bluuebunny/crossref_metadata_2025 huggingface dataset:
Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells
Authors: Jhamat Naveed , Guo Yongzhi , Han Jilong , Humblot Patrice , Bongcam-Rudloff Erik , Andersson Göran , Niazi Adnan
Published: September 2024

Endometritis is an inflammatory disease that negatively influences fertility and is common in milk-producing cows. An in vitro model for bovine endometrial inflammation was used to identify enrichment of cis-acting regulatory elements in differentially methylated regions (DMRs) in the genome of in vitro-cultured primary bovine endometrial epithelial cells (bEECs) before and after treatment with lipopolysaccharide (LPS) from E. coli, a key player in the development of endometritis. The enriched regulatory elements contain binding sites for transcription factors with established roles in inflammation and hypoxia including NFKB and Hif-1α. We further showed co-localization of certain enriched cis-acting regulatory motifs including ARNT, Hif-1α, and NRF1. Our results show an intriguing interplay between increased mRNA levels in LPS-treated bEECs of the mRNAs encoding the key transcription factors such as AHR, EGR2, and STAT1, whose binding sites were enriched in the DMRs. Our results demonstrate an extraordinary cis-regulatory complexity in these DMRs having binding sites for both inflammatory and hypoxia-dependent transcription factors. Obtained data using this in vitro model for bacterial-induced endometrial inflammation have provided valuable information regarding key transcription factors relevant for clinical endometritis in both cattle and humans.
Metabolomics-Assisted Breeding in Oil Palm: Potential and Current Perspectives
Authors: Nugroho Rizki Anjal P. , Zaag Ismail , Lamade Emmanuelle , Lukman Rudy , Caliman Jean-Pierre , Tcherkez Guillaume
Published: September 2024

Oil palm is presently the most important oil-producing crop worldwide in terms of oil production and consumption. However, oil palm cultivation faces important challenges such as adverse climatic conditions, expensive fertilization requirements, and fungal pathogens, including Ganoderma. Intense efforts in oil palm breeding are devoted to improving both oil production yield and resistance to environmental cues. Metabolomics can be of interest because it provides many quantitative traits and metabolic signatures that can be selected for to optimize oil palm performance. Here, we briefly review how metabolomics can help oil palm breeding, and to do so, we give examples of recent metabolomics analyses and provide a roadmap to use metabolomics-assisted breeding.
Osteochondral Tissue-On-a-Chip: A Novel Model for Osteoarthritis Research
Authors: González-Guede Irene , Garriguez-Perez Daniel , Fernandez-Gutierrez Benjamin
Published: September 2024

The existing in vitro and in vivo models for studying osteoarthritis have significant limitations in replicating the complexity of joint tissues. This research aims to validate a Tissue-On-a-Chip system for osteoarthritis research. Osteochondral tissues obtained from knee replacement surgeries of patients with osteoarthritis were cultured in an Organ-On-a-Chip system. This system was designed to supply oxygen and glucose to the cartilage from the bone. The distribution of oxygen and glucose was evaluated by fluorescence using Image-iT Green Hypoxia and 2-NBDG, respectively. Cytotoxicity was measured using lactate dehydrogenase (LDH) levels in chip cultures compared to plate cultures (12 tissues per method). Glycosaminoglycans (GAGs), alkaline phosphatase (ALP), Coll2-1, and procollagen type II N-terminal propeptide (PIINP) were measured in the perfused medium of the Tissue-On-a-Chip over a period of 70 days. Fluorescence of Image-iT Green Hypoxia was observed only in the cartilage area, while 2-NBDG was distributed throughout the tissue. An increase in LDH levels was noted in the plate cultures on day 24 and in the Tissue-On-a-Chip cultures on day 63. Compared to the start of the culture, GAG content increased on day 52, while ALP showed variations. A notable increase in GAG, ALP, and Coll2-1 levels was observed on day 59. PIINP levels remained stable throughout the experiment. The validated osteochondral Tissue-On-a-Chip system can replicate the joint microenvironment, with hypoxic conditions in cartilage and normoxic conditions in bone. Tissue survival and component stability were maintained for approximately two months. This platform is a useful tool for evaluating new drugs and represents a viable alternative to animal models.
Polymorphism and Pharmacological Assessment of Carbamazepine
Authors: Sá Filho Alberto , Martins Jose Luis Rodrigues , Costa Rafael Fernandes , Pedrino Gustavo Rodrigues , Duarte Vitor Santos , Silva Osmar Nascimento , Napolitano Hamilton Barbosa , Fajemiroye James Oluwagbamigbe
Published: September 2024

This work provides insight into carbamazepine polymorphs (Forms I, II, III, IV, and V), with reports on the cytoprotective, exploratory, motor, CNS-depressant, and anticonvulsant properties of carbamazepine (CBZ), carbamazepine formulation (CBZ-F), topiramate (TOP), oxcarbazepine (OXC), and diazepam (DZP) in mice. Structural analysis highlighted the significant difference in molecular conformations, which directly influence the physicochemical properties; and density functional theory description provided indications about CBZ reactivity and stability. In addition to neuron viability assessment in vitro, animals were treated orally with vehicle 10 mL/kg, as well as CBZ, CBZ-F, TOP, OXC, and DZP at the dose of 5 mg/kg and exposed to open-field, rotarod, barbiturate sleep induction and pentylenetetrazol (PTZ 70 mg/kg)-induced seizure. The involvement of GABAergic mechanisms in the activity of these drugs was evaluated with the intraperitoneal pretreatment of flumazenil (2 mg/kg). The CBZ, CBZ-F, and TOP mildly preserved neuronal viability. The CBZ-F and the reference AEDs potentiated barbiturate sleep, altered motor activities, and attenuated PTZ-induced convulsion. However, flumazenil pretreatment blocked these effects. Additional preclinical assessments could further establish the promising utility of CBZ-F in clinical settings while expanding the scope of AED formulations and designs.
FLASH Radiotherapy Versus Conventional Cancer Therapy: Promises, Paradoxes and Problems
Authors: Bondy Stephen C.
Published: September 2024

A novel means of applying radiotherapy in cancer treatment is the application of a radiation dose at a very high intensity for a very short time in FLASH radiotherapy (FLASH-RT). This technique involves the exposure of tumors to >40 Gy/s, usually for less than one second. Studies conducted in cell and preclinical models suggest that FLASH-RT seems less damaging to normal tissues from adverse effects relative to the same overall dose of radiation administered in conventional therapy (CONV-RT), which involves the administration of lower levels of radiation repeated intermittently over a protracted period. In contrast, the susceptibility of tumor tissues to FLASH-RT is not diminished relative to CONV-RT. Within solid tumors, both modes of dispensation of radiation produce an equivalent degree of cell damage. The differential treatment between normal and malignant material has been found in isolated tissues, animal studies and, more recently, in clinical trials. However, the classic radiation concept is that high-energy linear transfer radiation (LET) is more damaging than the equivalent total dose of low LET. Thus, the susceptibility of cells should be greater after short-term exposure to high LET. This article discusses the potential reasons that may account for this discrepancy. While the relative protection given to untransformed tissues by FLASH-RT relative to tumor tissue is a major step forward in radiation therapy for cancer, the processes that lie behind this phenomenon are incompletely understood and are considered here.
A Novel Transgenic Sf9 Cell Line for Quick and Easy Virus Quantification
Authors: Kim Kyu-Seek , Bae Jun-Su , Moon Hyuk-Jin , Kim Do-Young , Woo Soo-Dong
Published: September 2024

The following study was conducted to generate a transgenic Sf9 cell line for rapid and easy virus quantification in the baculovirus expression system (BES). The hr3 (homologous region 3) and 39K and p10 promoters were used as the expression structures to induce rapid and intense expression of the enhanced green fluorescent protein gene in cells in response to viral infection. Of 20 transgenic Sf9 cell lines generated using the piggyBac system, the cell line that showed the highest fluorescence expression in the shortest time in response to viral infection was selected and named Sf9-QE. The average diameter of the Sf9-QE cells was around 16 μm, which is 2 μm smaller than the average diameter of Sf9 cells, whereas the rate of cell proliferation was around 1.6 times higher in the Sf9-QE cells. Virus quantification using the Sf9-QE cell line did not produce significantly different results compared to the other cell lines; however, the time required for complete virus quantification was approximately 5.3 to 6.0 days for the Sf9-QE cells, which is around 4 to 6 days shorter than the time required for the other cell lines, enabling convenient and accurate virus quantification via fluorescence photometry within around 6.0 to 6.3 days. The properties of the Sf9-QE cells were stable for up to at least 100 passages.
Innovations in Liver Preservation Techniques for Transplants from Donors after Circulatory Death: A Special Focus on Transplant Oncology
Authors: Finotti Michele , Romano Maurizio , Grossi Ugo , Dalla Bona Enrico , Pelizzo Patrizia , Piccino Marco , Scopelliti Michele , Zanatta Paolo , Zanus Giacomo
Published: September 2024

Liver transplantation is the preferred treatment for end-stage liver disease. Emerging evidence suggests a potential role for liver transplantation in treating liver tumors such as colorectal liver metastases and cholangiocarcinoma. However, due to a limited donor pool, the use of marginal grafts from donation after circulatory death (DCD) donors is increasing to meet demand. Machine perfusion is crucial in this context for improving graft acceptance rates and reducing ischemia–reperfusion injury. Few studies have evaluated the role of machine perfusion in the context of transplant oncology. Perfusion machines can be utilized in situ (normothermic regional perfusion—NRP) or ex situ (hypothermic and normothermic machine perfusion), either in combination or as a complement to conventional in situ cold flush and static cold storage. The objective of this analysis is to provide an up-to-date overview of perfusion machines and their function in donation after circulatory death with particular attention to their current and likely potential effects on transplant oncology. A literature review comparing standard cold storage to machine perfusion methods showed that, so far, there is no evidence that these devices can reduce the tumor recurrence rate. However, some evidence suggests that these innovative perfusion techniques can improve graft function, reduce ischemia–reperfusion injury, and, based on this mechanism, may lead to future improvements in cancer recurrence.
Predictors of Satisfaction in Patients with Knee Osteoarthritis Treated with a Single Injection of Mannitol-Modified Crosslinked Hyaluronate Derivative
Authors: Balblanc Martin , Lohse Anne , Meyer Frederic , Rapp Charles , Bourgoin Charlotte , Balblanc Jean-Charles , Conrozier Thierry
Published: September 2024

Background/Objectives: There is a gap between the very positive opinion of patients and doctors regarding knee viscosupplementation (VS) and the contrasting results of controlled studies. The objective of this study was to evaluate the overall satisfaction and predictors of satisfaction with VS in patients with knee osteoarthritis treated with VS. Methods: Post-hoc analysis of a cross-sectional study in patients with knee OA treated with one injection of a mannitol-modified cross-linked HA (HANOX-M-XL). The primary outcome was satisfaction, self-assessed semi-quantitatively by the patients. Demographics, radiological features, comorbidities, OA and comorbidities treatments, and lifestyle associated with satisfaction were studied in bivariate and multivariate analysis. Results: 89 patients (124 knees) were analyzed. A total of 88.7% were satisfied with the treatment. Satisfaction was correlated with duration of effectiveness (DoE) and negatively correlated with BMI. Satisfaction was higher in active versus sedentary patients, in tibiofemoral involvement, in Kellgren-Lawrence grade 1–3 versus 4, and in subjects not requiring intraarticular corticosteroid (IACS) concomitantly to VS. Satisfied subjects were older than dissatisfied ones. In multivariate analysis, older age, K–L grade < 4, absence of IACS, and longer DoE were associated with higher rates of satisfaction. Conclusions: We identified several predictive factors of patient satisfaction after VS of the knee. Alongside these objective factors, there are probably subjective factors linked to patient beliefs, fears, and expectations impacting satisfaction.
Impact of Central Line-Associated Bloodstream Infections on Mortality and Hospital Stay in Adult Patients at a Tertiary Care Institution in Cali, Colombia, 2015–2018
Authors: Mosquera Jorge Mario Angulo , Assis Reveiz Jorge Karim , Barrera Lena , Liscano Yamil
Published: September 2024

Background: Central line-associated bloodstream infections (CLABSIs) are a significant healthcare challenge globally, increasing mortality risk and complicating central vascular catheter use. In Colombia, few studies have assessed the impact of CLABSIs on hospital stay and mortality. Objective: To determine the association between CLABSIs and discharge outcomes and hospital stay duration in adult patients at a tertiary care institution in Cali, Colombia, from 1 January 2015 to 31 December 2018. Methods: A nested case–control study was conducted. The odds of mortality associated with CLABSIs were estimated using conditional logistic regression. Non-conditional logistic regression was used to determine the odds of mortality when CLABSIs were caused by resistant microorganisms. Hospital stay duration, catheter duration, and time from catheter insertion to discharge were compared between patients with and without CLABSIs. The most frequent etiological agents were identified. Results: Patients with CLABSIs had 3.89 times the odds of mortality (95% CI [1.33–11.31], p = 0.013) compared to those without CLABSIs. The odds of mortality for patients with resistant microorganism CLABSIs were 4.04 times (95% CI [1.17–13.96], p = 0.027) higher than those with sensitive microorganism CLABSIs. Hospital stay duration (median = 51 days vs. 17 days; p = 0.000), catheter duration (median = 19 days vs. 7 days; p < 0.001), and time from catheter insertion to discharge (median = 40 days vs. 9 days; p < 0.001) were significantly longer in CLABSI patients. Klebsiella pneumoniae was the most isolated pathogen (20.2%), followed by Staphylococcus aureus (14.9%). Implications: CLABSI patients have longer catheter and hospitalization durations and higher mortality risk. Resistant microorganism CLABSIs are associated with elevated mortality risk. Conclusions: This study corroborates the positive relation between CLABSI and the mortality risk, which is influenced by resistant bacteria, though causality is not established. CLABSI is also linked to longer hospital stays, underscoring the need for improving infection control strategies
Chronic Unilateral Vestibular Hypofunction: Insights into Etiologies, Clinical Subtypes, Diagnostics and Quality of Life
Authors: Karabulut Mustafa , Viechtbauer Wolfgang , Van Laer Lien , Mohamad Alfarghal , Van Rompaey Vincent , Guinand Nils , Perez Fornos Angélica , Gerards Marie-Cecile , van de Berg Raymond
Published: September 2024

Background/Objectives: Chronic unilateral vestibular hypofunction (UVH) can lead to disabling vestibular symptoms and a decrease in quality of life. The aim of this study was to investigate etiologies, clinical subtypes, symptoms, and quality of life (QoL) in patients with chronic UVH. Methods: A retrospective study was performed on 251 UVH patients in a tertiary referral center. Inclusion criteria comprised reduced or absent caloric responses, with a caloric asymmetry ratio ≥25%. Patients with central vestibular pathology, symptom duration <3 months, and incomplete responses to questionnaires were excluded. Patient records were assessed for etiologies, secondary vestibular diagnoses, clinical subtypes, and questionnaires related to QoL. Additionally, multiple linear regression analysis was performed to evaluate factors influencing QoL. Results: Thirteen different etiologies were identified, with Menière’s Disease as the most prevalent (31%, n = 79). The most frequently reported secondary vestibular diagnoses were benign paroxysmal positional vertigo (BPPV) (21%, n = 54) and persistent postural perceptual dizziness (PPPD) (19%, n = 47). Five distinct clinical subtypes were identified: recurrent vertigo with UVH (47%), rapidly progressive UVH (25%), idiopathic/unknown UVH (18%), slowly progressive UVH (8%), and congenital UVH (2%). Over 80% of UVH patients experienced moderate-to-severe handicap, as indicated by the Dizziness Handicap Inventory. Approximately 20–25% of UVH patients exhibited moderate-to-severe depression and anxiety, based on the Hospital Anxiety and Depression Scale. Multiple linear regression analyses demonstrated that the presence of PPPD significantly reduced QoL in chronic UVH patients. Conclusions: Chronic UVH is a heterogeneous disorder. Secondary vestibular diagnoses like BPPV and PPPD often co-exist and can significantly impact QoL. A structured diagnostic approach and tailored interventions are crucial to address the diverse needs of UVH patients.
The Association of Weight Categories in Adolescence with Cardiovascular Morbidity in Young Adult Israeli Arabs—A Nationwide Study
Authors: Treister-Goltzman Yulia , Nemet Dan , Menashe Idan
Published: September 2024

Objectives. The health consequences of adolescent obesity are understudied in young adult Israeli Arabs. We aimed to evaluate the association of weight categories during adolescence with hypertension (HTN), diabetes mellitus type 2 (DM2), and the composite endpoint of ischemic stroke (IS), myocardial infarction (MI), and heart failure (HF) in young adult Israeli Arabs on a nationwide level. Methods. A retrospective cohort study of 53,726 Arab adolescents born from 1988–1992 was conducted. The cohort was followed, beginning with BMI measurements at ages 17–19 years, until whichever came first among the diagnosis of outcome disease, death, discontinuation of health insurance, or age of 30 years. Results. The incidence (95% CI) of HTN, DM2, and the composite endpoint of IS, MI, and HF was 138.2 (129.1–147.9), 136.7 (127.6–146.3), and 27.3 (23.3–31.7) cases per 105 person-years, respectively. The risk for DM and HTN increased gradually, starting from the ‘overweight’ category, and reaching fully adjusted HRs (95% CI) of 2.80 (1.82–4.30), and 1.97 (1.31–2.96), respectively, in the ‘class 3 obesity’ category. The Hazard ratio (HR) for the composite endpoint, its incidence and components, was highest in the ‘overweight’ category (aHR of 1.64 (1.08–2.50)). Conclusions. The findings emphasize the long-term health consequences of adolescent obesity in early adulthood and, hence, the need for interventions aimed at reducing the rate of adolescent overweight and obesity. The finding of a very high rate of DM2 incidence in early adulthood, even among adolescents without obesity, necessitates an integrated public health approach to all risk factors to prevent DM2 in this population.
The Importance of Cardiac Magnetic Resonance in the Assessment Risk of Cardiac Arrhythmias in Patients with Arterial Hypertension
Authors: Wysocki Andrzej , Macek Piotr , Dziadkowiec-Macek Barbara , Poręba Małgorzata , Gać Paweł , Poręba Rafał
Published: September 2024

Objectives: Arterial hypertension (AH) is one of the major risk factors for cardiovascular diseases. An association between untreated AH and arrhythmia is observed. Cardiac magnetic resonance (CMR) assesses myocardial fibrosis by detecting foci of late gadolinium enhancement (LGE). Clinical significance of LGE at the right ventricular insertion point (RVIP) is not fully established. This study aimed to assess the relationship between the presence of LGE at the RVIP determined by CMR and the incidence of arrhythmia in a group suffering from arterial hypertension. Methods: The study group consisted of 81 patients with AH (37 men and 44 women, age: 56.7 ± 7.1 years). All subjects underwent CMR and 24 h Holter ECG monitoring. Two subgroups were distinguished in the study group based on the criterion of the presence of LGE at the RVIP in CMR. The RVIP+ subgroup consisted of patients with LGE at the RVIP, while the RVIP− group consisted of patients without LGE at the RVIP. Results: The RVIP+ subgroup was characterized by higher maximum and minimum heart rates in 24 h Holter ECG recordings compared to the RVIP− subgroup (p < 0.05). The RVIP+ subgroup had a statistically significantly higher number of single premature supraventricular beats, supraventricular tachycardias, and single premature ventricular beats than the RVIP− subgroup (p < 0.05). Regression analysis documented that a longer duration of AH (counted from diagnosis) as well as the occurrence of LGE at the RVIP (assessed by CMR) are independent risk factors for arrhythmia (p < 0.05). Conclusions: Due to the possibility of detecting LGE at the RVIP, CMR may be a useful diagnostic method in estimating the risk of arrhythmias in the group of patients with AH.
Anterior Segment Optical Coherence Tomography for the Tailored Treatment of Mooren’s Ulcer: A Case Report
Authors: Lucchino Luca , Mastrogiuseppe Elvia , Giovannetti Francesca , Bruscolini Alice , Marenco Marco , Lambiase Alessandro
Published: September 2024

Background: Mooren’s ulcer (MU) is a rare and debilitating form of peripheral ulcerative keratitis (PUK), characterized by a crescent-shaped ulcer with a distinctive overhanging edge at the corneal periphery. If left untreated, MU can lead to severe complications such as corneal perforation and blindness. Despite various treatment approaches, including anti-inflammatory and cytotoxic drugs, as well as surgical interventions, there is no clear evidence of the most effective treatment due to the lack of randomized controlled trials. AS-OCT is a non-invasive imaging technique that provides high-resolution cross-sectional images of the anterior segment, allowing for accurate evaluation of corneal ulcer characteristics, including depth, extent, and disease progression. Methods: We present the case of a 20-year-old male patient with MU managed using a stepladder approach, which included local and systemic corticosteroids, limbal conjunctival resection, and Cyclosporine A 1% eye drops. The patient underwent consecutive AS-OCT examinations and strict follow-up to tailor systemic and topical therapy. Results: Complete healing of the corneal ulcer with resolution of the inflammatory process was achieved. There was no recurrence of the disease at the 7-month follow-up. AS-OCT demonstrated progressive reorganization and thickening of the stromal tissue until the complete recovery of stromal thickness. Conclusions: The AS-OCT imaging modality allowed for the accurate evaluation of corneal ulcer characteristics, facilitating informed decision-making regarding the use of systemic immunosuppression, surgical interventions, and local immunomodulation and providing detailed and precise assessment of disease progression. This approach enabled a tailored and effective treatment strategy for the patient and played a critical role in guiding the therapeutic approach.
Effects of Confined Microenvironments with Protein Coating, Nanotopography, and TGF-β Inhibitor on Nasopharyngeal Carcinoma Cell Migration through Channels
Authors: Hong Xiao , Xu Yuanhao , Pang Stella W.
Published: September 2024

Distant metastasis is the primary cause of unsuccessful treatment in nasopharyngeal carcinoma (NPC), suggesting the crucial need to comprehend this process. A tumor related to NPC does not have flat surfaces, but consists of confined microenvironments, proteins, and surface topography. To mimic the complex microenvironment, three-dimensional platforms with microwells and connecting channels were designed and developed with a fibronectin (FN) coating or nanohole topography. The potential of the transforming growth factor-β (TGF-β) inhibitor (galunisertib) for treating NPC was also investigated using the proposed platform. Our results demonstrated an increased traversing probability of NPC43 cells through channels with an FN coating, which correlated with enhanced cell motility and dispersion. Conversely, the presence of nanohole topography patterned on the platform bottom and the TGF-β inhibitor led to a reduced cell traversing probability and decreased cell motility, likely due to the decrease in the F-actin concentration in NPC43 cells. This study highlights the significant impact of confinement levels, surface proteins, nanotopography, and the TGF-β inhibitor on the metastatic probability of cancer cells, providing valuable insights for the development of novel treatment therapies for NPC. The developed platforms proved to be useful tools for evaluating the metastatic potential of cells and are applicable for drug screening.
Adjustability and Stability of Flow Control by Periodic Forcing: A Numerical Investigation
Authors: Li Hongbo , Yu Jiancheng , Chen Zhier , Ren Kai , Tan Zhiduo
Published: September 2024

The efficient and stable application of periodic forcing for drag-reduction can help underwater vehicles operate at high speed for long durations and improve their energy-utilization efficiency. This study considers flow control around a body-of-revolution model subjected to periodic blowing or suction through annular slots. The focus is on the boundary-layer structure, properties, and drag of the control fluid under a wide range of body variables (size, free-flow velocity, slot area, and blowing/suction velocity) and control parameters (normalized periodic-forcing amplitude and relative slot sizes). Body variables differ in their effects on the drag-reduction rate, with the surface pressure pushing the model vehicle when S and v are higher than S0 and v0. In particular, the lowest pressure drag was −26.4 N with v increasing, and the maximum drag-reduction rate of total drag exceeded 135%. At a fixed Reynolds number, increasing the values of the control parameters leads to larger-scale unstable vortex rings downstream from the slots; the surface-velocity gradient is reduced, effectively lowering the drag. A simple model relating the periodic fluctuation of pressure drag to the body variables is developed through quantitative analysis and used to determine navigational stability.
Non-Repetitive Time-Shifted Seismic Monitoring Study Based on Ocean Bottom Cable and Towed Streamer Data
Authors: Chen Fengying , Wang Xiangchun , Liu Wei , Li Yibin , Liu Zhendong
Published: September 2024

Time-shifted seismic research plays an important role in monitoring changes in the gas-water interface uplift, the weakening of amplitude attributes, and gas distribution due to mining. When time-shifted seismic research involves non-repeatable data with significant differences between data sets due to variations in seismic data acquisition parameters and seismic geometries, it necessitates consistent processing before time-shifted monitoring comparisons. In this paper, a study of time-shifted seismic monitoring using two non-repetitive data sets based on the ocean bottom cable (OBC) and towed streamer data is presented. First, amplitude, frequency, wavelet, and time difference are processed to achieve consistency for time-shifted comparisons. Secondly, three modes of seismic geometry normalization are compared to optimize the appropriate offset, azimuth, and signal-to-noise ratio (SNR). Finally, after eliminating the fault surface wave, the maximum trough amplitude attribute is extracted for the same position in the two data sets to analyze time-shifted differences under the three modes using the ratio method and difference method. The conclusions show the following: the OBC and towed streamer data can achieve consistency in terms of amplitude, frequency, wavelet, azimuth, SNR, and time difference; the data reconstruction method outperforms other methods in normalizing offset, azimuth, and SNR; and the time-shifted comparison method of the amplitude attribute ratio method proves more effective than the difference method. This study offers a reliable foundation for future time-shifted seismic research with non-repetitive data to monitor changes in subsurface oil and gas. It also provides a methodological basis for carbon capture and storage (CCS) monitoring technology.
WaterSAM: Adapting SAM for Underwater Object Segmentation
Authors: Hong Yang , Zhou Xiaowei , Hua Ruzhuang , Lv Qingxuan , Dong Junyu
Published: September 2024

Object segmentation, a key type of image segmentation, focuses on detecting and delineating individual objects within an image, essential for applications like robotic vision and augmented reality. Despite advancements in deep learning improving object segmentation, underwater object segmentation remains challenging due to unique underwater complexities such as turbulence diffusion, light absorption, noise, low contrast, uneven illumination, and intricate backgrounds. The scarcity of underwater datasets further complicates these challenges. The Segment Anything Model (SAM) has shown potential in addressing these issues, but its adaptation for underwater environments, AquaSAM, requires fine-tuning all parameters, demanding more labeled data and high computational costs. In this paper, we propose WaterSAM, an adapted model for underwater object segmentation. Inspired by Low-Rank Adaptation (LoRA), WaterSAM incorporates trainable rank decomposition matrices into the Transformer’s layers, specifically enhancing the image encoder. This approach significantly reduces the number of trainable parameters to 6.7% of SAM’s parameters, lowering computational costs. We validated WaterSAM on three underwater image datasets: COD10K, SUIM, and UIIS. Results demonstrate that WaterSAM significantly outperforms pre-trained SAM in underwater segmentation tasks, contributing to advancements in marine biology, underwater archaeology, and environmental monitoring.
Geometric Evaluation of the Hydro-Pneumatic Chamber of an Oscillating Water Column Wave Energy Converter Employing an Axisymmetric Computational Model Submitted to a Realistic Sea State Data
Authors: Pinto Júnior Édis Antunes , de Oliveira Sersana Sabedra , Oleinik Phelype Haron , Machado Bianca Neves , Rocha Luiz Alberto Oliveira , Gomes Mateus das Neves , dos Santos Elizaldo Domingues , Conde José Manuel Paixão , Isoldi Liércio André
Published: September 2024

In this research, considering the air methodology, an axisymmetric model was developed, validated, and calibrated for the numerical simulation of an Oscillating Water Column (OWC) converter subjected to a realistic sea state, representative of the Cassino beach, in the south of Brazil. To do so, the Finite Volume Method (FVM) was used, through the Fluent software (Version 18.1), for the airflow inside the hydro-pneumatic chamber and turbine duct of the OWC. Furthermore, the influence of geometric parameters on the available power of the OWC converter was evaluated through Constructal Design combined with Exhaustive Search. For this, a search space with 100 geometric configurations for the hydro-pneumatic chamber was defined by means of the variation in two degrees of freedom: the ratio between the height and diameter of the hydro-pneumatic chamber (H1/L1) and the ratio between the height and diameter of the smallest base of the connection, whose surface of revolution has a trapezoidal shape, between the hydro-pneumatic chamber and the turbine duct (H2/L2). The ratio between the height and diameter of the turbine duct (H3/L3) was kept constant. The results indicated that the highest available power of the converter was achieved by the lowest values of H1/L1 and highest values of H2/L2, with the optimal case being obtained by H1/L1 = 0.1 and H2/L2 = 0.81, achieving a power 839 times greater than the worst case. The values found are impractical in real devices, making it necessary to limit the power of the converters to 500 kW to make this assessment closer to reality; thus, the highest power obtained was 15.5 times greater than that found in the worst case, these values being consistent with other studies developed. As a theoretical recommendation for practical purposes, one can infer that the ratio H1/L1 has a greater influence over the OWC’s available power than the ratio H2/L2.
Metachromadora parobscura sp. nov. and Molgolaimus longicaudatus sp. nov. (Nematoda, Desmodoridae) from Mangrove Wetlands of China
Authors: Sun Jing , Huang Yong
Published: September 2024

Two new species of free-living marine nematodes, Metachromadora parobscura sp. nov. and Molgolaimus longicaudatus sp. nov., from mangrove wetlands of Beihai, Guangxi province in China, are described. Metachromadora parobscura sp. nov. is characterized by eight longitudinal rows of somatic setae arranged from the posterior part of the body, loop-shaped amphidial foveae with an open top and double contours, pharynx with bipartite cuticularized internal cavity, spicules with well-developed capitulum, gubernaculum canoe-shaped, without apophysis, 6–8 precloacal tubular supplements, and a short, conical tail with two ventral protuberances. It could be easily distinguished from the known species by spicule length and numbers of precloacal supplements. Molgolaimus longicaudatus sp. nov. is characterized by short cephalic setae, relatively small amphidial fovea, slender spicules ventrally bent with pronounced hooked capitulum and tapered distal end, two poriform precloacal supplements, and a relatively long conico-cylindrical tail. It differs from other species by the shape of spicules and long tail. Nearly full-length SSU sequences (1542–1592 bp) of the two species were provided, and phylogenetic trees based on maximum likelihood analyses supported the taxonomic position of the two new species. The combined use of traditional morphology-based taxonomy and molecular approaches has been proven to be a good choice for identification of free-living nematodes.
Genome-Wide Identification and Expression Analysis of the Cys2His2 Zinc Finger Protein Gene Family in Flammulina filiformis
Authors: Tong Zongjun , Han Xing , Duan Xinlian , Lin Junbin , Chen Jie , Xiao Jihong , Gan Ying , Gan Bingcheng , Yan Junjie
Published: September 2024

Zinc finger proteins (ZFPs) are essential transcription factors in eukaryotes, particularly the extensively studied C2H2 family, which is known for its involvement in various biological processes. This research provides a thorough examination and analysis of the C2H2-ZFP gene family in Flammulina filiformis. Using bioinformatics tools, 58 FfC2H2-ZFP genes spread across 11 chromosomes were identified and scrutinized in detail for their gene structures, protein characteristics, and phylogenetic relationships. The study of phylogenetics and synteny sheds light on the evolutionary relationships among C2H2-ZFPs in F. filiformis and other fungi, revealing a complex evolutionary past. The identification of conserved cis-regulatory elements in the gene promoter regions suggests intricate functionalities, particularly in the developmental and stress response pathways. By utilizing RNA-seq and qRT-PCR techniques, the expression patterns of these genes were explored across different developmental stages and tissues of F. filiformis, unveiling distinct expression profiles. Notably, significant expression variations were observed in the stipe elongation region and pilei of various sizes, indicating potential roles in fruiting body morphogenesis. This study enhances our knowledge of the C2H2-ZFP gene family in F. filiformis and lays the groundwork for future investigations into their regulatory mechanisms and applications in fungal biology and biotechnology.
The Absence of Typical Stroke Symptoms and Risk Factors Represents the Greatest Risk of an Incorrect Diagnosis in Stroke Patients
Authors: Jalali Rakesh , Bieniecka Aleksandra , Jankowski Marek , Michel Patryk Stanisław , Popielarczyk Marta , Majewski Mariusz Krzysztof , Zwiernik Jacek , Harazny Joanna Maria
Published: September 2024

Background: Stroke is one of the most misdiagnosed conditions that causes serious medical disabilities. Its early and accurate diagnosis by the emergency team is crucial for the patient’s survival. This study aimed to determine the percentage of brain strokes incorrectly diagnosed by paramedic teams and to analyze the factors influencing incorrect diagnoses. Methods: The data of 103 patients, mean age of 68.4 ± 14.96 years, admitted in 2019 to hospital emergency departments of the two hospitals in Olsztyn, Poland, were analyzed retrospectively. All patient data were obtained from their information cards. The parameters of the patients misdiagnosed and accurately diagnosed by paramedics were analyzed with Odds Ratio (OR) calculations using IBM SPSS version 23 software. Results: Stroke and transient ischemic attack were recognized in 77 cases (74.8%). In 26 patients (25.2%), the diagnosis made in the ambulance differed from that made in the hospital ward. The analysis of the Odds Ratio (OR) has shown that typical stroke risk factors, if present in a patient, facilitate the correct diagnosis. The greatest source of misdiagnosis of stroke by the paramedic team was the lack of hemiplegia (OR = 6.0). Conclusions: The absence of typical stroke risk factors and neurological stroke symptoms, such as smoking, hemiplegia, aphasia, hypercholesterolemia, arrhythmia, diabetes or a drooping corner of the mouth, constitutes a high risk of misdiagnosing stroke by the paramedic team.
Characterization of Tissue Immunity Defense Factors of the Lip in Primary Dentition Children with Bilateral Cleft Lip Palate
Authors: Ozola Laura , Pilmane Mara
Published: September 2024

Background: Bilateral cleft lip palate is a severe congenital birth defect of the mouth and face. Immunity factors modulate immune response, inflammation, and healing; therefore, they are vital in the assessment of the immunological status of the patient. The aim of this study is to assess the distribution of Gal-10, CD-163, IL-4, IL-6, IL-10, HBD-2, HBD-3, and HBD-4 in tissue of the bilateral cleft lip palate in primary dentition children. Methods: Five patients underwent cheiloplasty surgery, where five tissue samples of lip were obtained. Immunohistochemical staining, semi-quantitative evaluation, and non-parametric statistical analysis were used. Results: A statistically significant increase in HBD-2, HBD-3, and HBD-4 was found in skin and mucosal epithelium, hair follicles, and blood vessels. A notable increase was also noted in IL-4, IL-6, and IL-10 in the mucosal epithelium and CD163 in blood vessels. The connective tissue of patients presented with a statistically significant decrease in Gal-10, IL-10, and HBD-3. Spearman’s rank correlation revealed multiple significant positive and negative correlations between the factors. Conclusions: Upregulation of CD163 points to increased angiogenesis but the increase in IL-4 and IL-10 as well as the decrease in Gal-10 points to suppression of excessive inflammatory damage. Decreased connective tissue healing and excessive scarring are suggested by the decrease in HBD-3 and IL-10 and the increase in IL-6.
Assessing the Utility of Prediction Scores PAINT, ISARIC4C, CHIS, and COVID-GRAM at Admission and Seven Days after Symptom Onset for COVID-19 Mortality
Authors: Tanase Alina Doina , FNU Oktrian , Cristescu Dan-Mihai , Barata Paula Irina , David Dana , Petrescu Emanuela-Lidia , Bojoga Daliana-Emanuela , Hoinoiu Teodora , Blidisel Alexandru
Published: September 2024

The COVID-19 pandemic underscores the need for accurate prognostic tools to predict patient outcomes. This study evaluates the effectiveness of four prominent COVID-19 prediction scores—PAINT, ISARIC4C, CHIS, and COVID-GRAM—at two critical time points: at admission and seven days post-symptom onset, to assess their utility in predicting mortality among hospitalized patients. Conducted at the Clinical Emergency Hospital Pius Brînzeu in Timișoara, this retrospective analysis included adult patients hospitalized with confirmed SARS-CoV-2 infection. Eligible patients had complete data for the scores at both time points. Statistical analysis involved ROC curves and logistic regression to assess the scores’ predictive accuracy for mortality. The study included 215 patients, split into 139 survivors and 76 non-survivors. At admission, the PAINT, ISARIC4C, CHIS, and COVID-GRAM scores significantly differentiated between the survival outcomes (p < 0.0001). The best cutoff values at admission were 6.26 for PAINT, 7.95 for ISARIC4C, 5.58 for CHIS, and 0.63 for COVID-GRAM, corresponding to sensitivities of 85.47%, 80.56%, 88.89%, and 83.33% and specificities of 77.34%, 82.12%, 75.01%, and 78.45%, respectively. By day seven, the cutoff values increased, indicating deteriorating conditions in patients who eventually succumbed to the virus. The hazard ratios at admission for exceeding these cutoffs were significant: PAINT (HR = 3.45), ISARIC4C (HR = 2.89), CHIS (HR = 4.02), and COVID-GRAM (HR = 3.15), highlighting the scores’ abilities to predict severe outcomes. One week post symptom onset, these scores’ predictive values and corresponding hazard ratios increased, further validating their prognostic significance over time. The evaluated COVID-19 prediction scores robustly predict mortality at admission and become more predictive by the seventh day of symptom onset. These findings support the use of these scores in clinical settings to facilitate early identification and intervention for high-risk patients, potentially improving patient outcomes during the ongoing global health crisis.
Spatial and Seasonal Variation and the Driving Mechanism of the Thermal Effects of Urban Park Green Spaces in Zhengzhou, China
Authors: Feng Yuan , Zhang Kaihua , Li Ang , Zhang Yangyang , Wang Kun , Guo Nan , Wan Ho Yi , Tan Xiaoyang , Dong Nalin , Xu Xin , He Ruizhen , Wang Bing , Fan Long , Ge Shidong , Song Peihao
Published: September 2024

Greenscaping, a key sustainable practice, helps cities combat rising temperatures and climate change. Urban parks, a pivotal greenscaping element, mitigate the urban heat island (UHI) effect. In this study, we utilized high-resolution remote sensing imagery (GF-2 and Landsat 8, 9) and in situ measurements to analyze the seasonal thermal regulation of different park types in Zhengzhou, China. We calculated vegetation characteristic indices (VCIs) and landscape patterns (LMs) and employed boosted regression tree models to explore their relative contributions to land surface temperature (LST) across different seasons. Our findings revealed that urban parks lowered temperatures by 0.65 °C, 1.41 °C, and 2.84 °C in spring, summer, and autumn, respectively, but raised them by 1.92 °C in winter. Amusement parks, comprehensive parks, large parks, and water-themed parks had significantly lower LSTs. The VCI significantly influenced LST in autumn, with trees having a stronger cooling effect than shrubs. LMs showed a more prominent effect than VCIs on LST during spring, summer, and winter. Parks with longer perimeters, larger and more dispersed green patches, higher plant species richness, higher vegetation heights, and larger canopies were associated with more efficient thermal reduction in an urban setting. The novelty of this study lies in its detailed analysis of the seasonal thermal regulation effects of different types of urban parks, providing new insights for more effective urban greenspace planning and management. Our findings assist urban managers in mitigating the urban surface heat effect through more effective urban greenspace planning, vegetation community design, and maintenance, thereby enhancing cities’ potential resilience to climate change.
Reading and Memory Skills of Children with and without Dyslexia in Greek (L1) and English (L2) as a Second Language: Preliminary Results from a Cross-Linguistic Approach
Authors: Gkountakou Maria-Ioanna , Talli Ioanna
Published: September 2024

The focus of the present paper is twofold; the first objective is to examine how children with dyslexia (henceforward DYS children) and typically developing children (henceforward TD children) performed in Greek (first language; L1) compared to English (second language; L2) in reading, phonological awareness (PA), rapid automatized naming (RAN), working memory (WM), and short-term memory (STM) tasks. Our second goal is to investigate DYS children’s performance compared to that of TD children in the L1 and L2 domains mentioned above. Thirty-two (DYS = 16; TD = 16) school-aged children (9;7–11;9 years old; Mage = 130.41), basic users of English (level ranging from A1 to A2), carried out a battery test in L1 and L2, respectively, including reading, PA, STM, and WM tasks. More specifically, the tasks were the following: word and nonword decoding, reading accuracy and reading fluency, word and nonword reading per minute, PA, RAN, nonword repetition, as well as forward, backward, and digit span sequencing. This is a work-in-progress study, and preliminary results reveal that DYS students exhibit important reading and memory deficits in both languages. The data analysis indicated that DYS children have particular difficulties and statistically significant differences in L1 and L2 compared to TD in all tasks. In conclusion, this is the first study, at least in Greek, which assesses both reading and memory skills of DYS children in L2. The results reveal deficits in both languages, and the overall findings contribute to theories on the transfer of difficulties of linguistic skills between L1 and L2, while memory scores also underline this co-occurrence. Future implications of this study include a combination of reading and cognitive activities in the teaching methods of English teachers to improve DYS children’s overall performance in learning English as L2.
Comparative Tissue Identification and Characterization of Long Non-Coding RNAs in the Globally Distributed Blue Shark Prionace glauca
Authors: Bravo Scarleth , Zarate Patricia , Cari Ilia , Clavijo Ljubitza , Lopez Ignacio , Phillips Nicole M. , Vidal Rodrigo
Published: September 2024

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark (Prionace glauca) from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high-confidence lncRNAs were identified, with 8984 and 3067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations.