bluuebunny/crossref_metadata_2025 huggingface dataset:
It's About Time: Parent–Child Turn-Taking in Early Stuttering
Authors: Godsey Allison , Ratner Nan Bernstein
Published: December 2024

Purpose:

Most common treatments for stuttering offer advice that parents modify temporal features of conversational interaction to assist children who stutter (CWS). Advice includes but is not limited to slowing of adult speech, increasing turn-taking/response-time latencies (RTLs), and reducing interruptions. We looked specifically at RTL and parental speech rate in a longitudinal data set that included baseline behaviors.

Method:

We used data from baseline recordings (
CWNS
= 13 CWS-persistent, 28 CWS-recovered, 21 children who did not stutter) of the Illinois International Stuttering Research Project at FluencyBank, using CLAN software with audio linkage to Praat.

Results:

Group differences in speech rate and RTL at baseline were nonsignificant; parents of CWS-persistent spoke most slowly pre-advisement. No relationships between speech rate or RTL and child fluency were detected.

Conclusions:

This is a retrospective, observational study, and caution must be used in interpreting our findings. However, current results do not add evidentiary support for common advice to adjust temporal parameters of their interactions made to parents of CWS, in terms of therapeutic outcome or concurrent fluency. We are analyzing subsequent samples, after advisement, to determine potential benefits of such guidance not evident in this analysis. Suggestions for future research and implications for clinical focus and practice are offered.
The Active Ingredients of Semantic Naming Treatment: Evidence From Mandarin–English Bilingual Adults With Aphasia
Authors: Li Ran , Chen ShiMin , Kiran Swathi
Published: December 2024

Purpose:

Following the Rehabilitation Treatment Specification System (RTSS) framework, the current study investigated the active ingredients in the modified semantic feature analysis (mSFA) targeting either noun or verb retrieval in Mandarin–English bilingual adults with aphasia (BWA).

Method:

Twelve Mandarin–English BWA completed mSFA treatment for nouns and verbs. Eight of them completed both noun and verb treatment, while four completed either type of treatment. Performance in each step was scored and analyzed using mixed-effects modeling. Then, regression was performed to estimate the effect of treatment performance on the accuracy of naming probes for trained and semantically related items in both treated and untreated languages.

Results:

Participants demonstrated significant improvements in all treatment steps during both noun and verb treatment, yet the effect varied depending on the trained word category and treatment language. Moreover, all treatment components contributed significantly to the treatment outcomes. Better treatment performance in spontaneous naming was significantly associated with improved naming accuracy of the trained items in noun mSFA, while better treatment performance in spontaneous naming, feature analysis, and sentence production was significantly associated with enhanced naming of the semantically related untrained items in noun mSFA. Importantly, performance in all treatment steps of both noun and verb mSFA significantly predicted naming accuracy in the untreated language.

Conclusion:

Findings provided strong evidence of the potential active ingredients of semantic-based naming therapy in Mandarin–English BWA and highlighted the importance of examining treatment ingredients within the RTSS framework.

Supplemental Material:

https://doi.org/10.23641/asha.28003292
Search for hot subdwarf stars from SDSS images using a deep learning method: SwinBayesNet
Authors: Wu Huili , Bu Yude , Zhang JiangChuan , Zhang Mengmeng , Yi Zhenping , Liu Meng , Kong Xiaoming , Lei Zhenxin
Published: December 2024

Hot subdwarfs are essential for understanding the structure and evolution of low-mass stars, binary systems, astroseismology, and atmospheric diffusion processes. In recent years, deep learning has driven significant progress in hot subdwarf searches. However, most approaches tend to focus on modelling with spectral data, which are inherently more costly and scarce compared to photometric data. To maximise the reliable candidates, we used Sloan Digital Sky Survey (SDSS) photometric images to construct a two-stage hot subdwarf search model called SwinBayesNet, which combines the Swin Transformer and Bayesian neural networks. This model not only provides classification results but also estimates uncertainty. As negative examples for the model, we selected five classes of stars prone to confusion with hot subdwarfs, including O-type stars, B-type stars, A-type stars, white dwarfs (WDs), and blue horizontal branch stars. On the test set, the two-stage model achieved F1 scores of 0.90 and 0.89 in the two-class and three-class classification stages, respectively. Subsequently, with the help of Gaia DR3, a large-scale candidate search was conducted in SDSS DR17. We found 6804 hot-subdwarf candidates, including 601 new discoveries. Based on this, we applied a model threshold of 0.95 and Bayesian uncertainty estimation for further screening, refining the candidates to 3413 high-confidence objects, which include 331 new discoveries.
Weihnachtstrubel
Authors: Pintarelli-Rauschenbach Manuela
Published: December 2024

Haben Sie schon alle Geschenke und freuen sich auf die Weihnachtstage oder steht Ihnen noch Trubel und Hektik bevor? Oft sind es gerade die letzten Tage vor dem Fest, die uns in Hektik verfallen lassen. Diese Weihnachtszeit ist nicht wie immer – die Regierung ist vor wenigen Wochen geplatzt und Wahlvorbereitungen finden erstmalig neben Weihnachtsveranstaltungen statt. Und auch wir als Interessensverband für Physiotherapie engagieren uns besonders, informieren politische Entscheider über die Bedarfe der Berufsgruppe zu einer ungewöhnlichen Jahreszeit.
P
,
T
-odd effects in YbCu, YbAg, and YbAu
Authors: Polet Johan David , Chamorro Yuly , Pašteka Lukáš F. , Hoekstra Steven , Tomza Michał , Borschevsky Anastasia , Aucar I. Agustín
Published: December 2024

In this work, the molecular enhancement factors of the P,T-odd interactions involving the electron electric dipole moment (Wd) and the scalar–pseudoscalar nucleon–electron couplings (Ws) are computed for the ground state of the bimetallic molecules YbCu, YbAg, and YbAu. These systems offer a promising avenue for creating cold molecules by associating laser-cooled atoms. The relativistic coupled-cluster approach is used in the calculations, and a thorough uncertainty analysis is performed to give accurate and reliable uncertainties to the obtained values. Furthermore, an in-depth investigation of the different electronic structure effects that determine the magnitude of the calculated enhancement factors is carried out, and two different schemes for computing Wd are compared. The final values for the enhancement factors are (13.32±0.13)×1024hHzecm, (12.19±0.12)×1024hHzecm, and (2.36±0.48)×1024hHzecm for Wd and (−48.63 ± 0.53) h kHz, (−45.68 ± 0.60) h kHz, and (3.81 ± 2.58) h kHz for Ws, for YbCu, YbAg, and YbAu, respectively.
Study of balancing methods for parallel cable transmission lines
Authors: Bian Jiayin , Zhang Jue , Kong Shiqi , Quan Wanlin , He Weiming
Published: December 2024

Cables are of vital importance for the transmission and distribution of electricity within the power grid. However, as the demand for electricity continues to grow, the transmission capacity of a single high-voltage cable is no longer sufficient to meet the required standards. It is therefore imperative to increase the transmission capacity of cables. The deployment of parallel cable transmission represents the most effective strategy for enhancing transmission capacity. However, due to the complex electromagnetic coupling relationship between cables, there is a possibility of current imbalance between cable lines in the same phase, which will have an adverse effect on the normal operation of power equipment and pose a significant threat to the security of the power system. In light of the aforementioned considerations, this paper primarily investigates the mitigation of parallel cable line imbalance. Initially, it examines the parallel cable line current imbalance factors through a theoretical lens, encompassing cable impedance and electromagnetic coupling arrangement. Subsequently, it assesses the efficacy of two proposed methods for reducing the imbalance degree of the parallel cable, namely, the adjustable reactor in series and the addition of a magnetic ring device. Furthermore, finite element simulation software is employed to simulate the two methods and verify their efficacy. Ultimately, a parallel cable plus magnetic ring test is conducted to verify the effectiveness of the magnetic ring.
Modeling how and why aquatic vegetation removal can free rural households from poverty-disease traps
Authors: Doruska Molly J. , Barrett Christopher B. , Rohr Jason R.
Published: December 2024

Infectious disease can reduce labor productivity and incomes, trapping subpopulations in a vicious cycle of ill health and poverty. Efforts to boost African farmers’ agricultural production through fertilizer use can inadvertently promote the growth of aquatic vegetation that hosts disease vectors. Recent trials established that removing aquatic vegetation habitat for snail intermediate hosts reduces schistosomiasis infection rates in children, while converting the harvested vegetation into compost boosts agricultural productivity and incomes. We develop a bioeconomic model that interacts an analytical microeconomic model of agricultural households’ behavior, health status, and incomes over time with a dynamic model of schistosomiasis disease ecology. We calibrate the model with field data from northern Senegal. We show analytically and via simulation that local conversion of invasive aquatic vegetation to compost changes the feedback among interlinked disease, aquatic, and agricultural systems, reducing schistosomiasis infection and increasing incomes relative to the current status quo, in which villagers rarely remove aquatic vegetation. Aquatic vegetation removal disrupts the poverty-disease trap by reducing habitat for snails that vector the infectious helminth and by promoting the production of compost that returns to agricultural soils nutrients that currently leach into surface water from on-farm fertilizer applications. The result is healthier people, more productive labor, cleaner water, more productive agriculture, and higher incomes. Our model illustrates how this ecological intervention changes the feedback between the human and natural systems, potentially freeing rural households from poverty-disease traps.
Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase
Authors: He Runsheng , Dong Wenyang , Wang Zhi , Xie Chen , Gao Long , Ma Wenping , Shen Ke , Li Dubai , Pang Yuxuan , Jian Fanchong , Zhang Jiankun , Yuan Yuan , Wang Xinyao , Zhang Zhen , Zheng Yinghui , Liu Shuang , Luo Cheng , Chai Xiaoran , Ren Jun , Zhu Zhanxing , Xie Xiaoliang Sunney
Published: December 2024

Decades of research have established that mammalian transcription factors (TFs) bind to each gene’s regulatory regions and cooperatively control tissue specificity, timing, and intensity of gene transcription. Mapping the combination of TF binding sites genome wide is critically important for understanding functional genomics. Here, we report a technique to measure TFs’ binding sites on the human genome with a near single-base resolution by footprinting with deaminase (FOODIE) on a single-molecule and single-cell basis. Single-molecule sequencing reads after enzymatic deamination allow detection of the TF binding fraction on a particular footprint and the binding cooperativity of any two adjacent TFs, which can be either positive or negative. As a newcomer of single-cell genomics, single-cell FOODIE enables the detection of cell-type-specific TF footprints in a pure cell population in a heterogeneous tissue, such as the brain. We found that genes carrying out a certain biological function together in a housing-keeping correlated gene module (CGM) or a tissues-specific CGM are coordinated by shared TFs in the gene’s promoters and enhancers, respectively. Scalable and cost-effective, FOODIE allows us to create an open FOODIE database for cell lines, with applicability to human tissues and clinical samples.
Intrinsic adaptive plasticity in mouse and human sensory neurons
Authors: McIlvried Lisa A. , Del Rosario John Smith , Pullen Melanie Y. , Wangzhou Andi , Sheahan Tayler D. , Shepherd Andrew J. , Slivicki Richard A. , Lemen John A. , Price Theodore J. , Copits Bryan A. , Gereau Robert W.
Published: December 2024

In response to changes in activity induced by environmental cues, neurons in the central nervous system undergo homeostatic plasticity to sustain overall network function during abrupt changes in synaptic strengths. Homeostatic plasticity involves changes in synaptic scaling and regulation of intrinsic excitability. Increases in spontaneous firing and excitability of sensory neurons are evident in some forms of chronic pain in animal models and human patients. However, whether mechanisms of homeostatic plasticity are engaged in sensory neurons of the peripheral nervous system (PNS) is unknown. Here, we show that sustained depolarization (induced by 24-h incubation in 30 mM KCl) induces compensatory changes that decrease the excitability of mouse and human sensory neurons without directly opposing membrane depolarization. Voltage-clamp recordings show that sustained depolarization produces no significant alteration in voltage-gated potassium currents, but a robust reduction in voltage-gated sodium currents, likely contributing to the overall decrease in neuronal excitability. The compensatory decrease in neuronal excitability and reduction in voltage-gated sodium currents reversed completely following a 24-h recovery period in a normal medium. Similar adaptive changes were not observed in response to 24 h of sustained action potential firing induced by optogenetic stimulation at 1 Hz, indicating the need for prolonged depolarization to drive engagement of this adaptive mechanism in sensory neurons. Our findings show that mouse and human sensory neurons are capable of engaging adaptive mechanisms to regulate intrinsic excitability in response to sustained depolarization in a manner similar to that described in neurons in the central nervous system.
A misstep in the multistep process of fast inactivation
Authors: Short Ben
Published: December 2024

JGP study (Liu and Bezanilla. https://doi.org/10.1085/jgp.202413667) reveals that a sodium channel mutant blocks fast inactivation downstream of inactivation particle binding, diverting the channel into an alternative open state.
High spatial resolution PET detectors based on 10 mm × 10 mm linearly-graded SiPMs and 0.5 mm pitch LYSO arrays
Authors: Xie Jiahao , Wang Haibo , Merzi Stefano , Paternoster Giovanni , Gola Alberto , Qi Jinyi , Cherry Simon R , Du Junwei
Published: December 2024

Objective. Position-sensitive silicon photomultipliers (PS-SiPMs) are promising photodetectors for ultra-high spatial resolution small-animal positron emission tomography (PET) scanners. This paper evaluated the performance of the latest generation of linearly-graded SiPMs (LG-SiPMs), a type of PS-SiPM, for ultra-high spatial resolution PET applications using LYSO arrays from two vendors. Approach. Two dual-ended readout detectors were developed by coupling LG-SiPMs to both ends of the two LYSO arrays. Each LG-SiPM has an active area of 9.8 × 9.8 mm2. Both LYSO arrays consist of 20 × 20 arrays of 0.44 × 0.44 × 20 mm3 polished LYSOs with a pitch of 0.5 mm. The performance of the two detectors was compared in terms of flood histogram, energy resolution, timing resolution, and depth-of-interaction (DOI) resolutions. Main results. Flood histograms showed clear identification of all LYSO elements except for some edge crystals due to the larger size of the LYSO arrays compared to the active area of the LG-SiPMs and the misalignment between LG-SiPMs and LYSO arrays in the assembled detectors. At a bias voltage of 37.0 V, the detectors utilizing the Tianle LYSO array and EBO LYSO array provided energy resolutions of 17.5 ± 2.2 and 18.6 ± 2.0%, timing resolutions of 0.75 ± 0.03 and 0.78 ± 0.03 ns, and DOI resolutions of 2.16 ± 0.15 and 2.31 ± 0.12 mm, respectively. Significance. The results presented in this paper demonstrate that the new generation LG-SiPMs are promising photodetectors for ultra-high spatial resolution small-animal PET scanner applications.
Modulation instability induced by quadratic nonlinearity in optically anisotropic medium
Authors: Shafeeque Ali A K , Anas E , Maniparambath Mohamed Nishad , Basim M B
Published: December 2024

In anisotropic crystals, the inherent breakdown of circular symmetry due to anisotropy significantly impacts optical phenomena. This study theoretically investigates the effects of anisotropic diffraction on modulation instability (MI) spectra and subsequent optical filament formation. We model an anisotropic medium with quadratic nonlinearity, exhibiting noncritical phase-matched second-harmonic generation, using coupled nonlinear Schrödinger equations. Through linear stability analysis and numerical simulations, we examine MI in quasi-isotropic and anisotropic quadratic nonlinear media. Our results reveal that anisotropic diffraction induces asymmetry in the MI gain spectrum, leading to the formation of elliptical optical filaments for both fundamental and second harmonics. Notably, this asymmetry in the MI gain spectrum facilitates the generation of multiple filaments in high-gain MI region.
Stability and mechanical properties of Ti-Nb-Ta ternary alloys
Authors: Yuliza E , Wella S A , Amalia N
Published: December 2024

First-principles calculations were conducted to explore the influence of Ta incorporation on the stability, mechanical properties, and electronic structure of Ti50Nb(50−x)Ta
x
(0 ≤ x ≤ 50, x at.%) alloys. The results indicate that Ta addition increases lattice parameters and formation energy while maintaining structural stability across all compositions. Elastic constants confirm mechanical stability and reveal increasing stiffness with higher Ta content. Projected density of states (PDOS) analysis reveals that Ta enhances metallic bonding and alters the electronic environment near the Fermi level, which aligns with the observed mechanical improvements, including higher stiffness, rigidity, and hardness. The calculated Young’s modulus of 39–72 GPa offers better compatibility with bone than conventional implants, with Poisson’s ratio confirming sufficient ductility. These findings suggest that these alloys hold potential for biomedical applications, offering a balance between mechanical performance and structural stability.
Copper precursor-driven variations in structural, optical and electrical properties of SILAR-deposited CTS thin films
Authors: A K Sijo , P Sapna
Published: December 2024

This pioneering study elucidates, for the first time, the profound impact of copper precursors (copper acetate, copper sulfate, and copper chloride) on the structural, optical, and electrical properties of Copper Tin Sulfide (CTS) thin films synthesized via successive ionic layer adsorption and reaction (SILAR) deposition. Comprehensive characterization using x-ray diffraction (XRD), cross-sectional scanning electron microscopy (SEM), atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy, and electrical and optical measurements revealed significant variations in crystallite size (74.9–84.4 nm), film thickness (1.235–4.75 μm), and conductance (3.2–4.7 × 10−11 S). Notably, copper acetate-derived films exhibited enhanced surface morphology, whereas copper chloride-derived films demonstrated exceptional optoelectronic properties, including a maximum bandgap energy of 3.7 eV, highest conductance of 4.7 × 10−11 S, and unique optical characteristics, such as zero transmittance below 300 nm, low absorption above 300 nm, and a balanced absorption profile, rendering them suitable for photovoltaic cells, optical sensors, and UV-blocking applications. These results demonstrate the critical influence of copper precursors on CTS thin film properties, paving the way for tailored material design and enhanced device performance, with significant implications for the development of efficient and sustainable photovoltaic technologies.
Enhancement of dual autofocusing ability for ring Pearcey edge dislocation beams
Authors: Dong Shun , Jia Heping , Yang Rongcao , Kong Xianyi
Published: December 2024

When the ring with the maximum intensity deviates from the central point, the dual autofocusing performance of the ring Pearcey edge dislocation (RPED) beams in free space is gradually destroyed. To address the degradation in the dual autofocusing ability, we investigate the propagation dynamics of the RPED beams in a system with fractional diffraction effect or parabolic potential. The simulation results show that there exists a critical value for the Lévy index, that results in the RPED beams exhibiting an obvious dual autofocusing phenomenon with equal focusing intensities. When the Lévy index is near the critical value, the RPED beams have dual autofocusing characteristics, and the focusing intensity and focal distance can be controlled by changing the Lévy index. The introducing of the parabolic potential leads to the periodic evolution of the RPED beams, and the dual autofocusing property of the RPED beams with smaller radius can be restored within one evolution cycle by changing the potential depth. Moreover, the positions of the edge dislocation affect the focusing intensity, but have no effect on the number of foci. Our research provides some inspiration for the control of dual autofocusing beams, and has potential applications in optical manipulation and optical trapping.
Attosecond recollision dynamics in nonsequential double ionization of argon by orthogonally polarized two-color laser fields
Authors: Li Na , Qiao Xiaoxiao , Gao Feng , Lu Xiaolong , Liu Jun , Wang Zifeng , Xin Peipei
Published: December 2024

Electronic correlation, as a fundamental physical effect, is one of the most fascinating research topics in laser-matter interaction. Using the three dimensional classical ensemble model (CEM), we investigate the attosecond recollision dynamics in non-sequential double ionization (NSDI) of argon under orthogonally polarized two-color (OPTC) fields consisting of 800-nm and 400-nm laser pulses. We find that the probability distribution of recollision time and energy asymmetric sharing between two electrons, as well as the Coulomb repulsion of electron pairs all have an impact on the correlated behaviors of two electrons. Meanwhile, the emission directions of electrons pairs can be effectively controlled by manipulating the relative phase of the two-color field. By performing a classical trajectory analysis of two electrons, we reveal that not only the first return but also multiple returns of tunneling electrons can make a significant contribution to the recollision dynamics in NSDI.
Classification of static plane symmetric spacetime according to their self similar vector fields
Authors: Akhtar Sumaira Saleem , Shakeel Mehnaz , Zahir Hina , Khan Jamshed , Ahmad Imtiaz
Published: December 2024

This article discusses the use of self-similar symmetry to analyze static plane symmetric spacetime. A computer algorithm is employed to convert the symmetry equations, resulting in a tree structure known as a Riff tree, which is utilized for analyzing the aforementioned symmetry within the specified spacetime. The tree comprises several pivots and branches, with the pivots being subject to specific differential conditions on the metric functions. Furthermore, explicit formulas for the metrics and their corresponding self-similar vector fields (SSVFs) are derived by solving the set of equations using these constraints. Additionally, this work investigates the bounds for certain energy conditions as well as the kinematic variables.
Testing No slip model with pulsar timing arrays: NANOGrav and IPTA
Authors: Davari Mohammadreza , Allahyari Alireza , Khosravi Shahram
Published: December 2024

We perform an observational study of modified gravity considering a potential inflationary interpretation of pulsar timing arrays (PTA). We use a motivated model known as no slip in which the gravitational wave propagation is modified. Specifically, by using two different parametrizations for the model, we find the approximate transfer functions for tensor perturbations. In this way, we obtain the spectral energy density of gravitational waves and use NANOGrav and IPTA second data release to constrain parameters of the model. In parametrization I, ξ is degenerate with log
10
A and γ and in parametrization II, cM
is also degenerate with both log
10
A and γ.
For cM
, we only get an upper bound on the parameter. Thus, it is difficult to constrain them with percent level accuracy with the current PTA data.
diffSph: a Python tool to compute diffuse signals from dwarf spheroidal galaxies
Authors: Vollmann Martin , Welzmüller Finn , Gajović Lovorka
Published: December 2024

So far no diffuse emissions in dwarf spheroidal satellites of the Milky Way have ever been observed.
Given that dwarf galaxies are predominantly composed of Dark Matter, the discovery of these signals could offer valuable insights into understanding the nature of Dark Matter.
We present “diffSph”, a Python tool which in its present version provides fast predictions of such diffuse signals in radio frequencies.
It also features a very comprehensive module for the computation of “J” and “D” factors that are relevant for indirect Dark Matter detection using gamma rays.
Routines are coupled to parton-shower algorithms and Dark Matter halo mass functions from state-of-the-art kinematic fits.
This code is also useful for testing generic hypotheses (not necessarily associated with any Dark Matter candidate) about the cosmic-ray electron/positron sources in the dwarf galaxies.
The diffSph tool has already been employed in searches for diffuse signals from dwarf spheroidal galaxies using the LOw Frequency ARray (LOFAR).
Massive neutrinos and cosmic composition
Authors: Loverde Marilena , Weiner Zachary J.
Published: December 2024

Cosmological data probe massive neutrinos via their effects on the geometry of the
Universe and the growth of structure, both of which are degenerate with the late-time expansion
history. We clarify the nature of these degeneracies and the individual roles of both probes in
neutrino mass inference. Geometry is strongly sensitive to neutrino masses: within ΛCDM,
the primary cosmic microwave background anisotropies alone impose that the matter fraction
Ω
m
must increase fivefold with increasing neutrino mass. Moreover, large-scale structure
observables, like weak lensing of the CMB, are dimensionless and thus depend not on the matter
density (as often quoted) but in fact the matter fraction. We explore the consequential impact of
this distinction on the interplay between probes of structure, low-redshift distances, and CMB
anisotropies. We derive constraints on the neutrino's masses independently from their suppression
of structure and impact on geometry, showing that the latter is at least as important as the
former. While the Dark Energy Spectroscopic Instrument's recent baryon acoustic oscillation data
place stringent bounds largely deriving from their geometric incompatibility with massive
neutrinos, all recent type Ia supernova datasets drive marginal preferences for nonzero neutrino
masses because they prefer substantially larger matter fractions. Recent CMB lensing data,
however, neither exclude neutrinos' suppression of structure nor constrain it strongly enough to
discriminate between mass hierarchies. Current data thus evince not a need for modified dynamics
of neutrino perturbations or structure growth but rather an inconsistent compatibility with
massive neutrinos' impact on the expansion history. We identify two of DESI's measurements that
strongly influence its constraints, and we also discuss neutrino mass measurements in models that
alter the sound horizon.
Stability of volatile organic compounds in thermal desorption tubes and in solution
Authors: Kiland Kristian J , Martins Lucas , Borden Scott A , Lam Stephen , Myers Renelle
Published: December 2024

Exhaled breath volatile organic compounds (VOCs) are often collected and stored in sorbent tubes before thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) analysis. Information about the stability of VOCs during storage is needed to account for potential artifacts and monitor for losses. Additionally, information about the stability of VOC standards in solution is required to assess their performance as quality control and internal standards. We evaluated the stability of a standard mixture of 42 VOCs in dual-sorbent tubes containing Tenax® TA and Carbotrap 1TD over 60 d at commonly used storage conditions: room temperature (∼21 °C), 4 °C, and −80 °C. The same 42 VOCs were also evaluated for their stability in methanol over 60 d while stored at −20 °C. All samples were analyzed using TD-GC-MS. During storage, most VOCs were stable on sorbent after 60 d: 36/42 (86%), 39/42 (93%), and 41/42 (98%) had not statistically changed for room temperature, 4 °C and −80 °C, respectively, based on Spearman rank correlation coefficients and linear regression analysis. The isotopically labeled VOCs tested here are well-suited to serve as internal standards for pre-analysis or storage. Degradation of VOCs in solution was apparent after 60 d: 27/42 (64%) of VOCs had statistically decreased. The total VOC mixture had dropped to 90% of its original intensity after ∼22 d and a subset of VOCs typically used as internal standards dropped to 90% in ∼16 d. Analysts using similar mixtures should make a fresh solution at least every two weeks to ensure analytical accuracy. This study provides important insights into storage practices for both sorbent tubes and standard solutions, guiding analysts toward improved reliability and accuracy in exhaled breath analysis.
Room-temperature in-plane ferromagnetism in Co-substituted Fe5GeTe2 investigated by magnetic x-ray spectroscopy and microscopy
Authors: Heppell Emily , Fujita Ryuji , Gurung Gautam , Lin Jheng-Cyuan , May Andrew F , Foerster Michael , Waqas Khaliq M , Angel Niño Miguel , Valvidares Manuel , Herrero-Martín Javier , Gargiani Pierluigi , Watanabe Kenji , Taniguchi Takashi , Backes Dirk , van der Laan Gerrit , Hesjedal Thorsten
Published: December 2024

The exploration of two-dimensional (2D) van der Waals ferromagnets has revealed intriguing magnetic properties with significant potential for spintronics applications. In this study, we examine the magnetic properties of Co-doped Fe5GeTe2 using x-ray photoemission electron microscopy (XPEEM) and x-ray magnetic circular dichroism (XMCD), complemented by density functional theory calculations. Our XPEEM measurements reveal that the Curie temperature (

T
C

) of a bilayer of (Co
x
Fe

1
−
x

)

5
−
δ

GeTe2 (with x = 0.28) reaches ∼300 K—a notable enhancement over most 2D ferromagnets in the ultrathin limit. Interestingly, the

T
C

shows only a small dependence on film thickness (bulk

T

C

≈
340

 K), in line with the observed in-plane (IP) magnetic anisotropy and robust IP exchange coupling. XMCD measurements indicate that the spin moments for both Fe and Co are significantly reduced compared to the theoretical values. These insights highlight the potential of Co-doped Fe5GeTe2 for stable, high-temperature ferromagnetic applications in 2D materials.
Quantum optics with giant atoms in a structured photonic bath
Authors: Leonforte Luca , Sun Xuejian , Valenti Davide , Spagnolo Bernardo , Illuminati Fabrizio , Carollo Angelo , Ciccarello Francesco
Published: December 2024

We present a general framework to tackle quantum optics problems with giant atoms, i.e. quantum emitters each coupled non-locally to a structured photonic bath (typically a lattice) of any dimension. The theory encompasses the calculation and general properties of Green’s functions, atom-photon bound states, collective master equations and decoherence-free Hamiltonians (DFHs), and is underpinned by a formalism where a giant atom is formally viewed as a normal atom lying at a fictitious location. As a major application, we provide for the first time a general criterion to predict/engineer DFHs of giant atoms, which can be applied both in and out of the photonic continuum and regardless of the structure or dimensionality of the photonic bath. This is used to show novel DFHs in 2D baths such as a square lattice, photonic graphene and an extended photonic Lieb lattice.
NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture
Authors: Ahmed Fatma S , Aly Saleh , Liu Xiangrong
Published: December 2024

Antibody-mediated immunity is crucial in the vertebrate immune system. Nanobodies, also known as VHH or single-domain antibodies (sdAbs), are emerging as promising alternatives to full-length antibodies due to their compact size, precise target selectivity, and stability. However, the limited availability of nanobodies (Nbs) for numerous antigens (Ags) presents a significant obstacle to their widespread application. Understanding the interactions between Nbs and Ags is essential for enhancing their binding affinities and specificities. Experimental identification of these interactions is often costly and time-intensive. To address this issue, we introduce NABP-BERT, a deep-learning model based on the BERT architecture, designed to predict NANOBODY®-Ag binding solely from sequence information. Furthermore, we have developed a general pretrained model with transfer capabilities suitable for protein-related tasks, including protein-protein interaction tasks. NABP-BERT focuses on the surrounding amino acid contexts and outperforms existing methods, achieving an AUROC of 0.986 and an AUPR of 0.985.
GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites
Authors: Han Cheng , Fu Shanshan , Chen Miaomiao , Gou Yujie , Liu Dan , Zhang Chi , Huang Xinhe , Xiao Leming , Zhao Miaoying , Zhang Jiayi , Xiao Qiang , Peng Di , Xue Yu
Published: December 2024

Protein phosphorylation is dynamically and reversibly regulated by protein kinases and protein phosphatases, and plays an essential role in orchestrating a wide range of biological processes. Although a number of tools have been developed for predicting kinase-specific phosphorylation sites (p-sites), computational prediction of phosphatase-specific dephosphorylation sites remains to be a great challenge. In this study, we manually curated 4393 experimentally identified site-specific phosphatase–substrate relationships for 3463 dephosphorylation sites occurring on phosphoserine, phosphothreonine, and/or phosphotyrosine residues, from the literature and public databases. Then, we developed a hybrid learning framework, the group-based prediction system for the prediction of phosphatase-specific dephosphorylation sites (GPSD). For model training, we integrated 10 types of sequence features and utilized three types of machine learning methods, including penalized logistic regression, deep neural networks, and transformer neural networks. First, a pretrained model was constructed using 561 416 nonredundant p-sites and then fine-tuned to generate computational models for predicting general dephosphorylation sites. In addition, 103 individual phosphatase-specific predictors were constructed via transfer learning and meta-learning. For site prediction, one or multiple protein sequences in FASTA format could be inputted, and the prediction results will be shown together with additional annotations, such as protein–protein interactions, structural information, and disorder propensity. The online service of GPSD is freely available at https://gpsd.biocuckoo.cn/. We believe that GPSD can serve as a valuable tool for further analysis of dephosphorylation.
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling
Authors: Shen Yi , Liu Liya , Liu Enyan , Li Sida , Orlov Yuriy , Ivanisenko Vladimir , Chen Ming
Published: December 2024

Non-coding RNAs (ncRNAs) are traditionally considered incapable of encoding proteins, but new evidence suggests that small open reading frames (sORFs) within ncRNAs can actually encode biologically functional small peptides. Despite growing recognition of their importance, a systematic exploration of plant ncRNAs with coding potential has remained largely uncharted territory, especially in the context of their translational activities. By collecting and analyzing Ribo-Seq data from 226 Arabidopsis thaliana samples, we have integrated extensive information on Arabidopsis ncRNAs with coding potential and developed the AthRiboNC database, a novel and dedicated database that consolidates extensive information on ncRNAs with coding potential in Arabidopsis. AthRiboNC covers detailed information on 2743 long non-coding RNAs, 255 microRNAs, and 1871 circular RNA in Arabidopsis, along with 40 162 ORFs identified from these ncRNAs. The database also constructs co-expression networks for ncRNAs with coding potential, revealing correlations and potential biological function interpretations. With a commitment to accessibility and ease-of-use, AthRiboNC features a clear and intuitive interface. We hope that AthRiboNC will serve as a valuable resource for exploring the coding potential of plant ncRNAs.

Database URL: https://bis.zju.edu.cn/athribonc
Diversity and networking of uni-cyanobacterial cultures and associated heterotrophic bacteria from the benthic microbial mat of a desert hydrothermal spring
Authors: Lassoued Khaoula , Mahjoubi Mouna , Asimakis Elias , Bel Mokhtar Naima , Stathopoulou Panagiota , Ben Hamouda Refka , Bousselmi Olfa , Marasco Ramona , Masmoudi Ahmed Slaheddine , Daffonchio Daniele , Tsiamis George , Cherif Ameur
Published: December 2024

Thermal springs harbour microorganisms, often dominated by cyanobacteria, which form biofilms and microbial mats. These phototrophic organisms release organic exudates into their immediate surroundings, attracting heterotrophic bacteria that contribute to the diversity and functioning of these ecosystems. In this study, the microbial mats from a hydrothermal pool in the Ksar Ghilane oasis in the Grand Erg Oriental of the Desert Tunisia were collected to obtain cyanobacterial cultures formed by single cyanobacterial species. High-throughput analysis showed that while the microbial mat hosted diverse cyanobacteria, laboratory cultures selectively enriched cyanobacteria from the Leptolyngbya, Nodosilinea, and Arthronema. Per each of these genera, multiple non-axenic uni-cyanobacterial cultures were established, totalling 41 cultures. Cyanobacteria taxa mediated the assembly of distinct heterotrophic bacterial communities, with members of the Proteobacteria and Actinobacteria phyla dominating. The bacterial communities of uni-cyanobacterial cultures were densely interconnected, with heterotrophic bacteria preferentially co-occurring with each other. Our study highlighted the complex structures of non-axenic uni-cyanobacterial cultures, where taxonomically distinct cyanobacteria consistently associate with specific groups of heterotrophic bacteria. The observed associations were likely driven by common selection pressures in the laboratory, such as cultivation conditions and specific hosts, and may not necessarily reflect the microbial dynamic occurring in the spring microbial mats.
Improvement of Transmural Inflammation With Adalimumab Versus Immunomodulator Maintenance Therapy in Pediatric Crohn’s Disease: Single-Center Prospective Evaluation Using the Pediatric Inflammatory Crohn’s Magnetic Resonance Enterography Index
Authors: Scarallo Luca , McKay Hayley E , Schneider Rilla , Ricciuto Amanda , Walters Thomas D , Greer Mary-Louise C , Griffiths Anne M , Church Peter C
Published: December 2024

Background and Aims

Transmural healing, including as assessed by magnetic resonance enterography (MRE) has been associated with long-term favorable outcomes in Crohn’s Disease (CD), but data concerning MRE improvement and normalization with therapy are sparse. We performed a prospective longitudinal study utilizing the recently developed pediatric MRE-based multi-item measure of inflammation (PICMI) to examine the efficacy of adalimumab (ADA) and immunomodulator (IM) in attaining improvement of transmural inflammation of the small intestine.

Methods

Pediatric patients with CD involving small bowel and initiating ADA or IM were prospectively enrolled and followed with repeat MRE at 1 year. A single radiologist provided global assessment (RGA) and scored PICMI items (wall thickness, wall diffusion restriction, mural ulcers, comb sign, mesenteric edema) blinded to clinical information and to the timing of MRE. The primary outcome was mild improvement in PICMI at one year without a change in therapy.

Results

Sixty-two eligible patients were enrolled, 26 receiving ADA and 36 IM. On intent to treat basis, a decline in PICMI score of >20 points without change of therapy was observed more frequently in ADA versus IM-treated patients (54% vs 31%, P = .01). By RGA, 71% improved with ADA vs 42% with IM (P = .03). MRE normalization was rare with both treatments (9% vs 6%, P = .62). A change in PICMI of >20 points was confirmed as the best cut off for MRE improvement as assessed by RGA also for the small bowel.

Conclusions

ADA therapy was associated with objective improvement in MRE findings of inflammation more frequently than IM. The low rate of MRE normalization suggests that this is not yet a realistic target with existing therapies.
Cephalic ganglia transcriptomics of the American cockroach Periplaneta americana (Blattodea: Blattidae)
Authors: Levy Ilana , Arvidson Ryan
Published: December 2024

The American cockroach Periplaneta americana (L.) (Blattodea, Blattidae) has been a model organism for biochemical and physiological study for almost a century, however, its use does not benefit from the genetic tools found in key model species such as Drosophila melanogaster. To facilitate the use of the cockroach as a model system in neuroscience and to serve as a foundation for functional and translational experimentation, a transcriptome of the cephalic ganglia was assembled and annotated, and differential expression profiles between these ganglia were assessed. The transcriptome assembly yielded >400 k transcripts, with >40 k putative coding sequences. Gene ontology and protein domain searches indicate the cerebral and gnathal ganglia (GNG) have distinct genetic expression profiles. The developmental Toll signaling pathway appears to be active in the adult central nervous system (CNS), which may suggest a separate role for this pathway besides innate immune activation or embryonic development. The catabolic glycolytic and citric acid cycle enzymes are well represented in both ganglia, but key enzymes are more highly expressed in the GNG. Both ganglia express gluconeogenic and trehaloneogenic enzymes, suggesting a larger role of the CNS in regulating hemolymph sugar homeostasis than previously appreciated. The annotation and quantification of the cephalic ganglia transcriptome reveal both canonical and novel pathways in signaling and metabolism in an adult insect and lay a foundation for future functional and genetic analysis.
Intellectual property issues for open science practices in genomic-related health research and innovation in Africa
Authors: Adaji Aishatu Eleojo , Abdulrauf Lukman Adebisi
Published: December 2024

This paper considers the applicability and implications of intellectual property rights (IPRs) for open science practices in the context of genomic-related health research and innovation in Africa. The first part provides a brief background of the gaps in genomics and health research in Africa, highlighting the possible role of open science in facilitating collaborative research to address the peculiar health needs of the continent. The second part examines intellectual property protection in genomic-related health research and innovation in Africa, outlining some of the existing legal instruments and policies guiding the application of IPRs, focusing on patents and copyrights. Thereafter, the paper examined how intellectual property standards could impact the adoption of open science in genomics health research in Africa. In doing this, the paper considers the role they could play as enablers of open science practices in genomics health research and innovation and the potential challenges they pose. The paper concludes with recommendations regarding aspects of the intellectual property policies and legal frameworks in Africa that could be calibrated to overcome potential challenges and, thereby, stimulate the adoption of an open science model and promote open, collaborative genomics health research and innovation in the continent.
Drinking pattern and time lag of alcohol consumption with colorectal cancer risk in US men and women
Authors: Li Xinyi , Hur Jinhee , Zhang Yin , Song Mingyang , Smith-Warner Stephanie A , Liang Liming , Mukamal Kenneth J , Rimm Eric B , Giovannucci Edward L
Published: December 2024

Background

Association between light to moderate alcohol consumption and colorectal cancer (CRC) incidence remains understudied, especially regarding drinking pattern, beverage type, and temporal aspects.

Methods

Hazard ratios (HRs) and 95% confidence intervals (CIs) for time to CRC diagnosis were estimated among 137 710 participants. Estimates based on remote (eg, >10 years before follow-up) and recent (eg, the preceding 10 years before follow-up) alcohol intake, using different cutoffs (eg, 8, 10, 12 years) and mutual adjustment, enabled separating independent effects and investigating time lag of alcohol–CRC association.

Results

In total, 3599 CRC cases were documented over 3 decades. Light to moderate drinking was associated with an increased CRC risk only in men: HR (95% CI) for 5-14.9 and 15-29.9 vs 0 g/day of alcohol intake was 1.19 (1.01 to 1.41) and 1.38 (1.13 to 1.67). In women, that for 0.1-4.9 and 5-14.9 vs 0 g/day of alcohol was 1.07 (0.96 to 1.20) and 1.05 (0.91 to 1.20). Drinkers with both high drinking frequency and daily intake had the highest CRC risk, suggesting total alcohol intake was the critical factor. We estimated the time lag between alcohol consumption and CRC occurrence to be 8 to 12 years. Former drinkers did not experience a significant reduction in CRC risk even after 10 years of quitting or reducing consumption.

Conclusions

Based on 2 cohorts of health professionals, our findings suggest that the increased risk of CRC associated with alcohol intake is driven mainly by total quantity and remote intake. Former drinkers did not experience an immediate reduction in CRC risk after quitting or reducing consumption.