bluuebunny/crossref_metadata_2025 huggingface dataset:
Cervical cancer screening using DNA methylation triage in a real-world population
Authors: Schreiberhuber Lena , Barrett James E. , Wang Jiangrong , Redl Elisa , Herzog Chiara , Vavourakis Charlotte D. , Sundström Karin , Dillner Joakim , Widschwendter Martin
Published: June 2024

Cervical cancer (CC) screening in women comprises human papillomavirus (HPV) testing followed by cytology triage of positive cases. Drawbacks, including cytology’s low reproducibility and requirement for short screening intervals, raise the need for alternative triage methods. Here we used an innovative triage technique, the WID-qCIN test, to assess the DNA methylation of human genes DPP6, RALYL and GSX1 in a real-life cohort of 28,017 women aged ≥30 years who attended CC screening in Stockholm between January and March 2017. In the analysis of all 2,377 HPV-positive samples, a combination of WID-qCIN (with a predefined threshold) and HPV16 and/or HPV18 (HPV16/18) detected 93.4% of cervical intraepithelial neoplasia grade 3 and 100% of invasive CCs. The WID-qCIN/HPV16/18 combination predicted 69.4% of incident cervical intraepithelial neoplasia grade 2 or worse compared with 18.2% predicted by cytology. Cytology or WID-qCIN/HPV16/18 triage would require 4.1 and 2.4 colposcopy referrals to detect one cervical intraepithelial neoplasia grade 2 or worse, respectively, during the 6 year period. These findings support the use of WID-qCIN/HPV16/18 as an improved triage strategy for HPV-positive women.
AgEvidence: a dataset to explore agro-ecological effects of conservation agriculture
Authors: Atwood Lesley , Gannett Maria , Wood Stephen A.
Published: June 2024

Conservation agriculture (CA) is a set of principles thought to be able to enhance crop productivity while minimizing impacts on the environment. The evidence base for CA can be challenging to synthesize because it encompasses many different practices and social and agroecological outcomes. To facilitate synthesis of CA evidence we have created a dataset organizing 218 response variables from five common categories of CA: cover crops, tillage management, pest management, nutrient management, and crop diversification. These data cover the Midwestern United States (U.S.) from 1980–2020. The dataset is also summarized and visualized on the AgEvidence website, which enables users to interactively explore, filter, and download data. We hope this dataset will help a wide variety of stakeholders, including researchers, policy makers, advocacy groups, and growers access the evidence needed to make informed and impactful decisions about how to produce food with less negative environmental impact.
Multiparametric MRI dataset for susceptibility-based radiomic feature extraction and analysis
Authors: Fiscone Cristiana , Sighinolfi Giovanni , Manners David Neil , Motta Lorenzo , Venturi Greta , Panzera Ivan , Zaccagna Fulvio , Rundo Leonardo , Lugaresi Alessandra , Lodi Raffaele , Tonon Caterina , Castelli Mauro
Published: June 2024

Multiple sclerosis (MS) is a progressive demyelinating disease impacting the central nervous system. Conventional Magnetic Resonance Imaging (MRI) techniques (e.g., T2w images) help diagnose MS, although they sometimes reveal non-specific lesions. Quantitative MRI techniques are capable of quantifying imaging biomarkers in vivo, offering the potential to identify specific signs related to pre-clinical inflammation. Among those techniques, Quantitative Susceptibility Mapping (QSM) is particularly useful for studying processes that influence the magnetic properties of brain tissue, such as alterations in myelin concentration. Because of its intrinsic quantitative nature, it is particularly well-suited to be analyzed through radiomics, including techniques that extract a high number of complex and multi-dimensional features from radiological images. The dataset presented in this work provides information about normal-appearing white matter (NAWM) in a cohort of MS patients and healthy controls. It includes QSM-based radiomic features from NAWM and its tracts, and MR sequences necessary to implement the pipeline: T1w, T2w, QSM, DWI. The workflow is outlined in this article, along with an application showing feature reliability assessment.
A dataset describing chip parameters for rock breaking by chisel pick under deep-sea hydrostatic pressure
Authors: Liu Zenghui , Lv Rui , Chen Xinlei , Liu Kai , Wu Peng , Wei Changyun
Published: June 2024

Chip is a visual representation of rock breaking by cutter, and their related parameters are crucial for revealing the rock breaking mechanism in deep-sea mining. Based on sieving and three-dimensional size measurement methods widely used in mining engineering, this paper reports a dataset of chip parameters for rock breaking by chisel pick under deep-sea hydrostatic pressure. Specifically, we first designed an experimental setup that can accurately simulate deep-sea hydrostatic pressure, conducted rock breaking experiments and carefully collected chips. Subsequently, those chips were sieved, high-resolution images were collected, and the coarseness index (CI), chip size uniformity (n), absolute chip size (de), and fractal dimension (D) were measured. Finally, three-dimensional size (long, intermediate and short) was measured for 3064 chips with particle sizes greater than 4.75 mm. This dataset will be used by researchers to validate numerical simulations or optimize equipment structures related to deep-sea mining, including deep-sea rock mechanics, mining cutter and conveyor pipes.
Gap-free chromosome-level genomes of male and female spotted longbarbel catfish Hemibagrus guttatus
Authors: Yang Yexin , Liu Yi , Chen Fangcan , Wang Yuanyuan , Wu Yuli , He Zhichao , Liu Chao , Jiang Zhiyong , Mu Xidong , Bian Chao
Published: June 2024

Hemibagrus guttatus, also named as spotted longbarbel catfish, is an economical fish in China. However, their gender cannot be easily distinguished from their appearance, which largely impedes their artificial breeding. Therefore, we provided two gap-free chromosome-level genomes of male and female spotted longbarbel catfish by combining wtdbg2, LR_Gapcloser and TGS-GapCloser assembly approaches with Hi-C data and accurate Pacbio HiFi long-reads. We assembled 30 chromosomes without any gap. Their genome sizes are approximately 749.1 Mb and 747.8 Mb of male and female individuals. The completeness results of BUSCO evaluation show about 94.2% and 95.0%, representing a high-level of completeness of both genomes. We also obtained 35,277 and 34,571 protein-coding gene sets from male and female individuals. Both available gap-free chromosome-level genomes of H. guttatus will provide excellent references for resequencing of male and female individuals to identify accurate markers for distinguishing gender of this fish.
Experimental investigation on strengthening of Zea mays root fibres for biodegradable composite materials using potassium permanganate treatment
Authors: Kavitha S. Anne , Priya Retnam Krishna , Arunachalam Krishna Prakash , Avudaiappan Siva , Saavedra Flores Erick I. , Blanco David
Published: June 2024

Humans are the only species who generate waste materials that cannot be broken down by natural processes. The ideal solution to this waste problem would be to employ only compostable materials. Biodegradable materials play a key role in creating a safer and greener world. Biodegradability is the gift that keeps on giving, in the sense of creating an Earth worth living. The future is thus best served by green energy, sustainability, and renewable resources. To realize such goals, waste should be considered as a valuable resource. In this context,Zea mays(Zm) root fibres, which are normally considered as agricultural waste, can be used as reinforcing substances in polymer matrices to produce structural composite materials. Before being used in composites, such fibres must be analysed for their physical properties. Chemical treatments can be employed to improve the structural quality of fibres, and the changes due to such modification can be analysed. Therefore, the current work examines the effect of permanganate treatment on the surface properties of Zm fibres. The raw and potassium permanganate-treated samples were assayed for various properties. Physical analysis of the fibre samples yielded details concerning the physical aspects of the fibres. The thermal conductivity and moisture absorption behaviour of the samples were analysed. Chemical analysis was employed to characterize the composition of both treated and untreated samples. p-XRD was employed to examine the crystalline nature of the Zm fibres. Numerous functional groups present in each sample were analysed by FTIR. Thermogravimetric analysis was used to determine the thermal stability of Zm fibres. Elemental analysis (CHNS and EDS) was used to determine the elemental concentrations of both raw and treated samples. The surface alterations of Zm fibres brought on by treatment were described using SEM analysis. The characteristics of Zm roots and the changes in quality due to treatment were reviewed, and there were noticeable effects due to the treatment. Both samples would have applications in various fields, and each could be used as a potential reinforcing material in the production of efficient bio-composites.
Probiotics relieve perioperative postoperative cognitive dysfunction induced by cardiopulmonary bypass through the kynurenine metabolic pathway
Authors: Zhang Xiaodong , Yang Yanzhang , Ma Xinyi , Cao Huijuan , Sun Yingjie
Published: June 2024

Postoperative cognitive dysfunction (POCD) has become the popular critical post-operative consequences, especially cardiopulmonary bypass surgery, leading to an increased risk of mortality. However, no therapeutic effect about POCD. Probiotics are beneficial bacteria living in the gut and help to reduce the risk of POCD. However, the detailed mechanism is still not entirely known. Therefore, our research aims to uncover the effect and mechanism of probiotics in relieving POCD and to figure out the possible relationship between kynurenine metabolic pathway. 36 rats were grouped into three groups: sham operated group (S group, n = 12), Cardiopulmonary bypass group (CPB group, n = 12), and probiotics+CPB (P group, n = 12). After CPB model preparation, water maze test and Garcia score scale was performed to identify the neurological function. Immunofluorescence and Hematoxylin and eosin staining has been used for hippocampal neurons detection. Brain injury related proteins, oxidative stress factors, and inflammatory factors were detected using enzyme-linked immunosorbent assays (ELISA). Neuronal apoptosis was detected by TdT-mediated dUTP nick end-labeling (TUNEL) staining and western blot. High-performance liquid chromatography/mass spectrometry (HPLC/MS) was performed to detect the key factors of the kynurenine metabolic pathway. Our results demonstrated that probiotics improved neurological function of post-CPB rats. The administration of probiotics ameliorated memory and learning in spatial terms CPB rats (P < 0.05). Hematoxylin and eosin (H&E) staining data, S‐100β and neuron-specific enolase (NSE) data convinced that probiotics agonists reduced brain damage in CPB rats (P < 0.05). Moreover, probiotics regulated inflammatory factors, meanwhile attenuated hippocampal neuronal apoptosis. Probiotics alleviated POCD in rats with CPB through regulation of kynurenine metabolic signaling pathway.
A pre-Campanian Ignimbrite techno-cultural shift in the Aurignacian sequence of Grotta di Castelcivita, southern Italy
Authors: Falcucci Armando , Arrighi Simona , Spagnolo Vincenzo , Rossini Matteo , Higgins Owen Alexander , Muttillo Brunella , Martini Ivan , Crezzini Jacopo , Boschin Francesco , Ronchitelli Annamaria , Moroni Adriana
Published: June 2024

The Aurignacian is the first European technocomplex assigned toHomo sapiensrecognized across a wide geographic extent. Although archaeologists have identified marked chrono-cultural shifts within the Aurignacian mostly by examining the techno-typological variations of stone and osseous tools, unraveling the underlying processes driving these changes remains a significant scientific challenge. Scholars have, for instance, hypothesized that the Campanian Ignimbrite (CI) super-eruption and the climatic deterioration associated with the onset of Heinrich Event 4 had a substantial impact on European foraging groups. The technological shift from the Protoaurignacian to the Early Aurignacian is regarded as an archaeological manifestation of adaptation to changing environments. However, some of the most crucial regions and stratigraphic sequences for testing these scenarios have been overlooked. In this study, we delve into the high-resolution stratigraphic sequence of Grotta di Castelcivita in southern Italy. Here, the Uluzzian is followed by three Aurignacian layers, sealed by the eruptive units of the CI. Employing a comprehensive range of quantitative methods—encompassing attribute analysis, 3D model analysis, and geometric morphometrics—we demonstrate that the key technological feature commonly associated with the Early Aurignacian developed well before the deposition of the CI tephra. Our study provides thus the first direct evidence that the volcanic super-eruption played no role in this cultural process. Furthermore, we show that local paleo-environmental proxies do not correlate with the identified patterns of cultural continuity and discontinuity. Consequently, we propose alternative research paths to explore the role of demography and regional trajectories in the development of the Upper Paleolithic.
Using organ-on-a-chip technology to study haemorrhagic activities of snake venoms on endothelial tubules
Authors: Bittenbinder Mátyás A. , Bonanini Flavio , Kurek Dorota , Vulto Paul , Kool Jeroen , Vonk Freek J.
Published: June 2024

Snakebite envenomation is a major public health issue which causes severe morbidity and mortality, affecting millions of people annually. Of a diverse range of clinical manifestations, local and systemic haemorrhage are of particular relevance, as this may result in ischemia, organ failure and even cardiovascular shock. Thus far, in vitro studies have failed to recapitulate the haemorrhagic effects observed in vivo. Here, we present an organ-on-a-chip approach to investigate the effects of four different snake venoms on a perfused microfluidic blood vessel model. We assess the effect of the venoms of four snake species on epithelial barrier function, cell viability, and contraction/delamination. Our findings reveal two different mechanisms by which the microvasculature is being affected, either by disruption of the endothelial cell membrane or by delamination of the endothelial cell monolayer from its matrix. The use of our blood vessel model may shed light on the key mechanisms by which tissue-damaging venoms exert their effects on the capillary vessels, which could be helpful for the development of effective treatments against snakebites.
Revealing short-term dynamics of tropical cyclone wind speeds from satellite synthetic aperture radar
Authors: Avenas Arthur , Chapron Bertrand , Mouche Alexis , Platzer Paul , Vinour Léo
Published: June 2024

Both unresolved physics in numerical models and limited theoretical understanding of the small-scale diffusion processes occurring near the ocean surface hamper predictability of tropical cyclone (TC) wind changes. An analytical model is here developed to diagnose the short-term evolution of the TC wind profile. An effective frictional parameter is introduced to control the unknown diffusion effects. When this frictional parameter is adjusted to match the TC intensity change, solutions are consistent with observed high-resolution ocean surface wind speeds from satellite synthetic aperture radar (SAR). The initial high-resolution estimate of the near-core wind structure is then found to strongly modulate the wind profile evolution. The frictional parameter can, unfortunately, not efficiently be calibrated using outer-core wind speed changes. Low-resolution observations or standard numerical weather predictions may thus not be directly used to reinterpret and anticipate short-term TC wind changes. The expected accumulation of orbiting SAR sensors as well as improved measurements of the ocean-atmosphere boundary layer characteristics shall then become essential to more precisely monitor TC dynamics.
Study on coupled mode flutter parameters of large wind turbine blades
Authors: Zhuang Yong , Yuan Guangming
Published: June 2024

As the size of wind turbine blades increases, the flexibility of the blades increases. In actual operation, airflow flow can cause aerodynamic elastic instability of the blade structure. Long blades may experience coupled mode flutter due to the bending torsion coupling effect, leading to blade failure. Based on Euler Bernoulli beam theory combined with Theodorsen non directional aerodynamic loads, a blade flutter characteristic equation is established through finite element method. Taking NREL 5 MW wind turbine blades as an example, analyze the influence of parameter changes in different regions of the blades on flutter characteristics. Research has found that paramter changes in the tip region of blade have the greatest impact on flutter characteristics. The vibration frequency shows an overall upward trend with the increase of waving stiffness and torsional stiffness. The flutter velocity of the three regions tends to stabilize as the bending stiffness decreases. The blade flutter speed increases with the increase of torsional stiffness. The radius of gyration is inversely proportional to the flutter frequency and flutter velocity. The impact of centroid offset on blade structure flutter frequency is minimal, but the centroid offset in the tip region has a greater impact on flutter velocity. Increasing the torsional frequency can prevent coupled mode flutter and provide a theoretical basis for blade flutter prevention design.
The slopes of sub-barrier heavy-ion fusion excitation functions shed light on the dynamics of quantum tunnelling
Authors: Stefanini A. M. , Montagnoli G. , Del Fabbro M. , Corradi L. , Fioretto E. , Szilner S.
Published: June 2024

Quantum tunnelling plays a crucial role in heavy-ion fusion reactions at sub-barrier energies, especially in the context of nuclear physics and astrophysics. The nuclear structure of the colliding nuclei and nucleon transfer processes represent intrinsic degrees of freedom. They are coupled to the relative ion motion and, in general, increase the probability of tunnelling. The influence of couplings to nucleon transfer channels relatively to inelastic excitations, on heavy-ion fusion cross sections, is one of the still open problems in this field. We present a new analysis of several systems, based on the combined observation of the energy-weighted excitation functions $$E\sigma $$

E
σ

in relation to their first energy derivatives $$d(E\sigma )/dE$$

d
(
E
σ
)
/
d
E

. The relation between $$d(E\sigma )/dE$$

d
(
E
σ
)
/
d
E

and $$E\sigma $$

E
σ

removes the basic differences due to the varying Coulomb barrier when comparing different systems. We show that, depending on the nuclear structure and/or the presence of strong transfer channels, this representation reveals characteristic features below the barrier. The possible presence of cross section oscillations makes this analysis less clear for light- or medium-light systems.
An optimised patient-derived explant platform for breast cancer reflects clinical responses to chemotherapy and antibody-directed therapy
Authors: Demetriou Constantinos , Abid Naila , Butterworth Michael , Lezina Larissa , Sandhu Pavandeep , Howells Lynne , Powley Ian R. , Pringle James H. , Sidat Zahirah , Qassid Omar , Purnell Dave , Kaushik Monika , Duckworth Kaitlin , Hartshorn Helen , Thomas Anne , Shaw Jacqui A. , MacFarlane Marion , Pritchard Catrin , Miles Gareth J.
Published: June 2024

Breast Cancer is the most common cancer among women globally. Despite significant improvements in overall survival, many tumours are refractory to therapy and so novel approaches are required to improve patient outcomes. We have evaluated patient-derived explants (PDEs) as a novel preclinical platform for breast cancer (BC) and implemented cutting-edge digital pathology and multi-immunofluorescent approaches for investigating biomarker changes in both tumour and stromal areas at endpoint. Short-term culture of intact fragments of BCs as PDEs retained an intact immune microenvironment, and tumour architecture was augmented by the inclusion of autologous serum in the culture media. Cell death/proliferation responses to FET chemotherapy in BC-PDEs correlated significantly with BC patient progression-free survival (p = 0.012 and p = 0.0041, respectively) and cell death responses to the HER2 antibody therapy trastuzumab correlated significantly with HER2 status (p = 0.018). These studies show that the PDE platform combined with digital pathology is a robust preclinical approach for informing clinical responses to chemotherapy and antibody-directed therapies in breast cancer. Furthermore, since BC-PDEs retain an intact tumour architecture over the short-term, they facilitate the preclinical testing of anti-cancer agents targeting the tumour microenvironment.
Optimizing charge transport in hybrid GaN-PEDOT:PSS/PMMADevice for advanced application
Authors: Fakhri Makram A. , Salim Evan T. , Ketab Marwah R. , Jabbar Haneen D. , Ibrahim Omar A. , Azzahrani Ahmad S. , AbdulRazzaq Mohammed Jalal , Ismail Raid A. , Basem Ali , Alsultany Forat H. , Gopinath Subash C. B.
Published: June 2024

Organic–inorganic hybrid light-emitting devices have garnered significant attention in the last few years due to their potential. These devices integrate the superior electron mobility of inorganic semiconductors with the remarkable optoelectronic characteristics of organic semiconductors. The inquiry focused on analyzing the optical and electrical properties of a light-emitting heterojunction that combines p-type GaN with organic materials (PEDOT, PSS, and PMMA). This heterojunction is an organic–inorganic hybrid. The procedure entailed utilizing a spin-coating technique to apply a layer of either poly(methyl methacrylate) (PMMA) or a mixture of PMMA and poly(3,4ethylenedioxythiophene)-poly(styrene sulfonate) (PEDOT: PSS) onto an indium tin oxide (ITO) substrate. Subsequently, different Nd:YAG laser pulses (200, 250, and 300 pulses) were used to administer a GaN inorganic layer onto the prepared organic layer using a pulsed laser deposition approach. Subsequently, the thermal evaporation technique was employed to deposit an aluminum electrode on the top of the organic and inorganic layers, while laser pulses were fine-tuned for optimal performance. The Hall effect investigation verifies the p-type conductivity of the GaN material. The electroluminescence studies confirmed the production of blue light by the GaN-based devices throughout a range of voltage situations, spanning from 45 to 72 V.
Associations between HIV stigma and health-related quality-of-life among people living with HIV: cross-sectional analysis of data from HPTN 071 (PopART)
Authors: Hall Emily , Davis Katherine , Ohrnberger Julius , Pickles Michael , Gregson Simon , Thomas Ranjeeta , Hargreaves James R. , Pliakas Triantafyllos , Bwalya Justin , Dunbar Rory , Mainga Tila , Shanaube Kwame , Hoddinott Graeme , Bond Virginia , Bock Peter , Ayles Helen , Stangl Anne L. , Donnell Deborah , Hayes Richard , Fidler Sarah , Hauck Katharina ,   The HPTN 071 (PopART) study team, Hargreaves James R. , Watson-Jones Deborah , Godfrey-Faussett Peter , Sabapathy Kalpana , Hauck Katharina , Smith Peter C. , Cori Anne , Pickles Michael , Bell-Mandla Nomtha , Yang Blia , James Anelet , Vermaak Redwaan , Makola Nozizwe , Hoddinott Graeme , Naidoo Vikesh , Bond Virginia , Simwinga Musonda , Mwinga Alwyn , Kosloff Barry , Limbada Mohammed , Bwalya Justin , Ngulube Chepela , Fraser Christophe , Eshleman Susan , Agyei Yaw , Cummings Vanessa , Catalano Denni , Piwowar-Manning Estelle , Donnell Deborah , Emel Lynda , Bunts Lisa , Noble Heather , Burns David , Kouda Alain , Sista Niru , Moore Ayana , White Rhonda , Headen Tanette , Miller Eric , Hinson Kathy , Vermund Sten , Barnes Mark , Horn Lyn , Mwango Albert , Baldwin Megan , Wolf Shauna , Hughes Erin , el-Sadr Wafaa
Published: June 2024

People living with HIV (PLHIV) report lower health-related quality-of-life (HRQoL) than HIV-negative people. HIV stigma may contribute to this. We explored the association between HIV stigma and HRQoL among PLHIV. We used cross-sectional data from 3991 randomly selected PLHIV who were surveyed in 2017–2018 for HPTN 071 (PopART), a cluster randomised trial in Zambia and South Africa. Participants were 18–44 years, had laboratory-confirmed HIV infection, and knew their status. HRQoL was measured using the EuroQol-5-dimensions-5-levels (EQ-5D-5L) questionnaire. Stigma outcomes included: internalised stigma, stigma experienced in the community, and stigma experienced in healthcare settings. Associations were examined using logistic regression. Participants who had experienced community stigma (n = 693/3991) had higher odds of reporting problems in at least one HRQoL domain, compared to those who had not (adjusted odds ratio, aOR: 1.51, 95% confidence interval, 95% Cl: 1.16–1.98, p = 0.002). Having experienced internalised stigma was also associated with reporting problems in at least one HRQoL domain (n = 552/3991, aOR: 1.98, 95% CI: 1.54–2.54, p < 0.001). However, having experienced stigma in a healthcare setting was less common (n = 158/3991) and not associated with HRQoL (aOR: 1.04, 95% CI: 0.68–1.58, p = 0.850). A stronger focus on interventions for internalised stigma and stigma experienced in the community is required.
No free lunch for avoiding clustering vulnerabilities in distributed systems
Authors: Chitnelawong Pheerawich , Klishin Andrei A. , Mackay Norman , Singer David J. , van Anders Greg
Published: June 2024

Emergent design failures are ubiquitous in complex systems, and often arise when system elements cluster. Approaches to systematically reduce clustering could improve a design’s resilience, but reducing clustering is difficult if it is driven by collective interactions among design elements. Here, we use techniques from statistical physics to identify mechanisms by which spatial clusters of design elements emerge in complex systems modelled by heterogeneous networks. We find that, in addition to naive, attraction-driven clustering, heterogeneous networks can exhibit emergent, repulsion-driven clustering. We draw quantitative connections between our results on a model system in naval engineering to entropy-driven phenomena in nanoscale self-assembly, and give a general argument that the clustering phenomena we observe should arise in many distributed systems. We identify circumstances under which generic design problems will exhibit trade-offs between clustering and uncertainty in design objectives, and we present a framework to identify and quantify trade-offs to manage clustering vulnerabilities.
Genetic counseling and genetic testing for pathogenic germline mutations among high-risk patients previously diagnosed with breast cancer: a traceback approach
Authors: Abdel-Razeq Hikmat , Tamimi Faris , Iweir Sereen , Sharaf Baha , Abdel-Razeq Sarah , Salama Osama , Edaily Sarah , Bani Hani Hira , Azzam Khansa , Abaza Haneen
Published: June 2024

Genetic counseling and testing are more accessible than ever due to reduced costs, expanding indications and public awareness. Nonetheless, many patients missed the opportunity of genetic counseling and testing due to barriers that existed at that time of their cancer diagnoses. Given the identified implications of pathogenic mutations on patients’ treatment and familial outcomes, an opportunity exists to utilize a ‘traceback’ approach to retrospectively examine their genetic makeup and provide consequent insights to their disease and treatment. In this study, we identified living patients diagnosed with breast cancer (BC) between July 2007 and January 2022 who would have been eligible for testing, but not tested. Overall, 422 patients met the eligibility criteria, 282 were reached and invited to participate, and germline testing was performed for 238, accounting for 84.4% of those invited. The median age (range) was 39.5 (24–64) years at BC diagnosis and 49 (31–75) years at the date of testing. Genetic testing revealed that 25 (10.5%) patients had pathogenic/likely pathogenic (P/LP) variants; mostly in BRCA2 and BRCA1. We concluded that long overdue genetic referral through a traceback approach is feasible and effective to diagnose P/LP variants in patients with history of BC who had missed the opportunity of genetic testing, with potential clinical implications for patients and their relatives.
Suppressing mitochondrial inner membrane protein (IMMT) inhibits the proliferation of breast cancer cells through mitochondrial remodeling and metabolic regulation
Authors: Liu Li , Zhao Qingqing , Xiong Daigang , Li Dan , Du Jie , Huang Yunfei , Yang Yan , Chen Rui
Published: June 2024

Metabolic reprogramming is widely recognized as a hallmark of malignant tumors, and the targeting of metabolism has emerged as an appealing approach for cancer treatment. Mitochondria, as pivotal organelles, play a crucial role in the metabolic regulation of tumor cells, and their morphological and functional alterations are intricately linked to the biological characteristics of tumors. As a key regulatory subunit of mitochondria, mitochondrial inner membrane protein (IMMT), plays a vital role in degenerative diseases, but its role in tumor is almost unknown. The objective of this research was to investigate the roles that IMMT play in the development and progression of breast cancer (BC), as well as to elucidate the underlying biological mechanisms that drive these effects. In this study, it was confirmed that the expression of IMMT in BC tissues was significantly higher than that in normal tissues. The analysis of The Cancer Genome Atlas (TCGA) database revealed that IMMT can serve as an independent prognostic factor for BC patients. Additionally, verification in clinical specimens of BC demonstrated a positive association between high IMMT expression and larger tumor size (> 2 cm), Ki-67 expression (> 15%), and HER-2 status. Furthermore, in vitro experiments have substantiated that the suppression of IMMT expression resulted in a reduction in cell proliferation and alterations in mitochondrial cristae, concomitant with the liberation of cytochrome c, but it did not elicit mitochondrial apoptosis. Through Gene Set Enrichment Analysis (GSEA) analysis, we have predicted the associated metabolic genes and discovered that IMMT potentially modulates the advancement of BC through its interaction with 16 metabolic-related genes, and the changes in glycolysis related pathways have been validated in BC cell lines after IMMT inhibition. Consequently, this investigation furnishes compelling evidence supporting the classification of IMMT as prognostic marker in BC, and underscoring its prospective utility as a novel target for metabolic therapy.
Research on the generation and annotation method of thin section images of tight oil reservoir based on deep learning
Authors: Liu Tao , Liu Zongbao , Zhang Kejia , Li Chunsheng , Zhang Yan , Mu Zihao , Mu Mengning , Xu Mengting , Zhang Yue , Li Xue
Published: June 2024

The cast thin sections of tight oil reservoirs contain important parameters such as rock mineral composition and content, porosity, permeability and stratigraphic characteristics, which are of great significance for reservoir evaluation. The use of deep learning technology for intelligent identification of thin section images is a development trend of mineral identification. However, the difficulty of making cast thin sections, the complexity of the making process and the high cost of thin section annotation have led to a lack of cast thin section images, which cannot meet the training requirements of deep learning image recognition models. In order to increase the sample size and improve the training effect of deep learning model, we proposed a generation and annotation method of thin section images of tight oil reservoir based on deep learning, by taking Fuyu reservoir in Sanzhao Sag as the target area. Firstly, the Augmentor strategy space was used to preliminarily augment the original images while preserving the original image features to meet the requirements of the model. Secondly, the category attention mechanism was added to the original StyleGAN network to avoid the influence of the uneven number of components in thin sections on the quality of the generated images. Then, the SALM annotation module was designed to achieve semi-automatic annotation of the generated images. Finally, experiments on image sharpness, distortion, standard accuracy and annotation efficiency were designed to verify the advantages of the method in image quality and annotation efficiency.
Increase of secondary metabolites in sweet basil (Ocimum basilicum L.) leaves by exposure to N2O5 with plasma technology
Authors: Tateishi Rie , Ogawa-Kishida Natsumi , Fujii Nobuharu , Nagata Yuji , Ohtsubo Yoshiyuki , Sasaki Shota , Takashima Keisuke , Kaneko Toshiro , Higashitani Atsushi
Published: June 2024

Exposure to N2O5 generated by plasma technology activates immunity in Arabidopsis through tryptophan metabolites. However, little is known about the effects of N2O5 exposure on other plant species. Sweet basil synthesizes many valuable secondary metabolites in its leaves. Therefore, metabolomic analyses were performed at three different exposure levels [9.7 (Ex1), 19.4 (Ex2) and 29.1 (Ex3) μmol] to assess the effects of N2O5 on basil leaves. As a result, cinnamaldehyde and phenolic acids increased with increasing doses. Certain flavonoids, columbianetin, and caryophyllene oxide increased with lower Ex1 exposure, cineole and methyl eugenol increased with moderate Ex2 exposure and l-glutathione GSH also increased with higher Ex3 exposure. Furthermore, gene expression analysis by quantitative RT-PCR showed that certain genes involved in the syntheses of secondary metabolites and jasmonic acid were significantly up-regulated early after N2O5 exposure. These results suggest that N2O5 exposure increases several valuable secondary metabolites in sweet basil leaves via plant defense responses in a controllable system.
Sensorimotor tests in patients with neck pain and its associated disorders: a systematic review and meta-analysis
Authors: Särkilahti Niklas , Hirvonen Milka , Lavapuro Joona , Takatalo Jani , Löyttyniemi Eliisa , Tenovuo Olli
Published: June 2024

This systematic review aimed to synthesize the current evidence regarding neck sensorimotor testing in individuals with neck pain, assess the differences between neck pain groups and healthy controls, and recognize factors that might affect test results. We performed the data search using PubMed, Embase, PsycINFO, CINAHL, and Scopus databases. We used a two-step screening process to identify studies. Furthermore, we screened the reference lists for additional studies. Hedges g was used to present the difference between neck pain groups and asymptomatic individuals. We assessed the quality of the studies using the QUADAS tool. The final review included 34 studies, of which 25 were related to the joint position error test, four to the smooth pursuit neck torsion test and six to the balance test. Our meta-analysis showed poorer joint-position sense, oculomotor function, and wider postural sway in individuals with neck pain than healthy controls. The size of the difference between the groups seemed to be influenced by the intensity of the pain and the presence of dizziness. Therefore, it might be helpful in future studies to differentiate patients with neck pain into subgroups based on their symptom and demographic profiles to assess other factors that significantly affect cervical sensorimotor control.
Family migration and well-being of Chinese migrant workers’ children
Authors: Tang Ling , Xiang Xin , Liu Yang
Published: June 2024

This article aims to explore the effects of parental migration on the well-being of children and how to adjust social cognitive well-being through the interrelations among family relations and social cognitive well-being indicators using structural equation modelling. Two modified social cognitive well-being models were tested in 1682 Chinese migrant workers' children to examine the pathways among social cognitive well-being and family relation characteristics. The modified models are based on the social cognitive well-being model and the characteristics of Chinese migrant workers' children. The results show that caregiver-child communication frequency, caregiver-child regulation, caregiver-child conflicts, caregiver-child trust and communication, and coactivity positively impact children’s social cognitive well-being. In contrast, caregiver-child alienation negatively influences children’s social cognitive factors through caregiver-child trust and communication. Additionally, this research revealed that family-related characteristics (caregiver-child regulation, caregiver-child coactivities, caregiver-child communication frequency, caregiver-child alienation, caregiver-child conflicts, and caregiver-child trust and communication) are interconnected with social cognitive well-being indicators (academic satisfaction, outcome expectations, goal progress, lifelong satisfaction, environmental support, positive affect, negative affect, and self-efficacy). This suggests that family migration and relationships with caregiver(s) can significantly affect the well-being of migrant workers' children.
Preliminary evidence that eye appearance in parrots (Psittaciformes) co-varies with latitude and altitude
Authors: Duran Elif , Perea-García Juan Olvido , Piepenbrock Diede , Veefkind Celine , Kret Mariska E. , Massen Jorg J. M.
Published: June 2024

External eye appearance in avian taxa has been proposed to be driven by social and ecological functions. Recent research in primates suggests, instead, that, photoprotective functions are important drivers of external eye appearance. Using similar methods, we examined the variation in external eye appearance of 132 parrot species (Psittaciformes) in relation to their ecology and sociality. Breeding systems, flock size and sexual dimorphism, as well as species’ latitude and maximum living altitude, and estimated UV-B incidence in species’ ranges were used to explore the contribution of social and ecological factors in driving external eye appearance. We measured the hue and brightness of visible parts of the eye and the difference in measurements of brightness between adjacent parts of the eye. We found no link between social variables and our measurements. We did, however, find a negative association between the brightness of the inner part of the iris and latitude and altitude. Darker inner irises were more prevalent farther away from the equator and for those species living at higher altitudes. We found no link between UV-B and brightness measurements of the iris, or tissue surrounding the eye. We speculate that these results are consistent with an adaptation for visual functions. While preliminary, these results suggest that external eye appearance in parrots is influenced by ecological, but not social factors.
A 3-D interactive microbiology laboratory via virtual reality for enhancing practical skills
Authors: Chitra Ebenezer , Mubin Siti Azreena , Nadarajah Vishna Devi , Se Wong Pei , Sow Chew Fei , Er Hui Meng , Mitra Nilesh Kumar , Thiruchelvam Vinesh , Davamani Fabian
Published: June 2024

Virtual Reality (VR) laboratories are a new pedagogical approach to support psychomotor skills development in undergraduate programmes to achieve practical competency. VR laboratories are successfully used to carry out virtual experiments in science courses and for clinical skills training in professional courses. This paper describes the development and evaluation of a VR-based microbiology laboratory on Head-Mounted Display (HMD) for undergraduate students. Student and faculty perceptions and expectations were collected to incorporate into the laboratory design. An interactive 3-dimensional VR laboratory with a 360° view was developed simulating our physical laboratory setup. The laboratory environment was created using Unity with the (created) necessary assets and 3D models. The virtual laboratory was designed to replicate the physical laboratory environment as suggested by the students and faculty. In this VR laboratory, six microbiology experiments on Gram staining, bacterial streaking, bacterial motility, catalase test, oxidase test and biochemical tests were placed on the virtual platform. First-year biomedical science students were recruited to evaluate the VR laboratory. Students’ perception of the virtual laboratory was positive and encouraging. About 70% of the students expressed they felt safe using the VR laboratory and that it was engaging. They felt that the VR laboratory provided an immersive learning experience. They appreciated that they could repeat each experiment multiple times without worrying about mistakes or mishaps. They could personalise their learning by concentrating on the specific experiments. Our in-house VR-based microbiology laboratory was later extended to other health professions programmes teaching microbiology.
Research on the influencing factors of adult learners' intent to use online education platforms based on expectation confirmation theory
Authors: Pan Guoqiang , Mao Yu , Song Ziyuan , Nie Hui
Published: June 2024

This study addresses the understanding gap concerning the factors that influence the continuous learning intention of adult learners on online education platforms. The uniqueness and significance of this study stem from its dual focus on both platform features, such as service quality, and course features, including perceived interactivity and added value, aspects often overlooked in previous research. Rooted in Expectation Confirmation Theory, the study constructs a comprehensive model to shed light on the complex interplay of these factors. Empirical evidence collected from a survey of 1592 adult learners robustly validates the effectiveness of this model. The findings of the study reveal that platform service quality, perceived interactivity, and perceived added value significantly amplify adult learners' expectation confirmation and perceived usefulness. These elements subsequently enhance learner satisfaction, fostering their ongoing intention to use online education platforms. These insights offer practical guidance for online education providers, emphasizing the necessity to enhance platform service quality and course features to meet adult learners' expectations and perceived usefulness. The study provides valuable perspectives for devising strategies to boost user satisfaction and stimulate continuous usage intention among adult learners in the intensely competitive online education market. This study enriches the literature by uncovering the relationships among platform features, course features, expectation confirmation, perceived usefulness, and continuous usage intention. By proposing a comprehensive model, this study provides a novel theoretical basis for understanding how platform and course features impact adult learners' ongoing intention to use online education platforms, thereby aiding the evolution and refinement of relevant theories.
Bacteroidetes promotes esophageal squamous carcinoma invasion and metastasis through LPS-mediated TLR4/Myd88/NF-κB pathway and inflammatory changes
Authors: Wu Zhongbing , Guo Jianxin , Zhang Zhenhan , Gao Shuang , Huang Ming , Wang Yu , Zhang Yushuang , Li Qinghuan , Li Jing
Published: June 2024

Gut microbiota plays a crucial role in gastrointestinal tumors. Additionally, gut microbes influence the progression of esophageal cancer. However, the major bacterial genera that affect the invasion and metastasis of esophageal cancer remain unknown, and the underlying mechanisms remain unclear. Here, we investigated the gut flora and metabolites of patients with esophageal squamous cell carcinoma and found abundant Bacteroides and increased secretion and entry of the surface antigen lipopolysaccharide (LPS) into the blood, causing inflammatory changes in the body. We confirmed these results in a mouse model of 4NQO-induced esophageal carcinoma in situ and further identified epithelial–mesenchymal transition (EMT) occurrence and TLR4/Myd88/NF-κB pathway activation in mouse esophageal tumors. Additionally, in vitro experiments revealed that LPS from Bacteroides fragile promoted esophageal cancer cell proliferation, migration, and invasion, and induced EMT by activating the TLR4/Myd88/NF-κB pathway. These results reveal that Bacteroides are closely associated with esophageal cancer progression through a higher inflammatory response level and signaling pathway activation that are both common to inflammation and tumors induced by LPS, providing a new biological target for esophageal cancer prevention or treatment.
Evaluation of using micronized saudi calcite in ilmenite-weighted water-based drilling fluid
Authors: Shokry Amir , Basfar Salem , Elkatatny Salaheldin
Published: June 2024

A high-density water-based drilling fluid (WBDF) is crucial for maintaining wellbore stability, controlling formation pressures, and optimizing drilling performance in challenging subsurface conditions. In the present research, the effect of micronized calcium carbonate (calcite), extracted from the Aruma formation outcrop, is evaluated as one of the additives that could be added to the ilmenite-weighted WBDF to enhance and optimize its properties. Various concentrations of Calcite microparticles were introduced into identical fluid formulations to assess their impact. The concentrations ranged from 0, 10, 20, to 30 lb/bbl, providing a comprehensive examination of the effects of calcite microparticles across a spectrum of concentrations within the fluid. The results highlighted that adding Barite microparticles to the WBDF revealed a notable enhancement in rheological properties. Specifically, the yield point demonstrated an increase of 37%, 37%, and 11% for concentrations of 10, 20, and 30 lb/bbl of calcite, respectively. Equally significant, high-pressure-high-temperature (HPHT) filtration analysis indicated a considerable enhancement for the fluids containing calcite microparticles. A reduction of 14.5%, 24.6%, and 13% were observed in HPHT filtrate for concentrations of 10 lb/bbl, 20 lb/bbl, and 30 lb/bbl respectively. Simultaneously, there is a reduction in filter cake thickness by 20%, 40%, and 20%, respectively. No ilmenite settling was observed in the sample containing 20 lb/bbl of calcite, unlike the other concentrations. These diverse results strongly suggest that the optimal concentration for calcite microparticles is 20 lb/bbl. The combined utilization of the optimal concentration of calcite microparticles alongside the established additives proves to be an effective strategy for optimizing the ilmenite-weighted WBDF performance in terms of both thermal stability and rheological behavior.