bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases
Authors: Brissos Vânia , Borges Patrícia T. , Sancho Ferran , Lucas Maria Fátima , Frazão Carlos , Conzuelo Felipe , Martins Lígia O. 
Published: January 2024

AbstractHyperthermophilic (‘superheat-loving’) archaea found in high-temperature environments such as Pyrobaculum aerophilum contain multicopper oxidases (MCOs) with remarkable efficiency for oxidizing cuprous and ferrous ions. In this work, directed evolution was used to expand the substrate specificity of P. aerophilum McoP for organic substrates. Six rounds of error-prone PCR and DNA shuffling followed by high-throughput screening lead to the identification of a hit variant with a 220-fold increased efficiency (kcat/Km) than the wild-type for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) without compromising its intrinsic activity for metal ions. The analysis of the X-ray crystal structure reveals four proximal mutations close to the T1Cu active site. One of these mutations is within the 23-residues loop that occludes this site, a distinctive feature of prokaryotic MCOs. The increased flexibility of this loop results in an enlarged tunnel and one additional pocket that facilitates bulky substrate-enzyme interactions. These findings underscore the synergy between mutations that modulate the dynamics of the active-site loop enabling enhanced catalytic function. This study highlights the potential of targeting loops close to the T1Cu for engineering improvements suitable for biotechnological applications.
Graphical Abstract
Development and Validation of a 3D Resnet Model for Prediction of Lymph Node Metastasis in Head and Neck Cancer Patients
Authors: Lin Yi-Hui , Lin Chieh-Ting , Chang Ya-Han , Lin Yen-Yu , Chen Jen-Jee , Huang Chun-Rong , Hsu Yu-Wei , You Weir-Chiang 
Published: January 2024

AbstractThe accurate diagnosis and staging of lymph node metastasis (LNM) are crucial for determining the optimal treatment strategy for head and neck cancer patients. We aimed to develop a 3D Resnet model and investigate its prediction value in detecting LNM. This study enrolled 156 head and neck cancer patients and analyzed 342 lymph nodes segmented from surgical pathologic reports. The patients’ clinical and pathological data related to the primary tumor site and clinical and pathology T and N stages were collected. To predict LNM, we developed a dual-pathway 3D Resnet model incorporating two Resnet models with different depths to extract features from the input data. To assess the model’s performance, we compared its predictions with those of radiologists in a test dataset comprising 38 patients. The study found that the dimensions and volume of LNM + were significantly larger than those of LNM-. Specifically, the Y and Z dimensions showed the highest sensitivity of 84.6% and specificity of 72.2%, respectively, in predicting LNM + . The analysis of various variations of the proposed 3D Resnet model demonstrated that Dual-3D-Resnet models with a depth of 34 achieved the highest AUC values of 0.9294. In the validation test of 38 patients and 86 lymph nodes dataset, the 3D Resnet model outperformed both physical examination and radiologists in terms of sensitivity (80.8% compared to 50.0% and 91.7%, respectively), specificity(90.0% compared to 88.5% and 65.4%, respectively), and positive predictive value (77.8% compared to 66.7% and 55.0%, respectively) in detecting individual LNM + . These results suggest that the 3D Resnet model can be valuable for accurately identifying LNM + in head and neck cancer patients. A prospective trial is needed to evaluate further the role of the 3D Resnet model in determining LNM + in head and neck cancer patients and its impact on treatment strategies and patient outcomes.
Detecting Avascular Necrosis of the Lunate from Radiographs Using a Deep-Learning Model
Authors: Wernér Krista , Anttila Turkka , Hulkkonen Sina , Viljakka Timo , Haapamäki Ville , Ryhänen Jorma 
Published: January 2024

AbstractDeep-learning (DL) algorithms have the potential to change medical image classification and diagnostics in the coming decade. Delayed diagnosis and treatment of avascular necrosis (AVN) of the lunate may have a detrimental effect on patient hand function. The aim of this study was to use a segmentation-based DL model to diagnose AVN of the lunate from wrist postero-anterior radiographs. A total of 319 radiographs of the diseased lunate and 1228 control radiographs were gathered from Helsinki University Central Hospital database. Of these, 10% were separated to form a test set for model validation. MRI confirmed the absence of disease. In cases of AVN of the lunate, a hand surgeon at Helsinki University Hospital validated the accurate diagnosis using either MRI or radiography. For detection of AVN, the model had a sensitivity of 93.33% (95% confidence interval (CI) 77.93–99.18%), specificity of 93.28% (95% CI 87.18–97.05%), and accuracy of 93.28% (95% CI 87.99–96.73%). The area under the receiver operating characteristic curve was 0.94 (95% CI 0.88–0.99). Compared to three clinical experts, the DL model had better AUC than one clinical expert and only one expert had higher accuracy than the DL model. The results were otherwise similar between the model and clinical experts. Our DL model performed well and may be a future beneficial tool for screening of AVN of the lunate.
Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis
Authors: Erban Tomas , Sopko Bruno , Klimov Pavel B. , Hubert Jan 
Published: January 2024

AbstractBlomia tropicalis is an allergen-producing mite in the human environment in tropical regions. The microbiome of B. tropicalis was described using the barcode sequencing region of V4 16S rDNA and genome assemblage. Mixta mediterraneensis, previously isolated from human skin swabs, was identified as a B. tropicalis gut symbiont based on genome assembly. The microbiome contains two bacteria, Staphylococcus and M. mediterraneensis. The number of M. mediterraneensis 16S DNA copies was 106 per mite and 109 per feces in the rearing chamber based on qPCR quantification. The profile of this bacterium reached 50% of reads in the mite gut and feces. Genomic analyses revealed that the bacterium has several metabolic pathways that suggest metabolic cooperation with the mite host in vitamin and amino acid synthesis, nitrogen recycling, and antimicrobial defense. Lysozyme is present in the symbiotic bacterium but absent in the mite. The B. tropicalis microbiome contained Staphylococcus, which accelerates mite population growth. Mites can digest Staphylococcus by using specific enzymes with hydrolytic functions against bacterial cell walls (chitinases and cathepsin D), leading to endocytosis of bacteria and their degradation in lysosomes and phagosomes. Gene expression analysis of B. tropicalis indicated that phagocytosis was mediated by the PI3-kinase/Akt pathway interacting with the invasins produced by M. mediterraneensis. Moreover, the symbiont had metabolic pathways that allowed it to recycle the mite metabolic waste product guanine, known as a mite attractant. The mite host symbiont enhances mite aggregation in the feces, and the fecal–oral transmission route is excepted.
Key Grazing Behaviours of Beef Cattle Identify Specific Genotypes of the Glutamate Metabotropic Receptor 5 Gene (GRM5)
Authors: Moreno García Cristian Anibal , Perelman Susana Beatríz , Dynes Robyn , Maxwell Thomas M. R. , Zhou Huitong , Hickford Jonathan 
Published: January 2024

AbstractGenotype-phenotype associations between the bovine genome and grazing behaviours measured over time and across contexts have been reported in the past decade, with these suggesting the potential for genetic control over grazing personalities in beef cattle. From the large array of metrics used to describe grazing personality behaviours (GP-behaviours), it is still unclear which ones are linked to specific genes. Our prior observational study has reported associations and trends towards associations between genotypes of the glutamate metabotropic receptor 5 gene (GRM5) and four GP-behaviours, yet the unbalanced representation of GRM5 genotypes occurring in observational studies may have limited the ability to detect associations. Here, we applied a subsampling technique to create a genotypically-balanced dataset in a quasi-manipulative experiment with free ranging cows grazing in steep and rugged terrain of New Zealand’s South Island. Using quadratic discriminant analysis, two combinations of eleven GP-behaviours (and a total of fifteen behaviours) were selected to build an exploration model and an elevation model, respectively. Both models achieved ∼ 86% accuracy in correctly discriminating cows’ GRM5 genotypes with the training dataset, and the exploration model achieved 85% correct genotype prediction of cows from a testing dataset. Our study suggests a potential pleiotropic effect, with GRM5 controlling multiple grazing behaviours, and with implications for the grazing of steep and rugged grasslands. The study highlights the importance of grazing behavioural genetics in cattle and the potential use of GRM5 markers to select individuals with desired grazing personalities and built herds that collectively utilize steep and rugged rangelands sustainably.
Evaluation of a virtual reality training tool for firefighters responding to transportation incidents with dangerous goods
Authors: Berthiaume Maxine , Kinateder Max , Emond Bruno , Cooper Natalia , Obeegadoo Ishika , Lapointe Jean-François 
Published: January 2024

AbstractAccess to dangerous goods training for firefighters in remote areas is limited for financial and logistical reasons. Virtual reality (VR) is a promising solution for this challenge as it is cost-effective, safe, and allows to simulate realistic scenarios that would be dangerous or difficult to implement in the real world. However, rigorous evaluations of VR training tools for first responders are still scarce. In this exploratory user study, a simple VR training tool involving two dangerous goods scenarios was developed. In each scenario, trainees learned how to safely approach a jackknifed truck with a trailer and how to collect and communicate information about the transported materials. The tool was tested with a group of 24 professional firefighter trainees (n = 22) and instructors (n = 2), who each completed the two training scenarios. The main goal of the study was to assess the usability of the VR tool in the given scenarios. Participants provided feedback on cybersickness, perceived workload, and usability. They also filled out a knowledge test before and after the VR training and gave feedback at the end of the study. The VR tool recorded task completion duration and participants’ navigation and use of tools events. Overall, the tool provided good usability, acceptance, and satisfaction. However, a wide range in individuals’ responses was observed. In addition, no post-training improvement in participants' knowledge was found, likely due to the already high level of knowledge pre-training. Future directions for improving the VR tool, general implications for other VR training tools, and suggestions for future research are discussed.
Mountain masses as a determinant to genetic structure of char distributed in the Chugoku region, Japan
Authors: Kawai Koichiro , Matsuo Mahiro , Fujiwara Kazuki , Tani Shotaro , Tada Shohei , Saito Hidetoshi 
Published: January 2024

AbstractA mountain mass from which multiple river basins originate is a possible determinant of genetic structure of freshwater fishes. In this study, subspecies composition and genetic structure were examined for Japanese white-spotted char comprising of two subspecies, Salvelinus leucomaenis imbrius (Jordan and McGregor), “Gogi,” and S. l. pluvius (Hilgendorf), “Nikkoiwana,” collected in the 19 river basins originating from 6 mountain masses in the Chugoku Region, Japan, based on mitochondrial DNA sequences. In the western mountain masses, only Gogi was collected, while in the eastern mountain mass, only Nikkoiwana was collected. A total of 27 haplotypes were detected, among which only seven were shared by two subspecies and three were detected only in Nikkoiwana whereas 17 were detected only in Gogi. As many as 11 haplotypes were distributed only in the Oyorogi Mountain mass in the middle region. In the network, one group was exclusively constructed by the samples from the Oyorogi Mountain mass. Furthermore, in a tree of river basins based on average genetic distance of char, the Gono River basin originating from the Asa Mountain mass, situated in the western region, participated in a clade constructed by the rivers originating from the westernmost Sukegatake and the adjacent Asa Mountain masses, whereas the Gono River basin originating from the Oyorogi Mountain mass participated in a different clade constructed by the rivers originating from the Oyorogi to the easternmost Hyonosen Mountain masses. These results suggest that a mountain mass is a determinative factor to subspecies composition and genetic structure of char, with an implication of invasion of fish taking advantage of some geological events or conditions.
Semi-continuous cultivation for enhanced protein production using indigenous green microalgae and synthetic municipal wastewater
Authors: Umetani Ikumi , Sposób Michał , Tiron Olga 
Published: January 2024

AbstractCultivation of microalgae has gained significant interest as an alternative protein source, potentially becoming a target commodity recovered from microalgae-based wastewater treatment. This study examined a semi-continuous cultivation strategy to optimize protein accumulation of the indigenous freshwater chlorophytes, Lobochlamys segnis and Klebsormidium flaccidum, and simultaneously remove nutrients from wastewater efficiently. A strain-specific regime was made based on a fixed biomass concentration at the start of 24-h cultivation cycle, i.e., a constant initial cell density, which regulated harvesting and fresh medium supply volume according to the dilution rate. Six cultivation cycles were conducted in lab-scale 1L reactors with a synthetic municipal wastewater. Lobochlamys segnis and K. flaccidum grew exponentially in all cycles. The biomass productivity was 573 and 580 mg L–1 day–1, in which the total protein consisted of 62 and 45% of dry cell weight (dw), respectively. When a culture medium deficient in nitrogen and phosphorus was used, protein level was significantly reduced. L. segnis consumed all NH4+ and PO43– supplied by the medium replacement, giving the removal rate of 9.2 and 5.2 mg L–1 day–1. Whereas K. flaccidum removed 13.8 mg L–1 day–1 NH4+ without completing PO43– removal. The amino acid profile of both strains was characterized by glutamic acids content (4–5% dw). We concluded that the designed cultivation regime would support a constant biomass production with stable and high protein content, along with an efficient removal of nutrient from the wastewater.
A Hebrew Fragment in the Municipal Archive in Münster as a Witness to a Little-Known Ritual Practice
Authors: Kanarfogel Ephraim , Kogman-Appel Katrin 
Published: January 2024

AbstractThe Stadtarchiv in Münster, Germany holds a medieval Hebrew fragment with portions of the daily Shema Yisrael prayer. Measuring 510 mm in height, this fragment is but a quarter of a large-sized parchment sheet, which was designed to be hung on a wall. This study introduces the fragment and describes its material features and then suggests its possible function against the backdrop of talmudic discussions on biblical texts that are incorporated in prayer. In light of the halakhic position that biblical verses should not be recited from memory but only from a written text, the original sheet was intended to provide worshippers with an accessible copy of the Shema text, since many did not have personal prayerbooks.
Source parameters and scaling relationships of stress drop for shallow crustal seismic events in Western Europe
Authors: Yen Ming-Hsuan , Bindi Dino , Oth Adrien , Edwards Ben , Zaccarelli Riccardo , Cotton Fabrice 
Published: January 2024

AbstractFor an ω2-source model, moment-based estimates of the stress drop are obtained by combining corner frequency and seismic moment source parameters. Therefore, the moment-based estimates of the stress drop are informative about the amount of energy radiated at high frequencies by dynamic rupture processes. This study aims to systematically estimate such stress drop from the harmonized dataset at the European scale and to characterize the distributions of the stress drop for application in future stochastic simulations. We analyze the seismological records associated with shallow crustal seismic events that occurred in Western Europe between January 1990 and May 2020. We processed 220,000 high-quality records and isolated the contributions of the source, site, and path contributions using the Generalized Inversion Technique. The source parameters, including the corner frequency, moment magnitude, and stress drop, of 6135 seismic events are calculated. The events processed are mainly tectonic events (e.g., earthquakes of the central Italy 2009–2016 sequence), although non-tectonic events associated with the Groningen gas field and mining activities in Western Europe are also included in the analysis. The impact of different attenuation models and reference site choices are evaluated. Most of the obtained source spectra follow the standard ω2-model except for a few events where the data sampling considered does not allow an effective spectral decomposition. The resulting stress drop shows a positive correlation with moment magnitude between 3 and 4, and a self-similarity for magnitudes greater than 4 with a mean stress drop of 13.8 MPa.
Designing hardware for a robust high-speed cryptographic key generator based on multiple chaotic systems and its FPGA implementation for real-time video encryption
Authors: İnce Esra , Karakaya Barış , Türk Mustafa 
Published: January 2024

AbstractRecent advancements in communication technologies have highlighted the pivotal role of information security for all individuals and entities. In response, researchers are increasingly focusing on cryptographic solutions to ensure the reliability of confidential information. Recognizing the superiority of chaotic systems preference as entropy source of cryptographic systems, this paper proposes a novel true random number generator (TRNG) design by combining four different chaotic systems outputs, tailored for real-time video encryption application. These chaotic systems are continuous-time Lorenz and fractional-order Chen-Lee systems, as well as discrete-time Logistic and Tent maps. This study generates true random bit (TRB) sequences at a high bit rate (25 Mbps) through the hardware implementations of four distinct chaotic systems to have the best statistical randomness in the resulting output. Then, the cryptographic true random key bits (8-bit at 25 MHz frequency) are employed in the post-processing with real-time video data by using the XOR operation, a fundamental post-processing algorithm. The real-time video encryption application is executed on an experimental assembly, composed of a Field Programmable Gate Array (FPGA) development kit, an OV7670 camera module, a VGA monitor, and prototype circuit boards for the chaotic systems. To evaluate the effectiveness of the proposed encryption system, several security assessments are conducted. These include NIST SP 800 − 22 statistical tests, FIPS 140-1 standards, chi-square tests, histogram and correlation analysis, and NPCR and UACI differential attack resilience tests. Consequently, the findings suggest that the presented real-time embedded cryptosystem is robust and suitable for secure communications, particularly in the realm of video transmission.
Vital signs estimation in elderly using camera-based photoplethysmography
Authors: Caroppo Andrea , Manni Andrea , Rescio Gabriele , Siciliano Pietro , Leone Alessandro 
Published: January 2024

AbstractIn the context of Ambient Assisted Living, the demand for healthcare technologies development has been increased in the last two years by the current global health situation. The contagious nature of COVID-19 warrants inevitability to the thought of easing a continuous measurement of vital signs such as Heart Rate, Breath Rate, and SpO2 in a non-invasive manner, contributing of fundamental importance in the assessment of health status especially among frail and/or elderly individuals. A widely diffused method for contactless vital signs monitoring is remote photoplethysmography from facial video streams that, contrary to traditional contact measurement techniques, allows the measurement of vital parameters without the need for wearable sensors (generally considered uncomfortable, especially by the elderly), even with commercial and low-cost digital cameras. This paper proposes the design and implementation of a new pipeline for estimating Heart Rate, Breath Rate, and SpO2 values, and its integration on Raspberry Pi 4 as an elaboration unit. The pipeline provides specific algorithmic blocks to improve vital signs estimation in elderly subjects as it is made more difficult by the skin tone and the presence on the face of wrinkles, folds, and moles. Quantitative evaluations on our dataset containing the acquisition of only elderly older than 65 years of age demonstrate the validity of the proposed pipeline. For validation against the state of the art, tests were also conducted on three standard benchmark datasets containing video with subjects of varying ages. Again, the pipeline proved to be robust concerning the estimation of vital signs considered in the present work.
Predefined-time VFO control design for unicycle-like mobile robots
Authors: Sobański Rafał M. , Michałek Maciej M. , Defoort Michael 
Published: January 2024

AbstractThe paper presents a predefined-time Vector-Field-Orientation (VFO) control law for unicycle-like nonholonomic mobile robots. We consider a set-point control problem in the presence of strict time constraints, which has to guarantee satisfaction of a prescribed upper bound of the settling time for the configuration errors. The control law is based on the VFO methodology, which is characterized by non-oscillatory and well-predictable time evolution of transient states for unicycle-like robots. A formal stability analysis based on the Lyapunov theory is provided for the closed-loop dynamics. Then, the results of extensive numerical simulations as well as experimental tests illustrate the resultant control performance where time constraints are considered. The proposed approach is compared with an alternative predefined-time stabilizer, recently introduced for nonholonomic chained-form systems.