these new compounds induced a higher thrombotic risk than that related to the second-generation progestins. It appeared clear that the modulating action of progestins was against the procoagulant activity of estrogens. Lastly, at the end of the 2000s, OCs containing natural estrogens and a fourth-generation progestin (dienogest) became available. The prothrombotic effect of those natural products was not different from that of preparations containing second-generation progestins. Moreover, research over the years has produced much data on risk factors associated with OCs use such as age, obesity, cigarette smoking, and thrombophilia. These findings allowed us to better assess the individual thrombotic risk (both arterial and thrombotic) of each woman before offering an OC. Furthermore, research has shown that in high-risk people the use of single progestin is not dangerous as far as thrombosis is concerned. In conclusion, the OCs road has been long and difficult but has led to a great and unthinkable scientific and social enrichment since the 1960s.
Determination of nuclear level density based on a fully microscopic statistical partition function method for58Ni
Authors: Sepiani M , Nasrabadi M N 
Published: March 2023

AbstractNuclear level density (NLD) is calculated using the statistical partition function method for58Ni. The microscopic recursive approach based on the realistic single particle levels schemes obtained from various nuclear potentials is used to remove various simplifying approximations and accurately determine the NLD. The effect of these approximations is determined by comparing the results of this method with the usual and common calculations of the Fermi gas model. It is shown that such a fully microscopic approach represents the NLD behavior according to the available experimental data.
The effect of body position change on noninvasively acquired intracranial pulse waves
Authors: Boraschi Andrea , Spiegelberg Andreas , Karimi Fariba , Graf Kevin , Fallahi Arya , Neufeld Esra , Kuster Niels , Kurtcuoglu Vartan 
Published: March 2023

Abstract

Objective. Craniospinal compliance (CC) is an important metric for the characterization of space-occupying neurological pathologies. CC is obtained using invasive procedures that carry risks for the patients. Therefore, noninvasive methods for acquiring surrogates of CC have been proposed, most recently based on changes in the head’s dielectric properties during the cardiac cycle. Here, we have tested whether changes in body position, which are known to influence CC, are reflected in a capacitively acquired signal (hereinafter referred to as W) originating from dynamic changes of the head’s dielectric properties. Approach. eighteen young healthy volunteers were included in the study. After 10 min in supine position, subjects were tilted head-up (HUT), back to 0° (horizontal, control), and then head-down (HDT). Metrics related to cardiovascular action were extracted from W, including AMP, the peak-to-valley amplitude of the cardiac modulation of W. Computational electromagnetic simulations were performed to probe the association between intracranial volume change and W. Main results. AMP decreased during HUT (0°: 2869 ± 597 arbitrary units (au); +75°: 2307 ± 490 au, P = 0.002) and increased during HDT (−30°: 4403 ± 1428 au, P < 0.0001). The same behavior was predicted by the electromagnetic model. Significance. tilting affects the distribution of CC between cranial and spinal compartments. Cardiovascular action induces compliance-dependent oscillatory changes in the intracranial fluid composition, which causes corresponding variations in the head’s dielectric properties. These manifest as increasing AMP with decreasing intracranial compliance, which suggests that W may contain information related to CC, and that it might be possible to derive CC surrogates therefrom.
Investigation of trap characteristics under the inverse piezoelectric effect in AlGaN/GaN HEMT devices at room temperature and low temperature
Authors: Yao Zhiwen , Zhu Hui , Li Yilin , Xie Na , Sun Yerong , Zhang Yiqun , Liu Xing , Zhang Zhirang 
Published: March 2023

Abstract
Changes in the electrical properties and the trap characteristics of AlGaN/GaN high electron mobility transistors under the application of reverse bias stress at both room temperature and low temperature were investigated. When the critical stress voltage was reached, the gate current, which complied with the Poole–Frenkel conduction conditions, showed an abrupt increase. Furthermore, the magnitude of the critical stress voltage for occurrence of the inverse piezoelectric effect can be increased at 83 K. The transient current method was used to establish that the detrapping peak amplitudes of the traps increased, but the trap activation energy remained unchanged. The changes observed in both the time constant spectra and the pulsed current–voltage curves confirmed that the trap densities in the AlGaN barrier layer increased as a result of the inverse piezoelectric effect. However, the different degrees to which the numbers of traps increased at room temperature and at 83 K contributed to the occurrence of different degradations in the device.
Negative refraction in multilayered metal-dielectric metamaterials with ellipse-like isofrequence surfaces
Authors: Zhou Zhiyuan , Wang Xiao 
Published: March 2023

Abstract
Negative refraction in multilayered metal-dielectric metamaterials is usually based on negative refractive indices or hyperbolic-like isofrequency surfaces. In this study, we reveal that ellipse-like isofrequency surfaces can also lead to negative refraction. This phenomenon is theoretically demonstrated by analyzing the group velocities of refracted beams based on the exact transfer-matrix method and verified by numerical simulation based on the finite-element method. The corresponding physics mechanism is investigated through the energy flow of the ellipse-like modes in the metallic and dielectric layers. The results are also compared with the case of energy flow of hyperbolic-like modes. Moreover, negative double refraction is realized because negatively refracted beams can be enabled by ellipse-like and hyperbolic-like isofrequency surfaces simultaneously.
Data-driven discovery of Caputo fractional order systems
Authors: Fan Xuemeng , Wu Cong 
Published: March 2023

Abstract
Due to the peculiar non-locality of fractional order differential and integral operators, Caputo fractional order systems are harder than integer order systems to be discoverd from data. To solve this open problem, we propose a framework of method capable of discovering Caputo fractional order (autonomous and non-autonomous) systems from measurable data. The interior point method and genetic algorithm are embedded respectively in the framework. The former is mainly presented in text, while the latter is implemented for comparison and validation. The framework is designed to dynamically and coordinately update the fractional order and vector field function for the system to be discovered till the difference between the measured and discovered systems is minimized. It is computationally efficient, robust and illustrated by discovering the Caputo fractional order Lorenz system, Chua’s circuit and Duffing’s oscillator hidden in measured data. As thus, this work provides one way to uncover underlying Caputo fractional order mathematical models (or physical laws and governing equations).
Population density gratings produced by a pair of nonharmonic unipolar rectangular attosecond pulses in a resonant medium
Authors: Diachkova O O , Arkhipov R M , Arkhipov M V , Pakhomov A V , Rosanov N N 
Published: March 2023

Abstract
Recently, the possibility of obtaining non-harmonic unipolar electromagnetic pulses with a specific electric field strength’s dependence on time (e.g. a rectangular pulse) has been actively discussed in optics. Unipolar pulses have a nonzero electric area and a wide spectrum: from zero frequency up to the visible region. This could open up wide application of such pulses, for example, for faster and more efficient control of the quantum systems’ properties with a high temporal resolution compared to conventional bipolar multicycle pulses. In this paper, based on an approximate solution of the time dependent Schrödinger equation and a numerical solution of the equation system for the density matrix, we show the possibility of creating electromagnetically induced population density gratings in an atomic medium using a pair of unipolar rectangular attosecond light pulses that do not overlap in the medium. The formation of such gratings can be explained on the basis of the concept of ‘interference’ of electric pulse areas, recently introduced into optics.
Constant-tune cyclotrons
Authors: Planche Thomas 
Published: March 2023

Abstract
In this paper we demonstrate that cyclotrons can be made to
have precisely constant betatron tunes over wide energy ranges. In
particular, we show that the horizontal tune can be made constant
and does not have to follow the Lorentz factor γ, while still
perfectly satisfying the isochronous condition. To make this
demonstration we developed a technique based on the calculation of
the betatron tunes entirely from the geometry of realistic
non-hard-edge closed orbits. We present two particular cyclotron
designs, one compact cyclotron and one ring cyclotron. The compact
cyclotron design is backed up by a 3-dimensional finite element
magnet calculation, that we also present here.
Coupling resonance correction and avoidance for the TRIUMF 500 MeV cyclotron
Authors: Rao Yi-Nong , Zhang Lige 
Published: March 2023

Abstract
The linear coupling resonance νr
- νz
= 1 in a cyclotron
is driven by the first harmonic in the radial gradient of the radial
magnetic field. In the TRIUMF 500 MeV cyclotron, this resonance is
encountered multiple times. When the circulating beam is
off-centred radially passing through the resonance, the radial
betatron oscillation can be converted into vertical oscillation,
which can cause beam losses and radio-activation. We investigated
this resonance with goal to correct it by using the available
harmonic correction coils. Moreover, we improved the cyclotron
vertical tune measurement by using trim coils to create a flat-top
radial field, and thus confirmed an extra νr
- νz
= 1 coupling
resonance passage as this is unexpected from the historical tune
diagram. To avoid this passage, the local vertical tune is adjusted
to stay farther away from the resonance line by using the trim coils
axial field, but at the cost of a local excursion in
isochronism. After the correction and the avoidance of this
resonance, both the coherent and incoherent vertical oscillations
are decreased, thus helping to reduce the machine tank spills under
high intensity operation. In this paper, we present the results of
calculations and simulations as well as measurements that we
undertook.
Redundant field survey data of cyclotron with imperfect median plane
Authors: Zhang L.G. , Rao Y.-N. 
Published: March 2023

Abstract
An accurate and detailed field map is important for
cyclotron beam dynamics studies. During the long history of
cyclotron studies, many techniques have been developed by cyclotron
pioneers for the treatment of median plane field map. In this paper,
we take the TRIUMF 500 MeV cyclotron as an example to study the
asymmetric field resulting from imperfect median plane symmetry. The
“Gordon approach” and a highly accurate compact finite
differentiation method are used to investigate the historical field
survey data. The redundancy in the survey data is revealed by the
expansion method, which also makes it possible to correct the error
in the measurement. Finally, both the azimuthal field Bθ
and
the axial gradient of the axial field dBz
/dz in the median plane
are corrected using the radial field map Br
. The influence of the
correction is examined by recalculating the equilibrium orbit
properties of the TRIUMF cyclotron. The result shows significantly
increased vertical centering errors of the closed orbits. A further
simulation study suggests that these centering errors can be reduced
to below 1.5 cm by adjusting the trim coils' Br
field within the
output limits of our trim coils' power supplies. The error in the
measurement field data may explain why the calculated trim coils'
settings during the cyclotron commissioning in 1974 encountered
difficulty.
Lorentz dissociation of hydrogen ions in a cyclotron
Authors: Koay Hui Wen 
Published: March 2023

Abstract
Stripping extraction of hydrogen molecular ions has gained
interest in the cyclotron industry due to its high extraction
efficiency. However, the magnetic field could result in undesired
Lorentz dissociation of the hydrogen anion/molecular ions during
acceleration. Studies of dissociation under electric fields
comparable to that of a Lorentz-transformed magnetic field in a
typical cyclotron (a few MV/cm) are sparse. Hence, in order to fill
in the missing yet crucial information when designing a cyclotron,
this work compiles and summarizes the study of Lorentz dissociation
of H-, H+
2 and H+
3 for stripping extraction in a
cyclotron.
Editorial announcements and information — ICFA Beam Dynamics Newsletter No. 84
Authors: Cai Yunhai , Baartman Rick 
Published: March 2023

Abstract
This is a general information article of the ICFA Beam
Dynamics Newsletter No. 84. It contains two forewords from the
Editor-in-Chief and the issue editor, a workshop and conference
report section, a recent Ph.D. thesis section, a forthcoming beam
dynamics events section, and a section of announcements from the
beam dynamics panel.
Cyclotrons: Why/how are their dynamics different?
Authors: Baartman R. 
Published: March 2023

Abstract
For this issue, papers on the topic of cyclotron beam
physics have been solicited and chosen to highlight the main areas
both of historic interest and of active research. I take the
opportunity to outline the differences and similarities between
cyclotron dynamics as compared to other accelerator types. As well,
I try to introduce the major areas of interest, referring to papers
in this issue, as appropriate.
Long term operations experience with TR30 compact cyclotrons
Authors: Cojocaru G. 
Published: March 2023

Abstract
Negative ions compact cyclotrons serve many applications and
are known to be effective due to their simple and efficient
extraction as well as the large circulating currents without the
requirement of separated turns. TR30s are compact cyclotrons that
have continued to experience impressive technological advances over
the last few decades, driven primarily by medical isotope production
needs. Their space charge limits are in the range of 1 to 2 mA, and
we explored the combination of our machines' age and the challenges
of maintaining their performances. Certain subsystems are detailed
with specific examples from more than 30 years of around-the-clock,
quasi continuous operations with TR30 cyclotrons. The subsystems'
failures and their part in the overall downtime will be presented.