bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid modeling of thermoacoustic oscillations: Integrating signal processing and machine learning for accurate detection
Authors: Wei Dongwei , Zhang Zhedian
Published: February 2025

This study integrates machine learning models with traditional signal processing techniques to detect and analyze thermoacoustic instabilities in combustion systems. Time-domain analysis, Fourier transform, and phase space reconstruction methods are applied to pressure pulsation data to accurately identify the onset and evolution of thermoacoustic instabilities. Insights derived from these analyses are used to label datasets, which are subsequently employed as training data for two machine learning models: Extreme Gradient Boosting and Multilayer Perceptron. The trained models demonstrate high predictive accuracy in distinguishing between stable and unstable oscillatory states across multiple datasets. Moreover, quantitative comparisons with existing methods highlight the proposed approach's improvements in real-time monitoring capabilities, particularly in terms of prediction accuracy and computational efficiency. The study also evaluates two independent datasets and two public datasets to assess chaotic and irregular behaviors, further validating the models' robustness. The analysis reveals that the oscillatory states are characterized by distinct energy distributions across frequencies, as represented in the cumulative mass fraction diagram. These findings underscore the effectiveness of combining physical diagnostic methods with machine learning algorithms to enhance the detection, analysis, and real-time monitoring of thermoacoustic instabilities. This integrated methodology contributes significantly to the development of more efficient and reliable combustion systems.
Estimating viscosities of semiconductor-manufacturing gases
Authors: Gonzalez Esteban
Published: February 2025

Semiconductor manufacturing demands an accurate delivery of gases to the process chamber. To achieve this, accurate gas viscosities are needed. Hence, this paper compares viscosity models applied to pure gases and operating conditions relevant to semiconductor manufacturing and develops a method to design neural-network/multilayer-perceptron models of viscosity. Overall, the perceptron models give the smallest root-mean-square errors in comparison with experimental data, followed closely by a simplified variation of well-known models. Based on these findings, this paper uses a perceptron model to give viscosities of several semiconductor-manufacturing gases that are unavailable and gives recommendations on how to estimate these viscosities.
Flake production: A universal by-product of primate stone percussion
Authors: Proffitt Tomos , de Sousa Medeiros Paula , Martins Waldney Pereira , Luncz Lydia. V.
Published: February 2025

The evolution of stone tool technology marks a significant milestone in hominin development, enabling early humans to manipulate their environments. The oldest known evidence, dating to 3.3 Ma, indicates a combination of percussive and flake production activities. Studying the archaeological signature of percussive stone tool use in living primate provides a potential analog to the origin of stone flake technology in the hominin lineage. Here, we present a yellow-breasted capuchin (
Sapajus xanthosternos
) stone tool assemblage from Fazenda Matos, Brazil, to explore the variability of the material signatures associated with percussive tool use. Our analysis of this record demonstrates many archaeological features previously associated with intentional flake production. This includes hammerstones with substantial percussive damage and a range of flaked and detached pieces. Comparative analyses with other flaked primate and hominin assemblages reveals that, unintentional flake production is a universal component of stone hammer and anvil percussive behaviors, suggesting that similar behaviors by early hominins may have led to stone flake technology and that this record may have been highly variable. To fully understand the origins of hominin stone technology, a broad spectrum of material records including both hominin and primate must be considered.
Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel
Authors: Loiodice Mélanie , Drula Elodie , McIver Zak , Antonyuk Svetlana , Baslé Arnaud , Lima Marcelo , Yates Edwin A. , Byrne Dominic P. , Coughlan Jamie , Leech Andrew , Mesdaghi Shahram , Rigden Daniel J. , Drouillard Sophie , Helbert William , Henrissat Bernard , Terrapon Nicolas , Wright Gareth S. A. , Couturier Marie , Cartmell Alan
Published: February 2025

Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.
Additive manufactured microchannels: thermal insights from flow configuration and rough wall synergy
Authors: Nadarajah Puurnaraj , Mohamed Khairudin , Abdullah Jamaluddin , Devarajan Mutharasu
Published: February 2025

An additive-manufactured triangular microchannel heat sink (MCHS) with a hydraulic diameter of 650 µm and a relative wall surface roughness of 8% was fabricated using the direct metal laser sintering (DMLS) method. This experimental study investigates the effects of flow configurations and wall roughness on the MCHS’s thermal performance. Parameters such as the temperature gradient, pressure drop, Nusselt number, and thermal performance index (TPI) were evaluated and compared. At flow rates between 1 ml min−1 and 5 ml min−1, the counterflow configuration exhibited a more uniform temperature distribution, achieving a maximum improvement of 37.2% compared to parallel flow. Additionally, the counterflow resulted in a pressure drop reduction of at least 25% as the flow rate increased. Notably, the Nusselt number for parallel flow was 44% higher on average than in macro ducts, while counterflow offered a 22% improvement. This performance enhancement is attributed to the rough wall elements of the DMLS-printed MCHS, which promote heat dissipation by enhancing fluid mixing through the combined effects of increased inertial forces and surface roughness. The MCHS with parallel flow demonstrated a higher TPI compared to counterflow, averaging a 16% increase. However, to make valid comparisons with other DMLS-printed MCHS designs, studies at higher Reynolds number with an increased number of microchannels are needed. In conclusion, counterflow reduces the thermal gradient across the MCHS and is recommended for low heat-density electronic devices where thermo-mechanical reliability is critical. Conversely, parallel flow is better suited to high heat-density power electronics where efficient thermal management is a primary concern.
Applicability of universal machine learning interatomic potentials to the simulation of steels
Authors: Echeverri Restrepo Sebastián , Mohandas Naveen Karuthodi , Sluiter Marcel , Paxton Anthony T.
Published: February 2025

Bearing steels are complex materials composed of an iron matrix and a well defined and precise amount of several alloying elements.In order to improve sustainability and circularity, there is a tendency to increase the utilisation of scrap material for their production.The variability of the composition of scrap material has a direct impact on the properties of the final steels: There is less control on their composition due to the possible presence of larger amounts of tramp and alloying elements.One way to study the effect of tramp elements is by using universal machine learning interatomic potentials.These types of potential render the investigation of multielement systems possible.They permit the study of interactions between iron atoms in the matrix and multiple concurrent tramp and alloying elements, a feature that is currently not available in classical potentials.In this work, we present a benchmark of four state-of-the-art universal machine learning interatomic potentials (CHGNet [1] (v0.2.0 and v0.3.0 ), M3GNet [2], MACE [3]) and SevenNet [4], and study their applicability to the simulation of systems relevant to steels.For pure Fe, all potentials accurately predict the equilibrium lattice parameter, but the accuracy varies for other properties.For most solute-solute and solute-vacancy interactions all interatomic potentials tend to capture the general trends though there is a disparity in the predicted magnitudes.While currently “off-the-shelf” universal machine learning interatomic potentials fail to predict some key properties, some of them show significant potential to serve as starting point for further training and refinement.
Derived sequences of the (n, j)-bonacci sequences
Authors: Huang Yuke , Wen Zhiying
Published: February 2025

Derived sequence is an important theme in combinatorics on words. Let

S

n
,
j

be the infinite one-sided sequence over the alphabet

{

a
d

,
 
1
⩽
d
⩽
n
}

generated by the substitution

σ

n
,
j

(

a
d

)
=

a
1

j

a

d
+
1

for

1
⩽
d
<
n

and

σ

n
,
j

(

a
n

)
=

a
1

, which are natural generalizations of the Fibonacci sequence. In this paper, we determine the derived sequences of the (n, j)-bonacci sequences

S

n
,
j

for

n
⩾
2

and

j
⩾
1

.
Indirect detection of dark matter absorption in the Galactic Center
Authors: Boddy Kimberly K. , Dutta Bhaskar , Evans Addy J. , Huang Wei-Chih , Moltner Stacie , Strigari Louis E.
Published: February 2025

We consider the nuclear absorption of dark matter as an alternative to the typical
indirect detection search channels of dark matter decay or annihilation. In this scenario, an
atomic nucleus transitions to an excited state by absorbing a pseudoscalar dark matter particle
and promptly emits a photon as it transitions back to its ground state. The nuclear excitation of
carbon and oxygen in the Galactic Center would produce a discrete photon spectrum in the
𝒪(10) MeV range that could be detected by gamma-ray telescopes. Using the
BIGSTICK large-scale shell-model code, we calculate the excitation energies of carbon and
oxygen. We constrain the dark matter-nucleus coupling for current COMPTEL data, and provide
projections for future experiments AMEGO-X, e-ASTROGAM, and GRAMS for dark matter masses from
∼ 10 to 30 MeV. We find the excitation process to be very sensitive to the dark matter mass
and find that the future experiments considered would improve constraints on the dark
matter-nucleus coupling within an order of magnitude.
Primordial black hole formation from type II fluctuations with primordial non-Gaussianity
Authors: Shimada Masaaki , Escrivà Albert , Saito Daiki , Uehara Koichiro , Yoo Chul-Moon
Published: February 2025

This study investigates the formation of primordial black holes (PBHs) resulting from the
collapse of adiabatic fluctuations with large amplitudes and non-Gaussianity.
Ref. [1] showed that fluctuations with large amplitudes lead to the formation of
type B PBHs, characterized by the existence of the bifurcating trapping horizons, distinct from
the more common type A PBHs without a bifurcating trapping horizon. We focus on the local type
non-Gaussianity characterized by the curvature perturbation ζ given by a function of a
Gaussian random variable ζG as βζ=-ln(1-βζG) with a
parameter β. Then we examine how the non-Gaussianity influences the dynamics and the type
of PBH formed, particularly focusing on type II fluctuations, where the areal radius varies
non-monotonically with the coordinate radius. Our findings indicate that, for β > -2, the
threshold for distinguishing between type A and type B PBHs decreases with increasing β
similarly to the threshold for black hole formation. Additionally, for large positive values of
β, the threshold for type B PBHs approaches that for type II fluctuations. We also find
that, for a sufficiently large negative value of β ≲ -4.0, the threshold value is in
the type II region of μ, i.e., there are fluctuations of type II that do not form black holes.
Lastly, we calculate the PBH mass for several values of β. Then we observe that the final
mass monotonically increases with the initial amplitude within the parameter region of type A
PBHs, which differs from previous analytical expectations.
Theoretical research on effective generation of isolated attosecond pulse from the synthesized pulse laser with the optimized waveform
Authors: Zhan Kunzhen , yin yanben , Chen Gao
Published: February 2025

Mid-infrared femtosecond pulse laser with the single cycle and high intensity is an ideal driving light source for generating isolated attosecond pulse. Due to current experimental limitations, it is difficult to directly achieve this type of laser light source in the laboratory. In this paper, we obtain such an ideal light source by adding a Ti: sapphire pulse to the combined pulse laser consisting of two mid-infrared pulses. Specifically, by combining the synthesized pulse consisting of 8 fs/ 1200 nm / 1.62×1014 W/cm2 and 12 fs/ 1800 nm/ 2.71×1014 W/cm2 with an additional 8 fs/800 nm/ 1.26×1014 W/cm2 Ti: sapphire pulse, the resulting electric field waveform is very close to that of a 1170 nm femtosecond pulse with an intensity of 1.4×1015 W/cm2, a single-cycle pulse width, and a carrier-envelope phase of 0.25 π. Numerical simulations show that both cases produce high-order harmonic emission spectra with broadband supercontinuum spectra, however, the bandwidth of the supercontinuum spectra and the harmonic intensities in the synthesized pulses are significantly better than those in the single 1170nm pulse. After inverse Fourier transform, we obtain 66 as high-intensity isolated attosecond pulse, whose intensity is five orders of magnitude higher than that of a monochromatic field. Here, the phase differences between three combined pulse lasers have little effect on the numerical simulation results when they vary in the range of 0.3 π.
Power distribution over the wafer-scale monolithic pixel detector — MOSAIX for ALICE ITS3
Authors: Aglieri Rinella G. , Bugiel S. , Dobrijevic D. , Lemoine C. , Snoeys W. , Vicente Leitao P. ,   the ALICE collaboration
Published: February 2025

For the LS3 ALICE ITS3 upgrade the detector material budget reduction has been pushed to the limit by proposing a system composed almost exclusively of silicon wafer thinned down to 50μm. This improves performance, but adds complexity to the ASIC design. It requires a wafer-scale module with embedded power delivery network and on-chip data transfer, which were usually done through flexible printed circuit cable.

This contribution covers different aspects of the power delivery network design for a wafer-scale detector. It describes the difficulties, shows possible solutions and presents the power scheme design of the full-size ITS3 sensor prototype MOSAIX.
Prototype of SiC beam monitor for the COMET experiment at J-PARC
Authors: Kishishita T. , Okabe K. , Fujita Y. , Fukao Y. , Igarashi Y. , Hamada E. , Shoji M. , Xu X. , Kosugi R. , Kojima K. , Masumoto K. , Tanaka Y. , Yashima H. , Sakurai Y.
Published: February 2025

We have developed a prototype of the muon beam monitor (μBM) for the COMET experiment
at J-PARC. The COMET aims to search for the neutrino-less muon-to-electron conversion event in
the field of the nucleus, as a charged lepton flavor violation process. The SiC-based μBM
will be installed in a vacuum chamber and located in front of the muon-stopping target and the
main central drift chamber. The detector consists of SiC PN-diodes and dedicated readout
electronics. By tailing the 256 sensors in a matrix, the beam profile and bunch stability can be
extracted, and then, are utilized for the background estimation of the rare process. To validate
the μBM concept, we implemented the SiC sensors on the prototype Kapton-flex sensor board and
conducted a beam test at J-PARC. The pulse height of μ-events in the SiC sensor was linearly
correlated with an averaged coincidence of the decayed electrons by scintillators. We thus
conclude that the number of incident muons can be estimated from the pulse height information from
the μBM. The radiation tolerance of the sensor was also proven to be sufficient for the COMET
Phase-1 by irradiating fast neutrons with 1.7×1012/ cm2 fluence at research
nuclear reactor. The electronics designed in 65 nm CMOS is currently under testing. In the
lab.-testing, we confirmed the basic functionality as a required waveform digitizer and sufficient
signal-integrity to drive the 10 m cable length to the backend electronics.
Production of flex circuits for the ATLAS Inner Tracker Pixel Outer Barrel
Authors: Costanza F. , Chabanne E. , Gaglione R. , Levêque J. , Massol N. , Vilalte S.
Published: February 2025

The ATLAS ITk Pixel system requires large-scale flex circuits for low-voltage power, high-voltage sensor bias, and command/data transmission due to tight space constraints. This report focuses on the design and production of the services running from the modules to the first patch panel of the ITk Pixel Outer Barrel. The results from the quality control tests on the pre-production (10% of what is required to equip the final detector) will be discussed. In this report we also describe the procedure developed for the complex 3D bending needed to accommodate the routing and to respect the mechanical envelope.
A method for weld surface inspection and measurement based on AM U-Net
Authors: Shang Fei , Chen Huilin , Sun Bo , Han Yongquan , Cai Dandan , Wang Shaofeng , Gao Ting , Ji Chunsheng , Zhang Honghui
Published: February 2025

The quality of weld seams is critical to the performance and safety of industrial products. Traditional manual inspection methods are inefficient and prone to inaccuracies, particularly in complex environments. To address these challenges, this study introduces an automated weld seam inspection and dimensional measurement approach based on an enhanced U-Net architecture, termed AM U-Net. By integrating wavelet depth separable convolution, attention mechanisms, and multi-scale feature fusion, AM U-Net effectively captures intricate weld features while reducing computational complexity. Experimental results demonstrate that AM U-Net achieves a Dice coefficient of 0.94, outperforming the standard U-Net by 9.3%, and enhances inference speed by 33% with a 22.6% reduction in model parameters. Additionally, the proposed method for measuring weld seam dimensions combines sub-pixel edge detection with camera calibration, achieving millimeter-level accuracy with average relative errors of 0.16% for width and 0.25% for length measurements. This automated system offers a robust and efficient solution for weld seam inspection, meeting the precision requirements of industrial applications.
LTAU-FF: Loss Trajectory Analysis for Uncertainty in atomistic Force Fields
Authors: Vita Joshua A , Samanta Amit , Zhou Fei , Lordi Vincenzo
Published: February 2025

Model ensembles are effective tools for estimating prediction uncertainty in deep learning atomistic force fields. However, their widespread adoption is hindered by high computational costs and overconfident error estimates. In this work, we address these challenges by leveraging distributions of per-sample errors obtained during training and employing a distance-based similarity search in the model latent space. Our method, which we call LTAU (Loss Trajectory Analysis for Uncertainty), efficiently estimates the full probability distribution function of errors for any test point using the logged training errors, achieving speeds that are 2–3 orders of magnitudes faster than typical ensemble methods and allowing it to be used for tasks where training or evaluating multiple models would be infeasible. We apply LTAU towards estimating parametric uncertainty in atomistic force fields (LTAU-FF), demonstrating that it produces well-calibrated confidence intervals and predicts errors that correlate strongly with the true errors for data near the training domain. Furthermore, we show that the errors predicted by LTAU-FF can be used in practical applications for detecting out-of-domain data, tuning model performance, and predicting failure during simulations. We believe that LTAU will be a valuable tool for uncertainty quantification in atomistic force fields and is a promising method that should be further explored in other domains of machine learning.
Nanogel, a versatile nanoscopic platform for the simultaneous delivery of acyclovir and lignocaine for the treatment of Herpes simplex virus infection: formulation and characterizations
Authors: Aslam Adnan , Khan Barkat A , Khan M Khalid , Niazi Muhammad Bilal K
Published: February 2025

This study was designed to develop a nanogel formulation incorporating acyclovir and lignocaine (ALN). Various formulations were developed in which ALN-V (formulation-V) was optimized. ALN-V had an average spreadability of 32.3 ± 2.1, a pH of 5.8 ± 0.6 and was physically stable. The droplet size was 221.5 ± 0.5 nm while the surface charge was −7.59 ± 1.8 mV and the polydispersity was 0.145. ATR-FTIR analysis confirmed no interactions. The thermal analysis showed that the melting peak of lignocaine appeared at 65 °C, while that of acyclovir appeared at 256.54 °C. ALN-V showed approximately 72% release for acyclovir and 80% for lignocaine. The Higuchi model confirmed that the release mechanism follows controlled diffusion via a semipermeable membrane. ALN-V nanogels with pure acyclovir and blank nanogel formulations were tested for cytotoxicity and antiviral activity. ALN-V was capable of reducing the cytopathic effect of Herpes simplex virus (HSV) for up to 72 h. Moreover, the ALN-V nanogel inhibited (>95%) the virus titre even after 48 h, which confirmed that the ALN-V nanogel is nontoxic to cells and can effectively inhibit HSV. It was concluded that optimized nanogels can be loaded with combination drugs (lignocaine and acyclovir) and suitable candidates for transdermal delivery of both.
ImmunoTar—integrative prioritization of cell surface targets for cancer immunotherapy
Authors: Shraim Rawan , Mooney Brian , Conkrite Karina L , Hamilton Amber K , Morin Gregg B , Sorensen Poul H , Maris John M , Diskin Sharon J , Sacan Ahmet
Published: February 2025

Motivation

Cancer remains a leading cause of mortality globally. Recent improvements in survival have been facilitated by the development of targeted and less toxic immunotherapies, such as chimeric antigen receptor (CAR)-T cells and antibody-drug conjugates (ADCs). These therapies, effective in treating both pediatric and adult patients with solid and hematological malignancies, rely on the identification of cancer-specific surface protein targets. While technologies like RNA sequencing and proteomics exist to survey these targets, identifying optimal targets for immunotherapies remains a challenge in the field.

Results

To address this challenge, we developed ImmunoTar, a novel computational tool designed to systematically prioritize candidate immunotherapeutic targets. ImmunoTar integrates user-provided RNA-sequencing or proteomics data with quantitative features from multiple public databases, selected based on predefined criteria, to generate a score representing the gene's suitability as an immunotherapeutic target. We validated ImmunoTar using three distinct cancer datasets, demonstrating its effectiveness in identifying both known and novel targets across various cancer phenotypes. By compiling diverse data into a unified platform, ImmunoTar enables comprehensive evaluation of surface proteins, streamlining target identification and empowering researchers to efficiently allocate resources, thereby accelerating the development of effective cancer immunotherapies.

Availability

Code and data to run and test ImmunoTar are available at https://github.com/sacanlab/immunotar.

Supplementary information

Supplementary data are available at Bioinformatics online.
Engineered Extracellular Vesicles Derived from Pluripotent Stem Cells: A Cell-Free Approach to Regenerative Medicine
Authors: Wang Aline Yen Ling , Kao Huang-Kai , Liu Yen-Yu , Loh Charles Yuen Yung
Published: February 2025

The engineered extracellular vesicles (EVs) derived from pluripotent stem cells are a new concept in regenerative medicine. These vesicles are secreted from the embryonic stem cells as well as the induced pluripotent stem cells (iPSCs) and are involved in the transfer of bioactive molecules required for cell signaling. This review describes the possibilities for their use in the modification of therapeutic approaches in regenerative medicine and targeted therapies. Pluripotent stem cells can differentiate into various cell types which can be useful for tissue engineering or to generate models of diseases in a dish. Compared to cell therapies, engineered EVs are characterized by lower immunogenicity, higher targetability, and improved stability. Some of the applications are angiogenic, tissue restorative, immunomodulatory, and gene therapies for the treatment of certain diseases. iPSC-derived engineered EVs find application in regenerative medicine, drug delivery systems, diagnostics of diseases, and hydrogel systems. In regenerative medicine, they can promote the restoration of cardiac, bone, cartilage, and corneal tissues. Engineered EVs are also employed in drug targeting to particular sites as well as in the diagnosis of diseases based on biomarkers and improving image contrast. Hydrogels that contain EVs provide a depot-based delivery system to slowly release drugs in a controlled manner which enhances tissue repair. Thus, the results described above demonstrate the potential of engineered PSC-EVs for various biomedical applications. Future work will be directed toward expanding the knowledge of engineered PSC-EVs and their possibilities to create new therapeutic approaches based on the functions of these vesicles.
Improved Survival in Vascular Pythiosis with Surgery and Azithromycin, Doxycycline, and Itraconazole Therapy: A Phase II Multicenter, Open-Label, Single-Arm Trial
Authors: Torvorapanit Pattama , Worasilchai Navaporn , Manothummetha Kasama , Srisurapanont Karan , Thongkam Achitpol , Langsiri Nattapong , Leksuwankun Surachai , Meejun Tanaporn , Thanakitcharu Jaedvara , Lerttiendamrong Bhoowit , Susaengrat Nuttapon , Chuleerarux Nipat , Siriyakorn Nirada , Watcharasuwanseree Sureerat , Suparatanachatpun Pinyo , Chayangsu Sunee , Khemla Supphachoke , Kajeekul Rattagan , Wattanasoontornsakul Watchara , Bansong Ratiporn , Sakulkonkij Parichart , Wongkamha Thanyarak , Diewsurin Jaruwan , Laohasakprasit Kanokwan , Kongsakpaisal Prasopchai , Chayapum Poom , Chindamporn Ariya , Plongla Rongpong , Permpalung Nitipong
Published: February 2025

Background

Vascular pythiosis, caused by Pythium insidiosum, is a life-threatening disease with high mortality rate in patients with residual disease post-surgery. This study evaluated the effectiveness of a combination therapy of surgery, azithromycin, doxycycline, and itraconazole.

Methods

In this open-label, Phase II multicenter trial, 51 patients were enrolled. Patients were categorized based on residual disease post-surgery (unresectable lesions, incomplete resection, or persistent symptoms). Patients with residual disease received azithromycin (500 mg daily), doxycycline (100 mg twice daily), and itraconazole (200 mg thrice daily) until beta-d-glucan (BDG) levels were negative (< 80 pg/ml) for three months. Those without residual disease received the same regimen for six months. Outcomes included all-cause mortality at six months, adverse events, changes in BDG levels over time, and factors associated with residual disease and mortality.

Results

At six months, the all-cause mortality rate was 15.7%. Mortality in patients with residual disease was 31.5% compared to 6.25% for those without (p=0.04). Lesions above the popliteal artery were a significant predictor of residual disease (incidence rate ratio [IRR] 3.20, 95% confidence interval [CI] 1.08-11.70). BDG levels decreased over time (odds ratio [OR] 0.82, 95%CI 0.77-0.88 per week, p<0.001), but remained higher in the residual disease group (OR 4.29, 95% CI 1.55-11.92)

Conclusions

The combination therapy of surgery, azithromycin, doxycycline, and itraconazole improves survival in patients with vascular pythiosis, including those with residual disease. This regimen is well-tolerated and should be considered a standard of care, with further research needed for long-term outcomes.
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress
Authors: Huang Pingping , Cao Weilin , Li Zhaojun , Chen Qingshuai , Wang Guangchao , Zhou Bailing , Wang Jihua
Published: February 2025

The biotic stress significantly influences the production of potato (Solanum tuberosum L.) all over the world. Long noncoding RNAs (lncRNAs) play key roles in the plant response to environmental stressors. However, their roles in potato resistance to pathogens, insects, and other biotic stress are still unclear. The PotatoBSLnc is a database for the study of potato lncRNAs in response to major biotic stress. Here, we collected 364 RNA sequencing (RNA-seq) data derived from 12 kinds of biotic stresses in 26 cultivars and wild potatoes. PotatoBSLnc currently contains 18 636 lncRNAs and 44 263 mRNAs. In addition, to select the functional lncRNAs and mRNAs under different stresses, the differential expression analyses and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses related to the cis/trans-targets of differentially expressed lncRNAs (DElncRNAs) and to the differentially expressed mRNAs (DEmRNAs) were also conducted. The database contains five modules: Home, Browse, Expression, Biotic stress, and Download. Among these, the “Browse” module can be used to search detailed information about RNA-seq data (disease, cultivator, organ types, treatment of samples, and others), the exon numbers, length, location, and sequence of each lncRNA/mRNA. The “Expression” module can be used to search the transcripts per million/raw count value of lncRNAs/mRNAs at different RNA-seq data. The “Biotic stress” module shows the results of differential expression analyses under each of the 12 biotic stresses, the cis/trans-targets of DElncRNAs, the GO and KEGG analysis results of DEmRNAs, and the targets of DElncRNAs. The PotatoBSLnc platform provides researchers with detailed information on potato lncRNAs and mRNAs under biotic stress, which can speed up the breeding of resistant varieties based on the molecular methods.

Database URL: https://www.sdklab-biophysics-dzu.net/PotatoBSLnc
Comparison of bioprosthetic valves in primary isolated aortic valve replacement: a nationwide study
Authors: Kim Ji Seong , Kim Jinhee , Kang Yoonjin , Sohn Suk Ho , Hwang Ho Young , Kim Kyung Hwan , Kim Mi-Sook , Choi Jae Woong
Published: February 2025

OBJECTIVES

This study aimed to comprehensively compare the early and long-term clinical outcomes of bovine pericardial valve (BOV) and porcine valve (POV), specifically during the primary isolated aortic valve replacement (AVR), using data from the Korean National Health Insurance Service (NHIS) database.

METHODS

Using the Korean NHIS claimed data, all adult patients (age ≥19) who underwent primary isolated AVR using bioprosthetic valve from 2003 to 2019 were identified and propensity score matching (PSM) analysis was performed.

RESULTS

Overall, 5,470 patients with BOV (n = 3,947, Group B) or POV (n = 1,523, Group P) were enrolled, of whom 814 pairs were matched in a 1:1 ratio using PSM analysis. Early postoperative mortality and morbidities were comparable between the groups before and after PSM, considering inter-hospital clustering. The cumulative incidence of all-cause mortality was higher in Group P than in Group B in the total cohort (Group B 5.3%/patient-years vs Group P 6.4%/patient-years, adjusted hazard ratio: 1.20, P = 0.002), whereas those differences in call-cause mortality disappeared in PSM analysis (P = 0.24). The cumulative incidences of late stroke, reoperation, and infective endocarditis were not significantly different between the groups in PSM populations.

CONCLUSIONS

In Korean national database cohort patients with primary isolated AVR there was no significant difference in the early- and long-term clinical outcomes between BOV and POV.
Effects of perfluorooctane sulfonate (PFOS) on a novel reptilian toxicity test species, the brown anole (anolis sagrei)
Authors: Salice Christopher J , East Andrew , Weible Caitlin , Furst C Daniel , Rewerts Justin , Heron Christopher , Field Jennifer
Published: February 2025

Per- and polyfluoroalkyl substances (PFAS) are a broad class of chemicals with high environmental persistence and growing ecological and human health concern. Perfluorooctane sulfonate (PFOS) is among the most detected PFAS in environmental sampling and is often at high concentrations and has been measured in a variety of ecological receptors from around the globe. Despite the prevalence of PFOS, there are still important data gaps with regard to toxicity. For example, while studies have confirmed PFOS accumulation in tissues of wild reptiles, reptilian laboratory toxicity data are lacking. The purpose of this study was to first develop toxicity testing protocols using the brown anole, Anolis sagrei and, second, to conduct PFOS dosing studies to generate toxicity data to support ecological risk assessment of reptiles. We conducted two studies in which subadult males and then mature males were dosed with PFOS via pseudo-gavage with maximum doses in the range of 2 mg/kg/d. Subadults were exposed for 35 days while adult males were exposed for 90 days. While no significant mortality was observed, subadult male size and growth rate were significantly affected by PFOS at 2.98 mg/kg/d with a corresponding no effect level of 0.20 mg/kg/d and corresponding 10 and 20% effect levels for growth rate of 0.22 and 0.44 mg/kg/d, respectively. There were no significant effects on size metrics of mature male anoles from the 90-day study although several metrics showed dose-dependent decreases. These data may serve as the basis for toxicity reference values (TRVs) for use in ecological risk assessments of PFAS-contaminated sites in which reptiles may be exposed.
May Measurement Month 2022: an analysis of blood pressure screening results from Colombia
Authors: Lopez-Lopez Jose P , Otero Johanna , Urbina Zulma , Sanchez-Vallejo Gregorio , Narvaez Claudia , Camacho Paul A , Urina-Triana Miguel , Quintero Adalberto , Aroca Gustavo , Campos Alfonso , Arcos Edgar , Perez-Mayorga Maritza , Mosquera Walter , Garcia Luis , Beaney Thomas , Kerr Gabriele , Poulter Neil R , Lopez-Jaramillo Patricio
Published: February 2025

The May Measurement Month (MMM) campaign was carried out in Colombia in 2022 with the aim of raising awareness of raised blood pressure (BP). Here, we report on the findings of the campaign. Adults aged ≥ 18 years were recruited opportunistically at healthcare and public facilities in eleven departments. Three seated BP readings were taken for each participant, along with completion of a questionnaire on demographics, lifestyle factors, and comorbidities. Hypertension was defined as a systolic BP ≥ 140 mmHg and/or diastolic BP ≥ 90 mmHg or being on antihypertensive medication. Controlled BP was defined as being on antihypertensive medication with a BP <140/90 mmHg. Multiple imputation was used to estimate any missing BP readings. In total, 38 924 were screened, with a mean age of 46.3 years and 52.9% of whom were female. Of all participants, 10 738 (27.6%) had hypertension, of whom 7058 (65.7%) were aware, and 6925 (64.5%) were on antihypertensive medication. Of those on antihypertensive medication, 4600 (66.4%) had controlled BP, and of all participants with hypertension, 42.8% had controlled BP. However, those under 50 years had lower hypertension control (<30%). Women had a higher BP control than men (49.5 vs 36.3%). High education was associated with lower systolic BP (-2.37 mmHg). The MMM campaign in Colombia identified significant numbers of participants with either untreated or inadequately treated hypertension. MMM22 results point to the need to continue improving awareness and seek a broader implementation of strategies with proven efficacy in controlling hypertension.
Symposia Report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida
Authors: Rogina Blanka , Anderson Rozalyn , Lebrasseur Nathan , Curan Sean , Yousefzadeh Matthew J , Ghosh Bhaswati , Duque Gustavo , Howlett Susan , Austad Steven , Demuth Ilja , Gerstorf Denis , Korfhage Justin , Lombard David B , Abadir Peter , Christensen Kaare , Carey James R , Alberts Susan C , Campos Fernando , Palavicini Juan Pablo , Palmer Allyson , Bell Justice , Basisty Nathan , de Cabo Rafael , Gomes Ana , Dixit Vishwa Deep , Sen Payel , Baur Joseph A , Imai Shin-ichiro , Li Xiaoling , Valdez Gregorio , Orr Miranda E , Pletcher Scott , Andersen Julie , Jones Leanne , Castillo-Azofeida David , Bonaguidi Michael , Suh Yousin , Duncan Francesca E , Murray Anna , Wang Meng C, , Burkewitz Kristopher  , Henne Mike , Zhou Kai , Bouhrara Mustapha , Benjamini Dan , Kolind Shannon , Walker Keenan A , Reiter David A , Dean III Doug , Gorbunova Vera , Gladyshev Vadim N , Palovics Robert , Niedernhofer Laura J , Fan Rong , Bueckle Andreas D , Hurley Jennifer , Esser Karyn A , Kapahi Pankaj , Sato Shogo , Jiang Nisi , Ashiqueali Sarah A , Diaz Jose , Mishra Sidharth Prasad , Ralmundo Nuno , Banarjee Reema , Allsopp Richard , Reynolds Lindsay M , Zhang Bohan , Sebastiani Paola , Monti Stefano , Schork Nicholas , Rappaport Noa
Published: February 2025

The aging process is universal, and it is characterized by a progressive deterioration and decrease in physiological function leading to decline on the organismal level. Nevertheless, a number of genetic and non-genetic interventions have been described, which successfully extend healthspan and lifespan in different species. Furthermore, a number of clinical trials have been evaluating the feasibility of different interventions to promote human health. The goal of the annual Biological Sciences Section of the Gerontological Society of America meeting was to share current knowledge of different topics in aging research and provide a vision of the future of aging research. The meeting gathered international experts in diverse areas of aging research including basic biology, demography, and clinical and translational studies. Specific topics included metabolism, inflammaging, epigenetic clocks, frailty, senescence, neuroscience, stem cells, reproductive aging, inter-organelle crosstalk, comparative transcriptomics of longevity, circadian clock, metabolomics, and biodemography.
Azithromycin as Host-Directed Therapy for Pulmonary Tuberculosis: A Randomized Pilot Trial
Authors: Dekkers Bart G J , Kerstjens Huib A M , Breisnes Helene W , Leeming Diana J , Anthony Richard M , Frijlink Henderik W , van der Werf Tjip S , Kosterink Jos G W , Alffenaar Jan-Willem C , Akkerman Onno W
Published: February 2025

Background

Adjunctive host-directed therapies that modulate host immune responses to reduce excessive inflammation and prevent tissue damage in tuberculosis are being investigated. Macrolides, including azithromycin, were shown to possess anti-inflammatory and immune-modulatory effects in addition to their antibacterial effects. In the current trial, we investigated whether azithromycin enhances resolution of systemic and pulmonary inflammation and decreases extracellular matrix-related tissue turnover in tuberculosis patients.

Methods

An open-label, randomized, controlled trial was performed. Adult patients with drug-susceptible, pulmonary tuberculosis aged above 18 years were randomly assigned to receive standard antituberculosis care or azithromycin 250 mg orally once daily in addition to standard care (SOC) for 28 days.

Results

Twenty-eight patients were included within 4 weeks after initiating antituberculosis treatment. Twelve patients in both arms completed the trial. Participants were mostly young, male, had a history of smoking, and had no comorbidities. No differences in baseline characteristics were observed between the study arms. In blood, azithromycin treatment significantly enhanced the reduction of the tuberculosis marker interferon-γ-induced protein-10 (SOC plus azithromycin, −38% vs SOC alone, −24% vs SOC, P < .05) and the collagen type IV degradation product C4M (−26% vs −11%, P < .05). In sputum, treatment with azithromycin significantly reduced neutrophils (−24% vs 0%, P < .001), neutrophil elastase (−88% vs 75%, P < .01), and transforming growth factor-β (−86% vs −68%, P < .05). No significant effects were observed on other parameters. Treatment with azithromycin appeared to be safe.

Conclusions

The addition of azithromycin to standard antituberculosis treatment appears to diminish excess neutrophilic inflammation in patients with pulmonary tuberculosis.

Clinical Trials Registration. NCT03160638.
Internal Transcribed Spacers Enable Species-Level Metataxonomic Analysis of Ciliated Protozoa
Authors: Somasundaram Sripoorna , Yu Zhongtang
Published: February 2025

Traditional morphology-based ciliate classification is often time-consuming and inaccurate, necessitating molecular approaches. Although 18S rRNA gene sequencing is widely used for taxonomic analyses of ciliates, its high degree of conservation makes it challenging to achieve species-level resolution. This study explores the potential of internal transcribed spacers (ITS1 and ITS2) and the 28S rRNA gene to improve taxonomic resolution beyond that offered by 18S rRNA gene in free-living and host-associated ciliates. A comparative analysis of ITS, the 18S, and 28S rRNA gene sequences retrieved from public databases indicated that ITS regions exhibit greater inter- and intra-specific sequence dissimilarity compared to 18S rRNA gene, supporting existing literature. We then designed universal primers targeting the ITS and 28S rRNA gene for freshwater and rumen ciliates. These primers were rigorously evaluated for their inclusiveness, specificity, and amplification efficiency using in-silico PCR, experimental PCR, followed by sequencing and metataxonomic analyses of the ciliate communities. In-silico analyses revealed inclusiveness exceeding 80%, while experimental analyses validated their specificity. Metataxonomic analyses of ciliates demonstrated that the ITS and 28S rRNA gene captured significantly greater taxonomic diversity than 18S rRNA gene. Also, ITS1 offered superior taxonomic resolution by detecting the most ciliate species that went unnoticed by the 18S rRNA gene. These findings underscore the superiority of ITS1, and to a lesser extent ITS2, as taxonomic markers for enhancing the resolution of freshwater and rumen ciliate communities. We recommend ITS1 as an alternative marker to overcome the limitations of 18S rRNA gene-based approaches in free-living and host-associated ciliate taxonomy.
Synthetic DNA Spike-in Standards for Cross-Domain Absolute Quantification of Microbiomes by rRNA Gene Amplicon Sequencing
Authors: Tourlousse Dieter M , Sekiguchi Yuji
Published: February 2025

Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of twelve unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.
HSF1 and CPSF1 affect milk fat and protein synthesis by regulating the AKT/mTOR signaling pathway
Authors: Chen Zhujun , Zhang Xinyi , Teng Jun , Jiang Li , Zhang Qin
Published: February 2025

In our previous genome-wide association study on milk production traits in Chinese Holstein cows, HSF1 (heat shock factor 1) and CPSF1 (cleavage and polyadenylation specific factor 1) were found to be strongly associated with milk fat and protein percentages. However, their roles in milk fat and protein synthesis and the underlying mechanism are still largely unknown. In this study, we verified the effects of their expressions on milk fat and milk protein synthesis in MAC-T cells. We showed that HSF1 can participate in the AKT/mTOR signaling pathway, one of the most important pathways for fat and protein synthesis, through its interaction with the AKT protein, and influence the downstream genes in this pathway to regulate milk fat and milk protein synthesis. We also found that HSF1, as a transcription factor, can bind to the promoter region of CPSF1 to regulate its transcription and expression, which in turn modulates the expression of SREBP1 and thereby influences the synthesis of milk fat.
Empty Education: A Dialogue of Nishitani and Rancière
Authors: Kuusela Anttoni E A , Hietamäki Sari
Published: February 2025

In this article, we study the educational views of two philosophers from two different intellectual traditions: those of the East and West. We aim to explore comparative philosophy, a method intrinsic to the Kyoto School, as a practice, using it to engage the ideas of Nishitani Keiji and Jacques Rancière in dialogue. This dialogue takes place between Nishitani’s concept of emptiness and Rancière’s concept of equality. Taking inspiration from what Anton Luis Sevilla has termed ‘negative education’, we propose an alternative philosophy of education: empty education. To develop our new concept, we examine the importance of emptiness and equality in education, focusing on the fruitful and emancipatory encounters they promote. We contend that a reciprocal relationship between the I and the Thou is essential for bypassing the unequal relations and stultifying processes found in education.