bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic studies of odd-even staggering in isotopic cross sections with new difference formulas*
Authors: Mei 梅 Bo 波 , Guan 关 Yu-Tian 玉田 , Zeng 曾 Ning-Xin 宁馨 , Yu 余 Tian-Jun 天俊 , Tu 涂 Jia-Jun 家骏 , Mai 麦 Zi-Ying 子颖 , Ma 马 Hao-Tian 浩添 , Li 李 Ruo-Ya 若雅 , Pan 潘 Yu-Hao 宇浩 
Published: December 2024

Abstract
Although a 3rd-order difference formula has often been employed to investigate the odd-even staggering (OES) in experimental cross sections, other formulas can also be very useful. In this work, three formulas, the 2nd, 4th, and 5th-order difference formulas, are proposed for systematic OES studies. These new difference formulas with different orders are applied to extract the OES magnitudes in extensive accurate cross sections measured in different fragmentation and spallation reaction systems over a broad energy range. According to comparisons of these (2nd, 4th, and 5th-order) OES magnitudes derived from different reaction systems, they almost do not rely on the projectile-target combinations or the projectile energy. A similar universality was observed for the 3rd-order OES magnitudes obtained from various reaction systems in our previous studies of the 3rd-order OES. The weighted average values of the 2nd, 4th, and 5th-order OES magnitudes extracted from different experimental datasets are recommended as the 2nd, 4th, and 5th-order OES evaluations, respectively. Finally, comparisons of these (new) 2nd, 4th, 5th, and previous 3rd-order OES evaluations support that these OES evaluations with different orders are consistent and that all the difference formulas with different orders are applicable to OES studies.
Impact of nonextensivity on the transport coefficients of strongly interacting QCD matter*
Authors: Singh Dhananjay , Kumar Arvind 
Published: December 2024

Abstract
Tsallis nonextensive statistics is applied to study the transport coefficients of strongly interacting matter within the Polyakov chiral

quark mean field model (PCQMF). Nonextensivity is introduced within the PCQMF model through a dimensionless parameter q to examine the viscous properties, such as shear viscosity (η) and bulk viscosity (

), and conductive properties, such as electrical conductivity (

) and thermal conductivity (κ). Additionally, some key thermodynamic quantities relevant to the transport coefficients, such as the speed of sound (

) and specific heat at constant volume (

), are calculated. The temperature dependence of the transport coefficients is explored through a kinetic theory approach with the relaxation time approximation. The results are compared to those of the extensive case where q approaches 1. The nonextensive q parameter is found to have a significant effect on all transport coefficients. We find that the nonextensive behaviour of the medium enhances specific shear viscosity

, as well as conductive coefficients

and

. In contrast, the normalized bulk viscosity

is found to decrease as the nonextensivity of the medium increases. We also studied the transport coefficients for finite values of chemical potentials. The magnitudes of η,

, and κ increase at lower temperatures, while ζ

b
is found to decrease for systems with non-zero chemical potential.
Experimental results of the pFREYA16 ASIC for x-ray ptychography in continuous wave light sources
Authors: Lazzaroni P. , Hammer M. , Manghisoni M. , Miceli A. , Ratti L. , Re V. , Shi H. , Torilla G. 
Published: December 2024

Abstract
The pFREYA16, prototype Fast Readout for ptYchography Applications with 16 channels, ASIC is a pixellated 8-by-2 readout matrix developed for ptychography experiments based on fourth generation storage ring light sources, also known as diffraction-limited storage rings (DLSR), pushing towards continuous wave operation. The target of the experiment is to obtain a 128-by-128 matrix of pixels, working at a frame rate of 1 MHz with single-photon resolution, as well as low-noise and low-power figures, in a modest-size pixel area of 150 μm × 150 μm. The readout chain is composed of a switch-reset CSA and a semi-Gaussian unipolar RC-CR shaper, and includes signal discrimination, zero-suppression capabilities, and pixel-level analog to digital conversion. The ASIC is also configurable for 5, 9, 18, or 25 keV input photon energy, with a full well capacity of 256 equivalent photons in each mode, and four different peaking times are available for noise optimisation. The paper will focus on the characterisation of the CSA and the shaper stage.
Uncertainty in determining carbon dioxide removal potential of biochar
Authors: Kane Seth , Bin Thaneya Ahmad , Gursel Aysegul Petek , Fan Jin , Bose Baishakhi , Hendrickson Thomas P , Nordahl Sarah L , Scown Corinne D , Miller Sabbie A , Horvath Arpad 
Published: December 2024

Abstract
A quantitative and systematic assessment of uncertainty in life-cycle assessment is critical to informing sustainable development of carbon dioxide removal (CDR) technologies. Biochar is the most commonly sold form of CDR to date and it can be used in applications ranging from concrete to agricultural soil amendments. Previous analyses of biochar rely on modeled or estimated life-cycle data and suggest a cradle-to-gate range of 0.20–1.3 kg CO2 net removal per kg of biomass feedstock, with the range reported driven by differences in energy consumption, pyrolysis temperature, and feedstock sourcing. Herein, we quantify the distribution of CDR possible for biochar production with a compositional life-cycle inventory model paired with scenario-aware Monte Carlo simulation in a ‘best practice’ (incorporating lower transportation distances, high pyrolysis temperatures, high energy efficiency, recapture of energy for drying and pyrolysis energy requirements, and co-generation of heat and electricity) and ‘poor practice’ (higher transportation distances, lower pyrolysis temperatures, low energy efficiency, natural gas for energy requirements, and no energy recovery) scenarios. In the best-practice scenario, cradle-to-gate CDR (which is representative of the upper limit of removal across the entire life cycle) is highly certain, with a median removal of 1.4 kg of CO2e/kg biomass and results in net removal across the entire distribution. In contrast, the poor-practice scenario results in median net emissions of 0.090 kg CO2e/kg biomass. Whether this scenario emits (66% likelihood) or removes (34% likelihood) carbon dioxide is highly uncertain. The emission intensity of energy inputs to the pyrolysis process and whether the bio-oil co-product is used as a chemical feedstock or combusted are critical factors impacting the net carbon dioxide emissions of biochar production, together responsible for 98% of the difference between the best- and poor-practice scenarios.
Photon angular momentum and zero-point oscillations
Authors: Milonni Peter W , Jordan Maclay G 
Published: December 2024

Abstract
Radiation from certain oscillating charge distributions can have angular momentum that cannot be explained in classical electrodynamics. We consider the angular momentum of a single-photon field from an electric dipole oscillator and in particular compare the classical and quantum expressions for the mean-square field angular momentum. We show that differences in these expressions are attributable to zero-point oscillations of unexcited states of the dipole oscillator.
Stabilizing training of affine coupling layers for high-dimensional variational inference
Authors: Andrade Daniel 
Published: December 2024

Abstract
Variational inference with normalizing flows is an increasingly popular alternative to MCMC methods. In particular, normalizing flows based on affine coupling layers (Real NVPs) are frequently used due to their good empirical performance. In theory, increasing the depth of normalizing flows should lead to more accurate posterior approximations. However, in practice, training deep normalizing flows for approximating high-dimensional posterior distributions is often infeasible due to the high variance of the stochastic gradients. In this work, we show that previous methods for stabilizing the variance of stochastic gradient descent can be insufficient to achieve stable training of Real NVPs. As the source of the problem, we identify that, during training, samples often exhibit unusual high values. As a remedy, we propose a combination of two methods: (1) soft-thresholding of the scale in Real NVPs, and (2) a bijective soft log transformation of the samples. We evaluate these and other previously proposed modification on several challenging target distributions, including a high-dimensional horseshoe logistic regression model. Our experiments show that with our modifications, stable training of Real NVPs for posteriors with several thousand dimensions and heavy tails is possible, allowing for more accurate marginal likelihood estimation via importance sampling. Moreover, we evaluate several common training techniques and architecture choices and provide practical advise for training Real NVPs for high-dimensional variational inference. Finally, we also provide new empirical and theoretical justification that optimizing the evidence lower bound of normalizing flows leads to good posterior distribution coverage.
Ergodic recurrence and bounded gaps between primes
Authors: Pan Hao 
Published: December 2024

Let

(

X

,

B

X

,
μ
,
T
)

(\mathcal {X},\mathscr {B}_\mathcal {X},\mu ,T)

be a measure-preserving probability system with

T
T

is invertible. Suppose that

A
∈

B

X

A\in \mathscr {B}_\mathcal {X}

with

μ
(
A
)
>
0

\mu (A)>0

and

ϵ
>
0

\epsilon >0

. For any

m
≥
1

m\geq 1

, there exist infinitely many primes

p
0

,

p
1

,
…
,

p
m

p_0,p_1,\ldots ,p_m

with

p
0

>
⋯
>

p
m

p_0>\cdots >p_m

such that

μ
(
A
∩

T

−
(

p
i

−
1
)

A
)
≥
μ
(
A

)
2

−
ϵ

\begin{equation*} \mu (A\cap T^{-(p_i-1)}A)\geq \mu (A)^2-\epsilon \end{equation*}

for each

0
≤
i
≤
m

0\leq i\leq m

and

p
m

−

p
0

>

C

m
,
A
,
ϵ

,

\begin{equation*} p_m-p_0>C_{m,A,\epsilon }, \end{equation*}

where

C

m
,
A
,
ϵ

>
0

C_{m,A,\epsilon }>0

is a constant only depending on

m
m

,

A
A

and

ϵ
\epsilon

.
Pointwise convergence of multiple Fourier series over polytopes
Authors: Mastyło Mieczysław , Rodríguez-Piazza Luis 
Published: December 2024

For a convex polytope

P
P

in

R

d

\mathbb {R}^d

containing

0
0

in its interior, it is proved an interpolative estimate for the Carleson operator generated by the partial sums of multiple Fourier series over all dilated sets of

P
P

. This result is used to prove that this operator is bounded from the Arias-Reyna space

Q

A
(

T

d

)

Q\!A(\mathbb {T}^d)

to the weak

L

1

L^{1}

-space on the

d
d

-dimensional torus

T

d

\mathbb {T}^d

. As a by-product, it follows that the sums over

λ
P

\lambda P

of the multiple Fourier series of every function in

Q

A
(

T

d

)

Q\!A(\mathbb {T}^d)

converge almost everywhere to the function as

λ
\lambda

tends to

+
∞

+\infty

. It is shown that this statement holds for every function in a Lorentz space

Λ
φ

(

T

d

)

\Lambda _\varphi (\mathbb {T}^d)

, which contains the Orlicz space

L
(
log
⁡
L

)

d

log
⁡
log
⁡
log
⁡
L
(

T

d

)

L(\log L)^{d} \log \log \log L(\mathbb {T}^d)

and so

L
p

(

T

d

)

L^p(\mathbb {T}^d)

for all

p
∈
(
1
,
∞
]

p \in (1, \infty ]

. In particular, this extends Fefferman’s result on the almost everywhere convergence of the of multiple Fourier series over polygon in

R

2

\mathbb {R}^2

of functions in

L
p

(

T

2

)

L^p(\mathbb {T}^2)

.
Panacus: fast and exact pangenome growth and core size estimation
Authors: Parmigiani Luca , Garrison Erik , Stoye Jens , Marschall Tobias , Doerr Daniel 
Published: December 2024

Abstract

Motivation
Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).

Results
We introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in &lt;1 h.

Availability and implementation
Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus. Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html.
Extracorporeal membrane oxygenation as a bridge to transplant in severe pulmonary hypertension
Authors: Kruszona Sophie , Aburahma Khalil , Wand Philipp , de Manna Nunzio D , Avsar Murat , Bobylev Dmitry , Müller Carsten , Carlens Julia , Weymann Alexander , Schwerk Nicolaus , Welte Tobias , Liu Bin , Ruhparwar Arjang , Kuehn Christian , Salman Jawad , Greer Mark , Ius Fabio 
Published: December 2024

Abstract

OBJECTIVES
Severe pulmonary hypertension (PH) is the leading indication for a lung transplant in younger patients. Despite the availability of validated risk scores, their influence on lung allocation has been negligible, with continued reliance on decompensation and bridging with extracorporeal membrane oxygenation (ECMO).
This single-centre, retrospective study assessed outcome of ECMO bridging in lung transplant for PH and evaluated short-term predictability of ECMO bridging.

METHODS
Patients with PH listed for a lung transplant between January 2010 and March 2023 were included. Peri- and postoperative courses were compared dependent upon ECMO bridging status. Bridging risk analysis within 90 days of re-evaluation included patients not requiring ECMO at listing, with listing parameters evaluated using a univariate Cox proportional hazard regression.

RESULTS
A total of 114/123 patients listed underwent lung transplant. Twenty-eight required ECMO bridging. No differences in primary graft dysfunction grade 3 at 72 h (30 vs 20%; P = 0.28) or graft survival (1 year: 82 vs 88%; 5 years: 54 vs 59%; P = 0.84) were evident. ECMO bridging resulted in longer intensive care unit stays post-transplant (P = 0.002) and higher rates of both re-thoracotomy (P = 0.049) and vascular complications (P = 0.031). Factors increasing 90-day ECMO risk included N-terminal pro-B-type natriuretic peptide (P &lt; 0.001), 6-min walk distance (P = 0.03) and O2 requirement at rest (P = 0.006).

CONCLUSIONS
Lung transplant survival outcomes are not affected by ECMO bridging in patients with severe PH. It does, however, expose patients to additional risk, and efforts such as easy-to-measure parameters to pre-emptively identify patients requiring bridging to assist with effective allocation should be encouraged.
Contrasting patterns of diversity emerge depending on the initial drivers of speciation during adaptive radiation
Authors: Gillespie Rosemary G 
Published: December 2024

Abstract
I examine the spatial processes that shape species formation in adaptive radiation, and patterns that emerge from the different processes. I first consider situations that set the stage for diversification and conditions under which ecological diversity is maintained in populations without speciation, either due to balancing selection within a population or fluctuating selection between populations; the latter can be a precursor to speciation while the former can not. I then examine how speciation operates within the context of adaptive radiation: while species may diverge without ecological change within an adaptive radiation, I focus on ecological change, emphasizing two key processes through which nascent species may form, with initial divergence being attributed to either: (i) selection due to changes in the environment or substrate on which a species exists leading to ecological speciation; or (ii) geographic isolation leading to ecologically similar species that may subsequently compete and undergo character displacement in syntopy. There is good evidence for both processes in nature, but they lead to different predictions in terms of the production of ephemeral lineages and patterns of accumulation of species diversity. Initial ecological divergence along replicated environmental gradients may lead to predictable sets of allotopic ecomorphs, while initial divergence through geographic isolation may lead to initial supersaturation and predictable sets of syntopic ecomorphs.
Prophylactic cranial irradiation for small cell lung cancer in the era of immunotherapy and molecular subtypes
Authors: Pozonec Veronika , Pozonec Maria Dorothea , Aigner Clemens , Widder Joachim , Boettiger Kristiina , Megyesfalvi Zsolt , Dome Balazs 
Published: December 2024

Purpose of review
Small cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, whereas its metastatic capacity carries a predilection for the brain. Although prophylactic cranial irradiation (PCI) has been used to address this problem, upcoming alternatives might necessitate reflection of its application in SCLC treatment.

Recent findings
The addition of immunotherapy to treatment guidelines has provided a new strategy for the management of brain metastases. Complementation of immunotherapy with active MRI surveillance could potentially replace PCI and avoid irradiation-related cognitive side effects. SCLC's molecular profile is heterogeneous, with differential response to treatment modalities between subgroups. Investigation of these variances might be essential to improve therapeutic outcomes in SCLC patients.

Summary
The role of PCI in SCLC treatment must be examined in light of immunotherapy. We summarize recent results, bearing SCLC subtypes and therapeutic vulnerabilities in mind, to derive tailored treatment strategies for SCLC patients in future settings.
Therapeutic Drug Monitoring of Nirmatrelvir/Ritonavir (Paxlovid) in Patients Treated for COVID-19: Results from a Prospective Multicenter Observational Study
Authors: Böger Corinna R. , Martens-Lobenhoffer Jens , Worthmann Hans , Stichtenoth Dirk O. , Brod Torben 
Published: December 2024

Background:
Paxlovid is a combination of the antiviral agents nirmatrelvir and ritonavir indicated for the oral treatment of high-risk, symptomatic patients with coronavirus disease 2019 (COVID-19). As real-world data on the plasma concentrations of nirmatrelvir/ritonavir (Paxlovid) are limited, the aim of this study was to investigate nirmatrelvir/ritonavir plasma trough levels in a clinical setting using therapeutic drug monitoring.

Methods:
A prospective, noninterventional, multicenter, observational clinical study was conducted in which the plasma trough levels of nirmatrelvir/ritonavir were simultaneously determined by using liquid chromatography tandem mass spectrometry in patients with symptomatic COVID-19. The blood samples were collected on days 1, 3, and 5 after the first full-dose day (day 0), and patient data such as sex, height, weight, renal function, liver enzymes, and concomitant (co-) medications were obtained to describe the plasma levels with respect to potential influencing factors.

Results:
A total of 46 blood samples from 21 patients were analyzed. The geometric mean Cmin was 4997 ng/mL for nirmatrelvir and 529.4 ng/mL for ritonavir. The plasma concentrations covered a wide range, the highest being observed in patients with advanced age and renally excreted comedications. Patients older than 65 years had a significantly higher risk of achieving excessive plasma trough concentrations above 8840 ng/mL for nirmatrelvir and 1440 ng/mL for ritonavir compared with younger patients (odds ratio 11.2, 95% confidence interval 1.04–120.4).

Conclusions:
The plasma trough concentrations of nirmatrelvir and ritonavir in patients treated for symptomatic COVID-19 were higher than the reference values of 2210 ng/mL for nirmatrelvir and 360 ng/mL for ritonavir stated in the product characteristics. Advanced age and renally eliminated comedication were identified as possible influencing factors that warrant further investigation.
Beat-to-beat variability of aortic pulse wave velocity: implications for aortic stiffness measurements
Authors: Giudici Alessandro , Grillo Andrea , Scalise Filippo , Reesink Koen D. , Delhaas Tammo , Salvi Paolo , Spronck Bart , Parati Gianfranco 
Published: December 2024

Objectives:
Aortic pulse wave velocity (aPWV) predicts cardiovascular risk. Being the reference method for aortic stiffness evaluation, invasive aPWV is also recommended for validation of noninvasive devices. Because of intrinsic haemodynamic variability and processing issues, aPWV shows beat-to-beat variability. We aimed to quantify this variability and evaluate its implications for the reliability and use of aPWV as reference in validation and clinical application studies.

Methods:
The study included n = 84 patients, in whom two datasets of invasive data were recorded: 1) simultaneous ascending aorta and iliac pressure acquisitions using a dual-tip intra-aortic catheter, and 2) an additional ascending aorta pressure acquisition. By combining the iliac and ascending aorta pressure recordings from the first and second acquisitions, respectively, we evaluated how a sequential acquisition protocol affects variability. We compared three pressure waveform foot identification methods to investigate the effect of data processing on variability. Furthermore, we estimated how averaging over n
beats consecutive heartbeats affects the standard deviation (SD) of such n
beats-averaged estimate of aPWV.

Results:
The simultaneously acquired invasive aPWV showed a 5% beat-to-beat SD (variability), with small but significant differences between foot identification methods. The sequential acquisition protocol doubled aPWV variability compared to simultaneous acquisition. However, because averaging had a much stronger effect on sequentially measured aPWV, the two acquisition protocols yielded comparable variabilities at n
beats = 10 (2% vs. 3%).

Conclusions:
Our study suggests that, independently from the acquisition protocol and data processing, the intrinsic beat-to-beat variability of aPWV becomes manageable when aPWV values of at least ten heartbeats are averaged.