bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Newton polytopes of Lagrangian augmentations
Authors: Capovilla‐Searle Orsola , Casals Roger 
Published: February 2024

AbstractThis note explores the use of Newton polytopes in the study of Lagrangian fillings of Legendrian submanifolds. In particular, we show that Newton polytopes associated to augmented values of Reeb chords can distinguish infinitely many distinct Lagrangian fillings, both for Legendrian links and higher dimensional Legendrian spheres. The computations we perform work in finite characteristic, which significantly simplifies arguments and also allows us to show that there exist Legendrian links with infinitely many nonorientable exact Lagrangian fillings.
The higher regularity and decay estimates for positive solutions of fractional Choquard equations
Authors: Deng Yinbin , Yang Xian 
Published: February 2024

AbstractIn the paper, we study the higher regularity and decay estimates for positive solutions of the following fractional Choquard equations:

where , is a constant, , , , . Let be a positive solution of (). We obtain an optimal decay estimate for and reveal the relation between and the decay rate of for all permitting . We skillfully use the properties of Bessel kernel to deduce our main result by iteration. Moreover, by the decay estimates, the stronger regular estimates for are obtained.
A Volume-Averaged Hyperbolic System of Governing Equations for Granular Turbulent Flow Modeling With Phase Change
Authors: Balakrishnan Kaushik , Bellan Josette 
Published: February 2024

Abstract
A formulation is developed using volume-averaging and the concept of added mass to derive a hyperbolic system of governing equations for modeling turbulent, dense granular flows. The large eddy simulations (LES) framework is employed for the fluid phase, whereas the solid phase equations are based on enlarged Kinetic Theory concepts. To obtain the LES equations, the volume-averaged equations are filtered and the filtered terms not directly computable from the LES solution are generically modeled. Additionally, the pseudo-turbulent kinetic energy (PTKE) is included in the formulation and it is shown how its contribution is distinct from turbulence and leads to different terms that must be modeled in the conservation equations. Volume-averaging of the continuity, momentum and energy equations result in many integrals that are used to rigorously define the meaning of terms that have only been included heuristically in existing formulations. Simulations with this model are conducted in a configuration representing the interaction of a turbulent supersonic jet with a bed of solid particles. The results are analyzed to demonstrate hyperbolicity. Comparisons of results from a model including PTKE and one excluding it show that the inclusion of PTKE has no role in bestowing hyperbolicity to the model, and furthermore does not affect the macroscopic aspects of the crater. Comparisons between results obtained with a hyperbolic model and a model that is hyperbolic everywhere except in regions of particle/fluid interaction show that the macroscopic crater aspects are different, affecting the crater shape and topography.
In Situ Analysis of the Effect of Ultrasonic Cavitation on Electrochemical Polishing of Additively Manufactured Metal Surfaces
Authors: Jeon Ji Ho , Ahn Sung-Hoon , Melkote Shreyes N. 
Published: February 2024

Abstract
The effects of a hybrid process that combines ultrasonic cavitation and electrochemical polishing on the electrochemical behavior and the resulting surface characteristics of additively manufactured 316-L stainless steel were investigated. In situ potentiodynamic scans and electrochemical impedance spectroscopy (EIS) were conducted to gain a fundamental understanding of the effect of ultrasonic cavitation on the electrochemical processes involved, considering the influence of electrolyte temperature at 60 and 70 °C. The potentiodynamic scans revealed that increasing the ultrasonic excitation amplitude from 20 to 80 µm at 20 µm intervals and temperature from 60 to 70 °C led to reduced polishing resistance, and elevated passivation current density at equivalent applied potentials, thus leading to an increased polishing rate. These findings are attributed to intensified cavitation near the material surface, which promoted anodic dissolution reactions and accelerated the polishing rate. In situ EIS measurements provided valuable information on the charge transfer resistance and double-layer capacitance and their influence on the hybrid process. Specifically, higher ultrasonic amplitudes and elevated temperatures contributed to enhanced electrical double-layer formation and ion adsorption, resulting in a faster rate of polishing, indicating the efficacy of the hybrid process. These findings enhance our understanding of the complex interactions between ultrasonic cavitation and electrochemical dissolution processes that occur during ultrasonic cavitation-assisted electrochemical polishing. The research provides valuable insights for optimizing the process and its potential application in the post-processing of metal additive manufactured parts.
A Perspective on Plasticity, Dissipation and the Second Law of Thermodynamics
Authors: Needleman Alan 
Published: February 2024

Abstract
The requirement of a non-negative dissipation rate for all possible deformation histories is generally imposed on plastic constitutive relations. This is a constraint analogous to the Coleman–Noll [Coleman, B. D., and Noll, W., 1964, “The Thermodynamics of Elastic Materials With Heat Conduction and Viscosity,” Arch. Ration. Mech. Anal., 13, pp. 167–178. 10.1007/BF01262690] postulate that the Clausius–Duhem inequality needs to be satisfied for all possible deformation histories. The physical basis for the Clausius–Duhem inequality is as a statistical limit for a large number of discrete events for a long time and is not a fundamental physical requirement for small systems for a short time. The relation between the requirement of a non-negative dissipation rate and the Clausius–Duhem inequality is considered. The consequences of imposing a non-negative dissipation rate for all possible deformation histories are illustrated for: (i) a single crystal plasticity framework that accounts for elastic lattice curvature changes as well as elastic lattice straining and (ii) for discrete defect theories of plasticity, with attention specifically on discrete dislocation plasticity for crystalline solids and discrete shear transformation zone (STZ) plasticity for amorphous solids. Possible less restrictive conditions on the evolution of dissipation in plasticity formulations are considered as are implications for stability. The focus is on open questions and issues.
Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire
Authors: Shingai Masashi , Iida Sayaka , Kawai Naoko , Kawahara Mamiko , Sekiya Toshiki , Ohno Marumi , Nomura Naoki , Handabile Chimuka , Kawakita Tomomi , Omori Ryosuke , Yamagishi Junya , Sano Kaori , Ainai Akira , Suzuki Tadaki , Ohnishi Kazuo , Ito Kimihito , Kida Hiroshi 
Published: February 2024

ABSTRACT

Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future.

IMPORTANCE
As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis
Authors: P. Gomes Paulo Wender , Mannochio-Russo Helena , Mao Junhong , Zhao Haoqi Nina , Ancira Jacob , Tipton Craig D. , Dorrestein Pieter C. , Li Min 
Published: February 2024

ABSTRACT

Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence.
Staphylococcus
species, especially
S. aureus
, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL.
S. aureus
co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example
, Paracoccus
sp.,
Pseudomonas
sp.,
Prevotella bivia
,
Lactobacillus iners
,
Anaerococcus
sp.,
Micrococcus
sp.,
Corynebacterium ureicelerivorans
,
Corynebacterium massiliense
,
Streptococcus thermophilus
, and
Roseomonas mucosa
, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.

IMPORTANCE
This study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
First report of
bla
OXA-181
-carrying IncX3 plasmids in multidrug-resistant
Enterobacter hormaechei
and
Serratia nevei
recovered from canine and feline opportunistic infections
Authors: Leelapsawas Chavin , Sroithongkham Parinya , Payungporn Sunchai , Nimsamer Pattaraporn , Yindee Jitrapa , Collaud Alexandra , Perreten Vincent , Chanchaithong Pattrarat 
Published: February 2024

ABSTRACT

Whole-genome sequence analysis of six
Enterobacter hormaechei
and two
Serratia nevei
strains, using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing, revealed the presence of the epidemic
bla
OXA-181
-carrying IncX3 plasmids co-harboring
qnrS1
and ∆
ere
(A) genes, as well as multiple multidrug resistance (MDR) plasmids disseminating in all strains, originated from dogs and cats in Thailand. The subspecies and sequence types (ST) of the
E. hormaechei
strains recovered from canine and feline opportunistic infections included
E. hormaechei
subsp.
xiangfangensis
ST171 (
n
= 3), ST121 (
n
= 1), and ST182 (
n
= 1), as well as
E. hormaechei
subsp.
steigerwaltii
ST65 (
n
= 1). Five of the six
E. hormaechei
strains harbored an identical 51,479-bp
bla
OXA-181
-carrying IncX3 plasmid. However, the
bla
OXA-181
plasmid (pCUVET22-969.1) of the
E. hormaechei
strain CUVET22-969 presented a variation due to the insertion of IS
Kpn74
and IS
Sbo1
into the
virB
region. Additionally, the
bla
OXA-181
plasmids of
S. nevei
strains were nearly identical to the others at the nucleotide level, with IS
Ecl1
inserted upstream of the
qnrS1
gene. The
E. hormaechei
and
S. nevei
lineages from canine and feline origins might acquire the epidemic
bla
OXA-181
-carrying IncX3 and MDR plasmids, which are shared among Enterobacterales, contributing to the development of resistance. These findings suggest the spillover of significant OXA-181-encoding plasmids to these bacteria, causing severe opportunistic infections in dogs and cats in Thailand. Surveillance and effective hygienic practice, especially in hospitalized animals and veterinary hospitals, should be urgently implemented to prevent the spread of these plasmids in healthcare settings and communities.

IMPORTANCE

bla
OXA-181
is a significant carbapenemase-encoding gene, usually associated with an epidemic IncX3 plasmid found in Enterobacterales worldwide. In this article, we revealed six carbapenemase-producing (CP)
Enterobacter hormaechei
and two CP
Serratia nevei
strains harboring
bla
OXA-181
-carrying IncX3 and multidrug resistance plasmids recovered from dogs and cats in Thailand. The carriage of these plasmids can promote extensively drug-resistant properties, limiting antimicrobial treatment options in veterinary medicine. Since
E. hormaechei
and
S. nevei
harboring
bla
OXA-181
-carrying IncX3 plasmids have not been previously reported in dogs and cats, our findings provide the first evidence of dissemination of the epidemic plasmids in these bacterial species isolated from animal origins. Pets in communities can serve as reservoirs of significant antimicrobial resistance determinants. This situation places a burden on antimicrobial treatment in small animal practice and poses a public health threat.
Management of lower extremity vascular injuries in pediatric trauma patients: 20-year experience at a level 1 trauma center
Authors: Lyons Nicole B , Berg Arthur , Collie Brianna L , Meizoso Jonathan P , Sola Juan E , Thorson Chad M , Proctor Kenneth G , Namias Nicholas , Pizano Louis R , Marttos Antonio C , Sciarretta Jason D 
Published: February 2024

IntroductionPediatric lower extremity vascular injuries (LEVI) are rare but can result in significant morbidity. We aimed to describe our experience with these injuries, including associated injury patterns, diagnostic and therapeutic challenges, and outcomes.MethodsThis was a retrospective review at a single level 1 trauma center from January 2000 to December 2019. Patients less than 18 years of age with LEVI were included. Demographics, injury patterns, clinical status at presentation, and intensive care unit (ICU) and hospital length of stay (LOS) were collected. Surgical data were extracted from patient charts.Results4,929 pediatric trauma patients presented during the 20-year period, of which 53 patients (1.1%) sustained LEVI. The mean age of patients was 15 years (range 1–17 years), the majority were Black (68%), male (96%), and most injuries were from a gunshot wound (62%). The median Glasgow Coma Scale score was 15, and the median Injury Severity Score was 12. The most commonly injured arteries were the superficial femoral artery (28%) and popliteal artery (28%). Hard signs of vascular injury were observed in 72% of patients and 87% required operative exploration. There were 36 arterial injuries, 36% of which were repaired with a reverse saphenous vein graft and 36% were repaired with polytetrafluoroethylene graft. One patient required amputation. Median ICU LOS was three days and median hospital LOS was 15 days. There were four mortalities.ConclusionPediatric LEVIs are rare and can result in significant morbidity. Surgical principles for pediatric vascular injuries are similar to those applied to adults, and this subset of patients can be safely managed in a tertiary specialized center.Level of evidenceLevel IV, retrospective study.
Primordial black holes and secondary gravitational waves from generalized power-law non-canonical inflation with quartic potential
Authors: Heydari Soma , Karami Kayoomars 
Published: February 2024

AbstractHere, generation of PBHs and secondary GWs from non-canonical inflation with quartic potential have been probed. It is illustrated that, quartic potential in non-canonical setup with a generalized power-law Lagrangian density can source a consistent inflationary era with the latest observational data. Besides, we show that our model satisfies the swampland criteria. At the same time, defining a peaked function of inflaton field as non-canonical mass scale parameter $$M(\phi )$$

M
(
ϕ
)

of the Lagrangian, gives rise to slow down the inflaton in a while. In this span, namely Ultra-Slow-Roll (USR) stage, the amplitude of the curvature perturbations on small scales enlarges versus CMB scales. It has been illustrated that, further to the peaked aspect of the chosen non-canonical mass scale parameter, the amount of $$\alpha $$
α
parameter of the Lagrangian has enlarging impact on the amplitude of the scalar perturbations. As a consequence of adjusting three parameter Cases of this model, three Cases of PBHs in proper mass scopes to explain LIGO-VIRGO events, microlensing events in OGLE data and DM content in its totality, could be produced. In the end, power-law behavior of the current density parameter of gravitational waves $$\Omega _{\mathrm{GW_0}}$$

Ω

GW
0

in terms of frequency has been examined. Also, the logarithmic power index as $$n=3-2/\ln (f_c/f)$$

n
=
3
-
2
/
ln
(

f
c

/
f
)

in the infrared regime is obtained.
Choosing Wisely: Applying Value-Based Economic Principles to Population Science Research Investment
Authors: Frick Kevin D. , Helzlsouer Kathy J. 
Published: February 2024

Abstract
Scientific research requires a substantial investment of time, effort, and money by researchers and funders. The funding that would be needed for all meritorious proposals far exceeds available resources. Major funding organizations use a multistep process for allocating research dollars that follows and extends beyond scientific peer review with considerations including mission priority, budget, and potential duplication of past or ongoing research activities. At the level of programmatic review, the process tends to be less proscribed than scientific review, but considerations relate to and are akin to basic value-driven economic principles. We propose a framework that encompasses the elements of programmatic review and provide examples of how the economic principles of opportunity costs, diminishing marginal productivity, sunk costs, economic optimization, return on investment, and option value apply to both research planning and funding decisions. Examples use cancer control population science research, as the nature of observational and interventional research involves large population studies (large sample size, recruitment, and often long-duration follow-up costs) which demand a high level of resource utilization; the same principles can be applied throughout medical and population health research. Awareness of the aspects of programmatic review and context to focus discussion regarding funding decisions may help guide research planning, decision-making, and increase transparency of the overall review process.
Trends of Prostate Cancer Morbidity in Low-Incidence Countries from 1990–2019
Authors: Jiang Jinjiang , Chen Bo , Tang Bo , Yang Jie , Zhang Ting , Li Jinze , Tan Daqing , Wei Qiang 
Published: February 2024

Abstract

Background:
Our study was designed to elucidate the morbidity trends of prostate cancer in low-incidence countries.

Methods:
Data on prostate cancer were extracted from the 2019 Global Burden of Disease study. A cluster analysis of growth rates stratified by age was conducted, and correlation analyses were performed between age-standardized incidence rates (ASIR), estimated annual percent change (EAPC), and socio-demographic index (SDI).

Results:
Among 35 low-incidence countries for prostate cancer, predominantly located in Asia and North Africa, the SDI ranged from low to high-middle levels. Higher SDI regions exhibited considerably higher ASIR. With the exception of Kyrgyzstan, Kiribati, and Samoa that experienced a decrease in ASIR, the remaining 32 countries displayed an upward morbidity trend since 1990, with all their EAPCs exceeding the global average. In addition, men ages 90 years and above consistently exhibited the highest ASIR for prostate cancer. The most notable growth rate of ASIR was observed in individuals ages 20 to 44 years.

Conclusions:
Overall, low-incidence countries generally witnessed an increase in prostate cancer morbidity, albeit at levels lower than those seen in Western countries. Individuals ages 90 years and above consistently maintained the highest ASIR since 1990. Notably, more substantial increase of ASIR in younger age was also observed in low-incidence countries.

Impact:
This study offers a comprehensive overview of prostate cancer morbidity in low-incidence countries worldwide from 1990 to 2019. Future research should delve into the associations between incidence, clinical stages, PSA screening, environmental factors, lifestyle, and genetic risk in these low-incidence countries.
Cracking the Genomic Code of CDK4/6 Inhibitor Resistance
Authors: Wander Seth A. , Bardia Aditya 
Published: February 2024

SummaryThe therapeutic approach to metastatic hormone receptor–positive, human epidermal growth factor-2–negative metastatic breast cancer (HR+/HER2− MBC) has evolved rapidly over recent years. The cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) have become first-line targeted agents of choice, in combination with an antiestrogen. Simultaneously, the clinical landscape of therapeutic options has been rapidly shifting, with novel antiestrogens, signal transduction inhibitors, and next-generation CDK inhibitors in various stages of development. Given these dynamic changes, understanding the genomic and molecular landscape of resistance to currently available antiestrogen therapy and CDK4/6 inhibitors represents a major focus of translational breast cancer research globally.See related article by Goetz et al., p. 2233
Understanding Mechanisms of Response to CAR T-cell Therapy through Single-Cell Sequencing: Insights and Challenges
Authors: Haradhvala Nicholas J. , Maus Marcela V. 
Published: February 2024

Summary:
Single-cell RNA sequencing has emerged as a powerful technique to understand the molecular features of chimeric antigen receptor (CAR) T cells that associate with clinical outcomes. Here we discuss the common themes that have emerged from across single-cell studies of CAR T-cell therapy, and summarize the challenges in interpreting this complex data type.