bluuebunny/crossref_metadata_2025 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

Specific 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.
Inorganic non-carbon supported Pt catalysts and synergetic effects for oxygen reduction reaction
Authors: Sun Qi , Li Xin-Hao , Wang Kai-Xue , Ye Tian-Nan , Chen Jie-Sheng
Published: March 2023

In oxygen reduction reaction, Pt/C catalysts are prone to carbon corrosion, resulting in reduced activity. The use of non-carbon inorganic supports not only improves corrosion resistance, but also provides synergetic effects to increase activity and stability.
Detection and quantification of anthropogenic titanium-, cerium-, and lanthanum-bearing home dust particles
Authors: Nabi Md Mahmudun , Wang Jingjing , Baalousha Mohammed
Published: March 2023

Anthropogenic nanoparticles were identified in home dust samples collected from the surface of heating, ventilation, and air conditioning (HVAC) filters from eleven homes at different locations in Columbia, South Carolina, USA.
Interfacial interactions of humic acids with polystyrene nano-plastics in aqueous/ionic environments: a molecular dynamics exploration
Authors: Rama Prasad , Gallego-Urrea Julián A. , Abbas Zareen
Published: March 2023

TNB molecules exhibiting eco-corona on the surface of carboxylated polystyrene nano-plastic in the aquatic environment.
Exploration of the oxygen reduction reaction activity of four transition metal borates: synthesis, structure and characterization
Authors: Deng Yan-Ling , Chen An-Na , Li Wei , Xin Shu-Sheng , Pan Chun-Yang
Published: March 2023

Four new transition metal borates have been successfully synthesized. Borate-based catalysts were prepared at different temperatures and their electrocatalytic properties were explored. 1-CoB5/600 and 2-CoSB/450 exhibited ideal ORR activities.
Stop and restart of polycondensation reactions of highly reactive sol–gel precursors for nanoscale surface molding
Authors: Mizoshita Norihiro , Yamada Yuri
Published: March 2023

Reactivity-switchable sol–gel mixtures are obtained through acid-catalyzed transesterification and subsequent addition of amine compounds, which enables reproducible nanoimprinting of various organosilica and metal oxide films.
Fluid interfaces laden by force dipoles: towards active matter-driven microfluidic flows
Authors: Patel Kuntal , Stark Holger
Published: March 2023

Contractile force dipoles of active interfacial particles induce instability of the fluid–fluid interface. From the resulting viscous finger, a droplet breaks up.
Tailoring liquid crystalline self-assembly and de Vries behavior of azulenes via lateral and core substitution
Authors: Schulz Finn , Lutz Bettina , Rück Daniel , Batman Derman , Frey Wolfgang , Laschat Sabine
Published: March 2023

Variation of the mesomorphic 2-aryl-azulene core leads to SmA and SmC phases.
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

Go 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.
Guide chirurgical appliqué aux corticotomies d’accélération orthodontique sans lambeau : protocole de réalisation
Authors: Ameline Adrien , Mazoyer Christophe
Published: March 2023

Les corticotomies d’accélérations orthodontiques sont actuellement peu pratiquées, les praticiens et les patients restant réticents à cause des difficultés inhérentes à la chirurgie et des suites post-opératoires. La piézocision répond favorablement àces difficultés en proposant un protocole peu invasif, moins contraignant pour le patient tout en gardant une efficacité équivalente sur la création du Phénomène d’Accélération Régional. Toutefois, elle ne permet pas une bonne visibilité des pièges anatomiques tel que les racines dentaires. L’avènement des guides chirurgicaux dans de nombreux domaines de l’odontologie questionne sur la possibilité d’extrapoler les potentialités offertes par le numérique àla piézocision, de manière àpouvoir guider le geste du praticien et améliorer la prédictibilité de la chirurgie tout en réduisant les risques iatrogènes. Nous proposerons ici un protocole de réalisation d’un Guide de Piézocision conçu par Ordinateur (GPCO), en détaillant l’ensemble des étapes : l’élaboration du cahier des charges, le recueil des éléments cliniques, la planification numérique, la conception du guide et la fabrication par impression tridimensionnelle. Nous reprendrons ensuite l’ensemble du protocole de piézocision en utilisant le guide chirurgical.
Sohlenabszess (Pododermatitis purulenta superficialis) bei einem
Trampeltier – Diagnostik, Therapie und Heilungsverlauf
Authors: Eibl Cassandra , Schoiswohl Julia , Kofler Johann
Published: March 2023

Eine 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

The 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

Nuclear 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

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

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

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

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

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

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

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

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

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

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

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

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.
Quantum interference on the non-commutative plane and the quantum-to-classical transition
Authors: Pittaway I B , Scholtz F G
Published: March 2023

We explore a possible link between the structure of space at short length scales and the emergence of classical phenomena at macroscopic scales. To this end we adopt the paradigm of non-commutative space at short length scales and explicitly compute the outcomes of a double slit experiment and a von Neumann measurement in the non-commutative plane. A very consistent picture of a continuous quantum-to-classical transition emerges. The mechanism driving this transition is standard decoherence, which arises quite naturally from the tensor product structure of the non-commutative quantum Hilbert space. The double slit calculation enables us to establish a lower bound on the non-commutative parameter for this transition to become effective at particle numbers of the order of Avogadro’s number. Similarly, the result of the von Neumann measurement establishes a criterion involving the non-commutative parameter, apparatus size and coupling between system and apparatus for classicality to emerge.
Low-pressure-RF plasma modification of UiO-66 and its application in methylene blue adsorption
Authors: ZHOU Tian , YANG Douhao , WANG Yijun , CHENG Jiushan , CHEN Qiang , LIU Bowen , LIU Zhongwei
Published: March 2023

Defect engineering of metal-organic frameworks has attracted increasing attention in recent years for potential applications in gas storage and catalysis. In this study, defective UiO-66 is obtained by Ar and H2 plasma treatments. Compared with the pristine UiO-66, a new aperture with a size of ∼4 nm appears for a sample with the plasma modification, indicating the formation of mesopores within UiO-66 framework. Characterization results demonstrate that the pore volume, surface area and the number of Lewis and Brönsted acid sites can be easily tuned by varying the discharge parameters. The adsorption performance of UiO-66 is evaluated for the adsorption of methyl blue. In comparison to the pristine UiO-66 and the sample with H2 plasma treatment, the Ar plasma modified sample shows excellent adsorption activity due to the suitable pore size and volume. Equilibrium adsorption capacity as high as 40.6 mg·g−1 is achieved for the UiO-66 (Ar) sample.
PROSE: phenotype-specific network signatures from individual proteomic samples
Authors: Wong Bertrand Jern Han , Kong Weijia , Peng Hui , Goh Wilson Wen Bin
Published: March 2023

Proteomic studies characterize the protein composition of complex biological samples. Despite recent advancements in mass spectrometry instrumentation and computational tools, low proteome coverage and interpretability remains a challenge. To address this, we developed Proteome Support Vector Enrichment (PROSE), a fast, scalable and lightweight pipeline for scoring proteins based on orthogonal gene co-expression network matrices. PROSE utilizes simple protein lists as input, generating a standard enrichment score for all proteins, including undetected ones. In our benchmark with 7 other candidate prioritization techniques, PROSE shows high accuracy in missing protein prediction, with scores correlating strongly to corresponding gene expression data. As a further proof-of-concept, we applied PROSE to a reanalysis of the Cancer Cell Line Encyclopedia proteomics dataset, where it captures key phenotypic features, including gene dependency. We lastly demonstrated its applicability on a breast cancer clinical dataset, showing clustering by annotated molecular subtype and identification of putative drivers of triple-negative breast cancer. PROSE is available as a user-friendly Python module from https://github.com/bwbio/PROSE.
AMHMDA: attention aware multi-view similarity networks and hypergraph learning for miRNA–disease associations identification
Authors: Ning Qiao , Zhao Yaomiao , Gao Jun , Chen Chen , Li Xiang , Li Tingting , Yin Minghao
Published: March 2023

In recent years, many experiments have proved that microRNAs (miRNAs) play a variety of important regulatory roles in cells, and their abnormal expression can lead to the emergence of specific diseases. Therefore, it is greatly valuable to do research on the association between miRNAs and diseases, which can effectively help prevent and treat miRNA-related diseases. At present, effective computational methods still need to be developed to better identify potential miRNA–disease associations. Inspired by graph convolutional networks, in this study, we propose a new method based on Attention aware Multi-view similarity networks and Hypergraph learning for MiRNA-Disease Associations identification (AMHMDA). First, we construct multiple similarity networks for miRNAs and diseases, and exploit the graph convolutional networks fusion attention mechanism to obtain the important information from different views. Then, in order to obtain high-quality links and richer nodes information, we introduce a kind of virtual nodes called hypernodes to construct heterogeneous hypergraph of miRNAs and diseases. Finally, we employ the attention mechanism to fuse the outputs of graph convolutional networks, predicting miRNA–disease associations. To verify the effectiveness of this method, we carry out a series of experiments on the Human MicroRNA Disease Database (HMDD v3.2). The experimental results show that AMHMDA has good performance compared with other methods. In addition, the case study results also fully demonstrate the reliable predictive performance of AMHMDA.
On Conditional Edge-Fault-Tolerant Strong Menger Edge Connectivity Of Folded Hypercubes
Authors: Zhao Shijie , Li Pingshan
Published: March 2023

Edge connectivity is an important parameter for the reliability of the inter-connection network. A graph $G$ is strong Menger edge-connected ($SM$-$\lambda $ for short) if there exist min$\{\deg _{G}(u),\deg _{G}(v)\}$ edge-disjoint paths between any pair of vertices $u$ and $v$ of $G$. The conditional edge-fault-tolerance strong Menger edge connectivity of $G$, denoted by $sm_{\lambda }^{r}(G)$, is the maximum integer $m$ such that $G-F$ remains $SM$-$\lambda $ for any edge set $F$ with $|F|\leq m$ and $\delta (G-F)\geq r$, where $\delta (G-F)\geq r$ is the minimum degree of $G-F$. Most of the previous papers discussed $sm_{\lambda }^{r}(G)$ in the case of $r\leq 2$. In this paper, we show that $sm_{\lambda }^{r}(FQ_{n})=2^{r}(n-r+1)-(n+1)$ for $1\leq r\leq n-2$, where $n\geq 4$.
On the Removal of Asylum Seekers to Third Countries and the Scope of theEU–Turkey Readmission Agreement
Authors: Arıner Hakkı Onur , Kader Yiğit
Published: March 2023

The inclusion of asylum seekers within the scope of European Union (EU) readmission agreements signed with third countries remains contentious, especially considering that these agreements are instruments for removing irregular migrants to countries of origin or transit and do not regulate the responsibility for assessing asylum claims. Yet, the expulsion of asylum seekers from the EU to third countries is realized through a procedure whereby Member States are allowed the possibility of labelling third countries ‘safe’ according to criteria set out in EU law. The applications of asylum seekers arriving from safe third countries to the jurisdiction of the EU are deemed ‘inadmissible’, thus absolving Member States from assessing the applications on merit and enabling States to include asylum seekers within the scope of readmission agreements as irregular migrants. This article contends that the unique features of the EU–Turkey Readmission Agreement do not allow this practice in light of the main principles of international law, even assuming that Turkey can be labelled a ‘safe third country’. These features include treaty provisions obligating the sending State to make every effort to remove persons to their countries of origin, as well as Turkey’s explicitly declared position during the signing of the Agreement, which interprets the scope of the Agreement as not including asylum seekers. However, readmission of asylum seekers has taken place between the EU and Turkey through the EU–Turkey Statement of 18 March 2016 on the legal basis of the bilateral Greece–Turkey Readmission Agreement. It is argued that the EU’s attempts to institute the EU–Turkey Readmission Agreement as the legal basis for readmission of asylum seekers are destined to fail, due to the legal impossibility stemming from the said unique treaty provisions, as well as the absence of any indication from Turkey that it intends to change its initial official position in this regard.
Downregulation of RUNX1-Activated Osteopontin Facilitates Burn Wound Healing by Activating the MAPK Pathways
Authors: Ji Wei , Sun Zhibo , Yang Yanqing , Hu Meng , Zhang Qian , Fu Jie , Chen JunWei , Huang Yan , Cheng Yanyang
Published: March 2023

Burn wounds require intervention to ensure timely progression to reduce morbidity and mortality. The migrative and proliferative capabilities of keratinocytes are impaired in wounds. Matrix metalloproteinases (MMPs) can degrade the extracellular matrix (ECM), allowing epithelial cells to migrate. As reported, osteopontin can regulate cell migration, cell adhesion, and ECM invasion in endothelial and epithelial cells, and its expression is significantly increased in chronic wounds. Therefore, this study investigates the biological functions of osteopontin and its related mechanisms involved in burn wounds. We established cellular and animal models of burn injury. Levels of osteopontin, RUNX1, MMPs, collagen I, CK19, PCNA, and pathway-associated proteins were measured by RT-qPCR, western blotting, and immunofluorescence staining. Cell viability and migration were examined by CCK-8 and wound scratch assays. Histological changes were analyzed by hematoxylin and eosin staining and Masson’s trichrome staining. For in vitro analysis, osteopontin silencing facilitated the growth and migration of HaCaT cells and promoted ECM degradation in HaCaT cells. Mechanistically, RUNX1 bound to osteopontin promoter, and RUNX1 upregulation attenuated the promoting efficacy of osteopontin silencing on cell growth and migration and ECM degradation. Additionally, RUNX1-activated osteopontin inactivated the MAPK signaling pathway. For in vivo analysis, osteopontin depletion facilitated burn wound healing by promoting reepithelialization and ECM degradation. In conclusion, RUNX1 activates the osteopontin expression at the transcriptional level and osteopontin depletion facilitates the recovery of burn wounds by promoting the migration of keratinocytes and reepithelization and ECM degradation by activating the MAPK pathway.
Revisiting the cumulative incidence function with competing risks data
Authors: Zucker David M , Gorfine Malka
Published: March 2023

We consider estimation of the cumulative incidence function (CIF) in the competing risks Cox model. We study three methods. Methods 1 and 2 are existing methods while method 3 is a newly proposed method. Method 3 is constructed so that the sum of the CIF’s across all event types at the last observed event time is guaranteed, assuming no ties, to be equal to 1. The performance of the methods is examined via simulation, and they are illustrated on data from the field of computer code comprehension. The newly proposed method 3 exhibits performance comparable to that of methods 1 and 2 in terms of bias and variance, and better than that of Methods 1 and 2 in terms of confidence interval coverage rates.
10-year survival of pulmonary arterial hypertension associated with connective tissue disease: insights from a multicentre PAH registry
Authors: Chen Xiaoxi , Quan Ruilin , Qian Yuling , Yang Zhenwen , Yu Zaixin , Zhang Caojin , Yang Yuanhua , Zhang Gangcheng , Shen Jieyan , Wang Qian , Gu Qing , Xiong Changming , Jing Xiaoli , Han Huijun , He Jianguo
Published: March 2023

Objectives

To report the 10-year survival rate and prognostic factors of pulmonary arterial hypertension associated with CTD (CTD-PAH) patients, to compare treatment and survival between patients enrolled before and after 2015, and to validate the discrimination of the recommended four-strata model in predicting 10-year survival at follow-up in Chinese CTD-PAH patients.

Methods

This study was derived from a Chinese national multicentre prospective registry study from 2009 to 2019. Medical records were collected at baseline and follow-up, including PAH-targeted therapy and binary therapy (both CTD and PAH-targeted therapy).

Results

A total of 266 CTD-PAH patients were enrolled and the 10-year survival rate was 59.9% (median follow-up time: 4.85 years). Underlying CTD (SSc), baseline 6-min walking distance and SaO2 were independent risk factors for 10-year survival. The proportion of patients receiving PAH-targeted combination therapy increased from 10.1% (2009–2014) to 26.5% (2015–2019) and that of binary therapy increased from 14.8% to 35%. The 1-year survival rate increased from 89.8% (2009–2014) to 93.9%, and the 3-year survival rate increased from 80.1% (2009–2014) to 86.5% (both P > 0.05). The four-strata strategy performed well in predicting 10-year survival at follow-up (C-index = 0.742).

Conclusion

The 10-year survival rate of CTD-PAH patients was reported for the first time. The 10-year prognosis was poor, but there was a tendency for more standardized treatment and better survival in patients enrolled after 2015. The recommended four-strata model at follow-up can effectively predict 10-year survival in CTD-PAH patients.
State Nobility in the Field of International Criminal Justice: Divergent Elites and the Contest to Control Power over Capital
Authors: Christensen Mikkel Jarle
Published: March 2023

Criminal law was long considered as the sovereign domain of the state. However, after the end of the Cold War, states created new international criminal courts. These courts are part of a wider field of international criminal justice in which different elites work to develop, support, and critique legal ideas and practices that either complement or challenge the state. Inspired by Pierre Bourdieu’s sociology and based on a multiple correspondence analysis with sixty-four modalities, this article contributes a critical analysis of 365 elite agents active in this field. The analysis shows how different types and volumes of capital structure relations between these elites as well as between the field of international criminal justice and the state. Because these relations can turn state nobility against its national origins, international criminal justice poses a potential challenge to the state’s social fabric which goes beyond legal and political controversies: International criminal justice is emblematic of a competition over the value of and control over capital which plays out at the borders between the national and the international. This contest underlines that the state does necessarily control power over state capital and that, when its elites no longer reproduce its meta-capital, the state loses the semblance of being a unified actor on the world stage. Whereas the intensity of this contest over capital might be particular to the field of international criminal justice, similar battles of control are likely to affect the relations between the state and other globalized fields of law, justice, and politics.
Updating the biologically based dose-response model for the nasal carcinogenicity of inhaled formaldehyde in the F344 rat
Authors: Conolly Rory B , Schroeter Jeffry , Kimbell Julia S , Clewell Harvey , Andersen Melvin E , Gentry P Robinan
Published: March 2023

Chronic inhalation of formaldehyde by F344 rats causes nasal squamous cell carcinoma (SCC). This outcome is well-characterized: including dose-response and time course data for SCC, mechanistic endpoints, and nasal dosimetry. Conolly et al. (Toxicol. Sci. 75, 432–447, 2003) used these resources to develop a biologically based dose-response (BBDR) model for SCC in F344 rats. This model, scaled up to humans, has informed dose-response conclusions reached by several international regulatory agencies. However, USEPA concluded that uncertainties precluded its use for cancer risk assessment. Here, we describe an updated BBDR model that addresses uncertainties through refined dosimetry modeling, revised analysis of labeling index data, and an extended dataset where both inhaled (exogenous) and endogenous formaldehyde (exogF, endoF) form DNA adducts. Further, since Conolly et al. (ibid) was published, it has become clear that, when controls from all F344 inhalation bioassays are considered, accounting for over 4000 rats, at most one nasal SCC occurred. This low spontaneous incidence constrains possible contribution of endoF to the formation of nasal SCC via DNA reactivity. Further, since both exogF and endoF form DNA adducts, this constraint also applies to exogF. The revised BBDR model therefore drives SCC formation through the cytotoxicity of high concentration exogF. An option for direct mutagenicity associated with DNA adducts is retained to allow estimation of an upper bound on adduct mutagenicity consistent with the lack of a spontaneous SCC incidence. These updates represent an iterative refinement of the 2003 model, incorporating new data and insights to reduce identified model uncertainties.
Challenges and prospects of managing non-acute medical conditions among pastoral populations in sub-Saharan Africa
Authors: Ekeria Emmanuel , Opawoye Adefolarin , Abubakar Muhammad S , Iliyasu Garba , Habib Abdulrazaq G
Published: March 2023

In Africa, pastoral populations face several underrecognized health issues. The livelihoods of pastoralists revolve around possession of livestock and they are constantly moving in search of water and pasturage. They are predisposed to chronic zoonotic infections but may also suffer from non-acute non-zoonotic cosmopolitan infectious and non-infectious chronic medical conditions. Given their migratory lifestyle, livelihood, geographic inaccessibility, communication barriers, illiteracy and poverty, it is challenging for pastoralists to access lengthy inpatient clinical care and long-term periodic follow-up that may be required to achieve control or cure of subacute, chronic or lifelong diseases. The challenges and management modalities of complicated subacute bacterial endocarditis requiring critical clinical considerations, long-term medical and surgical interventions in a stateless Arab camel herder are described to highlight the plight of pastoralists. Innovative clinical and public health strategies are suggested to authorities and healthcare institutions to improve access to care for non-acute diseases among them.
High and dry: integrative taxonomy of the Andean spider genus Nerudia (Araneae: Pholcidae)
Authors: Huber Bernhard A , Meng Guanliang , Král Jiří , Ávila Herrera Ivalú M , Izquierdo Matias A , Carvalho Leonardo S
Published: March 2023

Ninetinae are a group of poorly known spiders that do not fit the image of ‘daddy long-legs spiders’ (Pholcidae), the family to which they belong. They are mostly short-legged, tiny and live in arid environments. The previously monotypic Andean genus Nerudia exemplifies our poor knowledge of Ninetinae: only seven adult specimens from two localities in Chile and Argentina have been reported in the literature. We found representatives of Nerudia at 24 of 52 localities visited in 2019, mostly under rocks in arid habitats, up to 4450 m a.s.l., the highest known record for Pholcidae. With now more than 400 adult specimens, we revise the genus, describing ten new species based on morphology (including SEM) and COI barcodes. We present the first karyotype data for Nerudia and for its putative sister-genus Gertschiola. These two southern South American genera share a X1X2X3Y sex chromosome system. We model the distribution of Nerudia, showing that the genus is expected to occur in the Atacama biogeographic province (no record so far) and that its environmental niche is phylogenetically conserved. This is the first comprehensive revision of any Ninetinae genus. It suggests that focused collecting may uncover a considerable diversity of these enigmatic spiders.