bluuebunny/crossref_metadata_2025 huggingface dataset:
X-ray assisted point defects creation in micron-size Zn, Mo oxide particles at liquid nitrogen temperature
Authors: Buryi M , Babin V , Remeš Z , Mičová J
Published: February 2024

Charge trapping processes induced by the X-ray irradiation in the heavy Mo doped ZnO and MoO3 micropowders synthesized by the hydrothermal growth method were investigated in detail. Electron paramagnetic resonance (EPR) and thermally stimulated luminescence (TSL) were applied in a correlated manner to discover the role of the Mo doping in the charge trapping processes in ZnO. Thermally unstable oxygen- and molybdenum-related charge trapping centers were studied. Molybdenum and oxygen created electron-hole trapping pairs in some cases were observed. Some part of the hole trapping centers seemed to be directly connected with the creation of Mo5+. The correlation between EPR and TSL data was found.
The Effect of Laser Beam on the Width of the Cut
Authors: Knedlová J , Kubišová M , Pata V , Marcaník M , Bočáková B
Published: February 2024

Conventional methods of dividing material due to their limitation to straight cuts have largely been replaced by non-conventional cutting methods, which include laser cutting. Laser cutting of polymer materials has become a priority for the manufacturing industry, mainly due to the constantly growing demand for these materials. The article discusses the effect of the laser beam on the width of the cut using lenses with different focal lengths, under different working conditions, on samples made of PMMA polymer material plates. For the experiment, the samples were produced using an ILS 3NM laser device, a CO2, with a wavelength of 10.6 μm and with maximum power 100 W, maximum feed speed 1524 mm · s-1. For the selected samples, it was studied how the dimension defined by the machining software differ from the dimension created by the machining.
Influence of selected parameters of drag finishing on tool microgeometry
Authors: Pätoprstý B , Buranský I , Jurina F
Published: February 2024

The aim of the experiment described in the paper was to determine how selected parameters of drag finishing such as process time, immersion depth and rotation frequency affect microgeometry of cutting edge. Four flute cemented carbide mills with diameter of 10 mm were used in this experiment. These mills were drag finished on prototype drag finishing machine developed on Faculty of Materials Science and Technology, Slovak University of Technology. Alicona Infinte Focus SL measuring machine was used to measure microgeometry of these mills. The main parameter of microgeometry of cutting edge was the size of the radius of cutting edge. In the article we compared which parameter has the biggest influence on size of cutting edge radius and also there was statistical evaluation carried out. The most significant parameter of drag finishing was determined to be the immersion depth.
Optimization of digital neutron-gamma discrimination methods in time and frequency domain
Authors: Singh Harleen , Mehra Rohit
Published: February 2024

Four digital methods are investigated for neutron-gamma
discrimination in organic scintillation detectors. A fast-digital
pulse processing system has been used to optimize the PSD methods
and to investigate a mixed radiation field with light output in the
range of 100 keV to 5 MeV from an Am-Be source. The methods used
for pulse shape discrimination are the charge comparison, the
simplified digital charge collection, the frequency gradient
analysis, and the discrete wavelet transform method. The performance
of each of these methods has been assessed by calculating the
figure-of-merit and the probability of misclassification. It has
been found that the frequency-domain algorithms perform more
effectively for low-energy pulses and require a smaller processing
gate width than the time-domain methods. They are therefore more
suited to environments with high count rates where pulse pileup is a
common attribute of data. In addition, frequency-domain methods are
more resistant to random noise present in the dataset compared to
time-domain methods.
Nitroprusside and metal nitroprusside nano analogues for cancer therapy
Authors: Tripathy Sanchita , Londhe Swapnali , Patra Chitta Ranjan
Published: February 2024

Sodium nitroprusside (SNP), U.S approved drug has been used in clinical emergency as a hypertensive drug for more than a decade. It is well established for its various biomedical applications such as angiogenesis, wound healing, neurological disorders including anti-microbial applications etc. Apart from that, SNP have been considered as excellent biomedical materials for its use as anti-cancer agent because of its behavior as NO-donor. Recent reports suggest that incorporation of metals in SNP/encapsulation of SNP in metal nanoparticles (metal nitroprusside analogues) shows better therapeutic anti-cancer activity. Although there are numerous reports available regarding the biological applications of SNP and metal-based SNP analogue nanoparticles, unfortunately there is not a single comprehensive review which highlights the anti-cancer activity of SNP and its derivative metal analogues in detail along with the future perspective. To this end, the present review article focuses the recent development of anti-cancer activity of SNP and metal-based SNP analogues, their plausible mechanism of action, current status. Furthermore, the future perspectives and challenges of these biomedical materials are also discussed. Overall, this review article represents a new perspective in the area of cancer nanomedicine that will attract a wider spectrum of scientific community.
Facile process of Hibiscus mucilage polymer formulation using Hibiscus rosa-sinensis leaves to treat second-degree burn and excision wounds
Authors: Saha Ishita , Ghosh Sourav , Roy Shubham , Basu Tarakdas , Karmakar Parimal
Published: February 2024

Mucilage is a sticky substance found in various plants and microorganisms and is made up of proteins and polysaccharides. Mucilage from Hibiscus rosa sinensisis is a complex polysaccharide traditionally used to treat different skin diseases. In our study, we fabricated mucilage polymer from Hibiscus rosa sinensis leaves and evaluated its potential application in second-degree burns and excision wounds. The physical properties of Hibiscus mucilage (HM) polymer were demonstrated by using Ultraviolet-visible absorption spectroscopy, x-ray diffraction, Fourier transform infrared spectroscopy, dynamic light scattering, Scanning electron microscopy, Brunauer–Emmett–Tellerand, Swelling ratio. The human cell lines WI-38, and HaCaT have been used for in-vitro experiments like MTT, scratch wound, BrdU, ROS scavenging assays, and western blot analysis. The results of the MTT, scratch-wound, and BrdU assay indicated that the HM polymer is nontoxic in nature and also enhances both the properties of cellular migration and proliferation, respectively. On the other hand, the result of the ROS scavenging assay suggested that HM polymer enhances the antioxidant activity of cells while the western blot analysis designated that the HM polymer treatment caused downregulation of the pro-inflammatory cytokine IFN-γ and upregulation of the pAkt (Serine 473) protein, and TGF-β1 signaling pathway. Therefore, all in-vitro experimental studies recommended that HM polymer is biocompatible and has antioxidant and anti-inflammatory effects. In the in vivo experiment, second-degree burns and excision wounds were created on the dorsal surface of male BALB/c mice. After the sixth day of HM polymer treatment have developed new tissue, hair follicles, blood vessels, α-SMA, and Collagen type-1 fiber on the burn and excision wound area while the 11th day of HM polymer treatment cured the wound area significantly. Therefore, it could be contemplated that HM polymer is a potential agent for treating different wounds in the near future.
An innovative environmental regulation tool for regional air pollution based on DEA-RFR
Authors: Hao Songze , Zhang Ke , Zhao Xiaohui , Huang Jin , Zhao Qingrui , Wang Chengyu , Zhang Hongpei , Wang Xiaodan , Zheng Binguo
Published: February 2024

Environmental regulation tools are one of the conventional means for pollution control in various countries. For large-scale urbanization regions, reasonable pre-allocation of pollutant emission amount for each area is an effective regulation to improve air quality. Treating pollutant emission quota as a resource element, a comprehensive input-output model has been established based on Data Envelopment Analysis (DEA) method, to evaluate the rationality of pollutant emission allocation and provide adjustment scheme, thus developing an environmental regulation tool. The index system includes factors of economy, environment, energy consumption, demographic and land-use as input indicators, regional GDP and environmental air quality index as output indicators. The regulation tool is applied to the current air pollutant emission management in Henan Province, China. The results show that 7 cities need to further adjust the allocation scheme, among which, Anyang, Xinxiang, Nanyang and Shangqiu are suggested to reduce the emission allocation quotas; Puyang and Zhumadian are suggested to increase the emission allocation quotas; Pingdingshan shall seek optimization paths through collaborative improvement. Further, to verify the effectiveness of the tool, by joint using Random Forest Regression (RFR), a DEA efficiency reassessment is conducted on the obtained new allocation scheme of Nanyang City. The results show that the efficiency of the new allocation scheme has reached optimal. This study provides a practical and effective regulation tool for regional management of pollutant emission, to balance economic growth and environmental protection.
Eco-friendly innovation: harnessing nature’s blueprint for enhanced photocatalysis and antimicrobial potential in multi-structured PN/ZnO nanoparticles
Authors: Gaur Jyoti , Kumar Sanjeev , Kaur Harpreet , Pal Mohinder , Supreet  , Bala Kanchan , Batoo Khalid Mujasam , Momoh Johnson Oshiobugie , Hussain Sajjad
Published: February 2024

This research unveils an innovative approach to green synthesis, detailed characterization, and multifunctional exploration of bio-functionalized zinc oxide nanoparticles (PN/ZnO NPs) adorned with phytochemicals from Piper nigrum (PN). Employing an extensive suite of spectroscopic techniques and physicochemical methods, including UV–vis spectroscopy, field emission scanning electron microscope (FESEM), high-resolution transmission electron microscope (HRTEM), energy dispersive x-ray (EDX) spectroscopy, Fourier-transform infrared (FTIR), x-ray diffraction (XRD), and Brunauer–Emmett–Teller (BET) analysis, the study delves into the unique properties of PN/ZnO NPs. XRD confirms the development of the wurtzite phase with a crystallite diameter of 47.77 nm. FTIR reveals ZnO functionalization by PN’s phytochemicals, while FESEM and HRTEM suggest diverse architectural features. Selected area electron diffraction patterns authenticate the crystalline structure. BET analysis showcases a large specific surface area of 80.72 m2 g−1 and a mesoporous structure. The absorption peak at 372 nm and an energy band gap (E
g) of 3.44 eV validate ZnO NP formation. The catalytic performance is demonstrated through the degradation of commercial reactive yellow-17 (RY-17) dye, with PN/ZnO (dosage 300 mg l−1) achieving 94.72% removal at a dose of 120 mg l−1. Pseudo-first-order kinetics govern the photodegradation process. PN-ZnO NPs showcase potent antimicrobial efficacy against both gram-negative and gram-positive bacteria, with varying clearance zones. This study stands as an impactful exploration, integrating green synthesis, detailed characterization, and versatile functionalities of PN/ZnO NPs.
Field-assisted machining of difficult-to-machine materials
Authors: Zhang Jianguo , Zheng Zhengding , Huang Kai , Lin Chuangting , Huang Weiqi , Chen Xiao , Xiao Junfeng , Xu Jianfeng
Published: February 2024

Difficult-to-machine materials (DMMs) are extensively applied in critical fields such as aviation, semiconductor, biomedicine, and other key fields due to their excellent material properties. However, traditional machining technologies often struggle to achieve ultra-precision with DMMs resulting from poor surface quality and low processing efficiency. In recent years, field-assisted machining (FAM) technology has emerged as a new generation of machining technology based on innovative principles such as laser heating, tool vibration, magnetic magnetization, and plasma modification, providing a new solution for improving the machinability of DMMs. This technology not only addresses these limitations of traditional machining methods, but also has become a hot topic of research in the domain of ultra-precision machining of DMMs. Many new methods and principles have been introduced and investigated one after another, yet few studies have presented a comprehensive analysis and summarization. To fill this gap and understand the development trend of FAM, this study provides an important overview of FAM, covering different assisted machining methods, application effects, mechanism analysis, and equipment design. The current deficiencies and future challenges of FAM are summarized to lay the foundation for the further development of multi-field hybrid assisted and intelligent FAM technologies.
Functional microfluidics: theory, microfabrication, and applications
Authors: Xie Mingzhu , Zhan Ziheng , Li Yinfeng , Zhao Junkai , Zhang Ce , Wang Zhaolong , Wang Zuankai
Published: February 2024

Microfluidic devices are composed of microchannels with a diameter ranging from ten to a few hundred micrometers. Thus, quite a small (10−9–10−18 l) amount of liquid can be manipulated by such a precise system. In the past three decades, significant progress in materials science, microfabrication, and various applications has boosted the development of promising functional microfluidic devices. In this review, the recent progress on novel microfluidic devices with various functions and applications is presented. First, the theory and numerical methods for studying the performance of microfluidic devices are briefly introduced. Then, materials and fabrication methods of functional microfluidic devices are summarized. Next, the recent significant advances in applications of microfluidic devices are highlighted, including heat sinks, clean water production, chemical reactions, sensors, biomedicine, capillaric circuits, wearable electronic devices, and microrobotics. Finally, perspectives on the challenges and future developments of functional microfluidic devices are presented. This review aims to inspire researchers from various fields—engineering, materials, chemistry, mathematics, physics, and more—to collaborate and drive forward the development and applications of functional microfluidic devices, specifically for achieving carbon neutrality.
A walking soft robot driven by electromagnetism inside the body
Authors: Zhu Yongqiang , Guo Qiang , Zhang Yuhan , Zhu Junru , Zhang Pingxia , Gao Mingming , Li Donglin , Liu Hao
Published: February 2024

Existing magnetically driven soft robots mainly rely on external electromagnetic, leading to a substantial energy consumption due to the requirement of a large external magnetic field. Moreover, the precise control of these soft robots relies on electric current, making them highly susceptible to disturbances and deviations induced by minute variations in the current. To overcome these challenges, we propose and evaluate a novel approach employing a miniature walking soft robot empowered by its internal electromagnets. The overall robot size is 18 mm × 6 mm × 12 mm (length × height× width). This design enables the robot to achieve precise and stable motion using a 240-mA current with a 6 V low voltage. In addition, the incorporation of specially designed sheet-leg mechanism with varying degrees of friction facilitates the transformation of linear motion into an effective forward gait. This paper outlines the principles and control strategies of the robot, illustrates the robot fabrication process, at the same time verifies the structural integrity through experimental validation. Further evaluations include comprehensive analysis of the robot’s gait and speed. The results show that the robot attains a speed of 2.86 mm s–1. This study marks a stride towards the realization of a fully autonomous, unrestrained, cost-effective, and energy-conserving magnetic soft robot.
Equivalent linearization of hyperelastic rubber rings in dynamic vibration absorber boring bar and simulation of its dynamic properties
Authors: Shi Haizhao , Ma Chicheng , Li Xinye , Wang Gang
Published: February 2024

A slight perturbation in high-speed precision cutting could cause violent vibration of boring bars, resulting in unexpected wear and failure of the structures. In this paper, the dynamical characteristic of a boring bar with a dynamic vibration absorber (DVA) is investigated. Considering that the nonlinear characteristics of the rubber ring play a significant role in improving the capacity of DVA, we proposed an equivalent linearization method for modeling hyperelastic rubber rings based on the experimental data of uniaxial tensile test. The relationship between the stiffness of rubber rings and the precompression parameter δ is established for two types of rubber. The equivalent linearization model shows good accuracy and calculation efficiency while the mass of the DVA is confined to a narrow space and the assumption of small strain is inherently satisfied. Numerical results show that the time cost of the equivalent linearization model is only 5% of the full hyperelastic model. Furthermore, the effect of different spring stiffnesses and damping on the dynamic characteristics of the boring bar is compared by using the equivalent linearization model, and the vibration peak of the DVA boring bar is found to be reduced about 45%. Our findings establish a simplified modeling scheme for choosing rubber rings in design of dynamic vibration absorbers with acceptable accuracy and little time cost, which could also give some reference for modeling of metal rubber and gel-like materials.
Changes in Northern Hemisphere extra-tropical cyclone frequency following volcanic eruptions
Authors: Andreasen L S , Cornér J , Abbott P M , Sinclair V A , Riede F , Timmreck C
Published: February 2024

Explosive volcanic eruptions are well known to influence Earth’s temperature. Changes in Earth’s temperature can affect temperature gradients which in turn could affect the isentropic slope and hence Northern Hemisphere high and mid-latitude weather. Yet, the possible influence of volcanic eruptions on these atmospheric circulation patterns and the potential spatial extent are not well understood. To address this issue, we pursue two independent lines of evidence. Firstly, we simulate volcanic eruptions with the MPI-ESM1.2 Earth System Model and use the TRACK algorithm to explore how extra-tropical cyclone (ETC) frequency is affected in the model experiments. Secondly, we query the Greenland ice core NEEM-2011-S1 for indications of increased Northern Hemisphere ETC frequency correlating with evidence for explosive volcanism by comparing the storm proxies sodium and calcium; with the eruption proxy sulphur. Both the model and proxy evidence suggest that large explosive volcanic eruptions increase storminess around the location of the ice core. Furthermore, the simulations indicate that the number of ETCs increases in the subtropics and at high latitudes, while they decrease in the mid-latitudes. A detailed interrogation of the simulated eruptions reveals that increases in cyclone frequency are linked to steepening of the isentropic slope due to a larger meridional temperature gradient and to a lower tropopause. The steepening is driven by a combination of warming of the tropical stratosphere from absorption of longwave radiation by volcanic aerosols and surface cooling due to the scattering of sunlight by the same aerosols, whereas the lower tropopause may be attributed to a warmer stratosphere.
Algebraic cobordism and a Conner–Floyd isomorphism for algebraic K-theory
Authors: Annala Toni , Hoyois Marc , Iwasa Ryomei
Published: February 2024

We formulate and prove a Conner–Floyd isomorphism for the algebraic K-theory of arbitrary qcqs derived schemes. To that end, we study a stable

∞
\infty

-category of non-

A

1

\mathbb {A}^1

-invariant motivic spectra, which turns out to be equivalent to the

∞
\infty

-category of fundamental motivic spectra satisfying elementary blowup excision, previously introduced by the first and third authors. We prove that this

∞
\infty

-category satisfies

P

1

\mathbb {P}^1

-homotopy invariance and weighted

A

1

\mathbb {A}^1

-homotopy invariance, which we use in place of

A

1

\mathbb {A}^1

-homotopy invariance to obtain analogues of several key results from

A

1

\mathbb {A}^1

-homotopy theory. These allow us in particular to define a universal oriented motivic

E

∞

\mathbb {E}_\infty

-ring spectrum

M
G
L

\mathrm {MGL}

. We then prove that the algebraic K-theory of a qcqs derived scheme

X
X

can be recovered from its

M
G
L

\mathrm {MGL}

-cohomology via a Conner–Floyd isomorphism
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper M normal upper G normal upper L Superscript asterisk asterisk Baseline left-parenthesis upper X right-parenthesis circled-times Subscript normal upper L Baseline double-struck upper Z left-bracket beta Superscript plus-or-minus 1 Baseline right-bracket asymptotically-equals normal upper K Superscript asterisk asterisk Baseline left-parenthesis upper X right-parenthesis comma">

M
G
L

∗
∗

(
X
)

⊗

L

Z

[

β

±
1

]
≃

K

∗
∗

(
X
)
,

\mathrm {MGL}^{**}(X)\otimes _{\mathrm {L}{}}\mathbb {Z}[\beta ^{\pm 1}]\simeq \mathrm {K}{}^{**}(X),

\]
where

L

\mathrm {L}{}

is the Lazard ring and

K

p
,
q

(
X
)
=

K

2
q
−
p

(
X
)

\mathrm {K}{}^{p,q}(X)=\mathrm {K}{}_{2q-p}(X)

. Finally, we prove a Snaith theorem for the periodized version of

M
G
L

\mathrm {MGL}

.
Fermented botanical fertilizer controls bacterial wilt of tomatoes caused by Ralstonia pseudosolanacearum
Authors: Hida Akiko , Okano Nanako , Tadokoro Chika , Fukunishi Myuji , Ahmed Asmaa Ali , Takenaka Kohei , Tateuchi Yusuke , Fujioka Kotaro , Torii Hideto , Tajima Takahisa , Kato Junichi
Published: February 2024

This study demonstrates the effect of fermented botanical product (FBP) on Ralstonia pseudosolanacearum-induced bacterial wilt disease and unravels its action mechanism. Soaking with diluted FBP solutions (0.1%-0.5%) significantly suppressed bacterial wilt in tomato plants, and FBP-treated tomato plants grew well against R. pseudosolanacearum infection. Growth assays showed that FBP had no antibacterial effect but promoted R. pseudosolanacearum growth. In contrast, few or no R. pseudosolanacearum cells were detected in aerial parts of tomato plants grown in FBP-soaked soil. Subsequent infection assays using the chemotaxis-deficient mutant (ΔcheA) or the root-dip inoculation method revealed that FBP does not affect pathogen migration to plant roots during infection. Moreover, FBP-pretreated tomato plants exhibited reduced bacterial wilt in the absence of FBP. These findings suggest that the plant, but not the pathogen, could be affected by FBP, resulting in an induced resistance against R. pseudosolanacearum, leading to a suppressive effect on bacterial wilt.
ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization
Authors: Yi Jia-Cai , Yang Zi-Yi , Zhao Wen-Tao , Yang Zhi-Jiang , Zhang Xiao-Chen , Wu Cheng-Kun , Lu Ai-Ping , Cao Dong-Sheng
Published: February 2024

Drug discovery and development constitute a laborious and costly undertaking. The success of a drug hinges not only good efficacy but also acceptable absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties. Overall, up to 50% of drug development failures have been contributed from undesirable ADMET profiles. As a multiple parameter objective, the optimization of the ADMET properties is extremely challenging owing to the vast chemical space and limited human expert knowledge. In this study, a freely available platform called Chemical Molecular Optimization, Representation and Translation (ChemMORT) is developed for the optimization of multiple ADMET endpoints without the loss of potency (https://cadd.nscc-tj.cn/deploy/chemmort/). ChemMORT contains three modules: Simplified Molecular Input Line Entry System (SMILES) Encoder, Descriptor Decoder and Molecular Optimizer. The SMILES Encoder can generate the molecular representation with a 512-dimensional vector, and the Descriptor Decoder is able to translate the above representation to the corresponding molecular structure with high accuracy. Based on reversible molecular representation and particle swarm optimization strategy, the Molecular Optimizer can be used to effectively optimize undesirable ADMET properties without the loss of bioactivity, which essentially accomplishes the design of inverse QSAR. The constrained multi-objective optimization of the poly (ADP-ribose) polymerase-1 inhibitor is provided as the case to explore the utility of ChemMORT.
BiGATAE: a bipartite graph attention auto-encoder enhancing spatial domain identification from single-slice to multi-slices
Authors: Tao Yuhao , Sun Xiaoang , Wang Fei
Published: February 2024

Recent advancements in spatial transcriptomics technology have revolutionized our ability to comprehensively characterize gene expression patterns within the tissue microenvironment, enabling us to grasp their functional significance in a spatial context. One key field of research in spatial transcriptomics is the identification of spatial domains, which refers to distinct regions within the tissue where specific gene expression patterns are observed. Diverse methodologies have been proposed, each with its unique characteristics. As the availability of spatial transcriptomics data continues to expand, there is a growing need for methods that can integrate information from multiple slices to discover spatial domains. To extend the applicability of existing single-slice analysis methods to multi-slice clustering, we introduce BiGATAE (Bipartite Graph Attention Auto Encoder) that leverages gene expression information from adjacent tissue slices to enhance spatial transcriptomics data. BiGATAE comprises two steps: aligning slices to generate an adjacency matrix for different spots in consecutive slices and constructing a bipartite graph. Subsequently, it utilizes a graph attention network to integrate information across different slices. Then it can seamlessly integrate with pre-existing techniques. To evaluate the performance of BiGATAE, we conducted benchmarking analyses on three different datasets. The experimental results demonstrate that for existing single-slice clustering methods, the integration of BiGATAE significantly enhances their performance. Moreover, single-slice clustering methods integrated with BiGATAE outperform methods specifically designed for multi-slice integration. These results underscore the proficiency of BiGATAE in facilitating information transfer across multiple slices and its capacity to broaden the applicability and sustainability of pre-existing methods.
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
Authors: Ermshaus Arik , Piechotta Michael , Rüter Gina , Keilholz Ulrich , Leser Ulf , Benary Manuela
Published: February 2024

Motivation

In precision oncology (PO), clinicians aim to find the best treatment for any patient based on their molecular characterization. A major bottleneck is the manual annotation and evaluation of individual variants, for which usually a range of knowledge bases are screened. To incorporate and integrate the vast information of different databases, fast and accurate methods for harmonizing databases with different types of information are necessary. An essential step for harmonization in PO includes the normalization of tumor entities as well as therapy options for patients.

preon is a fast and accurate library for the normalization of drug names and cancer types in large-scale data integration.

Availability and implementation

preon is implemented in Python and freely available via the PyPI repository. Source code and the data underlying this article are available in GitHub at https://github.com/ermshaua/preon/.
Bioframe: operations on genomic intervals in Pandas dataframes
Authors:   Open2C, Abdennur Nezar , Fudenberg Geoffrey , Flyamer Ilya M , Galitsyna Aleksandra A , Goloborodko Anton , Imakaev Maxim , Venev Sergey
Published: February 2024

Motivation

Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments.

Results

Bioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, NumPy and Pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features.

Availability and implementation

Bioframe is open-source under MIT license, cross-platform, and can be installed from the Python Package Index. The source code is maintained by Open2C on GitHub at https://github.com/open2c/bioframe.
The pathogenesis of endometriosis and adenomyosis: insights from single-cell RNA sequencing
Authors: Li Qiutong , Shi Jinghua , Yi Dai , Li Xiaoyan , Gu Zhiyue , Yan Hailan , Leng Jinhua
Published: February 2024

Endometriosis and adenomyosis are two similar gynecological diseases that are characterized by ectopic implantation and the growth of the endometrial tissue. Previous studies have reported that they share a common pathophysiology in some respects, such as a similar cellular composition and resistance to the progestogen of lesions, but their underlying mechanisms remain elusive. Emerging single-cell ribonucleic acid sequencing (scRNA-seq) technologies allow for the dissection of single-cell transcriptome mapping to reveal the etiology of diseases at the level of the individual cell. In this review, we summarized the published findings in research on scRNA-seq regarding the cellular components and molecular profiles of diverse lesions. They show that epithelial cell clusters may be the vital progenitors of endometriosis and adenomyosis. Subclusters of stromal cells, such as endometrial mesenchymal stem cells and fibroblasts, are also involved in the occurrence of endometriosis and adenomyosis, respectively. Moreover, CD8+ T cells, natural killer cells, and macrophages exhibit a deficiency in clearing the ectopic endometrial cells in the immune microenvironment of endometriosis. It seems that the immune responses are activated in adenomyosis. Understanding the immune characteristics of adenomyosis still needs further exploration. Finally, we discuss the application of findings from scRNA-seq for clinical diagnosis and treatment. This review provides fresh insights into the pathogenesis of endometriosis and adenomyosis as well as the therapeutic targets at the cellular level.
Limitation of life sustaining therapy in disorders of consciousness: ethics and practice
Authors: Lissak India A , Young Michael J
Published: February 2024

Clinical conversations surrounding the continuation or limitation of life-sustaining therapies (LLST) are both challenging and tragically necessary for patients with disorders of consciousness (DoC) following severe brain injury. Divergent cultural, philosophical and religious perspectives contribute to vast heterogeneity in clinical approaches to LLST—as reflected in regional differences and inter-clinician variability. Here we provide an ethical analysis of factors that inform LLST decisions among patients with DoC.

We begin by introducing the clinical and ethical challenge and clarifying the distinction between withdrawing and withholding life-sustaining therapy. We then describe relevant factors that influence LLST decision-making including diagnostic and prognostic uncertainty, perception of pain, defining a ‘good’ outcome, and the role of clinicians. In concluding sections, we explore global variation in LLST practices as they pertain to patients with DoC and examine the impact of cultural and religious perspectives on approaches to LLST.

Understanding and respecting the cultural and religious perspectives of patients and surrogates is essential to protecting patient autonomy and advancing goal-concordant care during critical moments of medical decision-making involving patients with DoC.
A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease
Authors: Aldous Sarah G , Smith Edward J , Landles Christian , Osborne Georgina F , Cañibano-Pico Maria , Nita Iulia M , Phillips Jemima , Zhang Yongwei , Jin Bo , Hirst Marissa B , Benn Caroline L , Bond Brian C , Edelmann Winfried , Greene Jonathan R , Bates Gillian P
Published: February 2024

The Huntington's disease mutation is a CAG repeat expansion in the huntingtin gene that results in an expanded polyglutamine tract in the huntingtin protein. The CAG repeat is unstable and expansions of hundreds of CAGs have been detected in Huntington's disease post-mortem brains. The age of disease onset can be predicted partially from the length of the CAG repeat as measured in blood. Onset age is also determined by genetic modifiers, which in six cases involve variation in DNA mismatch repair pathways genes. Knocking-out specific mismatch repair genes in mouse models of Huntington's disease prevents somatic CAG repeat expansion. Taken together, these results have led to the hypothesis that somatic CAG repeat expansion in Huntington's disease brains is required for pathogenesis. Therefore, the pathogenic repeat threshold in brain is longer than (CAG)40, as measured in blood, and is currently unknown.

The mismatch repair gene MSH3 has become a major focus for therapeutic development, as unlike other mismatch repair genes, nullizygosity for MSH3 does not cause malignancies associated with mismatch repair deficiency. Potential treatments targeting MSH3 currently under development include gene therapy, biologics and small molecules, which will be assessed for efficacy in mouse models of Huntington's disease. The zQ175 knock-in model carries a mutation of approximately (CAG)185 and develops early molecular and pathological phenotypes that have been extensively characterized. Therefore, we crossed the mutant huntingtin allele onto heterozygous and homozygous Msh3 knockout backgrounds to determine the maximum benefit of targeting Msh3 in this model.

Ablation of Msh3 prevented somatic expansion throughout the brain and periphery, and reduction of Msh3 by 50% decreased the rate of expansion. This had no effect on the deposition of huntingtin aggregation in the nuclei of striatal neurons, nor on the dysregulated striatal transcriptional profile. This contrasts with ablating Msh3 in knock-in models with shorter CAG repeat expansions. Therefore, further expansion of a (CAG)185 repeat in striatal neurons does not accelerate the onset of molecular and neuropathological phenotypes. It is striking that highly expanded CAG repeats of a similar size in humans cause disease onset before 2 years of age, indicating that somatic CAG repeat expansion in the brain is not required for pathogenesis.

Given that the trajectory for somatic CAG expansion in the brains of Huntington's disease mutation carriers is unknown, our study underlines the importance of administering treatments targeting somatic instability as early as possible.
Regulatory T-cell frequency and function in acute myocardial infarction patients and its correlation with ventricular dysfunction
Authors: Martínez-Shio Elena Berenice , Marín-Jáuregui Laura Sherell , Rodríguez-Ortega Alma Celeste , Doníz-Padilla Lesly Marsol , González-Amaro Roberto , Escobedo-Uribe Carlos David , Monsiváis-Urenda Adriana Elizabeth
Published: February 2024

A high percentage of patients with acute coronary syndrome develop heart failure due to the ischemic event. Regulatory T (Treg) cells are lymphocytes with suppressive capacity that control the immune response and include the conventional CD4+ CD25hi Foxp3+ cells and the CD4+ CD25var CD69+ LAP+ Foxp3− IL-10+ cells. No human follow-up studies focus on Treg cells’ behavior after infarction and their possible relationship with ventricular function as a sign of postischemic cardiac remodeling. This study aimed to analyze, by flow cytometry, the circulating levels of CD69+ Treg cells and CD4+ CD25hi Foxp3+ cells, their IL-10+ production as well as their function in patients with acute myocardial infarction (AMI), and its possible relation with ventricular dysfunction. We found a significant difference in the percentage of CD4+ CD25hi Foxp3+ cells and IL-10+ MFI in patients with AMI at 72 hours compared with the healthy control group, and the levels of these cells were reduced 6 months post-AMI. Regarding the suppressive function of CD4+ CD25+ regulatory cells, they were dysfunctional at 3 and 6 months post-AMI. The frequency of CD69+ Treg cells was similar between patients with AMI at 72 hours postinfarction and the control groups. Moreover, the frequency of CD69+ Treg cells at 3 and 6 months postischemic event did not vary over time. Treg cells play a role in regulating inflammation after an AMI, and its function may be compromised in this pathology. This work is the first report to evaluate CD69+ Foxp3− Treg cells in AMI patients.
Altered CD226/TIGIT expressions were associated with NK phenotypes in primary antiphospholipid syndrome and affected by IL-4/JAK pathway
Authors: Long Yan , Lu Ke-Jia , Xia Chang-Sheng , Feng Jing-Hong , Li Wen-Yi , Ma Yin-Ting , Sun Yuan-Yuan , Fan Chun-Hong , Li Chun
Published: February 2024

Natural killer (NK) cells were reported to be involved in the pathogenesis of primary antiphospholipid syndrome (pAPS). Immunosuppressive receptor T-cell immunoreceptor with Ig and ITIM domains (TIGIT) and activating receptor cluster of differentiation 226 (CD226) are specifically expressed on NK cells with competitive functions. This study aims to investigate the expression diversities of CD226/TIGIT on NK subsets and their associations with NK subsets activation phenotypes and potential clinical significance, furthermore, to explore potential cause for CD226/TIGIT expression diversities in pAPS. We comparatively assessed the changes of CD56brightNK, CD56dimNK, and NK-like cells in 70 pAPS patients compared with control groups, including systemic lupus erythematosus, asymptomatic antiphospholipid antibodies carriers (asymp-aPLs carriers), and healthy controls and their expression diversities of CD226/TIGIT by flow cytometry. CD25, CD69, CD107α expression, and interferon gamma (IFN-γ) secretion levels of NK subsets were detected to determine the potential association of CD226/TIGIT expression with NK subsets phenotypes. CD226/TIGIT expression levels were compared among different subgroups divided by aPLs status. Moreover, in vitro cultures were conducted to explore the potential mechanisms of CD226/TIGIT expression imbalance. CD56brightNK and CD3+CD56+NK-like cells were significantly increased while CD56dimNK cells were obviously decreased in pAPS, and CD56brightNK and NK-like cells exhibited significantly higher CD226 but lower TIGIT expressions. CD226+CD56brightNK and TIGIT-CD56brightNK cells show higher CD69 expression and IFN-γ secretion capacity, and CD226+NK-like and TIGIT-NK-like cells showed higher expressions of CD25 and CD69 but lower apoptosis rate than CD226− and TIGIT+CD56brightNK/NK-like cells, respectively. The imbalanced CD226/TIGIT expressions were most significant in aPLs triple-positive group. Imbalanced expressions of CD226/TIGIT on CD56brightNK and NK-like cells were aggravated after interleukin-4 (IL-4) stimulation and recovered after tofacitinib blocking. Our data revealed significant imbalanced CD226/TIGIT expressions on NK subsets in pAPS, which closely associated with NK subsets phenotypes and more complicated autoantibody status. CD226/TIGIT imbalanced may be affected by IL-4/Janus Kinase (JAK) pathway activation.
Measures of resting-state brain network segregation and integration vary in relation to data quantity: implications for within and between subject comparisons of functional brain network organization
Authors: Han Liang , Chan Micaela Y , Agres Phillip F , Winter-Nelson Ezra , Zhang Ziwei , Wig Gagan S
Published: February 2024

Measures of functional brain network segregation and integration vary with an individual’s age, cognitive ability, and health status. Based on these relationships, these measures are frequently examined to study and quantify large-scale patterns of network organization in both basic and applied research settings. However, there is limited information on the stability and reliability of the network measures as applied to functional time-series; these measurement properties are critical to understand if the measures are to be used for individualized characterization of brain networks. We examine measurement reliability using several human datasets (Midnight Scan Club and Human Connectome Project [both Young Adult and Aging]). These datasets include participants with multiple scanning sessions, and collectively include individuals spanning a broad age range of the adult lifespan. The measurement and reliability of measures of resting-state network segregation and integration vary in relation to data quantity for a given participant’s scan session; notably, both properties asymptote when estimated using adequate amounts of clean data. We demonstrate how this source of variability can systematically bias interpretation of differences and changes in brain network organization if appropriate safeguards are not included. These observations have important implications for cross-sectional, longitudinal, and interventional comparisons of functional brain network organization.
Caudally pronounced deficiencies in preplate splitting and migration underly a rostro-caudal progression of cortical lamination defects in the reeler brain
Authors: Mingo-Moreno Nieves , Truschow Pavel , Staiger Jochen F , Wagener Robin J
Published: February 2024

In mammalian neocortex development, every cohort of newborn neurons is guided toward the marginal zone, leading to an “inside-out” organization of the 6 neocortical layers. This migratory pattern is regulated by the extracellular glycoprotein Reelin. The reeler mouse shows a homozygous mutation of the reelin gene. Using RNA in situ hybridization we could demonstrate that the Reelin-deficient mouse cortex (male and female) displays an increasing lamination defect along the rostro-caudal axis that is characterized by strong cellular intermingling, but roughly reproduces the “inside-out” pattern in rostral cortex, while caudal cortex shows a relative inversion of neuronal positioning (“outside-in”). We found that in development of the reeler cortex, preplate-splitting is also defective with an increasing severity along the rostro-caudal axis. This leads to a misplacement of subplate neurons that are crucial for a switch in migration mode within the cortical plate. Using Flash Tag labeling and nucleoside analog pulse-chasing, we found an according migration defect within the cortical plate, again with a progressive severity along the rostro-caudal axis. Thus, loss of one key player in neocortical development leads to highly area-specific (caudally pronounced) developmental deficiencies that result in multiple roughly opposite rostral versus caudal adult neocortical phenotypes.
Distribution of initial caries lesions in relation to fixed orthodontic therapy. A systematic review and meta-analysis
Authors: Salerno Claudia , Grazia Cagetti Maria , Cirio Silvia , Esteves-Oliveira Marcella , Wierichs Richard J , Kloukos Dimitrios , Campus Guglielmo
Published: February 2024

Background

Initial caries lesion (ICLs) adjacent to orthodontic brackets are the most common side effect of orthodontic treatment with fixed appliances. The reported prevalence is uncertain and varies considerably across studies, from 27% to 97%.

Objectives

This paper was designed to evaluate and synthesize the available evidence on the prevalence and incidence rates of ICLs in relation to orthodontic treatment. Selection criteria: The review (Prospero protocol CRD42023412952) included randomized and non-randomized clinical trials of interventions, cohort studies, and cross-sectional studies, published after 1990 on the prevalence or incidence of ICLs during or after orthodontic treatment with fixed appliances. Search methods: Pubmed, Scopus, and Embase databases were searched from 1990 until 01 May 2023. The risk of bias assessment was performed with RoB 2 and ROBINS-I tool and the Joanna Briggs Institute Critical Appraisal Checklist. Data collection and analysis: The proportion of individuals with ICLs, reported as the number/percentage of individuals/teeth with ICLs or mean number of ICLs per subject, were used to synthesize results.

Results

The search yielded a total of 468 papers; 21 studies were included in the systematic review, 2 of which were not included in the meta-analysis. The prevalence rate [95%CI] of ICLs was 0.57% [0.48; 0.65] in 1448 patients, 0.22% [0.14; 0.33] in 11583 teeth, with a mean number of lesions equal to 2.24 [1.79; 2.70] in 484 patients evaluated. The incidence rate of new carious lesions developed during orthodontic treatment was 0.48% [0.33; 0.63] in 533 patients, 0.15% [0.08; 0.26] in 1890 teeth with a mean number of ICLs equal to 2.29 [1.12; 3.46] in 208 patients evaluated.

Limitations

Although the high number of included studies and the overall good quality, there was a significant heterogeneity in the collected data.

Conclusion

The prevalence and incidence rates of ICLs in subjects undergoing orthodontic treatment are quite high and raise some concerns in terms of risk assessment of orthodontic treatment. ICLs represent an alarming challenge for both patients and professionals. Effective caries prevention strategies during treatment need to be considered and implemented where appropriate.