bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoengineered chitosan functionalized titanium dioxide biohybrids for bacterial infections and cancer therapy
Authors: Shabib Akhtar Mohammad , Chandrasekaran Karthikeyan , Saminathan Sharmila , Rajalingam Siva Ranjani , Mohsin Nehal , Awad Alkarem Ahmed Khalid Altigani , Alhazmi Yasir , Walbi Ismail A. , Abdel-Wahab Basel A. , Gholap Amol D. , Faiyazuddin Md. , Sundaram Gowri 
Published: February 2024

AbstractNanoengineered chitosan functionalized titanium dioxide biohybrids (CTiO2@NPs) were prepared with Amomum subulatum Roxb extract via one-pot green method and assessed by UV–Vis spectroscopy, XRD, SEM and EDAX analyses. As revealed by XRD pattern, the nanohybrids exhibits a rutile TiO2 crystallites around 45 nm in size. The emergence of the Ti–O–Ti bond is identified by observing a peak between 400 and 800 cm−1. A wide bandgap (4.8 eV) has been observed in CTiO2@NPs, due to the quantum confinement effects and the oxygen vacancies reveal the intriguing potential of developed nanohybrids for various applications. Surface flaws were identified by observing an emission band at 382, 437, 482, 517, and 556 nm. They also exhibit better antibacterial performances using well diffusion method against Staphylococcus aureus, Bacillus substilis, Klebsiella pneumonia, and Escherichia coli. CTiO2@NPs were discovered to have free radical scavenging activity on DPPH analysis and exhibit IC50 value as 95.80 μg/mL and standard (Vitamin C) IC50 is 87.62 μg/mL. CTiO2@NPs exhibited better anticancer properties against the osteosarcoma (MG-63) cell line. All these findings suggest that there is a forum for further useful therapeutic applications. Therefore, we claim that nano-engineered carbohydrated TiO2 phytohybrid is a promising solution for bacterial infections and bone cancer.
Monte Carlo simulations of spherocylinders interacting with site-dependent square-well potentials
Authors: Yellam Kiranmai , Priyadarshi Anshuman , Jha Prateek K. 
Published: February 2024

AbstractMonte Carlo simulations are performed to study the self-assembly of a dilute system of spherocylinders interacting with square-well potential. The interactions are defined between randomly placed sites on the axis of the spherocylinder, akin to the interacting groups on a rigid rodlike molecule. This model therefore also serves as a minimal coarse-grained representation of a system of low molecular weight or stiff polymers with contour lengths significantly lower than the persistence length, interacting predominantly with short-range interactions (e.g., hydrogen bonding). The spherocylinder concentration, square-well interaction strength and range, and fraction of interacting sites are varied to study the phase behavior of the system. We observe the formation of dispersed, bundled, and network configurations of the system that may be compared with previous atomistic simulation results of weak polyelectrolytes.
Apolipoprotein L1 (APOL1) renal risk variant-mediated podocyte cytotoxicity depends on African haplotype and surface expression
Authors: Gupta Nidhi , Waas Bridget , Austin Daniel , De Mazière Ann M. , Kujala Pekka , Stockwell Amy D. , Li Tianbo , Yaspan Brian L. , Klumperman Judith , Scales Suzie J. 
Published: February 2024

AbstractHomozygous Apolipoprotein L1 (APOL1) variants G1 and G2 cause APOL1-mediated kidney disease, purportedly acting as surface cation channels in podocytes. APOL1-G0 exhibits various single nucleotide polymorphisms, most commonly haplotype E150K, M228I and R255K (“KIK”; the Reference Sequence is “EMR”), whereas variants G1 and G2 are mostly found in a single “African” haplotype background (“EIK”). Several labs reported cytotoxicity with risk variants G1 and G2 in KIK or EIK background haplotypes, but used HEK-293 cells and did not verify equal surface expression. To see if haplotype matters in a more relevant cell type, we induced APOL1-G0, G1 and G2 EIK, KIK and EMR at comparable surface levels in immortalized podocytes. G1 and G2 risk variants (but not G0) caused dose-dependent podocyte death within 48h only in their native African EIK haplotype and correlated with K+ conductance (thallium FLIPR). We ruled out differences in localization and trafficking, except for possibly greater surface clustering of cytotoxic haplotypes. APOL1 surface expression was required, since Brefeldin A rescued cytotoxicity; and cytoplasmic isoforms vB3 and vC were not cytotoxic. Thus, APOL1-EIK risk variants kill podocytes in a dose and haplotype-dependent manner (as in HEK-293 cells), whereas unlike in HEK-293 cells the KIK risk variants did not.
Changes of physicochemical and functional properties of processed cheese made with natural cheddar and mozzarella cheeses during refrigerated storage
Authors: Liu Tongji , Wu Jingwei , Aziz Tariq , Xue Rui , Khowdiary Manal M. , Yang Zhennai 
Published: February 2024

AbstractThe present study aimed to investigate changes of physicochemical and functional properties of the processed cheeses (PCs) made with Cheddar (PC1), Mozzarella (PC2) and both of them at a ratio of 1:1 (PC3) during storage at 4 °C for 4 months. The results showed that the type of natural cheese used affected the composition of PCs with lower fat content in PC2 due to the lower fat content of Mozzarella cheese used. PC2 with lower fat content showed decreased meltability and oil leakage compared with PC1 and PC3. The stretchability of all the samples significantly (P < 0.05) decreased during storage, and PC1 showed lower stretchability. This was confirmed by increased protein hydrolysis of all the samples during the storage with a higher level of proteolysis in PC1, leading to decreased stretchability of PCs. Further low-field nuclear magnetic resonance analysis indicated more entrapped water in cheese due to moisture migration into the cheese matrix that might squeeze the fat globules to aggregate, causing more fat leakage during later stages of storage. This was evidenced by microstructural analysis showing different extents of increase in fat particle sizes and decrease in free serum in all the PC samples over the storage time. Therefore, the present study provides further understanding of the mechanism of quality change of PC during refrigerated storage as affected by proteolytic properties and composition of natural cheese used.
Bifidobacterium longum 1714 improves sleep quality and aspects of well-being in healthy adults: a randomized, double-blind, placebo-controlled clinical trial
Authors: Patterson Elaine , Tan Hern Tze Tina , Groeger David , Andrews Mark , Buckley Martin , Murphy Eileen F. , Groeger John A. 
Published: February 2024

AbstractStress and sleep are linked with overall well-being.Bifidobacterium longum1714 has been shown to influence stress responses and modulate neural responses during social stress, and influence sleep quality during examination stress in healthy adults. Here, we explored the ability of this strain to alter sleep quality in adults using subjective and objective measures. Eighty-nine adults (18–45y) with impaired sleep quality assessed with the Pittsburgh Sleep Quality Index (PSQI) and with a global score ≥ 5 were randomized to receiveB. longum1714 or placebo daily for eight weeks. Assessing the effect of the strain on PSQI global score was the primary objective. Secondary objectives assessed sleep quality and well-being subjectively and sleep parameters using actigraphy objectively. While PSQI global score improved in both groups,B. longum1714 significantly improved the PSQI component of sleep quality (p < 0.05) and daytime dysfunction due to sleepiness (p < 0.05) after 4 weeks and social functioning (p < 0.05) and energy/vitality (p < 0.05) after 8 weeks, compared to placebo. No significant effect on actigraphy measures were observed. The 1714 strain had a mild effect on sleep, demonstrated by a faster improvement in sleep quality at week 4 compared to placebo, although overall improvements after 8 weeks were similar in both groups.B. longum1714 improved social functioning and increased energy/vitality in line with previous work that showed the strain modulated neural activity which correlated with enhanced vitality/reduced mental fatigue (ClinicalTrials.gov: NCT04167475).
Immunological mechanisms of the nucleocapsid protein in COVID-19
Authors: Edalat Fahime , Khakpour Niloofar , Heli Hossein , Letafati Arash , Ramezani Amin , Hosseini Seyed Younes , Moattari Afagh 
Published: February 2024

AbstractThe emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
An open-source, 3D printed inkjet DNA synthesizer
Authors: Kim Junhyeong , Kim Haeun , Bang Duhee 
Published: February 2024

AbstractSynthetic oligonucleotides have become a fundamental tool in a wide range of biological fields, including synthetic biology, biosensing, and DNA storage. Reliable access to equipment for synthesizing high-density oligonucleotides in the laboratory ensures research security and the freedom of research expansion. In this study, we introduced the Open-Source Inkjet DNA Synthesizer (OpenIDS), an open-source inkjet-based microarray synthesizer that offers ease of construction, rapid deployment, and flexible scalability. Utilizing 3D printing, Arduino, and Raspberry Pi, this newly designed synthesizer achieved robust stability with an industrial inkjet printhead. OpenIDS maintains low production costs and is therefore suitable for self-fabrication and optimization in academic laboratories. Moreover, even non-experts can create and control the synthesizer with a high degree of freedom for structural modifications. Users can easily add printheads or alter the design of the microarray substrate according to their research needs. To validate its performance, we synthesized oligonucleotides on 144 spots on a 15 × 25-mm silicon wafer filled with controlled pore glass. The synthesized oligonucleotides were analyzed using urea polyacrylamide gel electrophoresis.
Airborne imagery does not preclude detectability issues in estimating bird colony size
Authors: Couturier Thibaut , Gaillard Laurie , Vadier Almodis , Dautrey Emilien , Mathey Jérôme , Besnard Aurélien 
Published: February 2024

AbstractAerial images obtained by drones are increasingly used for ecological research such as wildlife monitoring. Yet detectability issues resulting from animal activity or visibility are rarely considered, although these may lead to biased population size and trend estimates. In this study, we investigated detectability in a census of Malagasy pond heron Ardeola idae colonies on the island of Mayotte. We conducted repeated drone flights over breeding colonies in mangrove habitats during two breeding seasons. We then identified individuals and nests in the images and fitted closed capture-recapture models on nest-detection histories. We observed seasonal variation in the relative abundance of individuals, and intra-daily variation in the relative abundance of individuals—especially immature birds—affecting the availability of nests for detection. The detection probability of nests estimated by capture–recapture varied between 0.58 and 0.74 depending on flyover days and decreased 25% from early to late morning. A simulation showed that three flyovers are necessary to detect a 5–6% decline in colonies of 50 to 200 nests. These results indicate that the detectability of nests of forest-canopy breeding species from airborne imagery can vary over space and time; we recommend the use of capture-recapture methods to control for this bias.
Spatial sequestration of activated-caspase 3 in aggresomes mediates resistance of neuroblastoma cell to bortezomib treatment
Authors: Berthenet Kévin , Aïmontché Eliézer , El Mrini Sara , Brière Johan , Pion Nathalie , Iacono Isabelle , Brejon Stéphanie , Monier Karine , Catez Frédéric , Ichim Gabriel , Combaret Valérie , Mertani Hichem C. , Diaz Jean-Jacques , Albaret Marie Alexandra 
Published: February 2024

AbstractNeuroblastoma (NB) is the most common pediatric tumor and is currently treated by several types of therapies including chemotherapies, such as bortezomib treatment. However, resistance to bortezomib is frequently observed by mechanisms that remain to be deciphered. Bortezomib treatment leads to caspase activation and aggresome formation. Using models of patients-derived NB cell lines with different levels of sensitivity to bortezomib, we show that the activated form of caspase 3 accumulates within aggresomes of NB resistant cells leading to an impairment of bortezomib-induced apoptosis and increased cell survival. Our findings unveil a new mechanism of resistance to chemotherapy based on an altered subcellular distribution of the executioner caspase 3. This mechanism could explain the resistance developed in NB patients treated with bortezomib, emphasizing the potential of drugs targeting aggresomes.
An animal study on the effectiveness of platelet-rich plasma as a direct pulp capping agent
Authors: Elkady Dina M. , Helaly Yara R. , El Fayoumy Hala W. , AbuBakr Huda O. , Yassin Aya M. , AbdElkader Naglaa A. , Farag Dina B. E. , El Aziz Possy M. Abd , Scarano Antonio , Khater Ahmad G. A. 
Published: February 2024

AbstractDirect pulp capping (DPC) is a conservative approach for preserving tooth vitality without requiring more invasive procedures by enhancing pulp healing and mineralized tissue barrier formation. We investigated the effectiveness of Platelet Rich Plasma (PRP) vs. Mineral Trioxide Aggregate (MTA) as a DPC agent. Forty-two teeth from three mongrel dogs were divided into two equal groups. After three months, the animals were sacrificed to evaluate teeth radiographically using cone-beam computerized tomography, histopathologically, and real-time PCR for dentin sialophosphoprotein (DSPP), matrix extracellular phosphoglycoprotein (MEPE), and nestin (NES) mRNA expression. Radiographically, hard tissue formation was evident in both groups without significant differences (p = 0.440). Histopathologic findings confirmed the dentin bridge formation in both groups; however, such mineralized tissues were homogenous without cellular inclusions in the PRP group, while was osteodentin type in the MTA group. There was no significant difference in dentin bridge thickness between the PRP-capped and MTA-capped teeth (p = 0.732). The PRP group had significantly higher DSPP, MEPE, and NES mRNA gene expression than the MTA group (p < 0.05). In conclusion, PRP enables mineralized tissue formation following DPC similar to MTA, and could generate better cellular dentinogenic responses and restore dentin with homogenous architecture than MTA, making PRP a promising alternative DPC agent.
Assessment of deep learning segmentation for real-time free-breathing cardiac magnetic resonance imaging at rest and under exercise stress
Authors: Schilling Martin , Unterberg-Buchwald Christina , Lotz Joachim , Uecker Martin 
Published: February 2024

AbstractIn recent years, a variety of deep learning networks for cardiac MRI (CMR) segmentation have been developed and analyzed. However, nearly all of them are focused on cine CMR under breathold. In this work, accuracy of deep learning methods is assessed for volumetric analysis (via segmentation) of the left ventricle in real-time free-breathing CMR at rest and under exercise stress. Data from healthy volunteers (n = 15) for cine and real-time free-breathing CMR at rest and under exercise stress were analyzed retrospectively. Exercise stress was performed using an ergometer in the supine position. Segmentations of two deep learning methods, a commercially available technique (comDL) and an openly available network (nnU-Net), were compared to a reference model created via the manual correction of segmentations obtained with comDL. Segmentations of left ventricular endocardium (LV), left ventricular myocardium (MYO), and right ventricle (RV) are compared for both end-systolic and end-diastolic phases and analyzed with Dice’s coefficient. The volumetric analysis includes the cardiac function parameters LV end-diastolic volume (EDV), LV end-systolic volume (ESV), and LV ejection fraction (EF), evaluated with respect to both absolute and relative differences. For cine CMR, nnU-Net and comDL achieve Dice’s coefficients above 0.95 for LV and 0.9 for MYO, and RV. For real-time CMR, the accuracy of nnU-Net exceeds that of comDL overall. For real-time CMR at rest, nnU-Net achieves Dice’s coefficients of 0.94 for LV, 0.89 for MYO, and 0.90 for RV and the mean absolute differences between nnU-Net and the reference are 2.9 mL for EDV, 3.5 mL for ESV, and 2.6% for EF. For real-time CMR under exercise stress, nnU-Net achieves Dice’s coefficients of 0.92 for LV, 0.85 for MYO, and 0.83 for RV and the mean absolute differences between nnU-Net and reference are 11.4 mL for EDV, 2.9 mL for ESV, and 3.6% for EF. Deep learning methods designed or trained for cine CMR segmentation can perform well on real-time CMR. For real-time free-breathing CMR at rest, the performance of deep learning methods is comparable to inter-observer variability in cine CMR and is usable for fully automatic segmentation. For real-time CMR under exercise stress, the performance of nnU-Net could promise a higher degree of automation in the future.
The effect of a startle-eliciting device on the foraging success of individual harbor seals (Phoca vitulina)
Authors: McKeegan Kathleen A. , Clayton Kate , Williams Rob , Ashe Erin , Reiss Stephanie , Mendez-Bye Andrea , Janik Vincent M. , Goetz Thomas , Zinkgraf Matthew , Acevedo-Gutiérrez Alejandro 
Published: February 2024

AbstractPinniped predation on commercially and ecologically important prey has been a source of conflict for centuries. In the Salish Sea, harbor seals (Phoca vitulina) are suspected of impeding the recovery of culturally and ecologically critical Pacific salmon (Oncorhynchus spp.). In Fall 2020, a novel deterrent called Targeted Acoustic Startle Technology (TAST) was deployed at Whatcom Creek to deter harbor seals from preying on fall runs of hatchery chum (O. keta) and Chinook (O. tshawytscha) salmon in Bellingham, Washington, USA. Field observations were conducted in 2020 to compare the presence and foraging success of individual harbor seals across sound exposure (TAST-on) and control (TAST-off) conditions. Observations conducted the previous (2019) and following (2021) years were used to compare the effects observed in 2020 to two control years. Using photo-identification, individual seals were associated with foraging successes across all 3 years of the study. Generalized linear mixed models showed a significant 45.6% reduction in the duration (min) individuals remained at the creek with TAST on, and a significant 43.8% reduction in the overall foraging success of individuals. However, the observed effect of TAST varied across individual seals. Seals that were observed regularly within one season were more likely to return the year after, regardless of TAST treatment. Generalized linear models showed interannual variation in the number of seals present and salmon consumed. However, the effect of TAST in 2020 was greater than the observed variation across years. Our analyses suggest TAST can be an effective tool for managing pinniped predation, although alternate strategies such as deploying TAST longer-term and using multi-unit setups to increase coverage could help strengthen its effects. Future studies should further examine the individual variability found in this study.
Explainable hybrid vision transformers and convolutional network for multimodal glioma segmentation in brain MRI
Authors: Zeineldin Ramy A. , Karar Mohamed E. , Elshaer Ziad , Coburger Jan , Wirtz Christian R. , Burgert Oliver , Mathis-Ullrich Franziska 
Published: February 2024

AbstractAccurate localization of gliomas, the most common malignant primary brain cancer, and its different sub-region from multimodal magnetic resonance imaging (MRI) volumes are highly important for interventional procedures. Recently, deep learning models have been applied widely to assist automatic lesion segmentation tasks for neurosurgical interventions. However, these models are often complex and represented as “black box” models which limit their applicability in clinical practice. This article introduces new hybrid vision Transformers and convolutional neural networks for accurate and robust glioma segmentation in Brain MRI scans. Our proposed method, TransXAI, provides surgeon-understandable heatmaps to make the neural networks transparent. TransXAI employs a post-hoc explanation technique that provides visual interpretation after the brain tumor localization is made without any network architecture modifications or accuracy tradeoffs. Our experimental findings showed that TransXAI achieves competitive performance in extracting both local and global contexts in addition to generating explainable saliency maps to help understand the prediction of the deep network. Further, visualization maps are obtained to realize the flow of information in the internal layers of the encoder-decoder network and understand the contribution of MRI modalities in the final prediction. The explainability process could provide medical professionals with additional information about the tumor segmentation results and therefore aid in understanding how the deep learning model is capable of processing MRI data successfully. Thus, it enables the physicians’ trust in such deep learning systems towards applying them clinically. To facilitate TransXAI model development and results reproducibility, we will share the source code and the pre-trained models after acceptance athttps://github.com/razeineldin/TransXAI.