bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPIRED-Fitness: an end-to-end framework for the prediction of protein structure and fitness from single sequence
Authors: Gong Haipeng , Chen Yinghui , Xu Yunxin , Liu Di , Xing Yaoguang 
Published: March 2024

Abstract

Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction accuracy, showing promise for many downstream prediction tasks. Here, we propose SPIRED, a novel single-sequence-based structure prediction model that exhibits comparable performance to the state-of-the-art methods but with approximately 5-fold acceleration in inference and at least one order of magnitude reduction in training consumption. By integrating SPIRED with downstream neural networks, we compose an end-toend framework named SPIRED-Fitness for the rapid prediction of both protein structure and fitness from single sequence. SPIRED-Fitness and its derivative SPIRED-Stab achieve state-of-the-art performance in predicting the mutational effects on protein fitness and stability metrics, respectively.
Production of carbon-11 for PET preclinical imaging using a high-repetition rate laser-driven proton source
Authors: Peñas Juan , Alejo Aaron , Bembibre Adrián , Apiñaniz Jon Imanol , García-García Enrique , Guerrero Carlos , Henares José Luis , Hernández-Palmero Irene , Méndez Cruz , Millán-Callado María Ángeles , Puyuelo-Valdés Pilar , Seimetz Michael , Benlliure José 
Published: March 2024

Abstract
Most advanced medical imaging techniques, such as positron-emission tomography (PET), require tracers that are produced in conventional particle accelerators. This paper focuses on the evaluation of a potential alternative technology based onlaser-driven ion acceleration for the production of radioisotopes for PET imaging. We report for the first time the use of ahigh-repetition rate, ultra-intense laser system for the production of carbon-11 in multi-shot operation. Proton bunches with energies up to 10 – 14 MeV were systematically accelerated in long series at pulse rates between 0.1 and 1 Hz using a PW-class laser. These protons were used to activate a boron target via the 11B(p,n)11C nuclear reaction. A peak activity of 234 kBq was obtained in multi-shot operation with laser pulses with an energy of 25 J. Significant carbon-11 production was also achieved for lower pulse energies. The experimental carbon-11 activities measured in this work are comparable to the levels required for preclinical PET, which would be feasible by operating at the repetition rate of current state-of-the-art technology (10Hz). The scalability of next-generation laser-driven accelerators in terms of this parameter for sustained operation over time could increase these overall levels into the clinical PET range.
Endocrine islet β-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients
Authors: Gu guoqiang , Brown Monica , Agan Verda , Nevills Simone , Hu Ruiying , Simmons Alan , Xu Yanwen , Yang Yilin , Yagan Mahircan , Najam Sadia , Dadi Prasanna , Sampson Leesa , Magnuson Mark , Jacobson David , Lau Ken , Hodges Emily 
Published: March 2024

Abstract
Endocrine islet b cells comprise heterogenous cell subsets. Yet when/how these subsets are produced and how stable they are remain unknown. Addressing these questions is important for preventing/curing diabetes, because lower numbers of b cells with better secretory function is a high risk of this disease. Using combinatorial cell lineage tracing, scRNA-seq, and DNA methylation analysis, we show here that embryonic islet progenitors with distinct gene expression and DNA methylation produce b-cell subtypes of different function and viability in adult mice. The subtype with better function is enriched for genes involved in vesicular production/trafficking, stress response, and Ca2+-secretion coupling, which further correspond to differential DNA methylation in putative enhancers of these genes. Maternal overnutrition, a major diabetes risk factor, reduces the proportion of endocrine progenitors of the b-cell subtype with better-function via deregulating DNA methyl transferase 3a. Intriguingly, the gene signature that defines mouse b-cell subtypes can reliably divide human cells into two sub-populations while the proportion of b cells with better-function is reduced in diabetic donors. The implication of these results is that modulating DNA methylation in islet progenitors using maternal food supplements can be explored to improve b-cell function in the prevention and therapy of diabetes.
Insights to the Damaging Effects of August 7, 2020 (Mw 5.0) Mila Earthquake and Seismic Hazard Analysis of Northeast Algeria
Authors: Mouloud Hamidatou , Hallal Nassim Hallal , Lebdioui Saad , Agius Matthew R. , Sawires Rashad 
Published: March 2024

Abstract

Here, we present a seismic hazard evaluation for the August 7, 2020 (Mw 5.0) Mila earthquake that occurred in northeast Algeria. The study addresses the environmental factors that could contribute significantly to the highly damaging impact of this event. The following aspects were included in an interdisciplinary methodology that was adopted: the earthquake catalog, the coseismic geologic impacts with respect to the Environmental Seismic Intensity (ESI) scale standards, and estimations of peak ground acceleration values based on both probabilistic and deterministic seismic hazard approach. A comprehensive study of main and secondary impacts was performed for three districts (El-Kherba, Grareme-Gouga, and Azzeba), to obtain a good seismic intensity assessment. A PSHA- and DSHA based hazard analysis for the region concluded that the unique intensity values were related to the Modified Mercalli Intensity (MMI) and PGA distributions. Our work shows that the considered hazard estimation processes can result in very diverse values of the PGA distributions. Furthermore, PGA values frequently deviate significantly from macroseismic intensity levels derived using the ESI scale. As a result, the combination of the environmental factors attached to the hazard assessments seems to be necessary to obtain an additional accurate seismic assessment. In the final phase, seismic hazard assessment methods were applied to obtain the estimated damage distributions at the risky locations for 50 years of exposure time. The results show the importance of taking precautions to reduce earthquake casualties in vulnerable old urban centers. This work proposes a probable methodology for conducting site-specific hazard and vulnerability estimations to mitigate earthquake hazards and support risk reduction measures.
Wireless Brain Oscillation Control via Magnetoelectric Stimulation with Millisecond Precision
Authors: Cheng Chao-Chun , Chen Li-Ling , Huang Mu-Yun , Tseng Chih-Ning , Ting Yen-Jing , Tseng Guan-Jhong , Huang Jun-Xuan , Wu Chih-Hsuan , Chiang Po-Han 
Published: March 2024

Abstract
Electrical deep brain stimulation (DBS) is a pivotal technology in treating neurological disorders and advancing neuroscience research. Minimizing the invasiveness of conventional DBS can reduce the risk of large hardware implants. Our study introduces a novel wireless magnetoelectric neuromodulation method termed Magnetic-driven Torque-Induced Electrical Stimulation (MagTIES). Diverging from traditional magnetostriction-based magnetoelectric stimulation approaches, we utilized the torque force from magnetic nanodiscs during alternating magnetic fields (AMF) to induce a piezoelectric effect on piezoelectric nanoparticles. This technique triggered neuronal activity in vitro and in vivo at millisecond-scale temporal precision using weak AMF at slow frequency. Importantly, it allows fine-tuning brain oscillations in deep brain areas through AMF frequency adjustments. MagTIES represents a significant advancement in neuromodulation, providing a minimally invasive, transgene-free approach for precise and wireless brain activity control, with vast potential for neurological therapies and neuroscience research.
The role of voltage-gated calcium channel α2δ-1 in the occurrence and development in myofascial orofacial pain
Authors: Lu Yang , Wang Jingfu , Li Li , Zhang Xiaodong 
Published: March 2024

Abstract

Patients who suffer from myofascial orofacial pain could affect their quality of life deeply. The pathogenesis of pain is still unclear. Our objective was to assess Whether Voltage-gated calcium channel α2δ-1（Cavα2δ-1） is related to myofascial orofacial pain. Rats were divided into the masseter tendon ligation group and the sham group. Compared with the sham group, the mechanical pain threshold of the masseter tendon ligation group was reduced on the 4th, 7th, 10th and 14th day after operation(P<0.05). On the 14th day after operation, Cavα2δ-1 mRNA expression levels in trigeminal ganglion（TG） and the trigeminal spinal subnucleus caudalis and C1-C2 spinal cervical dorsal horn (Vc/C2) of the masseter tendon ligation group were increased (PTG=0.021, PVc/C2=0.012). Rats were divided into three groups. On the 4th day after ligating the superficial tendon of the left masseter muscle of the rats, 10 ul Cavα2δ-1 antisense oligonucleotide, 10 ul Cavα2δ-1 mismatched oligonucleotides and 10 ul normal saline was separately injected into the left masseter muscle of rats in Cavα2δ-1 antisense oligonucleotide group, Cavα2δ-1 mismatched oligonucleotides group and normal saline control group twice a day for 4 days. The mechanical pain threshold of the Cavα2δ-1 antisense oligonucleotides group was higher than Cavα2δ-1 mismatched oligonucleotides group on the 7th and 10th day after operation (P<0.01). After PC12 cells were treated with lipopolysaccharide, Cavα2δ-1 mRNA expression level increased（P<0.001）. Cavα2δ-1 may be involved in the occurrence and development in myofascial orofacial pain.
sLZIP functions as a key modulator of bone remodeling by regulating the crosstalk between osteoblasts and osteoclasts
Authors: Ko Jesang , Park Sungyeon , Kim Jeonghan 
Published: March 2024

Abstract

Human small leucine zipper protein (sLZIP) regulates differentiation of both osteoblasts (OBs) and osteoclasts (OCs). However, the regulatory role of sLZIP in bone remodeling and its involvement in bone disorders remain unclear. In this study, we investigated the role of sLZIP in bone remodeling and its significance in the development of cell therapies for the treatment of bone diseases. sLZIP increased bone mass in an osteoporosis mouse model. However, bone mass was lower in mesenchymal stem cell-specific murine LZIP-1/2 knockout (Osx-LZIP-1/2fl/fl) mice than in control LZIP-1/2fl/fl mice. Osx-LZIP-1/2fl/fl mice showed delayed bone fracture healing in osteoporosis compared with control mice. Conditioned medium (CM) of OBs differentiated from adipose-derived stem cells (ADSCs) in Osx-LZIP-1/2fl/fl mice attenuated OC formation and migration of bone marrow-derived macrophages. However, CM of OCs from sLZIP transgenic mice induced OB differentiation and migration. sLZIP regulates secretion of OC-derived sphingosine-1-phosphate, which induces OB differentiation. sLZIP also regulates OB-derived WNT16, which inhibits OC differentiation. Therefore, sLZIP functions as a key modulator of the crosstalk between OBs and OCs and promotes bone remodeling and fracture healing in osteoporosis. In addition, sLZIP-overexpressing ADSCs promoted bone formation and repair in osteoporosis. sLZIP is an excellent target for the stem cell-based treatment of osteoporosis.
Nonlinear Amplification of Vesicle Membrane Concavity on the Critical Response Threshold to Biosignals
Authors: YAN Qiang , LI Xuefeng , Liang Xin , Yang Cuiqin 
Published: March 2024

Abstract

Polymer nanoparticles that can sharply sense and detect biological signals in cells are promising candidates for biomedical and theranostic nanomaterials. However, the response ability of current polymer assemblies poorly match the requirement of trace concentration level (10-6~10-9 mol/L) of cellular biosignals due to their linear signal input-to-function output mode, which impedes their practical applications in vivo. Here we report a kind of bowl-shaped polymer vesicle system with pH-tunable membrane invaginated morphology that can nonlinearly amplify the response abilities toward biosignals by modulating the membrane concavity. Compared to conventional spherical nanoparticles, non-spherical concave vesicles reduce the critical response threshold of polymers by up to 5 orders of magnitude, from millimole to nanomole level, covering most of biosignal concentration windows. Moreover, we find that this nonlinear signal gain effect is originated from the collective impact of a single signal on transitioning the polymer chain aggregation state of individual assemblies, rather than just altering a certain unit or chain. This nonlinear signal-to-response mechanism is potential to solve the tricky problems of probing and sensing endogenous signals with extremely low physiological concentration.
RETRACTED: Late HCC occurrence in patients achieving SVR after DAAs therapy: a matter of follow-up or something else?
Authors: Perrella Alessandro , de Sio Ilario , Bellopede Pasquale , Maddaloni Adelaide , Vitale Luigi , Rinaldi Barbara , Mormone Andrea , Izzi Antonio , Sbreglia Costanza , Bernardi Francesca , Trama Ugo , Berretta Massimiliano , Galiero Raffaele , caturano alfredo , Sasso Ferdinando , Marfella Raffaele , franci gianluigi , rinaldi luca 
Published: March 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
Development and evaluation of lyophilization protocol for colorimetric RT-LAMP diagnostic assay for COVID-19
Authors: Prado Nayra Olivera , Marin Anelis Maria , Lalli Larissa Araújo , Sanchuki Heloisa Bruna Soligo , Wosniaki Denise Kusma , Nardin Jeanine Marie , Morales Hugo Manoel Paz , Blanes Lucas , Zanette Dalila Luciola , Aoki Mateus Nóbrega 
Published: March 2024

Abstract

Molecular diagnosis involving nucleic acids (DNA and RNA) is considered an extremely functional tool. During the 2020 global health crisis, the race began to optimize the production and delivery of molecular diagnostic kits to detect SARS-CoV-2. In this period, the RT-LAMP gained attention. However, due to the thermolability of the reagents used in this technique, transport, storage, and conservation require special infrastructure at low temperatures. Such parameters limit the distribution capacity, requiring adaptations that increase the costs of the process. Thus, the present report focused on the development of a lyophilization protocol for reagents in a colorimetric RT-LAMP diagnostic kit to detect SARS-CoV-2, enabling transport and storage at room temperature. Tests were carried out to define the ideal excipients to maintain the molecular integrity of the reagents, as well as to guarantee their stability in storage and transport at room temperature. The condition chosen as adequate was the addition of 5% PEG 8,000 and 75 mM trehalose to the RT-LAMP reaction, allowing stability at room temperature for up to 28 days and showing an analytical and diagnostic sensitivity and specificity of 83.33% and 90%, respectively, for detection of SARS-CoV-2. This study provides results of lyophilized colorimetric RT-LAMP COVID-19 detection assay with a diagnostic sensitivity and specificity similar to RT-qPCR, especially in high-viral load.
Numerical and Experimental Investigation of Friction Damping in Shrouded Blades
Authors: Du Chenhong , Wang Yanrong 
Published: March 2024

Abstract

The blade is a critical turbine engine component that faces a high risk of high-cycle fatigue (HCF). To reduce its vibration, shrouded blades are often employed. However, the dynamic behavior of the shrouded blade is complex, making it challenging to accurately predict its damping ratio and resonance frequency. In this study, an economical experimental setup was designed, which requires only two blades to investigate the dynamic characteristics of shrouded blades. A novel method was adapted to measure the contact force and friction coefficient of the shrouds. Sinusoidal excitations were executed, and frequency response functions (FRFs) were recorded. Subsequently, study established a relationship between resonance frequency to vibrational stress using these FRFs. Additionally, the experiment was simulated by the harmonic balance method (HBM). A hysteresis spring contact model was adapted to simulate the contact of the shrouds. Vibrational stress, resonance frequency and damping ratio were computed base on the displacement outcomes from the HBM simulation. The consistency between the obtained simulation outcomes and experimental results was found to be satisfactory, indicating that the proposed approach effectively captured the complex behavior of the shrouded blades.
Indigenous Peoples’ evaluation of health risks when facing mandatory evacuation for birth during the COVID-19 pandemic: An Indigenous feminist analysis
Authors: Murdock Melanie , Campbell Erika , Durant Sarah , Couchie Carol , Meekis Carmel Theresa , Rae Charity , Kenequanash Julie , Jeyamohan Arthi Erika , Barry Jacob , Lawford Karen 
Published: March 2024

Abstract

Background
Indigenous Peoples living on Turtle Island are comprised of First Nations, Inuit, and Métis people and because of the Government of Canada’s mandatory evacuation policy, those living in rural and remote regions of Ontario are required to travel to urban, tertiary care centres to give birth. When evaluating the risk of travelling for birth, Indigenous Peoples understand, evaluate, and conceptualise health risks differently than Eurocentric biomedical models of health. Also, the global COVID-19 pandemic changed how people perceived risks to their health. Our research goal was to better understand how Indigenous parturients living in rural and remote communities conceptualised the risks associated with evacuation for birth before and during the COVID-19 pandemic.
Methods
To achieve this goal, we conducted semi-structured interviews with 11 parturients who travelled for birth during the pandemic and with 5 family members of those who were evacuated for birth.
Results
Participants conceptualised evacuation for birth as riskier during the COVID-19 pandemic and identified how the pandemic exacerbated existing risks of travelling for birth. In fact, Indigenous parturients noted the increased risk of contracting COVID-19 when travelling to urban centres for perinatal care, the impact of public health restrictions on increased isolation from family and community, the emotional impact of fear during the pandemic, and the decreased availability of quality healthcare.
Conclusions
Using Indigenous Feminist Methodology and Indigenous Feminist Theory, we critically analysed how mandatory evacuation for birth functions as a colonial tool and how conceptualizations of risk empowered Indigenous Peoples to make decisions that reduced risks to their health during the pandemic. With the results of this study, policy makers and governments can better understand how Indigenous Peoples conceptualise risk related to evacuation for birth before and during the pandemic, and prioritise further consultation with Indigenous Peoples to collaborate in the delivery of the health and care they need and desire.
The set-up errors and influencing factors of thoracic cancer patients receiving radiotherapy in different seasons in northwest China：a real world study
Authors: Yang lin , Zhang Junxia , Liu Zixuan , Cai Rong , Yao Xiaowei , Huo Tongjun , Zhao Lina , Bai Fei 
Published: March 2024

Abstract
Objective: This study aims to measure the set-up errors in thoracic cancer patients undergoing VMAT radiotherapy and weekly cone-beam computed tomography (CBCT), and to evaluate the impact of different seasons on set-up errors.
Methods: The CBCT verification results of 168 chest tumor patients in our department from November 2019 to 2021 to January 21 were collected as winter cohort, and a total of 840 sets of off-line CBCT images were collected. CBCT verification results for 139 patients from June 2021 to August 2022, and 717 sets of off-line CBCT images were collected.then the Mann-Whitney U test was performed.The PTV margin were then calculated according to the formula MPTV=2.5Σ+ 0.7δ. Gender, age, disease type, and arm position were also included for multivariate analysis.
Results: Set-up error of summer vs.winter cohort, LR direction:1(1,2) vs.1(1,2) mm. SI direction: 2(1,3) vs. 2(1,3) mm,AP direction: 1(1,3)vs.1(1,2)mm. Rtn direction 0.3(0.1,0.55)°vs. 0.3(0.1,0.50)°. The PTV margins in the LR, SI, and AP directions were 4.18mm,4.85mm,4.59mm in the summer cohort,and 4.40mm,5.01mm,3.90mm in the winter cohort. Multivariate analysis showed that sex was statistically significant in the LR direction (b=0.164, t=1.993, p=0.048). The effect of the arm placement was statistically different in the SI direction (b= -0.46, t=4.84, P <0.001).
Conclusion: It is found that for the patients with chest tumor fixation, the set-up error in the AP direction in the winter cohort was significantly smaller than that in the summer cohort. The conventional 5mm outer release boundary from CTV to PTV is sufficient for the summer cohort, but 4mm for the AP direction of the winter cohort. In the SI direction, the set-up error of the arm placed body side is significantly smaller than the arm raised on the forehead. Female patients greater set-up error in the LR direction than in male patients.
Reliability and Reproducibility of the Venous Excess Ultrasound (VExUS) Score, A Multi-Site Prospective Study Validating a Novel Ultrasound Technique for Comprehensive Assessment of Volume Status
Authors: Longino August A , Martin Katharine C , Leyba Katarina R , Siegel Gabriel , Sharma Vibhu M , Riscinti Matthew , Lopez Carolina O , Gill Edward A 
Published: March 2024

Abstract
Though the novel Venous Excess Ultrasound (VExUS) score is increasingly used as a noninvasive ultrasonographic method to measure venous congestion, the inter-rater reliability (IRR) and inter-user reproducibility (IUR) of this procedure have not been established. For this reason, we conducted a multi-site study of the IRR and IUR of the VExUS score between a wide range of physicians, reporting the Kappa statistic (KS) and Intraclass Correlation Coefficient (ICC) for IRR and IUR. We found that when VExUS images were interpreted by physicians specializing in cardiology, pulmonology, hospital medicine, and emergency medicine, there was substantial IRR, with a KS of 0.71 and ICC of 0.83 for the overall VExUS grade (p < 0.001), and IUR, with a KS 0.63 and ICC of 0.8, suggesting that the VExUS score is likely to be a reliable and reproducible measure interpretable by clinicians with diverse backgrounds.