bluuebunny/crossref_metadata_2025 huggingface dataset:
Distributionally robust optimal power flow based on multi‐transport hyperrectangle ambiguity set
Authors: Ou Weizhen , Li Peijie , Weng Zonglong , Xiao Jiawen , Bai Xiaoqing
Published: February 2025

The Wasserstein distributionally robust optimization has become the preferred method for addressing the uncertainties in optimal power flow problems caused by renewable energy sources. However, when the system involves high‐dimensional random variables, such as multiple solar or wind farms, the curse of dimensionality associated with this method leads to a slow convergence rate of Wasserstein ambiguity sets. Therefore, it is essential to explore novel ambiguity sets which can effectively address the dimensionality problem. This paper proposes a distributionally robust optimal power flow model based on a multi‐transport hyperrectangle ambiguity set to tackle the uncertainties in wind power. First, this paper presents the multi‐transport hyperrectangle, which resolves the curse of dimensionality issue associated with Wasserstein ambiguity sets. Furthermore, the wind power curtailment cost in the objective function is reformulated into a tractable form using duality theory, enabling commercial solvers to provide efficient solutions. Finally, tests conducted on the modified IEEE 14‐bus and IEEE 118‐bus systems demonstrate that the proposed ambiguity set maintains a stable convergence rate under high‐dimensional random variables without rapid deterioration as the sample size increases. Moreover, the model achieves significant cost reductions while ensuring system stability.
Predicting core losses in power converters based on open source database
Authors: Zhou Yan , Zhang Minmin
Published: February 2025

Core losses are closely related to flux densities, frequencies, temperatures, exciting waveforms, and DC biases. Hysteresis losses and dynamic losses are considered the main components of core losses. A method for predicting core losses based on an open‐source database and a data‐driven physical model is proposed. To a certain predicted point, two paths in the procedure can be executed automatically. First, if there are two points in the database with similar working conditions to the predicted point, core loss power density can be directly predicted based on separate equations. Secondly, if loss power density for specific waveforms in the database are missing, hysteresis loss power density and dynamic loss power density under sinusoidal excitations can be utilized to estimate core loss power density for specific waveforms. Based on the proposed method, the impact of temperature on hysteresis loss power density and dynamic loss power density can also be individually fitted and analysed. The proposed concepts demonstrate good flexibility in handling various complex waveforms in power electronics and have been accurately verified using the loss data of N49 and N87 in the MagNet database.
Deriving pulsar pair-production multiplicities from pulsar wind nebulae using H.E.S.S. and LHAASO observations
Authors: Spencer S. T. , Mitchell A. M. W.
Published: February 2025

Context. Pulsar wind nebulae (PWNe) dominate the galactic gamma-ray sky at very high energies and they are major contributors to the leptonic cosmic ray flux. However, the question of whether or not pulsars also accelerate ions to comparable energies has not yet been experimentally confirmed.

Aims. We aim to constrain the birth period and pair-production multiplicity for a set of pulsars. In doing so, we aim to constrain the proportion of ions in the pulsar magnetosphere and, hence, the proportion of ions that could enter the pulsar wind.

Methods. We estimated possible ranges of the value of the average pair production multiplicity for a sample of 26 pulsars in the Australia Telescope National Facility (ATNF) catalogue, which have also been observed by the High Energy Stereoscopic System (H.E.S.S.) telescopes. We then derived lower limits for the pulsar birth periods and average pair production multiplicities for a subset of these sources where the extent of the pulsar wind nebula and surrounding supernova shell have been measured in the radio. We also derived curves for the average pair production multiplicities as a function of birth period for sources recently observed by the Large High Altitude Air Shower Observatory (LHAASO).

Results. We show that there is a potential for hadrons entering the pulsar wind for most of the H.E.S.S. and LHAASO sources we consider here, which is dependent upon the efficiency of luminosity conversion into particles. We also present estimates of the pulsar birth period for six of these sources, all falling into the range of ≃10–50 ms.
Mapping the Milky Way with Gaia Bp/Rp spectra I: Systematic flux corrections and atmospheric parameters for 68 million stars
Authors: Ye Xianhao , Wu Wenbo , Allende Prieto Carlos , Aguado David S. , Zhao Jingkun , González Hernández Jonay I. , Rebolo Rafael , Zhao Gang , Li Zhuohan , del Burgo Carlos , Chen Yuqin
Published: February 2025

Gaia Bp/Rp spectrophotometry for over two hundred million stars has been publicly released as part of Gaia Data Release 3 (DR3). These data have great potential for mapping metallicity across the Milky Way. Several recent studies have analyzed this data set to derive atmospheric parameters and identify new metal-poor stars. In addition, systematics in the fluxes of the Bp/Rp spectra have also been identified and characterized. We aim to construct an alternative catalog of atmospheric parameters from Gaia Bp/Rp spectra by fitting them with synthetic spectra based on model atmospheres, and provide corrections to the Bp/Rp fluxes according to stellar colors, magnitudes, and interstellar extinction. We use GaiaXPy to obtain calibrated spectra and apply FER R E to match the corrected Bp/Rp spectra with models and infer atmospheric parameters. We train a neural network (NN) using stars in the Apache Point Observatory Galactic Evolution Experiment (APOGEE) to predict flux corrections as a function of wavelength for each target. Based on the comparison with APOGEE parameters, we conclude that our estimated parameters have systematic errors and uncertainties in T_ eff log g, and M/H about -38 ± 167 K, $0.05 ± 0.40$ dex, and -0.12 ± 0.19 dex, respectively, for stars in the range $4000 eff 7000$ K. The corrected Bp/Rp spectra show improved agreement with both models and Hubble Space Telescope (HST) CALSPEC data. Our correction increases the precision of the relative spectrophotometry of the Bp/Rp data from $3.2% - 3.7%$ to $1.2% - 2.4%$. We also compare our results with other similar catalogs from the literature and validate them using star clusters. Finally, we have built a catalog of atmospheric parameters for stars within $4000 eff 7000$ K, comprising $68,394,431$ sources, along with a subset of $124,188$ stars with M/H -2.5. Our catalogs and flux correction code are publicly available. Our results confirm that the Gaia Bp/Rp flux calibrated spectra show systematic patterns as a function of wavelength that are tightly related to colors, magnitudes, and extinction. Our optimization algorithm can give us accurate atmospheric parameters of stars with a clear and direct link to models of stellar atmospheres, and can be used to efficiently search for extremely metal-poor (EMP) stars.
VLTI/GRAVITY upper limit on near-infrared emission from the nearby 33 M⊙ black hole Gaia BH3
Authors: Kervella Pierre , Panuzzo Pasquale , Gallenne Alexandre , Mérand Antoine , Arenou Frédéric , Caffau Elisabetta , Lacour Sylvestre , Mazeh Tsevi , Holl Berry , Babusiaux Carine , Nardetto Nicolas , Clavel Maïca , Le Bouquin Jean-Baptiste , Ségransan Damien
Published: February 2025

Context. The recent astrometric discovery of the nearby (590 pc) massive (33 M⊙) dormant black hole candidate Gaia BH3 offers the possibility to angularly resolve the black hole from its companion star by using optical interferometry.

Aims. Our aim is to detect emission in the near-infrared K band from the close-in environment of Gaia BH3 caused by accretion.

Methods. Gaia BH3 was observed with the GRAVITY instrument using the four 8-meter Unit Telescopes of the VLT Interferometer. We searched for the signature of emission from the black hole in the interferometric data using the CANDID, PMOIRED, and exoGravity tools.

Results. With a present separation of 18 mas, the Gaia BH3 system can be well resolved angularly by GRAVITY. We did not detect emission from the black hole at a contrast level of Δm = 6.8 mag with respect to the companion star, that is, fBH/f⋆ < 0.2%. This corresponds to an upper limit on the continuum flux density of fBH < 1.9 × 10−16 W m−2 μm−1 in the K band. In addition, we did not detect emission from the black hole in the hydrogen Brγ line.

Conclusions. The non-detection of near-infrared emission from the black hole in Gaia BH3 indicates that its accretion of the giant star wind is presently occurring at most at a very low rate. This is consistent with the limit of fEdd < 4.9 × 10−7 derived previously on the Eddington ratio for an advection-dominated accretion flow. Deeper observations with GRAVITY may be able to detect the black hole as the companion star approaches periastron around 2030.
Patient Blood Management – Wunsch und Realität
Authors: Holzhäuer Inci , De Rop Christiane , Hermsen Derik , Fischer Johannes , Hoffmann Till
Published: February 2025

Die Anämiebehandlung durch Versorgung mit Eisen, Folsäure und Vitamin B12 und
Stimulation der Erythropoese mit Erythropoetin bei Patienten, welche
Bluttransfusionen ablehnen, ist eine paradigmatische Herausforderung an das
Patient Blood Management (PBM), insbesondere in Notfallsituationen. Je nach
Anämieausprägung muss mit mindestens 14 Tagen für eine vollständige
Anämiekorrektur gerechnet werden. Wir stellen die Dynamik der Anämie-Entwicklung
und -Erholung bei unter ‚real life‘-Bedingungen verzögertem Patient Blood
Management im Fall eines Patienten vor, der Transfusionen aus religiösen Gründen
ablehnte.
Neuer Heftaufbau von „Nephrologie aktuell“
Authors: Schäfer Christian
Published: February 2025

Wie Sie, liebe Leserinnen und Leser, wahrscheinlich mit dem Blick auf das Editorial bemerkt haben, hat sich der Heftaufbau der „Nephrologie aktuell“ mit dieser Ausgabe etwas geändert. Dies habe ich zwar in Ausgabe 10/2024 in meinem Editorial angekündigt, aber eventuell haben es nicht alle gelesen. Daher möchte ich meine entsprechenden Worte im Folgenden sinngemäß wiederholen.
Shoulder Arthroplasty: Preoperative Evaluation and Postoperative Imaging
Authors: Vaswani Devin , Cohn Randy M. , Walsh Pamela J.
Published: February 2025

Shoulder arthroplasty procedures have increased over the past few years. Several different arthroplasty options are available for varying indications, such as humeral head resurfacing, hemiarthroplasty, anatomical total shoulder arthroplasty, and reverse total shoulder arthroplasty, with ongoing modifications of prosthesis components and surgical techniques. Arthroplasty complications are encountered from the acute postoperative period to several years postoperatively. This article reviews the more common types of shoulder arthroplasties: their imaging appearances, multimodality imaging assessments for preoperative planning, and complications.
Peripheral Nerve Injuries: Preoperative Evaluation and Postoperative Imaging
Authors: Daniels Steven P. , Hacquebord Jacques H. , Azad Ali , Adler Ronald S.
Published: February 2025

Imaging plays an important role in evaluating peripheral nerves. In the preoperative setting, imaging helps overcome pitfalls of electrodiagnostic testing and provides key anatomical information to guide surgical management. In the postoperative setting, imaging also offers key information for treating physicians, although it comes with several challenges due to postsurgical changes and alteration of normal anatomy. This article reviews our approach to peripheral nerve imaging, including how we use imaging in the pre- and postoperative setting for several common indications.
Femoroacetabular Impingement: Preoperative Evaluation and Postoperative Imaging
Authors: Cantarelli Rodrigues Tatiane , Morais André Queiroz de , Cabrita Henrique Antônio Berwanger de Amorim , Godoy Ivan Rodrigues Barros , Skaf Abdalla
Published: February 2025

Femoroacetabular impingement (FAI) is a significant orthopaedic condition that primarily affects young active adults. It is characterized by abnormal contact between the femoral head and the acetabulum, leading to joint damage and osteoarthritis. This syndrome presents in three forms: pincer, cam, and mixed impingement, each with distinct morphological characteristics that can cause labral tears and cartilage damage. Over the last 20 years, the diagnosis and management of FAI has evolved considerably with advancements in imaging technologies and surgical techniques, especially hip arthroscopy.

This article reviews the pathophysiology, diagnostic imaging criteria, surgical treatments, and postoperative outcomes of FAI, providing essential insights for radiologists and surgeons. The importance of early and accurate diagnosis through advanced imaging is emphasized to prevent the progression of FAI and to plan effective surgical interventions aimed at joint preservation. Challenges remain in the postoperative setting, where residual symptoms can require revision surgeries. Future directions in the management of FAI will likely focus on refining imaging protocols and surgical techniques to enhance the success rates of primary procedures and reduce the need for subsequent interventions.
Postoperative Imaging in the Throwing Athlete
Authors: Flores Dyan V. , Huang Brady K.
Published: February 2025

Overhead throwing subjects the shoulder and elbow to substantial stresses, resulting in unique injury patterns that need to be recognized to allow appropriate treatment and return to sport. At the elbow, the ulnar collateral ligament (UCL) is the primary static restraint to valgus stress and the most commonly injured structure. UCL reconstruction is the most frequent surgical procedure in throwers and may be performed along with ulnar nerve transposition and flexor-pronator mass procedures. Posteromedial impingement and valgus extension overload syndrome are related entities that result in intra-articular pathology, such as osteophytes or bodies lodged within the olecranon fossa, also warranting excision at the time of UCL reconstruction. Shoulder injuries involve the rotator cuff (partial-thickness articular-sided tear), labrum (superior anteroposterior labral tear), and capsule (glenohumeral internal rotation deficit). Surgical options such as cuff repair, labral debridement or repair, and capsular release or tightening therefore target these structures.
Bibliometric analysis and systematic review of digital competence in education
Authors: Ma Huiling , Ismail Lilliati
Published: February 2025

The ubiquity of digital technologies has profoundly transformed communication and education in the 21st century, making the development of digital competence essential for both teachers and students to be prepared for the digital age. However, existing reviews predominantly focus on the teachers’ perspective with a limited scope and methodology. This literature review combines bibliometric analysis and systematic literature review to provide a comprehensive analysis of existing research. Bibliometric analysis evaluates performance and science mapping to identify influential journals, countries, and authors while visualizing trends in the field. Content analysis identifies five major themes: (1) digital competence levels, (2) factors and variables, (3) digital competence and teacher education, (4) students’ digital competence, and (5) digital competence and academic performance. The study also outlines seven future research directions: (1) integrating digital competence into curricula, (2) initial training in digital competence for future professions, (3) subject-specific development, (4) expanding research samples to include younger students, (5) addressing limitations of self-assessment, (6) understanding the needs of teachers and students, and (7) strengthening administrative support. Overall, the review highlights challenges in measuring digital competence and underscores the need for its integration into education systems, offering insights into opportunities for future research.
On the shape of Gaussian scale-free polymer networks
Authors: Blavatska Viktoria , Holovatch Yurij
Published: February 2025

We consider the model of complex hyperbranched polymer structures formed on the basis of scale-free graphs, where functionalities (degrees) k of nodes obey a power-law decaying probability

p
(
k
)
∼

k

−
α

. Such polymer topologies can be considered as generalization of regular hierarchical dendrimer structures with fixed functionalities. The conformational size and shape characteristics, such as averaged asphericity

⟨

A
3

⟩

and size ratio g of such polymer networks are obtained numerically by application of Wei’s method, which defines the configurations of any complex Gaussian network in terms of eigenvalue spectra of the corresponding Kirchhoff matrix. Our quantitative results indicate, in particular, an increase of compactness and symmetry of network structures with the decrease of parameter α.
Effectiveness of troubleshooting activities in the instruction phase of productive failure in 8th-graders studying simple electric circuits
Authors: Safadi Rafi’ , Diab Ali
Published: February 2025

Productive failure engages students in a problem-solving phase that requires them to solve novel problems targeting yet-to-be-learned accepted ideas before the instruction phase. A few studies have explored students working individually during the instruction phase, where they diagnose a fictitious student’s erroneous examples; i.e. identify and explain classical errors embedded in them, by comparing these erroneous examples with worked examples involving a step-by-step description of the correct solutions (dubbed ‘ungraded-troubleshooting’ activity). However, these studies have yielded inconsistent results, leaving it unclear whether all students benefit equally from this instruction phase or not. In the current study, which was part of a larger project, seven 8th-grade classes from three different middle schools completed a pretest/intervention/posttest before studying simple electric circuits. The intervention consisted of two productive failure sessions targeting yet-to-be-learned accepted ideas. In the instruction phase of each session, the students in each class were randomly assigned to four activities, two of which were examined here: an ungraded-troubleshooting activity (49 students) and a graded-troubleshooting activity (50 students). It was hypothesized that students would show greater performance gains on the graded-troubleshooting activity that scaffolded the instruction phase by asking students to score erroneous examples on a rubric portraying the worked examples, in addition to diagnosing them. Contrary to predictions, the ungraded-troubleshooting activities led to better learning outcomes. The instructional implications and directions for future research are discussed.
Detection of occult hemorrhage using multivariate non-invasive technologies: a porcine study
Authors: Rashedi Navid , Murphy Ethan K , Klein Samuel B , Hamlin Alexandra , Anderson Justin E , Minichiello Joseph M , Lindqwister Alexander L , Moodie Karen L , Wanken Zachary J , Read Jackson T , Borza Victor A , Elliott Jonathan T , Halter Ryan J , Vaze Vikrant S , Paradis Norman A
Published: February 2025

Objective. Occult hemorrhage (OH) can emerge subtly post-trauma, especially when internal bleeding is not yet severe enough to result in noticeable hemodynamic changes or shock. Despite normal appearances of traditional vital signs like heart rate (HR) and blood pressure (BP), clinically significant OH may be present, posing a critical diagnostic challenge. Early detection of OH, before vital signs begin to deteriorate, is vital as delays in identifying such conditions are linked to poorer patient outcomes. We analyze the performance of poly-anatomic multivariate technologies—including electrical impedance tomography (EIT), near-infrared spectroscopy (NIRS), electrical impedance spectroscopy (EIS), plethysmography (Pleth), and ECG—in a porcine model of OH. The goal was to detect OH without the need to know the subject’s pre-established normal baseline. Approach. Forty female swine were bled at slow rates to create an extended period of subclinical hemorrhage, during which the animals’ HR and BP remained stable before hemodynamic deterioration. Continuous vital signs, Pleth, and continuous non-invasive data were recorded and analyzed with the objective of developing an improved means of detecting OH. This detection was set up as a supervised voting classification problem where the measurement of each technology (minimally transformed) was used to train a classifier. A soft majority voting classification technique was then used to detect the existence of OH. Main Results. When comparing the prediction performance of the most significant univariate technology (EIT) to that of a poly-anatomic multivariate approach, the latter achieved higher area-under-the-curve (AUC) values from receiver operating characteristic analyses in almost every observation interval duration. In particular, after 21 min of continuous observation, the best AUC of the multivariate approach was 0.98, while that of the univariate approach was 0.92. The best multivariate technologies, in descending order, appeared to be EIT on the thorax, NIRS on the abdomen, and EIS on the thorax. Significance. In this clinically relevant porcine model of clinically OH, multivariate non-invasive measurements may be superior to univariate ones in detecting OH. Advanced technologies such as EIT, NIRS, and EIS exhibit considerably greater potential to accurately predict OH than standard physiological measurements. From a practical standpoint, our approach would not require the medical device to have prior access to non-hemorrhage baseline data for each patient. Early detection of OH using these technologies could improve patient outcomes by allowing for timely intervention before vital signs begin to deteriorate.
Carbon aggregation effects on electronic properties of Ge: a first-principles study
Authors: Wang Jinghang , Xia Shilong , Yu Fangqi , Wen Yuhua , Li Cheng
Published: February 2025

Germanium (Ge) is a promising candidate in the field of Si-based optoelectronic integration. The introduction of C may modify the energy band of Ge and thus has scientific and technical significance. In this work, we performed first-principles calculations to investigate the C aggregation behavior in Ge and its effect on the electronic properties. Our results show that for a single C impurity, the substitutional site is more energetically favorable than the interstitial site. The formation energy per C atom decreases with the number of C atoms, indicating the tendency of C clustering in Ge. In particular, the C quadruplet in regular tetrahedral shape is found to be the most stable configuration in Ge. Formation energy calculations of C-related defects with various charge states demonstrate that, for single C doping, the (0/−1) and (−1/−2) transition levels are respectively located at 0.41 and 0.64 eV above VBM, displaying the potential acceptor characteristic. The band structure calculations show the vanishing of the direct band gap characteristic with the aggregation of C atoms in Ge.
Prediction of aerodynamic pass-by noise for a high-speed train pantograph by combining the wind tunnel model and the Farassat_1A formula
Authors: Zhang Shumin , Shi Jiawei , Wang Haoran
Published: February 2025

To effectively control noise emission from a high-speed train in early stage of design, it is necessary to predict the pass-by noise accurately. In the past, wind tunnel model was widely used to predict noise emission at a fixed far-field point, with the train remaining stationary and the wind blowing head-on at high speed. By doing so however, no Doppler effect is predicted. However, if the movement of the source considered, a sliding mesh or overset mesh will be used, which will generate the so-called interfaces between the sliding region and other stationary regions for flow field data exchange, and the existence of such interfaces may have a negative effect on calculation accuracy. Therefore, in this paper, a method is proposed combining the wind tunnel model and the Farassat_1A formula without using sliding mesh or overset mesh. In order to verify the effectiveness of the written program, a moving monopole and dipole source are given first. Based on the verified model, a typical high-speed train pantograph is studied. The subdomain method is used to obtain the sound source data, and then pass-by noise at different far-field observer points is calculated. The contribution of different pantograph components to the standard far-field noise is studied. Results show that due to the Doppler effect, the peak at the vortex shedding frequency of the pan-head is distributed over a frequency range.
Experimental study of charge composition of diffuse vacuum arc in axial magnetic field by optical spectra
Authors: Belostotskii Artemii , Melnikov Anton Dmitrievich , Usmanov Ravil , Gavrikov Andrei , Smirnov Valentin
Published: February 2025

One of the issues of plasma technologies is a design of a high-performance plasma source. A diffusevacuum arc discharge can be one of the promising options due to its properties. In this work, the dependenceof the charge composition of a diffuse vacuum arc plasma with a hot cathode on the value of the externalaxial magnetic field and discharge voltage was investigated. The study was conducted with thermionicgadolinium cathode. Monitoring the charge composition was done by analyzing the emission spectra of theplasma. Steady-states of arc discharge were obtained for a range of parameters: the arc currents were 30and 40 A, the arc voltage was up to 29 V and the external magnetic field was varied from 0 to 20 mT. Itwas found that in the presence of the eternal magnetic field the defining factor of the charge compositionwas the arc voltage. Moreover, for a fixed arc voltage, the increase in the magnitude causes the growth ofintensities of all atomic and ionic plasma components (Gd, Gd+, Gd++). The potential causes of this effectwere discussed. It was established that in an axial magnetic field it is possible to implement dischargemodes with predominance of single-charge ions by increasing the magnitude of external magnetic field.Potentially these discharge modes will be of use for the implementation of plasma methods of reprocessingspent nuclear fuel.
Partial Submandibular Gland Resection With Ultrasonic Dissector vs Electrocautery
Authors: Buckner Hallie , Shah Anil R
Published: February 2025

Background

The superficial aspect of the submandibular gland can be removed to improve the aesthetic appearance of the face and neck. This study describes a novel surgical technique to resect part of the submandibular gland during a deep neck or face lift.

Objectives

Describe technique to remove the superficial lobe of the submandibular gland using an ultrasonic dissector. Analyze the association between use of ultrasonic technology and reduced post-operative complications. Compare rates of post-operative complications between standard electrocautery and ultrasonic dissection.

Methods

Experimental and control groups were established. A Sonicision ultrasonic dissector (Covidien, Dublin, Ireland) was used for resection in the experimental group, while electrocautery was used for resection in the control group. Post-operative outcomes of neuropraxia, hematoma, seroma, and sialocele formation were collected. Statistical analysis was performed using a Fisher’s exact test in RStudio.

Results

Control patients (n=32) experienced 1 hematoma, 3 seromas, 3 sialoceles, and 3 neuropraxias. Experimental patients (n=48) experienced 2 seromas with no hematomas, sialoceles, or neuropraxia. No association of statistical significance between reduced risk of complications and use of ultrasonic dissection was found.

Conclusions

This novel technique has potential to improve the safety and efficacy of partial submandibular gland resection. However, a follow-up study with greater sample size and without confounding variables, such as intraoperative injection of Botulinum toxin, is necessary.
A conditional denoising VAE-based framework for antimicrobial peptides generation with preserving desirable properties
Authors: Zhao Weizhong , Hou Kaijieyi , Shen Yiting , Hu Xiaohua
Published: February 2025

Motivation

The widespread use of antibiotics has led to the emergence of resistant pathogens. Antimicrobial peptides (AMPs) combat bacterial infections by disrupting the integrity of cell membranes, making it challenging for bacteria to develop resistance. Consequently, AMPs offer a promising solution to addressing antibiotic resistance. However, the limited availability of natural AMPs cannot meet the growing demand. While deep learning technologies have advanced AMP generation, conventional models often lack stability and may introduce unforeseen side effects.

Results

This study presents a novel denoising VAE-based model guided by desirable physicochemical properties for AMP generation. The model integrates key features (e.g. molecular weight, isoelectric point, hydrophobicity, etc.), and employs position encoding along with a Transformer architecture to enhance generation accuracy. A customized loss function, combining reconstruction loss, KL divergence, and property preserving loss ensure effective model training. Additionally, the model incorporates a denoising mechanism, enabling it to learn from perturbed inputs, thus maintaining performance under limited training data. Experimental results demonstrate that the proposed model can generate AMPs with desirable functional properties, offering a viable approach for AMP design and analysis, which ultimately contributes to the fight against antibiotic resistance.

Availability and implementation

The data and source codes are available both in GitHub (https://github.com/David-WZhao/PPGC-DVAE) and Zenodo (DOI 10.5281/zenodo.14730711).
Tracking the neurophysiological effects of proteinopathy into the pre-clinical stage of Alzheimer’s disease
Authors: Wiesman Alex I , Flores-Alonso Santiago I
Published: February 2025

This scientific commentary refers to ‘Amyloid-β deposition predicts oscillatory slowing of magnetoencephalography signals and a reduction of functional connectivity over time in cognitively unimpaired adults’, by Scheijbeler et al. (https://doi.org/10.1093/braincomms/fcaf018).
A simple method for preparation of poly(2,2′-bithiophene) flexible electrochromic devices in ionic liquids
Authors: Cao Yudi , Chen Qingshan , Wang Lei , Yang Mingqing , Zhang Shiyu , Niu Chunhui , Lv Yong
Published: February 2025

In this study, we develop a simple method for efficiently preparing poly(2,2′-bithiophene) flexible electrochromic devices. The poly(2,2′-bithiophene) films are fabricated in the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate. The poly(2,2′-bithiophene) films are characterized by Fourier transform infrared spectroscopy, scanning electron microscope, and ultraviolet-visible absorbance spectroscopy. The poly(2,2′-bithiophene) films exhibit electrochromic behavior, transitioning from an orange-red color in its reduced state to a dark green upon oxidation, particularly pronounced in the near-infrared region. Further studies demonstrate that poly(2,2′-bithiophene) films exhibits flexibility, allowing it to be bent and folded. This method for fabricating poly(2,2′-bithiophene) films shows promising potential for future applications.
New insight into slow earthquake activities from continuous ocean bottom seismometers at the Guerrero seismic gap, Mexico
Authors: Chen Yanhan , Ito Yoshihiro , Plata-Martinez Raymundo , Dominguez Luis Antonio , Ohyanagi Shukei , Garcia Emmanuel Soliman , Flores Ketzallina , Cruz-Atienza Victor M , Shinohara Masanao , Yamashita Yusuke
Published: February 2025

The Guerrero seismic gap in the Mexican subduction zone exhibits a slip behaviour distinct from that of adjacent segments, which typically experience large earthquakes. With the acquisition of offshore seismic data in this region and the discovery of shallow tectonic tremors, the study of slow earthquakes has gradually increased. This study presents the detection of tectonic tremors and low frequency earthquakes (LFEs) in the Guerrero seismic gap using a combination of a modified envelope cross-correlation method and a matched filter applied to ocean bottom seismometer data for a continuous two-year observational period. The modified envelope cross-correlation method was used to detect and locate tremors, and the matched filter technique enabled the detection of LFEs. These methods allowed for better constraints on the depths of the detected events, offering new insights into tremors and LFE activity offshore the Guerrero seismic gap. Our results show that the spatial distribution of these phenomena, along with seismicity, residual gravity anomalies and seafloor topography, suggests that a section of the shallow plate interface within the gap has experienced stable slip. This study builds on previous work by enhancing the detection and location accuracy of these slow earthquakes, contributing to a more comprehensive understanding of subduction dynamics in the region.
Co-silencing of PhENO1 and PhPPT alters anthocyanin production by reducing phosphoenolpyruvate supply in petunia flower
Authors: Li Xin , Cao Jiahao , Jiang Guiyun , Deng Wenqi , Deng Huimin , Yang Weiyuan , Yu Yixun , Liu Juanxu
Published: February 2025

The shikimate pathway is crucial for the production of aromatic amino acids and various secondary plant products, including anthocyanins. Phosphoenolpyruvate (PEP) is an important source for shikimate production. The pre-chorismate part of the shikimate pathway is confined to plastids. There are three sources of PEP in plastids. PEP can be imported into the plastids from cytoplasm via the PEP/phosphate translocator (PPT), and it can also be generated in plastids via enolase (ENO) and pyruvate orthophosphate dikinase (PPDK) catalysis. A large number of anthocyanins are synthesized in the flowers of most ornamental plants in the coloring stage. However, the source of PEP, the precursor of anthocyanin synthesis, is still unknown. Herein, Petunia hybrida PhENO1, PhPPT and PhPPDK genes were identified and their subcellular localization and expression patterns were analyzed. Silencing PhENO1, PhPPT and PhPPDK alone and co-silencing of PhENO1 and PhPPDK or PhPPT and PhPPDK did not exhibit any visible phenotypic change compared with the control, while co-silencing of PhENO1 and PhPPT resulted in the flower color change from purple to light purple. The content of PEP, shikimate, flavonoids, anthocyanins and aromatic amino acids were all significantly decreased in PhENO1 and PhPPT co-silenced plants. Co-silencing PhENO1 and PhPPT did not affect the expression level of key genes in anthocyanin synthesis and shikimate pathways. Furthermore, co-silencing of PhENO1, PhPPT and PhPPDK resulted in a phenotype similar to the co-silencing of PhENO1 and PhPPT. Altogether, our study suggested that PEP used for anthocyanin synthesis is mainly provided by PhENO1 and PhPPT, rather than PhPPDK.
Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks
Authors: Negishi Hiroki , Ichikawa Ayumi , Takahashi Saori , Kano Hiroshi , Makino Seiya
Published: February 2025

The gut microbiome plays a crucial role in human health, and certain bacterial species, such as Faecalibacterium prausnitzii, are particularly beneficial. This study conducted a comprehensive investigation of prebiotic compounds that showed potential for specifically promoting beneficial gut bacteria. Using in vitro fecal cultures and a human intervention study, we identified maltobionic acid and lactobionic acid as compounds that specifically promoted Faecalibacterium growth both in vitro and in vivo without significantly affecting Bifidobacterium, which is typically increased by traditional prebiotics. In a human intervention study (n = 27), a significant increase was observed in Faecalibacterium abundance following maltobionic acid supplementation, with effectiveness correlating with the initial Parabacteroides abundance. Mechanistic investigations revealed a cross-feeding pathway between gut bacteria. In this pathway, Parabacteroides species converted the gluconic acid moiety of maltobionic and lactobionic acids to glucuronic acid, which was then preferentially utilized by Faecalibacterium. These findings suggest that gluconic acid-containing oligosaccharides are promising prebiotics for the targeted enhancement of beneficial Faecalibacterium and underscore the importance of microbial interactions in prebiotic research, offering new avenues for personalized microbiome modulation strategies.
Multifaceted roles of neutrophils in cardiac disease
Authors: Morrissey Samantha , Kirkland Logan G , Phillips Tasha K , Levit Rebecca D , Hopke Alex , Jensen Brian C
Published: February 2025

Neutrophils, the most abundant leukocytes in human blood, have long been recognized as critical first responders in the innate immune system's defense against pathogens. Some of the more notable innate anti-microbial properties of neutrophils include generation of superoxide free radicals like myeloperoxidase (MPO), production of proteases that reshape the extracellular matrix allowing for easier access to infected tissues, and release of neutrophil extracellular traps (NETs), extruded pieces of DNA that ensnare bacterial and fungi. These mechanisms developed to provide neutrophils with a vast array of specialized functions to provide the host defense against infection in an acute setting. However, emerging evidence over the past few decades has revealed a far more complex and nuanced role for these neutrophil-driven processes in various chronic conditions, particularly in cardiovascular diseases.

The pathophysiology of cardiac diseases involves a complex interplay of hemodynamic, neurohumoral, and inflammatory factors. Neutrophils, as key mediators of inflammation, contribute significantly to this intricate network. Their involvement extends far beyond their classical role in pathogen clearance, encompassing diverse functions that can both exacerbate tissue damage and contribute to repair processes. Here we consider the contributions of neutrophils to myocardial infarction, heart failure, cardiac arrhythmias and non-ischemic cardiomyopathies. Understanding these complex interactions is crucial for developing novel therapeutic strategies aimed at modulating neutrophil functions in these highly morbid cardiac diseases.
Occupational health topics series on the effects of chemicals: epidemiological and toxicological risk assessments of ortho-toluidine for bladder cancer
Authors: Nakano Makiko , Gi Min , Toyooka Tatsushi , Suzuki Shugo , Wanibuchi Hideki , Takebayashi Toru
Published: February 2025

Objectives

Our aim was to report integrative evidence for the health risk assessment of ortho-toluidine (OT) in bladder cancer in a mini-review of the recent studies of humans, experimental animals, and OT skin permeability.

Methods

Bladder cancer cases were identified in workers in Japan who were occupationally exposed in 2014-2017 to aromatic amines, primarily to the human carcinogen OT.

Results

A key epidemiological study of 98 aromatic amine–exposed workers in Japan showed a clear OT exposure–response relationship with a standardized incidence ratio. A rat model experimental study also indicated that OT and acetoaceto-o-toluidine are potent bladder carcinogens. Multiple mechanisms of OT-related bladder cancer have been proposed: metabolic activation to reactive metabolites that bind DNA and proteins, mutagenicity, oxidative DNA damage, chromosomal damage, and cytotoxicity by OT. Recent comprehensive analyses of DNA adducts in rats identified a number of common oxidative DNA adducts, including 8-OHdG, in the rat urothelium and indicated that oxidative stress may play a crucial role in the development of urinary cancer caused by OT. The skin permeability of 6 aromatic amines (o-toluidine, aniline, p-toluidine, o-anisidine, 2,4-dimethylaniline, and o-chloroaniline) was examined with the use of a 3-dimensional (3D) reconstructed human skin model; ~70%-80% of the 6 aromatic amines had permeated through the 3D skin within 8 hours. Genotoxic potency testing in a human urothelial cell line using γ-H2AX, a marker of DNA damage, suggested that OT exhibited strong γ-H2AX generation.

Conclusions

Prolonged dermal exposure to OT along with other genotoxic aromatic amines over many years may contribute to the development of bladder cancer.
A tale of too many trees: a conundrum for phylogenetic regression
Authors: Adams Richard , Roa Lozano Jenniffer , Duncan Mataya , Green Jack , Assis Raquel , DeGiorgio Michael
Published: February 2025

Just exactly which tree(s) should we assume when testing evolutionary hypotheses? This question has plagued comparative biologists for decades. Though all phylogenetic comparative methods require input trees, we seldom know with certainty whether even a perfectly estimated tree (if this is possible in practice) is appropriate for our studied traits. Yet, we also know that phylogenetic conflict is ubiquitous in modern comparative biology, and we are still learning about its dangers when testing evolutionary hypotheses. Here we investigate the consequences of tree-trait mismatch for phylogenetic regression in the presence of gene tree-species tree conflict. Our simulation experiments reveal excessively high false positive rates for mismatched models with both small and large trees, simple and complex traits, and known and estimated phylogenies. In some cases, we find evidence of a directionality of error: assuming a species tree for traits that evolved according to a gene tree sometimes fares worse than the opposite. We also explored the impacts of tree choice using an expansive, cross-species gene expression dataset as an arguably “best-case” scenario in which one may have a better chance of matching tree with trait. Offering a potential path forward, we found promise in the application of a robust estimator as a potential, albeit imperfect, solution to some issues raised by tree mismatch. Collectively, our results emphasize the importance of careful study design for comparative methods, highlighting the need to fully appreciate the role of accurate and thoughtful phylogenetic modeling.
Coding Genes Helped the Origination and Diversification of Intragenic MicroRNAs
Authors: Liu Chengzhang , Zhang Xiaojun , Yuan Jianbo , Xiang Jianhai , Li Fuhua
Published: February 2025

Noncoding microRNAs tend to evolve within introns of coding genes that provide them with transcriptional opportunity. As an outcome of natural selection, the intragenic position of microRNAs is crucial for their expression, evolution, and functional cooperation with the host gene. Therefore, understanding the evolution of intragenic microRNA structures may bring novel insights into genetic and phenotypic evolution. However, it remains largely unexplored. Here, by analyzing microRNA genomics in 34 metazoan species, we found that the majority (630/1,154) of microRNA families originated from introns of coding genes that provided them with initial transcriptional capacity. The most rapid expansion of intragenic microRNAs happened at the advent of vertebrates when 21 microRNA families emerged from introns of neural genes and reorganized the gene regulatory network, leading to the rise of vertebrate-specific neural crest cells, which transformed the invertebrate head and enabled the ecological shift from filter feeding to active predation. Intragenic microRNAs gradually gain independence from their host genes, which is accelerated by whole-genome duplications. After a whole-genome duplication, the purging of redundant host genes often set an orphaned microRNA “free” to diversify with the transcriptional elements inherited from the host. Whole-genome duplications facilitated a dramatic microRNA diversification during the initial divergence of vertebrates, as the intragenic status of 12 neural crest-regulating microRNAs was retained in jawed vertebrates but was lost in jawless cyclostomes, which diverged their neural crest development. We propose that coding genes not only facilitate the origination of new microRNAs, but also “sacrifice” themselves to help microRNA diversification.
Metamorphic evolution of kyanite-bearing garnet pyroxenites from the Variscan orogenic root: Gföhl Unit, Moldanubian Zone, Austria
Authors: Asenbaum Rene , Zelinková Tereza , Racek Martin , Janoušek Vojtěch , Hauzenberger Christoph , Abart Rainer
Published: February 2025

Kyanite-bearing garnet pyroxenites occurring in centimetre to several hundred metres sized lenses of (ultra-)mafic lithologies embedded in felsic granulites of the Gföhl Unit in the south-eastern part of the Moldanubian Zone recorded a polyphase metamorphic evolution. An early high-pressure–high-temperature (HP–HT) stage at temperatures of 900 °C to 1000 °C and pressures in excess of 2 GPa is represented by the assemblage garnet–kyanite–omphacitic clinopyroxene–rutile (± quartz). Subsequent re-crystallisation under medium-pressure–high-temperature (MP–HT) conditions of about 1.0–1.3 GPa and 900–1000 °C is documented by the replacement of omphacitic clinopyroxene by symplectic intergrowth of diopsidic clinopyroxene and plagioclase, formation of sapphirine-bearing symplectites after kyanite, and a pronounced secondary compositional zoning of pre-existing garnet. Systematic compositional variations in the garnet cores over mm- to cm-sized mineralogically and microstructurally distinct domains indicate that equilibration volumes were small during the early HP–HT stage. In contrast, the compositions of the minerals that formed, or re-crystallised, during the MP–HT overprint are uniform throughout the samples, indicating substantially larger equilibration volumes during that stage. The metamorphic evolution is discussed in the light of deep subduction and relamination of felsic metaigneous crust, which subsequently experienced buoyancy-driven exhumation to mid-crustal levels and incorporated slivers of mafic and ultramafic material from the lithospheric mantle and lower crust en route.
Engineering of anti-cancer human IgA equipped with albumin for enhanced plasma half-life
Authors: Mester Simone , Chan Chilam , Lustig Marta , Foss Stian , Jansen J H Marco , Leangen Herigstad Marie , Evers Mitchell , Nilsen Jeannette , Reiding Karli R , Damen J Mirjam A , Burger Renate , Grevys Algirdas , Dalhus Bjørn , Valerius Thomas , Sandlie Inger , Leusen Jeanette H W , Andersen Jan Terje
Published: February 2025

Most therapeutic antibodies are based on immunoglobulin G (IgG) due to their potent effector functions and long plasma half-life. However, also monomeric IgA has emerged as an attractive candidate for cancer treatment as, upon specific binding to tumor cells, it can activate myeloid cells, like polymorphonuclear leukocytes and macrophages, to kill the tumor cells by engaging the Fc α receptor I (FcαRI). Despite this favorable property, human IgA has a short plasma half-life in both mice and humans, which is clearly limiting preclinical studies in a translational perspective. Here, we report on albumin-equipped designs of human IgA antibodies that are long-acting due to tailored binding to the human form of neonatal Fc receptor (FcRn), which is a natural plasma half-life regulator of albumin. Importantly, this was achieved without compromising the ability of IgA to engage and activate FcαRI-expressing effector cells for tumor cell killing in vitro and in vivo in a new mouse model transgenic for the human forms of FcRn and FcαRI. We further show that the potency of the engineered long-acting human IgA against tumor cells with intermediate target antigen expression levels could be enhanced by myeloid checkpoint inhibitors targeting the signal regulatory protein α - CD47 axis.