bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of flexibility of protein backbone in simulations of protein–ligand interactions using steered molecular dynamics
Authors: Truong Duc Toan , Ho Kiet , Pham Dinh Quoc Huy , Chwastyk Mateusz , Nguyen-Minh Thai , Nguyen Minh Tho 
Published: May 2024

AbstractTo ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein’s heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
A comparative study of an on premise AutoML solution for medical image classification
Authors: Elangovan Kabilan , Lim Gilbert , Ting Daniel 
Published: May 2024

AbstractAutomated machine learning (AutoML) allows for the simplified application of machine learning to real-world problems, by the implicit handling of necessary steps such as data pre-processing, feature engineering, model selection and hyperparameter optimization. This has encouraged its use in medical applications such as imaging. However, the impact of common parameter choices such as the number of trials allowed, and the resolution of the input images, has not been comprehensively explored in existing literature. We therefore benchmark AutoKeras (AK), an open-source AutoML framework, against several bespoke deep learning architectures, on five public medical datasets representing a wide range of imaging modalities. It was found that AK could outperform the bespoke models in general, although at the cost of increased training time. Moreover, our experiments suggest that a large number of trials and higher resolutions may not be necessary for optimal performance to be achieved.
Gold nanostructure-enhanced immunosensing: ultra-sensitive detection of VEGF tumor marker for early disease diagnosis
Authors: Yarjoo Sadaf , Siampour Hossein , Khalilipour Mehrsa , Sajedi Reza H. , Bagheri Hassan , Moshaii Ahmad 
Published: May 2024

AbstractWe present an advanced electrochemical immunosensor designed to detect the vascular endothelial growth factor (VEGF) precisely. The sensor is constructed on a modified porous gold electrode through a fabrication process involving the deposition of silver and gold on an FTO substrate. Employing thermal annealing and a de-alloying process, the silver is eliminated from the electrode, producing a reproducible porous gold substrate. Utilizing a well-defined protocol, we immobilize the heavy-chain (VHH) antibody against VEGF on the gold substrate, facilitating VEGF detection through various electrochemical methods. Remarkably, this immunosensor performs well, featuring an impressive detection limit of 0.05 pg/mL and an extensive linear range from 0.1 pg/mL to 0.1 µg/mL. This emphasizes it’s to measure biomarkers across a wide concentration spectrum precisely. The robust fabrication methodology in this research underscores its potential for widespread application, offering enhanced precision, reproducibility, and remarkable detection capabilities for the developed immunosensor.
Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes
Authors: Luo Diou , Ottesen Eric W. , Lee Ji Heon , Singh Ravindra N. 
Published: May 2024

AbstractSpinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A–2B–3–4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A–2B–3–4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4172 genes) by C2A–2B–3–4. About half of the affected genes by C2A–2B–3–4 remained unaffected by L2A–2B–3–4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/2. These findings underscore the unique role of the structural context of C2A–2B–3–4 in gene regulation. A surprisingly high number of upregulated genes by C2A–2B–3–4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/2 transcripts, C2A–2B–3–4 and L2A–2B–3–4 upregulated and downregulated SMN1/2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A–2B–3–4 with very limited overlap with those affected by L2A–2B–3–4. Independent validations confirmed the effect of C2A–2B–3–4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A–2B–3–4, and expands our understanding of functions of SMN1/2 genes.
Continuous monitoring using thermography can capture the heat oscillations maintaining body temperature in neonates
Authors: Morimoto Aya , Nakamura Shinji , Koyano Kosuke , Nishisho Sae , Nakao Yasuhiro , Arioka Makoto , Inoue Kota , Inoue Eri , Nishioka Katsufumi , Morita Hirosuke , Konishi Yukihiko , Hirao Konomu , Kusaka Takashi 
Published: May 2024

AbstractThe body temperature of infants at equilibrium with their surroundings is balanced between heat production from metabolism and the transfer of heat to the environment. Total heat production is related to body size, which is closely related to metabolic rate and oxygen consumption. Body temperature control is a crucial aspect of neonatal medicine but we have often struggled with temperature measures. Contactless infrared thermography (IRT) is useful for vulnerable neonates and may be able to assess their spontaneous thermal metabolism. The present study focused on heat oscillations and their cause. IRT was used to measure the skin temperature every 15 s of neonates in an incubator. We analyzed the thermal data of 27 neonates (32 measurements), calculated the average temperature within specified regions, and extracted two frequency components—Components A and B—using the Savitzky–Golay method. Furthermore, we derived an equation describing the cycle—named cycle T—for maintaining body temperature according to body weight. A positive correlation was observed between cycle T and Component B (median [IQR]: 368 [300–506] s). This study sheds light on the physiological thermoregulatory function of newborns and will lead to improved temperature management methods for newborns, particularly premature, low-birth-weight infants.
Long-term stimulation by implanted pacemaker enables non-atrophic treatment of bilateral vocal fold paresis in a human-like animal model
Authors: Walluks Kassandra , Hoffmann Bianca , Svensson Carl-Magnus , Förster Gerhard , Müller Andreas H. , Jarvis Jonathan , Perkins Justin , Figge Marc Thilo , Arnold Dirk 
Published: May 2024

AbstractA wide variety of treatments have been developed to improve respiratory function and quality of life in patients with bilateral vocal fold paresis (BVFP). One experimental method is the electrical activation of the posterior cricoarytenoid (PCA) muscle with a laryngeal pacemaker (LP) to open the vocal folds. We used an ovine (sheep) model of unilateral VFP to study the long-term effects of functional electrical stimulation on the PCA muscles. The left recurrent laryngeal nerve was cryo-damaged in all animals and an LP was implanted except for the controls. After a reinnervation phase of six months, animals were pooled into groups that received either no treatment, implantation of an LP only, or implantation of an LP and six months of stimulation with different duty cycles. Automated image analysis of fluorescently stained PCA cross-sections was performed to assess relevant muscle characteristics. We observed a fast-to-slow fibre type shift in response to nerve damage and stimulation, but no complete conversion to a slow-twitch-muscle. Fibre size, proportion of hybrid fibres, and intramuscular collagen content were not substantially altered by the stimulation. These results demonstrate that 30 Hz burst stimulation with duty cycles of 40% and 70% did not induce PCA atrophy or fibrosis. Thus, long-term stimulation with an LP is a promising approach for treating BVFP in humans without compromising muscle conditions.
Study on the dynamic response characteristics of lining structures in large-section tunnel blasting using JH-2 model analysis
Authors: Li Fengting , Wu Ke , Li Shengrui , Wang Cao , Liu Yajun , Dou Zhongyu 
Published: May 2024

AbstractThe lining structures of tunnels are typically constructed using sprayed or cast concrete materials, and their performance and quality during tunnel excavation and blasting are crucial for the stability and safety of tunnels. Therefore, the safe distance between the lining structure and blasting source should be determined to avoid concrete damage caused by blasting vibrations. In this study, taking the subway tunnel of Danshan Station in Qingdao as an example, the JH-2 model is introduced as the constitutive model of the tunnel blasting simulation, and the JH-2 model parameters of the local surrounding rock are obtained by experiments, and finally the numerical simulation and theoretical verification are carried out to study the safety distance of shotcrete under various safety judgment standards. The results indicate that the JH-2 model can effectively simulate the propagation of stress waves under different media conditions, and the closer the strength parameters and pressure constant of the lining structure are to those of the surrounding rock, the safer the concrete–rock bonding interface. During tunnel blasting construction using the ring blasting method, the peak particle velocity (PPV) of the lining structure increases with an increase in the arch angle. Based on the numerical simulation results, we recommend that concrete lining be constructed at a distance of at least 62 m from the blasting source to avoid damage caused by vibrations. The effect of concrete tensile failure caused by longitudinal stress is much smaller than the damage to the bonding interface caused by the PPV and can be neglected.
Stroke walking and balance characteristics via principal component analysis
Authors: Cho Jieun , Ha Sunghe , Lee Jooyoung , Kim Minseok , Kim Hogene 
Published: May 2024

AbstractBalance impairment is associated gait dysfunction with several quantitative spatiotemporal gait parameters in patients with stroke. However, the link between balance impairments and joint kinematics during walking remains unclear. Clinical assessments and gait measurements using motion analysis system was conducted in 44 stroke patients. This study utilised principal component analysis to identify key joint kinematics characteristics of patients with stroke during walking using average joint angles of pelvis and bilateral lower limbs in every gait-cycle percentile related to balance impairments. Reconstructed kinematics showed the differences in joint kinematics in both paretic and nonparetic lower limbs that can be distinguished by balance impairment, particularly in the sagittal planes during swing phase. The impaired balance group exhibited greater joint variability in both the paretic and nonparetic limbs in the sagittal plane during entire gait phase and during terminal swing phase respectively compared with those with high balance scores. This study provides a more comprehensive understanding of stroke hemiparesis gait patterns and suggests considering both nonparetic and paretic limb function, as well as bilateral coordination in clinical practice. Principal component analysis can be a useful assessment tool to distinguish differences in balance impairment and dynamic symmetry during gait in patients with stroke.
Prominin 1 is crucial for the early development of photoreceptor outer segments
Authors: Yanardag Sila , Rhodes Scott , Saravanan Thamaraiselvi , Guan Tongju , Ramamurthy Visvanathan 
Published: May 2024

AbstractProminin 1 (PROM1) is a pentaspan transmembrane glycoprotein localized on the nascent photoreceptor discs. Mutations in PROM1 are linked to various retinal diseases. In this study, we assessed the role of PROM1 in photoreceptor biology and physiology using the PROM1 knockout murine model (rd19). Our study found that PROM1 is essential for vision and photoreceptor development. We found an early reduction in photoreceptor response beginning at post-natal day 12 (P12) before eye opening in the absence of PROM1 with no apparent loss in photoreceptor cells. However, at this stage, we observed an increased glial cell activation, indicative of cell damage. Contrary to our expectations, dark rearing did not mitigate photoreceptor degeneration or vision loss in PROM1 knockout mice. In addition to physiological defects seen in PROM1 knockout mice, ultrastructural analysis revealed malformed outer segments characterized by whorl-like continuous membranes instead of stacked disks. In parallel to the reduced rod response at P12, proteomics revealed a significant reduction in the levels of protocadherin, a known interactor of PROM1, and rod photoreceptor outer segment proteins, including rhodopsin. Overall, our results underscore the indispensable role of PROM1 in photoreceptor development and maintenance of healthy vision.
No evidence that averaging voices influences attractiveness
Authors: Ostrega Jessica , Shiramizu Victor , Lee Anthony J. , Jones Benedict C. , Feinberg David R. 
Published: May 2024

AbstractVocal attractiveness influences important social outcomes. While most research on the acoustic parameters that influence vocal attractiveness has focused on the possible roles of sexually dimorphic characteristics of voices, such as fundamental frequency (i.e., pitch) and formant frequencies (i.e., a correlate of body size), other work has reported that increasing vocal averageness increases attractiveness. Here we investigated the roles these three characteristics play in judgments of the attractiveness of male and female voices. In Study 1, we found that increasing vocal averageness significantly decreased distinctiveness ratings, demonstrating that participants could detect manipulations of vocal averageness in this stimulus set and using this testing paradigm. However, in Study 2, we found no evidence that increasing averageness significantly increased attractiveness ratings of voices. In Study 3, we found that fundamental frequency was negatively correlated with male vocal attractiveness and positively correlated with female vocal attractiveness. By contrast with these results for fundamental frequency, vocal attractiveness and formant frequencies were not significantly correlated. Collectively, our results suggest that averageness may not necessarily significantly increase attractiveness judgments of voices and are consistent with previous work reporting significant associations between attractiveness and voice pitch.
Influence of operating pressure on the durability of a satellite hydraulic motor supplied by rapeseed oil
Authors: Sliwinski Pawel 
Published: May 2024

AbstractThis article describes the results of a durability test of a hydraulic satellite motor supplied by rapeseed oil. The tests were carried out on a test stand in a power recuperation system. The tests of the motor were carried out at a constant shaft speed for three fixed pressure drops in the motor. This made it possible to demonstrate the influence of the motor operating pressure on the durability of the satellite mechanism. The influence of the pressure drop in the motor and the influence of the operating time on the motor absorbency, on the torque on the motor shaft and the influence on the volumetric and hydraulic-mechanical efficiency are also shown. The basic relationship between the efficiency of the motor and the temperature rise in the motor is also described. The results of the calculations of the temperature rise in the motor are compared with the experimental results. The article also shows which components of the motor’s working mechanism wear out the fastest. The cause of the wear and failure is also explained.
Universal and cultural factors shape body part vocabularies
Authors: Tjuka Annika , Forkel Robert , List Johann-Mattis 
Published: May 2024

AbstractEvery human has a body. Yet, languages differ in how they divide the body into parts to name them. While universal naming strategies exist, there is also variation in the vocabularies of body parts across languages. In this study, we investigate the similarities and differences in naming two separate body parts with one word, i.e., colexifications. We use a computational approach to create networks of body part vocabularies across languages. The analyses focus on body part networks in large language families, on perceptual features that lead to colexifications of body parts, and on a comparison of network structures in different semantic domains. Our results show that adjacent body parts are colexified frequently. However, preferences for perceptual features such as shape and function lead to variations in body part vocabularies. In addition, body part colexification networks are less varied across language families than networks in the semantic domains of emotion and colour. The study presents the first large-scale comparison of body part vocabularies in 1,028 language varieties and provides important insights into the variability of a universal human domain.
Committing to the wrong artificial delegate in a collective-risk dilemma is better than directly committing mistakes
Authors: Terrucha Inês , Fernández Domingos Elias , Simoens Pieter , Lenaerts Tom 
Published: May 2024

AbstractWhile autonomous artificial agents are assumed to perfectly execute the strategies they are programmed with, humans who design them may make mistakes. These mistakes may lead to a misalignment between the humans’ intended goals and their agents’ observed behavior, a problem of value alignment. Such an alignment problem may have particularly strong consequences when these autonomous systems are used in social contexts that involve some form of collective risk. By means of an evolutionary game theoretical model, we investigate whether errors in the configuration of artificial agents change the outcome of a collective-risk dilemma, in comparison to a scenario with no delegation. Delegation is here distinguished from no-delegation simply by the moment at which a mistake occurs: either when programming/choosing the agent (in case of delegation) or when executing the actions at each round of the game (in case of no-delegation). We find that, while errors decrease success rate, it is better to delegate and commit to a somewhat flawed strategy, perfectly executed by an autonomous agent, than to commit execution errors directly. Our model also shows that in the long-term, delegation strategies should be favored over no-delegation, if given the choice.
Comparison of preventive effects of combined furosemide and mannitol versus single diuretics, furosemide or mannitol, on cisplatin-induced nephrotoxicity
Authors: Takagi Ayaka , Miyoshi Takanori , Hayashi Toshinobu , Koizumi Hinako , Tsumagari Kyouichi , Yokota Chiaki , Nakano Takafumi , Matsuo Koichi , Egawa Takashi 
Published: May 2024

AbstractCisplatin (CDDP)-induced nephrotoxicity is a common dose-limiting toxicity, and diuretics are often administered to prevent nephrotoxicity. However, the efficacy and optimal administration of diuretics in preventing CDDP-induced nephrotoxicity remain to be established. This study aimed to evaluate the efficacy of combining furosemide and mannitol to prevent CDDP-induced nephrotoxicity. This was a post-hoc analysis of pooled data from a multicenter, retrospective, observational study, including 396 patients who received one or two diuretics for CDDP-based chemotherapy, compared using propensity score matching. Multivariate logistic regression analyses were used to identify risk factors for nephrotoxicity. There was no significant difference in the incidence of nephrotoxicity between the two groups (22.2% vs. 28.3%, P = 0.416). Hypertension, CDDP dose ≥ 75 mg/m2, and no magnesium supplementation were identified as risk factors for nephrotoxicity, whereas the use of diuretics was not found to be a risk factor. The combination of furosemide and mannitol showed no advantage over a single diuretic in preventing CDDP-induced nephrotoxicity. The renal function of patients receiving CDDP-based chemotherapy (≥ 75 mg/m2) and that of those with hypertension should be carefully monitored. Magnesium supplementation is important for these patients.
Configurational entropy of ice XIX and its isotope effect
Authors: Gasser Tobias M. , Thoeny Alexander V. , Fortes A. Dominic , Loerting Thomas 
Published: May 2024

AbstractIce XIX is a partly hydrogen-ordered polymorph related to disordered ice VI, similar to ice XV. We here investigate the order–order–disorder sequence ice XIX→ice XV→ice VI based on calorimetry at ambient pressure both for D2O and H2O-ice XIX. From these data we extract configurational entropy differences between ice XIX, ice XV and ice VI. This task is complex because, unlike for all other ices, the order–disorder transition from ice XIX to ice VI takes place in two steps via ice XV. Even more challenging, these two steps take place in an overlapping manner, so that careful separation of slow kinetics is necessary. This is evidenced best by changing the heating rate in calorimetry experiments: For fast heating experiments the second step, disordering of ice XV, is suppressed because the first step, formation of ice XV from ice XIX, is too slow. The transient state ice VI‡ that is initially produced upon ice XIX decay then does not have enough time to convert to ice XV, but remains disordered all along. In order to tackle the challenge to determine the entropy difference between ice XIX and VI as well as the entropy difference between ice XV and VI we employ two different approaches that allow assessing the impact of kinetics on the entropy change. “Single peak integration” defines a kinetically limited result, but “combined peak integration” allows estimation of the true thermodynamic values. Our best estimate for the true value shows ice XIX to be much more ordered than ice XV (25 ± 3% vs 9 ± 4% of the Pauling entropy). For D2Oice XIX samples we obtain 28% of order, but only when a small number of fast H-isotope defects are used. In the second part we use these results to estimate the location of the ice XIX phase boundary both for protiated and deuterated ice XIX. The initial Clapeyron slope at ambient pressure is determined from the combination of neutron powder diffraction volume differences and calorimetry entropy differences data to be 21 K GPa−1 with an order–disorder transition temperature To-d(0.0 GPa) = 103 ± 1 K. An in situ bracketing experiment at 1.8 GPa yields To-d(1.8 GPa) = 116 ± 3 K, i.e., the phase boundary slope flattens at higher pressures. These data allow us to determine the region of thermodynamic stability of ice XIX in the phase diagram and to explain the surprising isotope shift reversal at 1.6 GPa compared to 0.0 GPa, i.e., why D2O-ice XIX disorders at lower temperatures than H2O-ice XIX at 1.6 GPa, but at higher temperatures at ambient pressures.