bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3
Authors: Shiraishi Nao , Konuma Tsuyoshi , Chiba Yoshie , Hokazono Sayaka , Nakamura Nao , Islam Md Hadiul , Nakanishi Makoto , Nishiyama Atsuya , Arita Kyohei 
Published: June 2024

AbstractDNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 85VRT87 motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.
GOAT: efficient and robust identification of gene set enrichment
Authors: Koopmans Frank 
Published: June 2024

AbstractGene set enrichment analysis is foundational to the interpretation of high throughput biology. Identifying enriched Gene Ontology (GO) terms or disease-associated gene sets within a list of gene effect sizes that represent experimental outcomes is an everyday task in life science that crucially depends on robust and sensitive statistical tools. We here present GOAT, a parameter-free algorithm for gene set enrichment analysis of preranked gene lists. The algorithm can precompute null distributions from standardized gene scores, enabling enrichment testing of the GO database in one second. Validations using synthetic data show that estimated gene set p-values are well calibrated under the null hypothesis and invariant to gene list length and gene set size. Application to various real-world proteomics and gene expression studies demonstrates that GOAT identifies more significant GO terms as compared to current methods. GOAT is freely available as an R package and user-friendly online tool for gene set enrichment analyses that includes interactive data visualizations: https://ftwkoopmans.github.io/goat.
Changes in tornado risk and societal vulnerability leading to greater tornado impact potential
Authors: Strader Stephen M. , Gensini Victor A. , Ashley Walker S. , Wagner Amanda N. 
Published: June 2024

AbstractTornado risk, as determined by the occurrence of atmospheric conditions that support tornado incidence, has exhibited robust spatial trends in the United States Southern Plains and Mid-South during recent decades. The consequences of these risk changes have not been fully explored, especially in conjunction with growing societal vulnerability. Herein, we assess how changes in risk and vulnerability over the last 40 years have collectively and individually altered tornado-housing impact potential. Results indicate that escalating vulnerability and exposure have outweighed the effects of spatially changing risk. However, the combination of increasing risk and exposure has led to a threefold increase in Mid-South housing exposure since 1980. Though Southern Plains tornado risk has decreased since 1980, amplifying exposure has led to more than a 50% increase in mean annual tornado-housing impact potential across the region. Stakeholders should use these findings to develop more holistic mitigation and resilience-building strategies that consider a dynamically changing tornado disaster landscape.
Meta‐analysis and systematic review for anomaly network intrusion detection systems: Detection methods, dataset, validation methodology, and challenges
Authors: Maseer Ziadoon K. , Kadhim Qusay Kanaan , Al‐Bander Baidaa , Yusof Robiah , Saif Abdu 
Published: June 2024

AbstractIntrusion detection systems built on artificial intelligence (AI) are presented as latent mechanisms for actively detecting fresh attacks over a complex network. The authors used a qualitative method for analysing and evaluating the performance of network intrusion detection system (NIDS) in a systematic way. However, their approach has limitations as it only identifies gaps by analysing and summarising data comparisons without considering quantitative measurements of NIDS's performance. The authors provide a detailed discussion of various deep learning (DL) methods and explain data intrusion networks based on an infrastructure of networks and attack types. The authors’ main contribution is a systematic review that utilises meta‐analysis to provide an in‐depth analysis of DL and traditional machine learning (ML) in notable recent works. The authors assess validation methodologies and clarify recent trends related to dataset intrusion, detected attacks, and classification tasks to improve traditional ML and DL in NIDS‐based publications. Finally, challenges and future developments are discussed to pose new risks and complexities for network security.
Energy estimation of small-scale jets from the quiet-Sun region
Authors: Shi Fanpeng , Li Dong , Ning Zongjun , Xu Jun , Song Yuxiang , Yang Yuzhi 
Published: June 2024

Context. Solar jets play a role in coronal heating and the supply of solar wind.
Aims. In this study, we calculate the energies of 23 small-scale jets emerging from a quiet-Sun region in order to investigate their contributions to coronal heating.
Methods. We used data from the High-Resolution Imager (HRI) of the Extreme Ultraviolet Imager (EUI) on board the Solar Orbiter. Small-scale jets were observed by the HRIEUV 174 Å passband in the high cadence of 6 s. These events were identified by the time–distance stacks along the trajectories of jets. Using the simultaneous observation from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO), we also performed a differential emission measure (DEM) analysis on these small-scale jets to obtain the physical parameters of plasma, which enabled us to estimate the kinetic and thermal energies of the jets.
Results. We find that most of the jets exhibit common unidirectional or bidirectional motions, while some show more complex behaviors; namely, a mixture of unidirection and bidirection. A majority of jets also present repeated eruption blobs (plasmoids), which may be signatures of the quasi-periodic magnetic reconnection that has been observed in solar flares. The inverted Y-shaped structure can be recognized in several jets. These small-scale jets typically have a width of ∼0.3 Mm, a temperature of ∼1.7 MK, an electron number density of ≳109 cm−3, with speeds in a wide range from ∼20–170 km s−1. Most of these jets have an energy of 1023–1024 erg, which is marginally smaller than the energy of typical nanoflares. The thermal energy fluxes of 23 jets are estimated to be (0.74–2.96)×105 erg cm−2 s−1, which is almost on the same order of magnitude as the energy flow required to heat the quiet-Sun corona, although the kinetic energy fluxes vary over a wide range because of their strong dependence on velocity. Furthermore, the frequency distribution of thermal energy and kinetic energy both follow the power-law distribution N(E)∝E−α.
Conclusions. Our observations suggest that although these jets cannot provide sufficient energy to heat the whole quiet-Sun coronal region, they are likely to account for a significant portion of the energy demand in the local regions where the jets occur.
Jet formation in post-AGB binaries
Authors: De Prins T. , Van Winckel H. , Ferreira J. , Verhamme O. , Kamath D. , Zimniak N. , Jacquemin-Ide J. 
Published: June 2024

Context. Jets are launched from many classes of astrophysical objects, including post-asymptotic giant branch (post-AGB) binaries with a circumbinary disc. Despite dozens of detections, the formation of these post-AGB binary jets and their connection to the inter-component interactions in their host systems remains poorly understood.
Aims. Building upon the previous paper in this series, we consider cold self-similar magnetohydrodynamic (MHD) disc wind solutions to describe jets that are launched from the circumcompanion accretion discs in post-AGB binaries. Resulting predictions are matched to observations. This both tests the physical validity of the MHD disc wind paradigm and reveals the accretion disc properties.
Methods. Five MHD solutions are used as input to synthesise spectral time-series of the Hα line for five different post-AGB binaries. A fitting routine over the remaining model parameters is developed to find the disc wind models that best fit the observed time-series.
Results. Many of the time-series’ properties are reproduced well by the models, though systematic mismatches, such as overestimated rotation, remain. Four targets imply accretion discs that reach close to the secondary’s stellar surface, while one is fitted with an unrealistically large inner radius at ≳20 stellar radii. Some fits imply inner disc temperatures over 10 000 K, seemingly discrepant with a previous observational estimate from H band interferometry. This estimate is, however, shown to be biased. Fitted mass-accretion rates range from ∼10−6 − 10−3 M⊙/yr. Relative to the jets launched from young stellar objects (YSOs), all targets prefer winds with higher ejection efficiencies, lower magnetizations and thicker discs.
Conclusions. Our models show that current cold MHD disc wind solutions can explain many of the jet-related Hα features seen in post-AGB binaries, though systematic discrepancies remain. This includes, but is not limited to, overestimated rotation and underestimated post-AGB circumbinary disc lifetimes. The consideration of thicker discs and the inclusion of irradiation from the post-AGB primary, leading to warm magnetothermal wind launching, might alleviate these.
Planet-driven spirals in protoplanetary discs: Limitations of the semi-analytical theory for observations
Authors: Fasano D. , Winter A. J. , Benisty M. , Rosotti G. , Ruzza A. , Lodato G. , Toci C. , Hilder T. , Izquierdo A. , Price D. 
Published: June 2024

Context.Detecting protoplanets during their formation stage is an important but elusive goal of modern astronomy. Kinematic detections via the spiral wakes in the gaseous disc are a promising avenue to achieve this goal.Aims.We aim to test the applicability of a commonly used semi-analytical model for planet-induced spiral waves to observations in the low and intermediate planet mass regimes. In contrast to previous works that proposed using the semi-analytical model to interpret observations, in this study we analyse for the first time both the structure of the velocity and density perturbations.Methods.We ran a set of FARGO3D hydrodynamic simulations and compared them with the output of the semi-analytic model in the codeWAKEFLOW. We divided the disc into two regions. We used the density and velocity fields from the simulation in the linear region, where density waves are excited. In the non-linear region, where density waves propagate through the disc, we then solved Burgers’ equation to obtain the density field, from which we computed the velocity field.Results.We find that the velocity field derived from the analytic theory is discontinuous at the interface between the linear and nonlinear regions. After ~0.2rpfrom the planet, the behaviour of the velocity field closely follows that of the density perturbations. In the low mass limit, the analytical model is in qualitative agreement with the simulations, although it underestimates the azimuthal width and the amplitude of the perturbations, predicting a stronger decay but a slower azimuthal advance of the shock fronts. In the intermediate regime, the discrepancy increases, resulting in a different pitch angle between the spirals of the simulations and the analytic model.Conclusions.The implementation of a fitting procedure based on the minimisation of intensity residuals is bound to fail due to the deviation in pitch angle between the analytic model and the simulations. In order to apply this model to observations, it needs to be revisited so that it can also account for higher planet masses.
Is a Biopsy Required to Classify Patients with Idiopathic
Retroperitoneal Fibrosis as IgG4-RPF or Non-IgG4-RPF?
Authors: Misirci Salim , Ekin Ali , Coskun Belkis Nihan , Yagız Burcu , Yılmaz Özgür , Yıldız Abdulmecit , Dalkılıç Ediz , Pehlivan Yavuz 
Published: June 2024

Abstract
Objective Our aim was to group cases of idiopathic retroperitoneal
fibrosis (IRPF) into those associated with immunoglobulin (Ig) G4-related
disease (IgG4-RD) (IgG4-RPF) and those not associated with IgG4-RD
(non-IgG4-RPF) and to compare the clinical presentation, laboratory findings,
imaging, and treatment methods.
Methods A total of 46 patients were included in the study. According to
the assessment by two experienced rheumatologists and the IgG4-RPF
classification criteria published by the American College of
Rheumatology/European League Against Rheumatism (ACR/EULAR) in 2019, 11 patients
who were admitted as IgG4-RPF were included in the IgG4-RPF group and 35
patients who were not admitted as IgG4-RPF were included in the non-IgG4-RPF
group. The clinical and demographic characteristics, affected sites, laboratory
results and treatments were retrospectively evaluated and compared.
Results The mean age of our patients was 50.69 (±11.33) in the
non-IgG4-RPF group and 55.36 (±7.80) in the IgG4-RPF group and was similar in
both groups (p=0.340). The male gender dominated in both groups. Although there
was no significant difference between the groups in terms of acute renal failure
(p=0.074), this was more frequent in the IgG4-RPF group (81.82%). An increased
IgG4 concentration was found in about half (n=6, 54.55%) of the patients in the
IgG4-RPF group, while this was present in only 5.71% (n=2) of the patients in
the non-IgG4-RPF group (p=0.001). The most commonly used diagnostic imaging
modality was computed tomography. Biopsy was performed in almost all patients
(n=10, 90.91%) in the IgG4-RPF group and 11 (31.43%) in the non-IgG4-RPF group
(p<0.001). Drug treatment alone and drug treatment in combination with
interventional treatment were the most commonly used treatment modalities in the
non-IgG4-RPF group (n=12, 34.29% for both). In the IgG4-RPF group, the
combination of medical and interventional treatment was the most commonly used
treatment modality (n=5, 45.45%). No significant difference was found between
the two groups in the assessment of treatment success (p>0.05).
Conclusion IRPF can present with similar clinical and imaging findings in
IgG4-RPF and non-IgG4-RPF groups. Since a similar treatment success can be
achieved in both groups with similar therapeutic agents, we believe that a
biopsy is not necessary in patients with an uncertain diagnosis of IRPF.
Highly Regio-/Stereoselective Synthesis of Carbohydrates with Unsaturated Glycosyl Donors under Mild Conditions
Authors: Wang Nengzhong , Huang Nianyu , Yao Hui , Gao Xinyu , Ren Keke , Ma Lijuan 
Published: June 2024

AbstractCarbohydrates and their conjugates play important roles in life activities and drug development. Our group was committed to the general and effective glycosylation methods and their application in chemical biology using unsaturated glycosyl donors. In the past five years, we have reported several synthetic strategies with high stereoselectivity and milder conditions compared with previous works. In particular, high chemo-/regio- and stereoselective O-glycosylation, C-glycosylation and S-glycosylation could be achieved via palladium catalysis under open-air conditions at room temperature. In this Account, we will introduce our research progress in constructing four types of glycosides.1	Introduction2	Stereoselective Synthesis of O-Glycosides3	Stereoselective Synthesis of C-Glycosides4	Stereoselective Synthesis of N-Glycosides5	Stereoselective Synthesis of S-Glycosides6	Conclusion
Dehydration in Water: A Reagentless and Straightforward Synthesis of Tetrahydroquinazolines under Microwave Irradiation or by Stirring at Room Temperature, and Their Subsequent Conversion into Quinazolines in a Micellar Medium
Authors: Panjikar Padmini. C. , Pinheiro Abigail. B. , Chatterjee Amrita , Banerjee Mainak , Saha Soumik 
Published: June 2024

AbstractUsing a reagent- and catalyst-free approach, a series of 2-substituted 1,2,3,4-tetrahydroquinazolines is synthesized by cyclocondensation between aldehydes and 2-aminobenzylamines via dehydration in water. The reactions are complete in 2 minutes under microwave irradiation and proceed well under stirring at room temperature, affording tetrahydroquinazolines in high to excellent yields. The products are water-insoluble and are isolated by simple filtration, avoiding a conventional work-up step and offering an organic-solvent-free process. Furthermore, the tetrahydroquinazolines are efficiently oxidized in a micellar medium derived from cetyltrimethylammonium bromide (CTAB) using a cheap commercial bleaching solution (4% NaOCl in water) to give quinazolines in high yields. This sustainable protocol has a near zero E-factor.
Synthesis and Reactivity of α-Diazo-β-keto Sulfonamides
Authors: Collins Stuart G. , Maguire Anita R. , Judge Evan R. , O’Shaughnessy Keith , Lawrence Simon E. 
Published: June 2024

AbstractCopper-mediated reactions of α-diazo-β-keto sulfonamides led to a range of products, including alkynesulfonamides, enamines, and α-halosulfonamides, with no evidence for intramolecular C–H insertion in any of the reactions, in contrast to the reactivity of the comparable α-diazo-β-oxo sulfones. Use of copper(II) triflate (5 mol%) led to the isolation of a series of alkynesulfonamides (up to 12% yield) and enamines (up to 64% yield). Use of copper(II) chloride (5 mol%) led to the formation, in addition, of α-halosulfonamides; use of stoichiometric amounts of copper(II) chloride/bromide enabled facile halogenation of the β-keto sulfonamide to form α-halosulfonamides (up to 63% yield).
Reproducing the normal and the pathological in personalized cancer medicine clinical trials
Authors: Even Chorev Nadav , Filc Dani 
Published: June 2024

AbstractThe medical practice termed Personalized Medicine ideally uses all the patient’s possible characteristics in predicting disease predisposition and response to therapy, but primarily employs the individual’s unique molecular make-up in the tailoring of treatment. This change in medical practice also entails an epistemic shift towards ‘molecularization’: individuals and disease are now understood and governed through life’s basic building blocks. In this paper we argue that underlying personalized medicine is a continued understanding of the pathological state as a quantitative deviation from a normal state. In this we build on the critique of French philosopher Georges Canguilhem who positioned the quantitative interpretation of the pathological in nineteenth century medical thinking. Personalized cancer medicine takes each patient’s cancer as singular, implying that there is no ‘normal’ baseline for comparing individual pathology. We analyze cases of personalized cancer clinical trials from recent years to show that each displays a quantitative understanding of the pathological reminiscent of past thinking in two main modes: a molecularized interpretation of cancer pathology and a quantitative measuring of targeted therapy efficacy. We situate the analysis in broader discussions of historical medical shifts and in current studies of personalized medicine, to outline implications of this form of continuity.
Cultivating inclusivity in introductory undergraduate STEM course syllabi
Authors: Bernardi Francesca , Brown Crystal , Davis Lindsay , Ephraim Michelle , Moody Rebecca , Trubko Raisa 
Published: June 2024

AbstractSyllabi are widely used at higher education institutions in the United States to present students with course-related information before or at the beginning of a new class. The timing and versatility of these documents allows instructors to set the tone of a course with (or without) an eye towards inclusivity. This can be important for all students but affects, in particular, students from marginalized groups as they navigate STEM courses. We report a study about inclusive practices in course syllabi at a STEM institution by addressing whether they: (a) list instructors’ pronouns, (b) utilize readings and materials authored by women and gender minority scholars, and (c) contain inclusivity statements. We report and compare perspectives on these three aspects from two datasets: 163 syllabi analyzed based on a rubric that we developed and results from an undergraduate student survey, both from Worcester Polytechnic Institute. The two complementary datasets provide a way to benchmark whether there is a link between student and faculty perceptions of syllabi use and desired content. We find sharp differences between students’ expectations and actual syllabi content for all three of our topics of interest with students wanting inclusive practices at the forefront of course development regardless of subject and faculty lagging behind. We provide suggestions on how to incorporate inclusive practices in syllabi design and propose further questions to explore.
How far can we see back in time in high-energy collisions using charm hadrons?
Authors: Gyulai László , Bíró Gábor , Vértesi Róbert , Barnaföldi Gergely Gábor 
Published: June 2024

Abstract
We use open charm production to estimate how far we can see back in time in high-energy hadron-hadron collisions. We analyze the transverse momentum distributions of the identified D mesons from pp, p–Pb and A–A collisions at the ALICE and STAR experiments covering the energy range from

s

NN

=
200

GeV

up to 7 TeV. Within a non-extensive statistical framework, the common Tsallis parameters for D mesons represent higher temperature and more degrees of freedom than that of light-flavour hadrons. Assuming Bjorken-expansion, the production of D mesons corresponds to a significantly earlier proper time, τ
D = (0.18 ± 0.06)τ
LF.
Lepton flavour violation signal of the singly charged scalar singlet at the ILC
Authors: Yue Chong-Xing , Sun Xiao-Chen , Zhang Na-Qian , Bu Yang-Yang 
Published: June 2024

Abstract
The singly charged SU(2)
L
singlet scalar is one of the very interesting new particles, as it can generate neutrino masses at loop level, produce contributions to various flavour observables. We study the possibility of detecting this kind of scalar predicted by the singly-charged scalar model at ILC via the lepton flavour violation process

e

+

e

−

→

S

+

S

−

→
μ
e
+

E

. Considering the constraints on the free parameters, we obtain the expected sensitivities of the ILC with the center of mass energy

s

=
1

TeV

and the integrated luminosity

L
=

1.5 ab−1 to the parameter space of the singly-charged scalar model. The prospective excluded mass range at 95% C.L. is M

S
≳ 470 GeV, 410 GeV for the branching ratio

B

μ
e

= 100% , 50%, respectively, while the scalar with M

S
≳ 300 GeV is excluded at 95% C.L. for

B

μ
e

= 30%.