bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitigation of thermal artifacts in 100 kHz ultrafast 2D IR spectroscopy
Authors: Esterly Harrison J. , Shivani Shivani T. , Farrell Kieran M. , Zanni Martin T.
Published: December 2024

Ytterbium lasers make possible shot-to-shot data collection of two-dimensional infrared (2D IR) spectra at 100 kHz and higher repetition rates. At those rates, the power absorbed by the sample is appreciable and creates a steady state temperature rise and an accumulated thermal grating artifact in the spectra that can obscure weak or low concentration IR chromophores. We report the magnitude of the temperature rise, the pulse ordering by which it is created, and ways to mitigate it. Using a calibrant molecule, we measured a steady-state temperature up to 32.5 and 45 °C for laser light at 4 µm in H2O and 6 µm in D2O, respectively, for a typical optical density used in 2D IR experiments. The temperature reached a steady state in ∼60 s. The temperature rise scales with the integrated optical density of the sample across the laser spectrum. By cooling the sample cell, we returned the steady state temperature to room temperature within the laser focus. For samples that undergo rotation, the accumulated thermal grating artifact is removed using a perpendicular ⟨XXYY⟩ polarization because the permuted time-orderings of the thermal grating artifact has the orientational response ⟨XYXY⟩, which decays to zero during the delay between consecutive laser pulses. The procedure described in this study can be used to characterize and minimize the thermal effects in experiments where repetition rate and/or pulse energy cause an appreciable temperature rise.
Characterization of gliding arc plasma ignition in aeroengine swirl combustion chamber
Authors: Zhang Lei , Yu Jinlu , Su Wenhao , Ma Shuaihao , Wu Xing , Wang Xiaomin
Published: December 2024

Gliding arc plasma-enhanced combustion is a relatively new combustion technology. This paper describes a gliding arc plasma combustion dome that improves the ignition characteristics of aeroengines. The ignition characteristics are studied using an experimental platform consisting of a single-combustion-dome swirl combustion chamber. A flame spontaneous radiation imaging technique is adopted to collect the C2* groups formed during the ignition process. We focus on the ignition mode, flame kernel propagation mechanism, ignition delay time, and ignition boundary of the gliding arc ignition process. The gliding arc ignition process has five stages with different characteristics: flame kernel stabilization, flame kernel expansion, intense combustion, combustion decay, and stable combustion. During the flame kernel propagation stage, the main flame kernel in the combustion dome splits into flame kernel 1, located in the recirculation zone of the upper wall, and flame kernel 2, located in the recirculation zone of the lower wall under the action of airflow. The main flame kernel reflects the direct action of the gliding arc. Unconsumed energy and active particles included in the main flame kernel are added to flame kernels 1 and 2 through sporadic splitting of the main kernel. This promotes the expansion rate of the fire nucleus in the combustion chamber. Compared with electric spark ignition, gliding arc plasma-enhanced combustion significantly widens the ignition boundary and shortens the ignition delay time of the combustion chamber. The ignition delay time can be shortened by up to 81.53% under an inlet flow rate of 55 m/s and a residual gas coefficient of 3; the ignition boundary can be widened by a maximum of 115.9% under an inlet flow rate of 5 m/s.
Novel predefined-time stability theory and its application in sliding mode control of synchronizing chaotic systems
Authors: Liu Jingang , Li Ruiqi
Published: December 2024

Aiming at predefined-time synchronization for chaotic systems, a new predefined-time sliding mode control method is proposed. First, based on the definition of predefined-time stability, a novel predefined-time inequality is proposed, along with a detailed mathematical proof. This inequality differs from existing Lyapunov inequalities and offers greater flexibility. Second, a new sliding mode surface and sliding mode controller are proposed based on this inequality. Since the sliding mode controller introduced in this paper is tunable, the actual convergence time can be adjusted freely within the predefined time. Finally, two sets of numerical simulations demonstrate that the proposed method offers advantages in terms of short synchronization time and high regulatory performance compared to traditional predefined-time sliding mode control, finite-time sliding mode control, and fixed-time sliding mode control.
A high-order no image point sharp interface immersed boundary method for compressible flows
Authors: Huang Chuyun , Yang Yantao , Cai Qingdong
Published: December 2024

A high-order no-image point sharp interface immersed boundary method for compressible flow is presented. The method comprises a stable high-order compact scheme and a ghost point value determination method. By regulating dissipation, the stability of the compact scheme for either Dirichlet or Neumann boundary conditions is validated by the von Neumann method in one dimension. With regard to the use of ghost points, mirror points or Lagrange points are no longer employed. The boundary conditions at the intersection of arbitrary geometries and Cartesian grids are imposed on the basis function of Taylor polynomial interpolation, along with weighted least squares error minimization, in order to determine the values of the ghost points. Third-order accuracy is maintained for both subsonic and supersonic inviscid flow. Numerical simulations of several two-dimensional benchmark problems are carried out to provide evidence about the convergence order of the method.
TRPC6 is a mechanosensitive channel essential for ultrasound neuromodulation in the mammalian brain
Authors: Matsushita Yumi , Yoshida Kaede , Yoshiya Miyuki , Shimizu Takahiro , Tsukamoto Satoshi , Kudo Nobuki , Takeuchi Yuichi , Higuchi Makoto , Shimojo Masafumi
Published: December 2024

Ultrasound neuromodulation has become an innovative technology that enables noninvasive intervention in mammalian brain circuits with high spatiotemporal precision. Despite the expanding utility of ultrasound neuromodulation in the neuroscience research field and clinical applications, the molecular and cellular mechanisms by which ultrasound impacts neural activity in the brain are still largely unknown. Here, we report that transient receptor potential canonical 6 (TRPC6), a mechanosensitive nonselective cation channel, is essential for ultrasound neuromodulation of mammalian neurons in vitro and in vivo. We first demonstrated that ultrasound irradiation elicited rapid and robust Ca
2+
transients mediated via extracellular Ca
2+
influx in cultured mouse cortical and hippocampal neurons. Ultrasound-induced neuronal responses were massively diminished by blocking either the generation of action potential or synaptic transmission. Importantly, both pharmacological inhibition and genetic deficiency of TRPC6 almost completely abolished neuronal responses to ultrasound. Furthermore, we found that intracerebroventricular administration of a TRPC6 blocker significantly attenuated the number of neuronal firings in the cerebral cortex evoked by transcranial ultrasound irradiation in mice. Our findings indicate that TRPC6 is an indispensable molecule of ultrasound neuromodulation in intact mammalian brains, providing fundamental understanding of biophysical molecular mechanisms of ultrasound neuromodulation as well as insight into its future feasibility in neuroscience and translational research in humans.
Caspase-8-dependent autophagy regulates neutrophil infiltration in oral squamous cell carcinoma
Authors: Bernabé-Rubio Miguel , Watt Fiona M.
Published: December 2024

Oral squamous cell carcinoma (OSCC) is a subtype of head and neck cancer that arises in the multilayered epithelia of the mouth and lips. Although inactivating mutations in
CASP8
are frequently found in human OSCC their role in the disease is unknown. To investigate this, we deleted
Casp8
in the oral epithelium of adult mice. Loss of Caspase-8 resulted in defects in the tongue epithelial barrier and triggered a neutrophil-rich immune infiltrate distinct from that observed on epidermal
Casp8
deletion. Oral
Casp8
deletion led to activation of autophagy. Inhibition of autophagy partially rescued epithelial integrity in
Casp8
−/−
mice, while induction of autophagy in wild type mice resulted in oral barrier defects and excessive neutrophil infiltration. On treatment with the carcinogen 4-nitroquinoline-1-oxide
Casp8
−/−
mice showed increased susceptibility to developing oral tumors. Depletion of neutrophils reduced tumor incidence, which correlated with a reduction in reactive oxygen species and decreased epithelial DNA damage. Our findings establish a functional link between epithelial integrity, autophagy, and the tumor immune microenvironment, placing Caspase-8 at the center of these processes.
Active doping controls the mode of failure in dense colloidal gels
Authors: Zhou Tingtao , Brady John F.
Published: December 2024

Mechanical properties of disordered materials are governed by their underlying free energy landscape. In contrast to external fields, embedding a small fraction of active particles within a disordered material generates nonequilibrium internal fields, which can help to circumvent kinetic barriers and modulate the free energy landscape. In this work, we investigate through computer simulations how the activity of active particles alters the mechanical response of deeply annealed polydisperse colloidal gels. We show that the “swim force” generated by the embedded active particles is responsible for determining the mode of mechanical failure, i.e., brittle vs. ductile. We find, and theoretically justify, that at a critical swim force the mechanical properties of the gel decrease abruptly, signaling a change in the mode of mechanical failure. The weakening of the elastic modulus above the critical swim force results from the change in gel porosity and distribution of attractive forces among gel particles, while below the critical swim force, the ductility enhancement is caused by an increase of gel structural disorder. Above the critical swim force, the gel develops a pronounced heterogeneous structure characterized by multiple pore spaces, and the mechanical response is controlled by dynamical heterogeneities. We contrast these results with those of a simulated monodisperse gel that exhibits a nonmonotonic trend of ductility modulation with increasing swim force, revealing a complex interplay between the gel energy landscape and embedded activity.
Permafrost thaw subsidence, sea-level rise, and erosion are transforming Alaska’s Arctic coastal zone
Authors: Creel Roger , Guimond Julia , Jones Benjamin M. , Nielsen David M. , Bristol Emily , Tweedie Craig E. , Overduin Pier Paul
Published: December 2024

Arctic shorelines are vulnerable to climate change impacts as sea level rises, permafrost thaws, storms intensify, and sea ice thins. Seventy-five years of aerial and satellite observations have established coastal erosion as an increasing Arctic hazard. However, other hazards at play—for instance, the cumulative impact that sea-level rise and permafrost thaw subsidence will have on permafrost shorelines—have received less attention, preventing assessments of these processes’ impacts compared to and combined with coastal erosion. Alaska’s Arctic Coastal Plain (ACP) is ideal for such assessments because of the high-density observations of topography, coastal retreat rates, and permafrost characteristics, and importance to Indigenous communities and oilfield infrastructure. Here, we produce 21st-century projections of Arctic shoreline position that include erosion, permafrost subsidence, and sea-level rise. Focusing on the ACP, we merge 5 m topography, satellite-derived coastal lake depth estimates, and empirical assessments of land subsidence due to permafrost thaw with projections of coastal erosion and sea-level rise for medium and high emissions scenarios from the Intergovernmental Panel on Climate Change’s AR6 Report. We find that by 2100, erosion and inundation will together transform the ACP, leading to 6-8x more land loss than coastal erosion alone and disturbing 8-11x more organic carbon. Without mitigating measures, by 2100, coastal change could damage 40 to 65% of infrastructure in present-day ACP coastal villages and 10 to 20% of oilfield infrastructure. Our findings highlight the risks that compounding climate hazards pose to coastal communities and underscore the need for adaptive planning for Arctic coastlines in the 21st century.
Glutamine is critical for the maintenance of type 1 conventional dendritic cells in normal tissue and the tumor microenvironment
Authors: Lobel Graham P. , Han Nanumi , Molina Arocho William A. , Silber Michal , Shoush Jason , Noji Michael C. , To Tsun Ki Jerrick , Zhai Li , Lesner Nicholas P. , Simon M. Celeste , Haldar Malay
Published: December 2024

Proliferating tumor cells take up glutamine for anabolic processes, engendering glutamine deficiency in the tumor microenvironment. How this might impact immune cells is not well understood. Using multiple mouse models of soft tissue sarcomas, glutamine antagonists, as well as genetic and pharmacological inhibition of glutamine utilization, we found that the number and frequency of conventional dendritic cells (cDCs) is dependent on microenvironmental glutamine levels. cDCs comprise two distinct subsets—cDC1s and cDC2s, with the former subset playing a critical role in antigen cross-presentation and tumor immunity. While both subsets show dependence on glutamine, cDC1s are particularly sensitive. Notably, glutamine antagonism did not reduce the frequency of DC precursors but decreased the proliferation and survival of cDC1s. Further studies suggest a role of the nutrient sensing mechanistic target of rapamycin (mTOR) signaling pathway in this process. Taken together, these findings uncover glutamine dependence of cDC1s that is coopted by tumors to escape immune responses.
Direct simulation and machine learning structure identification unravel soft martensitic transformation and twinning dynamics
Authors: Fukuda Jun-ichi , Takahashi Kazuaki Z.
Published: December 2024

Phase transition between ordered phases has garnered attention from the viewpoint of materials science as well as statistical physics. One interesting example is martensitic transformation and the resulting formation of twin structures, in which atoms or molecules that form one crystalline phase move in a concerted and diffusionless manner toward another crystalline phase. Recently martensitic transformation has been observed experimentally also in various soft materials. However, the complex internal structures involving many molecules have eluded direct investigation of the dynamical processes of martensitic transformation. Here, we carry out a direct simulation of mesoscale structural transition of a liquid crystalline blue phase (BP) of cubic symmetry, known as BP II. The dynamics is simulated by a Langevin-type equation for the orientational order parameter with thermal fluctuations. We demonstrate that machine-learning-aided analysis of local structures successfully unravels the transformation process from a perfect lattice of BP II to a twinned lattice of another BP (BP I). The nucleation of BP I is initiated by the breakup of junctions of line defects (disclinations), followed by the deformation of disclination network. We further show that twinned BP I is reversibly transformed to a perfect lattice of BP II by temperature variation. Order-parameter-based simulations with machine-learning-aided local structure identification provide valuable insights into not only the martensitic transformation of soft materials but also a wider class of complex structural transitions between ordered phases.
Structure of yeast RAVE bound to a partial V
1
complex
Authors: Wang Hanlin , Tarsio Maureen , Kane Patricia M. , Rubinstein John L.
Published: December 2024

Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V
1
subcomplex and a membrane-embedded proton-translocating V
O
subcomplex. The V
1
and V
O
subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V
1
and V
O
requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast
Saccharomyces cerevisiae
, RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V
1
. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V
1
. Only Rav1p interacts with V
1
, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V
1
is in a rotational state suitable for binding the free V
O
complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V
1
complex with RAVE appears poised for reassembly with V
O
.
Quantum oscillations in the hole-doped cuprates and the confinement of spinons
Authors: Bonetti Pietro M. , Christos Maine , Sachdev Subir
Published: December 2024

A long-standing problem in the study of the under-hole-doped cuprates has been the description of the Fermi surfaces underlying the high magnetic field quantum oscillations, and their connection to the higher temperature pseudogap metal. Harrison and Sebastian [
Phys. Rev. Lett.
106
, 226402 (2011)] proposed that the pseudogap “Fermi arcs” are reconstructed into an electron pocket by field-induced charge density wave order. But computations on such a model [Zhang and Mei,
Europhys. Lett.
114
, 47008 (2016)] show an unobserved additional oscillation frequency from a Fermi surface arising from the backsides of the hole pockets completing the Fermi arcs. We describe a transition from a fractionalized Fermi liquid (FL*) model of the pseudogap metal, to a metal with bidirectional charge density wave order without fractionalization. We show that the confinement of the fermionic spinon excitations of the FL* across this transition can eliminate the unobserved oscillation frequency.
Morphological complexity as a predictor of cognitive effort in neural machine translation post-editing
Authors: Abu-Rayyash Hussein , Alhawamdeh Shatha
Published: December 2024

This study examines how morphological complexity affects cognitive effort in neural machine translation (NMT)
post-editing across six languages. Analysis of the DivEMT dataset shows that morphologically richer target languages like
Ukrainian and Turkish require more editing time, keystrokes, and frequent pauses, indicating higher cognitive demands. Vietnamese,
despite simpler morphology, also showed high cognitive effort, suggesting other factors like syntax influence processing load.
Mean Size of Paradigm (MSP) analysis confirmed Ukrainian and Turkish’s high morphological complexity compared to isolating
languages like Vietnamese. Higher error rates in morphologically rich languages demonstrate increased editing needs. While user
perceptions varied, the data reveals that greater linguistic distance correlates with higher cognitive effort in NMT post-editing,
showing typological divergence impacts beyond morphology alone.
One step 4× and 12× 3D-ExM enables robust super-resolution microscopy of nanoscale cellular structures
Authors: Norman Roshan X. , Chen Yu-Chia , Recchia Emma E. , Loi Jonathan , Rosemarie Quincy , Lesko Sydney L. , Patel Smit , Sherer Nathan , Takaku Motoki , Burkard Mark E. , Suzuki Aussie
Published: December 2024

Super-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared with traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4× and 12× 3D-ExM). 3D-ExM is a straightforward expansion microscopy technique featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12× 3D-ExM achieves a lateral resolution of <30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein–Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.
Genetic and environmental risks for clonal hematopoiesis and cancer
Authors: Franco Stephanie , Godley Lucy A.
Published: December 2024

Somatic variants accumulate in all organs with age, with a positive selection of clonal populations that provide a fitness advantage during times of heightened cellular stress leading to clonal expansion. Easily measured within the hematopoietic compartment, clonal hematopoiesis (CH) is now recognized as a common process in which hematopoietic clones with somatic variants associated with hematopoietic neoplasms exist within the blood or bone marrow of individuals without evidence of malignancy. Most cases of CH involve a limited number of genes, most commonly DNMT3A, TET2, and ASXL1. CH confers risk for solid and hematopoietic malignancies as well as cardiovascular and numerous inflammatory diseases and offers opportunities for cancer prevention. Here, we explore the genetic and environmental factors that predispose individuals to CH with unique variant signatures and discuss how CH drives cancer progression with the goals of improving individual cancer risk stratification, identifying key intervention opportunities, and understanding how CH impacts therapeutic strategies and outcomes.
Embedding unicritical connectedness loci
Authors: Mukundan Malavika
Published: December 2024

In this article, for degree

d
≥
1

d\geq 1

, we construct an embedding

Φ
d

\Phi _d

of the connectedness locus

M

d
+
1

\mathcal {M}_{d+1}

of the polynomials

z

d
+
1

+
c

z^{d+1}+c

into the connectedness locus of degree

2
d
+
1

2d+1

bicritical odd polynomials.
Connections between metric differentiability and rectifiability
Authors: Caamaño Iván , Durand-Cartagena Estibalitz , Jaramillo Jesús , Prieto Ángeles , Soultanis Elefterios
Published: December 2024

We combine Kirchheim’s metric differentials with Cheeger charts in order to establish a non-embeddability principle for any collection

C

\mathcal C

of Banach (or metric) spaces: if a metric measure space

X
X

bi-Lipschitz embeds in some element in

C

\mathcal C

, and if every Lipschitz map

X
→
Y
∈

C

X\to Y\in \mathcal C

is differentiable, then

X
X

is rectifiable. This gives a simple proof of the rectifiability of Lipschitz differentiability spaces that are bi-Lipschitz embeddable in Euclidean space, due to Kell–Mondino. Our principle also implies a converse to Kirchheim’s theorem: if all Lipschitz maps from a domain space to arbitrary targets are metrically differentiable, the domain is rectifiable. We moreover establish the compatibility of metric and

w
∗

w^*

-differentials of maps from metric spaces in the spirit of Ambrosio–Kirchheim.
Anytime valid and asymptotically efficient inference driven by predictive recursion
Authors: Dixit Vaidehi , Martin Ryan
Published: December 2024

Distinguishing two candidate models is a fundamental and practically important statistical problem. Error rate control is crucial to the testing logic but, in complex nonparametric settings, can be difficult to achieve, especially when the stopping rule that determines the data collection process is not available. This paper proposes an e-process construction based on the predictive recursion algorithm originally designed to recursively fit nonparametric mixture models. The resulting predictive recursion process affords anytime valid inference and is asymptotically efficient in the sense that its growth rate is first-order optimal relative to the predictive recursion’s mixture model.
Artificial intelligence and digital tools for design and execution of cardiovascular clinical trials
Authors: Hu Jiun-Ruey , Power John R , Zannad Faiez , Lam Carolyn S P
Published: December 2024

Recent advances have given rise to a spectrum of digital health technologies that have the potential to revolutionize the design and conduct of cardiovascular clinical trials. Advances in domain tasks such as automated diagnosis and classification, synthesis of high-volume data and latent data from adjacent modalities, patient discovery, telemedicine, remote monitoring, augmented reality, and in silico modelling have the potential to enhance the efficiency, accuracy, and cost-effectiveness of cardiovascular clinical trials. However, early experience with these tools has also exposed important issues, including regulatory barriers, clinical validation and acceptance, technological literacy, integration with care models, and health equity concerns. This narrative review summarizes the landscape of digital tools at each stage of clinical trial planning and execution and outlines roadblocks and opportunities for successful implementation of digital tools in cardiovascular clinical trials.
On Liftings of Modules of Finite Projective Dimension
Authors: KC Nawaj , Soto Levins Andrew J
Published: December 2024

We introduce and study a notion of Serre liftable modules; these are modules that are liftable to modules of the maximal possible dimension over a regular local ring. We establish new cases of Serre’s positivity conjecture over ramified regular local rings by proving it for Serre liftable modules. Furthermore, we show that the length of a nonzero Serre liftable module is bounded below by the Hilbert–Samuel multiplicity of the local ring. This establishes special cases of the Length Conjecture of Iyengar–Ma–Walker.
Oral ciprofloxacin biofilm activity in a catheter-associated urinary tract infection model
Authors: Abbott Iain J , Anderson Connor R B , van Gorp Elke , Wallis Steve C , Roberts Jason A , Meletiadis Joseph , Peleg Anton Y
Published: December 2024

Background

Catheter-associated urinary tract infections (CA-UTIs) are a common hospital-acquired infection. We examined ciprofloxacin activity in a novel CA-UTI in vitro model.

Methods

Three ATCC strains [Escherichia coli (ECO)-25922, Klebsiella pneumoniae (KPN)-700721, Pseudomonas aeruginosa (PAE)-27853] and 45 clinical urinary isolates were assessed. Biofilm mass and planktonic bacterial density were quantified during drug-free incubation (72 h) and following ciprofloxacin exposure (equivalent 750 mg orally q12h, 3 days).

Results

ECO produced smaller biofilms (6.3 ± 1.1 log10 cfu/cm2) compared with KPN (7.1 ± 0.7 log10 cfu/cm2) and PAE (7.0 ± 1.2 log10 cfu/cm2), which extended along the entire catheter length. Following ciprofloxacin, all isolates with MIC > 4 mg/L had minimal biofilm disruption or planktonic kill. Ciprofloxacin resistance was most common in PAE isolates (10/16 isolates), compared with ECO (3/16 isolates) and KPN (6/16 isolates). Greater ciprofloxacin exposure (AUC0–24/MIC) was required for a 3 log10 biofilm kill for KPN (5858; R2 = 0.7774) compared with ECO (2117; R2 = 0.7907) and PAE (2485; R2 = 0.8260). Due to persistent growth in the bladder, ECO required greater ciprofloxacin exposure for a 3 log10 planktonic kill (5920; R2 = 0.8440) compared with KPN (2825; R2 = 0.9121) and PAE (1760; R2 = 0.8781). Monte Carlo simulation supported a 95% PTA for both a 3 log10 biofilm and planktonic kill for ECO and KPN isolates with MIC ≤ 0.5 mg/L and PAE isolates with MIC ≤ 1 mg/L.

Conclusions

In a novel CA-UTI model, following simulated ciprofloxacin therapy, KPN biofilms were comparatively more difficult to disrupt, ECO planktonic growth frequently persisted in the bladder, and PAE had greater propensity for emergence of ciprofloxacin resistance.
Combining density forecast accuracy tests: an application to agricultural, energy, and metal commodities
Authors: Algieri Bernardina , Leccadito Arturo , Sicoli Danilo , Tunaru Diana
Published: December 2024

This study develops a new methodology for combining density forecast accuracy tests and assessing the relevance of psychological indicators in predicting commodity returns. Density forecasts provide a complete description of the uncertainty associated with a prediction and are highly requested by policymakers, central bankers, and financial operators to define policy actions, manage financial risks, and assess portfolio selection. The proposed methodology combines different tests and derives the p-value of the resulting test statistic by Monte Carlo simulations. To assess the power of the proposed methodology, we implement a set of experiments for several data-generating processes. Based on an empirical forecasting exercise applied to agricultural, energy, and metal commodities, we find that sentiment variables and psychological factors improve the density forecasts of commodity futures returns, especially for agricultural commodities. Additionally, combinations of sentiment variables are more powerful in predicting returns than considering them separately.
Personalized dynamic super learning: an application in predicting hemodiafiltration convection volumes
Authors: Chatton Arthur , Bally Michèle , Lévesque Renée , Malenica Ivana , Platt Robert W , Schnitzer Mireille E
Published: December 2024

Obtaining continuously updated predictions is a major challenge for personalized medicine. Leveraging combinations of parametric regressions and machine learning algorithms, the personalized online super learner (POSL) can achieve such dynamic and personalized predictions. We adapt POSL to predict a repeated continuous outcome dynamically and propose a new way to validate such personalized or dynamic prediction models. We illustrate its performance by predicting the convection volume of patients undergoing hemodiafiltration. POSL outperformed its candidate learners with respect to median absolute error, calibration-in-the-large, discrimination, and net benefit. We finally discuss the choices and challenges underlying the use of POSL.
Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression
Authors: Hajheidari Mohsen , Sunyaev Shamil , de Meaux Juliette
Published: December 2024

Variation in complex traits is controlled by multiple genes. The prevailing assumption is that such polygenic complex traits are underpinned by variation in elementary molecular traits, such as gene expression, which themselves have a simple genetic basis. Here, we review recent advances that reveal the captivating complexity of gene regulation: the cell type, time point, and magnitude of gene expression are not merely dependent on a couple of regulators; rather, they result from a probabilistic process shaped by cis- and trans-regulatory elements collaboratively integrating internal and external cues with the tightly regulated dynamics of DNA. In addition, the finding that genetic variants linked to complex diseases in humans often do not co-localize with quantitative trait loci modulating gene expression, along with the role of nonfunctional transcription factor (TF) binding sites, suggests that some of the genetic effects influencing gene expression variation may be indirect. If the number of genomic positions responsible for TF binding, TF binding site search time, DNA conformation and accessibility as well as regulation of all trans-acting factors is indeed vast, is it plausible that the complexity of elementary molecular traits approaches the complexity of higher-level organismal traits? Although it is hard to know the answer to this question, we motivate it by reviewing the complexity of the molecular machinery further.
Perspectives on the use of ChatGPT in academic publications
Authors: Kardes Guzin , Tuna Oran Nazan
Published: December 2024

The use of ChatGPT, an artifcial intelligence-based language model, in article writing has raised ethical issues such as authorship, plagiarism, and errors in references. In this research, we aimed to examine the use of ChatGPT in academic publications from an ethical perspective. In the procedures published by many publishers, it is stated that ChatGPT cannot be accepted as an author, but support can be received from them in cases such as translation, and this support should be clearly stated in the acknowledgment section of the article. However, there is a need for programs that can objectively evaluate the sections where ChatGPT is used, rather than relying on the subjective statements of the authors regarding for which parts of the article they have received support from ChatGPT. With the correct use of this technology, it is thought that concerns in the field of academia can be eliminated in the near future.
New fungicide options for managing Sclerotinia blight of peanut
Authors: Batista da Silva Mychele , Langston David
Published: December 2024

Late leaf spot (LLS), caused by Nothopassalora personata, and Sclerotinia blight (SB), caused by Sclerotinia minor, are significant diseases affecting peanut production in Virginia. Field trials were conducted in 2020 - 2022 at two locations per year to identify fungicide programs that manage both diseases. In 2020, pydiflumetofen applied independently, as well as in combination with a premix of azoxystrobin + benzovindiflupyr, provided effective protection against both LLS and SB. This combination demonstrated potential as a cost-effective alternative to fluazinam. Years 2021 and 2022 focused on the most effective timing of pydiflumetofen and the premix of azoxystrobin + benzovindiflupyr. Results demonstrated that the combination of pydiflumetofen and the premix of azoxystrobin + benzovindiflupyr applied 60 and 90 days after planting was most consistent in providing the greatest efficacy against both diseases while improving yield. The tank-mix/premix combination of pydiflumetofen and azoxystrobin + benzovindiflupyr offers effective and economical management of both LLS and SB compared to fungicide programs where fluazinam is added for SB management only.
Pregnancy and Pregnancy Outcomes in a National Population Cohort of Patients Treated for Substance Use Disorders
Authors: Bretteville-Jensen Anne Line , Williams Jenny
Published: December 2024

Objectives

The objectives of this study were to i) provide population-level prevalence rates of pregnancy, birth, elective termination, and miscarriage among females treated for SUDs and their demographic counterparts and ii) examine associations between SUD treatment and pregnancy and elective terminations.

Methods

Data were analyzed from a prospective registry-linkage study of all females (15–45 years) recorded as treated for SUDs in the Norwegian Patient Registry over a 2-year period (n = 6470) and a non-treated frequency-matched cohort of females from the general population (n = 6286). Pregnancy and pregnancy outcomes over a 4-year follow-up were retrieved from the Norwegian Patient Registry. Multivariable logistic regression models tested for associations of SUD treatment with pregnancy and with elective termination among pregnant females.

Results

Annual pregnancy and elective termination rates per 1000 females were significantly higher for the SUD cohort than the non-treated cohort (94.2 vs 71.3 for pregnancy, P < 0.001; 54.7 vs 17.8 for elective termination, P < 0.001), the annual birth rate was lower for the SUD cohort (25.3 vs 41.8, P < 0.001), and the rate of miscarriage did not differ across cohorts. Multivariable analysis showed that SUD treatment was associated with a significant increase in the odds of pregnancy (adjusted Odds Ratio 1.34, Confidence Interval [1.18–1.54]) and the odds of an elective termination, conditional on pregnancy (aOR 2.55, Confidence Interval [1.97–3.29]).

Conclusions

Females treated for SUDs had substantially higher odds of pregnancy and elective terminations than the non-treated cohort. To improve their reproductive health, targeted interventions such as free long-acting contraception and integration of family planning guidance into substance use treatment should be considered.
Increased Wound Prevalence in those Exposed to Xylazine and Fentanyl Compared to Those Exposed to Fentanyl: An Observational Study
Authors: Semancik Carolanne E.
Published: December 2024

Objectives

The aim of this study is to determine the difference, if any, in prevalence of wounds in individuals who were exposed to xylazine and fentanyl compared to individuals who were exposed to fentanyl and not xylazine.

Methods

A large inpatient substance use disorder specialty hospital provided medical records over an 8-month period from July 2023 to February 2024. Individuals were admitted to an American Society of Addiction Medicine 3.7 level of care where a urine drug screen and skin assessment was conducted on admission. If the urine screen noted a presence of fentanyl, the sample was then tested for xylazine exposure. Patients were considered positive for wounds on admission to treatment if any wound was noted during the skin assessment during the admission process.

Results

A total of 282 medical records were identified. A chi square test of association was completed and revealed a statistically significant association between xylazine exposure and wounds (P = 0.002, odds ratio = 2.420, 95% confidence interval = 1.376–4.254).

Conclusions

This study provides early support for the previously theorized connection between xylazine exposure and wounds.
Comparison of 2 Methods for Measuring Chronotropic Response to Exercise: Heart Rate–Work Rate Slope Versus Percent Change in Heart Rate–Work Rate Slope—A Cross-Sectional Study
Authors: Scott Rachel , Taylor J. David , Allen Melissa , Fletcher James , Mathis Ruth Ann , McGee Margaret , Rainey Jacquie
Published: December 2024

Purpose:

Chronotropic response to exercise (CRE) is an indicator of cardiovascular health and is evaluated using different methodologies. The purpose of this cross-sectional investigation was to compare 2 methods for measuring CRE: heart rate (HR)–work rate slope versus percent change in HR–work rate slope.

Methods:

Thirty-three participants met the inclusion criteria. Participants completed a two-stage graded exercise protocol. Heart rate and work rate data were recorded at rest (0 watts), the final minute of stage 1, and the final minute of stage 2. Heart rate–work rate slope was defined as the slope of HR increase relative to work rate increase. Percent change in HR–work rate slope was calculated as the percent change in HR–work rate slope between stage 1 and stage 2.

Results:

Spearman correlation coefficient indicated a significant, but relatively low, correlation between the 2 measurements (rs = 0.388, P = .01). The 95% limits of agreement (z-scores) between the 2 measurements were −2.29 to 2.29, suggesting considerable disagreement.

Conclusions:

The findings of this study indicated that HR–work rate slope and percent change in HR–work rate slope were not comparable. The low correlation and lack of agreement between the 2 methods could be explained by the possible measurement of different constructs (cardiorespiratory fitness vs coronary artery disease risk). Because of considerable disagreement, clinicians should not make decisions related to patient care using the 2 methodologies interchangeably. The findings of this investigation support the perspective that a standardized procedure for measuring CRE is warranted.
Early Retinal Detachments Following Open Globe Repair: Incidence and Risk Factors
Authors: Sheth Neil , Chang Arthur Y. , Bharadwaj Arthi , Wu David , Ivakhnitskaia Evguenia , Mieler William F.
Published: December 2024

Purpose:

Risk factors for the development of rhegmatogenous retinal detachments (RRDs) in the early postoperative period following open globe repair (OGR) are not well understood. RRDs are often diagnosed late after OGIs, which can negatively impact visual prognosis. We assessed the incidence and risk factors that predict the development of this complication.

Methods:

We conducted a retrospective case-control study of all OGIs at a single ocular trauma center from January 2016 to September 2021 where at baseline the retina was attached. Cases were defined as postoperative RRDs that developed within 90 days of OGR.

Results:

Of 96 eyes included, 40 (41.7%) subsequently developed RRD. Univariate analysis revealed initial visual acuity (VA) of light perception (LP) or worse (OR 7.64; 95% CI, 3.03-19.22; p < .01), zone 3 injuries (OR 7.54; 95% CI, 2.64-21.54; p < .01), no view of the lens (OR 4.26; 95% CI, 1.77-10.26; p < .01), and the presence of injuries external to the globe (OR 5.33; 95% CI, 2.09-13.63; p < .01) to be associated with early RRD development. On multivariate analysis, presenting VA of LP (p < .001), the presence of external injuries (p = .001), and zone 3 injuries (p = .037) remained significant. Of the 40 patients with early RD, 34 (85%) remained attached following repair, with variable visual outcomes.

Conclusion:

Presenting VA of LP, zone 3 injuries, and external injuries to the globe confer increased risk of early postoperative RRD after OGR. The majority of RRDs can be successfully repaired.
Decreasing outer retina traumatism of ILM peeling in diabetic eyes with foveal sparing technique
Authors: Caporossi Tomaso , Crincoli Emanuele , Culiersi Carola , Scampoli Alessandra , Governatori Lorenzo , Bernardinelli Patrizio , Baldascino Antonio , Rizzo Stanislao
Published: December 2024

Purpose:

To evaluate the effect on outer retina integrity of foveal sparing internal limiting membrane (ILM) peeling compared to standard ILM peeling on proliferative diabetic retinopathy (PDR) eyes affected by diabetic macular edema (DME) and epiretinal membrane (ERM).

Materials and methods:

Eyes diagnosed with PDR, DME and ERM eligible for vitrectomy were prospectively recruited and randomly assigned to either foveal sparing (FS) group and no foveal sparing (nFS) group. Ellipsoid zone (EZ) lesion size, EZ reflectivity and external limiting membrane (ELM) integrity and angular sign of Henle Fiber Layer Hyperreflectivity (ASHH) were assessed preoperatively and 1 year postoperatively.

Results:

Twelve (12) eyes and fifteen (15) eyes were included in FS and nFS group respectively. The two groups showed no differences in terms of EZ lesion size (p=0.549), EZ reflectivity (p=0.657) and ELM integrity (0.999) at preoperative examination. A significant increase in EZ lesion size was noted in nFS group between preoperative and postoperative examination (p=0.040) which was not present in FS group (p=0.862). Moreover, nFS group showed a higher prevalence of ASHH and a lower EZ reflectivity at follow up compared to FS group (respectively p=0.047 and p=0.041).

Conclusions:

Vitrectomy with FS ILM peeling may result in a better preservation of the Muller-photoreceptors complex in PDR complicated with DME and ERM.
TNF-α Suppression Attenuates Limbal Stem Cell Damage in Ocular Injury
Authors: Zhou Chengxin , Lei Fengyang , Mittermaier Mirja , Dana Reza , Dohlman Claes H. , Chodosh James , Paschalis Eleftherios I.
Published: December 2024

Purpose:

Ocular chemical injuries often cause uveal inflammation, upregulation of TNF-α at the limbus, and subsequent limbal stem cell (LSC) damage. In this study, we investigate the protective role of TNF-α suppression in LSC survival.

Methods:

Corneal alkali injuries were performed using NaOH as previously described by our group. Anterior chamber pH elevation in the absence of corneal alkali exposure was achieved by cannulation. A CX3CR1+/EGFP::CCR2+/RFP bone marrow chimera was used to study the role of innate immune cells in LSC damage, which was assessed by TUNEL assay, ABCB5, cytokeratin 12 and 13 staining, flow cytometry, in situ hybridization, and qPCR. Corneal neovascularization and conjunctivalization were evaluated by light microscopy. Intraperitoneal injection of 6.25 mg/kg infliximab was administered after irrigation. A TNFR1/2 knockout mouse was used to confirm the findings by a second method.

Results:

Systemic administration of 6.25 mg/kg infliximab suppressed uveal inflammation after anterior chamber pH elevation or corneal alkali injury and led to reduction of TNF-α secreting CCR2+ and CX3CR1+ monocytes in the basal limbal tissue. In turn, this led to LSC survival (P < 0.01) and allowed reestablishment of K12+ epithelium (P < 0.05) on the injured cornea. Moreover, it led to less corneal neovascularization, conjunctivalization, and scarring, as compared with untreated animals. The protective effect of TNF-α suppression was confirmed in TNFR1/2 knockout mice.

Conclusions:

Prompt systemic administration of TNF-α inhibitor prevents LSC deficiency and facilitates corneal reepithelialization after alkali burn. TNF-α suppression may benefit the outcomes of other ocular injuries that cause LSC deficiency.
Evaluating diurnal rhythms of host responses to enteric norovirus infection in mouse models
Authors: Zhang Jianglin , Orchard Robert C. , Kuang Zheng
Published: December 2024

Norovirus is a leading cause of gastroenteritis worldwide. The factors required for the life cycle and pathogenesis of norovirus in humans remain unclear. Mouse models of norovirus infection have been widely used to explore the crosstalk between norovirus and the host. The circadian clock entrains biological processes and behaviors including eating and sleeping in response to day–night cycles. How the mucosal immunity is diurnally programmed in response to norovirus infection remains largely unknown. Here, we provide procedures for preparing a murine norovirus strain CR6 and for infection in mouse models under normal day/night light cycles or jet-lag conditions. We also present procedures to quantify viral copies and antiviral response transcripts in host tissues. These protocols will help facilitate studies of norovirus infection and immunometabolic responses from the circadian perspective.