bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of transcutaneous electrical nerve stimulation based on wrist-ankle acupuncture theory for pain relief during colonoscopy without anesthesia: a randomized controlled trial
Authors: Huang Xiaonan , Wang Hao , Shi Lei , Xu Lifan , Lv Can , Song Wenjuan , Huang Lele , Yan Feihu , Shi Ping , Cai Mengcheng , Fang Fanfu 
Published: July 2024

Abstract
Background Colonoscopy is essential for diagnosing colorectal diseases but can cause pain during the procedure. This study explored the analgesic effects of transcutaneous electrical nerve stimulation based on wrist-ankle acupuncture theory (TENS-WAA) in colonoscopy without anesthesia.
Methods This prospective study included 120 participants undergoing colonoscopies without anesthesia. The trial group received low-frequency, high-intensity TENS-WAA adjusted to the maximum tolerable current, while the control group received minimal current. The primary outcome was the retrospective pain score on a visual analog scale (VAS). Secondary outcomes included time, heart rate, and credibility/expectancy questionnaire (CEQ) scores.
Results Participants who received TENS-WAA reported significantly lower pain VAS scores than the control group (estimated median difference –1.1, 95%CI –2 to –0.4; P = 0.002). Male participants in the trial group experienced significantly lower pain scores than the control group (mean difference –1.4, 95%CI –2.41 to –0.39; P = 0.008). The trial group showed significantly less variation in heart rates (P<0.001) and higher CEQ scores (P = 0.001) than the control group. No adverse events were reported.
Conclusion TENS-WAA effectively reduced pain during colonoscopy without anesthesia, especially in male participants, providing a promising noninvasive analgesic method.
Antenatal Screening for Congenital Heart Disease: A Single Center 11-Year Study of the Incidence, Antenatal Detection Rate, and Outcomes of Fetal Cardiac Anomalies
Authors: Clark Eilidh , Palaniappan Nithiya , Clegg Isobel 
Published: July 2024

Abstract
Objectives This article describes the incidence, detection rate, and birth outcomes of congenital heart disease (CHD) within a single center over an 11-year period.
Methods A database of patients diagnosed with CHD on antenatal ultrasound or within 12 months of delivery was collated from January 2010 to December 2020. A retrospective review of records was performed to establish the incidence of CHD and the antenatal detection rate (ADR). A Fisher's exact test was used to investigate the association between the type of CHD, the presence of a genetic abnormality, extracardiac anomalies, and the ADR.
Results The incidence of CHD was 4.3 per 1,000 maternities (n = 161). Fifty-five percent of anomalies were diagnosed antenatally. Twenty-seven percent underwent termination of pregnancy. Seventy-three percent of cases were alive at the end of follow-up. Patients with a major form of CHD were more likely to receive an antenatal diagnosis compared with those with other forms of CHD (64.9% vs. 39.1%, p 0.002). The presence of extracardiac abnormalities was associated with a higher ADR.
Conclusion The incidence of CHD was 4.3 per 1,000 maternities. Most major cardiac anomalies were diagnosed antenatally. Detection rates varied depending on the nature of the lesion and the presence of other congenital anomalies.
Implications for Clinical Practice Cardiac anomalies are the most common form of birth defect. Reported incidence rates lie between 4 and 20 per 1,000 live births. This study describes the incidence, pregnancy outcomes, and ADR of cardiac anomalies within one Scottish health board. It provides insight into the effectiveness of a national screening program in detecting CHD and the factors that influence ADR. Therefore, it can be used to more effectively counsel patients on the strengths and limitations of antenatal ultrasound for detecting CHD.
Two liquid states of distinguishable helium-4: The existence of another non-superfluid frozen by heating
Authors: Tsujimoto Momoko , Kinugawa Kenichi 
Published: July 2024

We show that two liquid states can exist in distinguishable helium-4 (4He) obeying Boltzmann statistics by path integral centroid molecular dynamics (CMD) simulations. This is an indication of quantum liquid polyamorphism induced by the nuclear quantum effect. For 0.08–3.3 K and 1–500 bar, we extensively conducted the isothermal–isobaric CMD simulations to explore not only possible states and state diagram but also the state characteristics. The distinguishable 4He below 25 bar does not freeze down to 0.1 K even though it includes no Bosonic exchange effect and, therefore, no Bose condensation. One liquid state, low quantum-dispersion liquid (LQDL), is nearly identical to normal liquid He-I of real 4He. The other is high quantum-dispersion liquid (HQDL) consisting of atoms with longer quantum wavelength. This is another non-superfluid existing below 0.5 K or the temperatures of LQDL. The HQDL is also a low-entropy and fragile liquid to exhibit, unlike conventional liquids, rather gas-like relaxation of velocity autocorrelation function, while there the atoms diffuse without noticeable contribution from quantum tunneling. The LQDL–HQDL transition is not a thermodynamic phase transition but a continuous crossover accompanied by the change in the expansion factor of quantum wavelength. Freezing of HQDL into the low quantum-dispersion amorphous solid occurs by heating from 0.2 to 0.3 K at 40–50 bar, while this P-T condition coincides with the Kim–Chan normal–supersolid phase boundary of real 4He. The obtained state diagram was compared to that of the confined subnano-scale 4He systems, where Bosonic correlation is considerably suppressed.
The initial measurement of a compact D–T neutron spectrometer based on a single-crystal chemical vapor deposition diamond stack for fusion plasma diagnostic
Authors: Liao L. Y. , Ogawa K. , Sangaroon S. , Paenthong W. , Kusaka S. , Tamaki S. , Murata I. , Isobe M. 
Published: July 2024

For developing and characterizing a novel compact D–T neutron spectrometer based on a single-crystal chemical vapor deposition diamond stack for plasma diagnostics toward future D–T fusion reactors, the initial measurement was performed using the accelerator-based D–T neutron sources OKTAVIAN at Osaka University. This neutron spectrometer was designed for the detection of 3–17 MeV neutrons and operated in the proton recoil telescope configuration by installing a polyethylene converter in front of the diamond stack. The measured neutron energy spectra were obtained by summing the energy of the recoil protons deposited in the diamond stack after the coincidence of the recoil protons identified by the time coincidence analysis. The neutron energy peaks measured by the compact D–T neutron spectrometer were almost in agreement with those obtained by the Monte Carlo N-Particle transport (MCNP) simulation. The energy resolution of the compact D–T neutron spectrometer was emulated to be about 4%–5% in D–T neutron measurement. In future work, the design of the compact D–T neutron spectrometer would be optimized to measure the fusion neutron for plasma diagnostics.
Determination of dark matter distribution in Ursa Major III and constraints on dark matter annihilation*
Authors: Zhao 赵 Yi 熠 , Bi 毕 Xiao-Jun 效军 , Lin 林 Su-Jie 苏杰 , Yin 殷 Peng-Fei 鹏飞 
Published: July 2024

Abstract
The recently discovered satellite dwarf galaxy Ursa Major III provides a promising opportunity to explore the signatures resulting from dark matter (DM) annihilation owing to its proximity and large J-factor. Given the absence of an excess of γ-ray signatures originating from Ursa Major III, observations of γ-rays, such as those from Fermi-LAT, can be utilized to set constraints on the DM annihilation cross-section. In this study, we determined the DM density profile and considered the relationship between DM density and velocity dispersion at different locations within Ursa Major III through Jeans analysis. We calculated the J-factor of Ursa Major III for s-wave annihilation along with the effective J-factors for p-wave and Sommerfeld enhanced annihilation scenarios. Employing these derived J-factors, we set stringent constraints on DM annihilation cross-sections in three scenarios. Given the substantial impact of member star identification on the J-factor of Ursa Major III, we further calculated J-factors under the exclusion of the largest velocity outlier. Our analysis reveals a notable reduction in the median value and an increase in the deviation of J-factors, thereby leading to considerably weaker constraints.
The minimal projective bundle dimension and toric 2-Fano manifolds
Authors: Araujo Carolina , Beheshti Roya , Castravet Ana-Maria , Jabbusch Kelly , Makarova Svetlana , Mazzon Enrica , Viswanathan Nivedita 
Published: July 2024

Motivated by the problem of classifying toric

2
2

-Fano manifolds, we introduce a new invariant for smooth projective toric varieties, the minimal projective bundle dimension. This invariant

m
(
X
)
∈
{
1
,
…
,
dim
⁡
(
X
)
}

m(X)\in \{1, \dots ,\dim (X)\}

captures the minimal degree of a dominating family of rational curves on

X
X

or, equivalently, the minimal length of a centered primitive relation for the fan of

X
X

. We classify smooth projective toric varieties with

m
(
X
)
≥
dim
⁡
(
X
)
−
2

m(X)\geq \dim (X)-2

, and show that projective spaces are the only

2
2

-Fano manifolds among smooth projective toric varieties with

m
(
X
)
∈
{
1
,
dim
⁡
(
X
)
−
2
,
dim
⁡
(
X
)
−
1
,
dim
⁡
(
X
)
}

m(X)\in \{1, \dim (X)-2,\dim (X)-1,\dim (X)\}

.
Faith and diversity
Authors: Trigg Roger 
Published: July 2024

Abstract
Religious beliefs in many forms have been universal features of human life, as recent research in cognitive science of religion indicates. Religious faith, for good or ill, is deep-rooted in the way humans are. There may be common strands between its different forms, but we must be wary of interpreting everything in terms familiar to our own society. Faith needs reason and understanding, and belief in God needs further special revelation. This gives rise to diversity between religions, and divergent claims within religion, including Christianity. Claims to religious revelation have to be tested. If reason plays a part in faith, we must face the fact of disagreement within and between religions, and about all religion.
survivalContour: visualizing predicted survival via colored contour plots
Authors: Shi Yushu , Zhang Liangliang , Do Kim-Anh , Jenq Robert R , Peterson Christine B 
Published: July 2024

Abstract

Summary
Advances in survival analysis have facilitated unprecedented flexibility in data modeling, yet there remains a lack of tools for illustrating the influence of continuous covariates on predicted survival outcomes. We propose the utilization of a colored contour plot to depict the predicted survival probabilities over time. Our approach is capable of supporting conventional models, including the Cox and Fine–Gray models. However, its capability shines when coupled with cutting-edge machine learning models such as random survival forests and deep neural networks.

Availability and implementation
We provide a Shiny app at https://biostatistics.mdanderson.org/shinyapps/survivalContour/ and an R package available at https://github.com/YushuShi/survivalContour as implementations of this tool.
ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration
Authors: Lai Jhih-Siang , Burley Stephen K , Duarte Jose M 
Published: July 2024

Abstract

Motivation
Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools.

Results
This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics.

Availability and implementation
ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.
SpatialQC: automated quality control for spatial transcriptome data
Authors: Mao Guangyao , Yang Yi , Luo Zhuojuan , Lin Chengqi , Xie Peng 
Published: July 2024

Abstract

Summary
The advent of spatial transcriptomics has revolutionized our understanding of the spatial heterogeneity in tissues, providing unprecedented insights into the cellular and molecular mechanisms underlying biological processes. Although quality control (QC) critical for downstream data analyses, there is currently a lack of specialized tools for one-stop spatial transcriptome QC. Here, we introduce SpatialQC, a one-stop QC pipeline, which generates comprehensive QC reports and produces clean data in an interactive fashion. SpatialQC is widely applicable to spatial transcriptomic techniques.

Availability and implementation
source code and user manuals are available via https://github.com/mgy520/spatialQC, and deposited on Zenodo (https://doi.org/10.5281/zenodo.12634669).
GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization
Authors: Montoto-Louzao Julián , Gómez-Carballa Alberto , Bello Xabier , Pardo-Seco Jacobo , Camino-Mera Alba , Viz-Lasheras Sandra , Martín María J , Martinón-Torres Federico , Salas Antonio 
Published: July 2024

Abstract

Summary
Most tools for normalizing NanoString gene expression data, apart from the default NanoString nCounter software, are R packages that focus on technical normalization and lack configurable parameters. However, content normalization is the most sensitive, experiment-specific, and relevant step to preprocess NanoString data. Currently this step requires the use of multiple tools and a deep understanding of data management by the researcher. We present GUANIN, a comprehensive normalization tool that integrates both new and well-established methods, offering a wide variety of options to introduce, filter, choose, and evaluate reference genes for content normalization. GUANIN allows the introduction of genes from an endogenous subset as reference genes, addressing housekeeping-related selection problems. It performs a specific and straightforward normalization approach for each experiment, using a wide variety of parameters with suggested default values. GUANIN provides a large number of informative output files that enable the iterative refinement of the normalization process. In terms of normalization, GUANIN matches or outperforms other available methods. Importantly, it allows researchers to interact comprehensively with the data preprocessing step without programming knowledge, thanks to its easy-to-use Graphical User Interface (GUI).

Availability and implementation
GUANIN can be installed with pip install GUANIN and it is available at https://pypi.org/project/guanin/. Source code, documentation, and case studies are available at https://github.com/julimontoto/guanin under the GPLv3 license.
Tomivosertib reduces ectopic activity in dorsal root ganglion neurons from patients with radiculopathy
Authors: Li Yan , Uhelski Megan L , North Robert Y , Mwirigi Juliet M , Tatsui Claudio E , McDonough Kathleen E , Cata Juan P , Corrales German , Dussor Greg , Price Theodore J , Dougherty Patrick M 
Published: July 2024

Abstract
Spontaneous activity in dorsal root ganglion (DRG) neurons is a key driver of neuropathic pain in patients suffering from this largely untreated disease. While many intracellular signalling mechanisms have been examined in preclinical models that drive spontaneous activity, none have been tested directly on spontaneously active human nociceptors.
Using cultured DRG neurons recovered during thoracic vertebrectomy surgeries, we showed that inhibition of mitogen-activated protein kinase interacting kinase (MNK) with tomivosertib (eFT508, 25 nM) reversibly suppresses spontaneous activity in human sensory neurons that are likely nociceptors based on size and action potential characteristics associated with painful dermatomes within minutes of treatment.
Tomivosertib treatment also decreased action potential amplitude and produced alterations in the magnitude of after hyperpolarizing currents, suggesting modification of Na+ and K+ channel activity as a consequence of drug treatment. Parallel to the effects on electrophysiology, eFT508 treatment led to a profound loss of eIF4E serine 209 phosphorylation in primary sensory neurons, a specific substrate of MNK, within 2 min of drug treatment. Our results create a compelling case for the future testing of MNK inhibitors in clinical trials for neuropathic pain.
Decoding the muscle transcriptome of patients with late-onset Pompe disease reveals markers of disease progression
Authors: Monceau Alexandra , Nath Rasya Gokul , Suárez-Calvet Xavier , Musumeci Olimpia , Toscano Antonio , Kierdaszuk Biruta , Kostera-Pruszczyk Anna , Domínguez-González Cristina , Hernández-Lain Aurelio , Paradas Carmen , Rivas Eloy , Papadimas George , Papadopoulos Constantinos , Chrysanthou-Piterou Margarita , Gallardo Eduard , Olivé Montse , Lilleker James , Roberts Mark E , Marchese Domenica , Lunazzi Giulia , Heyn Holger , Fernández-Simón Esther , Villalobos Elisa , Clark James , Katsikis Panos , Collins Catherine , Mehra Priyanka , Laidler Zoe , Vincent Amy , Tasca Giorgio , Marini-Bettolo Chiara , Guglieri Michela , Straub Volker , Raben Nina , Díaz-Manera Jordi 
Published: July 2024

Abstract
Late-onset Pompe disease (LOPD) is a rare genetic disorder caused by the deficiency of acid alpha-glucosidase leading to progressive cellular dysfunction owing to the accumulation of glycogen in the lysosome. The mechanism of relentless muscle damage (a classic manifestation of the disease) has been studied extensively by analysing the whole-muscle tissue; however, little, if anything, is known about transcriptional heterogeneity among nuclei within the multinucleated skeletal muscle cells. This is the first report of application of single-nucleus RNA sequencing to uncover changes in the gene expression profile in muscle biopsies from eight patients with LOPD and four muscle samples from age- and sex-matched healthy controls. We matched these changes with histological findings using GeoMx spatial transcriptomics to compare the transcriptome of control myofibres from healthy individuals with non-vacuolated (histologically unaffected) and vacuolated (histologically affected) myofibres of LODP patients.
We observed an increase in the proportion of slow and regenerative muscle fibres and macrophages in LOPD muscles. The expression of the genes involved in glycolysis was reduced, whereas the expression of the genes involved in the metabolism of lipids and amino acids was increased in non-vacuolated fibres, indicating early metabolic abnormalities. Additionally, we detected upregulation of autophagy genes and downregulation of the genes involved in ribosomal and mitochondrial function leading to defective oxidative phosphorylation. Upregulation of genes associated with inflammation, apoptosis and muscle regeneration was observed only in vacuolated fibres. Notably, enzyme replacement therapy (the only available therapy for the disease) showed a tendency to restore dysregulated metabolism, particularly within slow fibres. A combination of single-nucleus RNA sequencing and spatial transcriptomics revealed the landscape of the normal and diseased muscle and highlighted the early abnormalities associated with disease progression. Thus, the application of these two new cutting-edge technologies provided insight into the molecular pathophysiology of muscle damage in LOPD and identified potential avenues for therapeutic intervention.
Absence of lung tumor promotion with reduced tumor size in mice after inhalation of copper welding fumes
Authors: Zeidler-Erdely Patti C , Kodali Vamsi , Falcone Lauryn M , Mercer Robert , Leonard Stephen S , Stefaniak Aleksandr B , Grose Lindsay , Salmen Rebecca , Trainor-DeArmitt Taylor , Battelli Lori A , McKinney Walter , Stone Samuel , Meighan Terence G , Betler Ella , Friend Sherri , Hobbie Kristen R , Service Samantha , Kashon Michael , Antonini James M , Erdely Aaron 
Published: July 2024

Abstract
Welding fumes are a Group 1 (carcinogenic to humans) carcinogen as classified by the International Agency for Research on Cancer. The process of welding creates inhalable fumes rich in iron (Fe) that may also contain known carcinogenic metals such as chromium (Cr) and nickel (Ni). Epidemiological evidence has shown that both mild steel (Fe-rich) and stainless steel (Fe-rich + Cr + Ni) welding fume exposure increases lung cancer risk, and experimental animal data support these findings. Copper-nickel (CuNi) welding processes have not been investigated in the context of lung cancer. Cu is intriguing, however, given the role of Cu in carcinogenesis and cancer therapeutics. This study examines the potential for a CuNi fume to induce mechanistic key characteristics of carcinogenesis in vitro and to promote lung tumorigenesis, using a two-stage mouse bioassay, in vivo. Male A/J mice, initiated with 3-methylcholanthrene (MCA; 10 µg/g), were exposed to CuNi fumes or air by whole-body inhalation for 9 weeks (low deposition-LD and high deposition-HD) and then sacrificed at 30 weeks. In BEAS-2B cells, the CuNi fume-induced micronuclei and caused DNA damage as measured by γ-H2AX. The fume exhibited high reactivity and a dose–response in cytotoxicity and oxidative stress. In vivo, MCA/CuNi HD and LD significantly decreased lung tumor size and adenomas. MCA/CuNi HD exposure significantly decreased gross-evaluated tumor number. In summary, the CuNi fume in vitro exhibited characteristics of a carcinogen, but in vivo, the exposure resulted in smaller tumors, fewer adenomas, less hyperplasia severity, and with HD exposure, less overall lung lesions/tumors.