bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised abnormality detection in neonatal MRI brain scans using deep learning
Authors: Raad Jad Dino , Chinnam Ratna Babu , Arslanturk Suzan , Tan Sidhartha , Jeong Jeong-Won , Mody Swati 
Published: July 2023

AbstractAnalysis of 3D medical imaging data has been a large topic of focus in the area of Machine Learning/Artificial Intelligence, though little work has been done in algorithmic (particularly unsupervised) analysis of neonatal brain MRI’s. A myriad of conditions can manifest at an early age, including neonatal encephalopathy (NE), which can result in lifelong physical consequences. As such, there is a dire need for better biomarkers of NE and other conditions. The objective of the study is to improve identification of anomalies and prognostication of neonatal MRI brain scans. We introduce a framework designed to support the analysis and assessment of neonatal MRI brain scans, the results of which can be used as an aid to neuroradiologists. We explored the efficacy of the framework through iterations of several deep convolutional Autoencoder (AE) unsupervised modeling architectures designed to learn normalcy of the neonatal brain structure. We tested this framework on the developing human connectome project (dHCP) dataset with 97 patients that were previously categorized by severity. Our framework demonstrated the model’s ability to identify and distinguish subtle morphological signatures present in brain structures. Normal and abnormal neonatal brain scans can be distinguished with reasonable accuracy, correctly categorizing them in up to 83% of cases. Most critically, new brain anomalies originally missed during the radiological reading were identified and corroborated by a neuroradiologist. This framework and our modeling approach demonstrate an ability to improve prognostication of neonatal brain conditions and are able to localize new anomalies.
A randomised controlled test of emotional attributes of a virtual coach within a virtual reality (VR) mental health treatment
Authors: Wei Shu , Freeman Daniel , Rovira Aitor 
Published: July 2023

AbstractWe set out to test whether positive non-verbal behaviours of a virtual coach can enhance people's engagement in automated virtual reality therapy. 120 individuals scoring highly for fear of heights participated. In a two-by-two factor, between-groups, randomised design, participants met a virtual coach that varied in warmth of facial expression (with/without) and affirmative nods (with/without). The virtual coach provided a consultation about treating fear of heights. Participants rated the therapeutic alliance, treatment credibility, and treatment expectancy. Both warm facial expressions (group difference = 7.44 [3.25, 11.62], p = 0.001, $${eta}_{p}^{2}$$

eta

p

2

=0.10) and affirmative nods (group difference = 4.36 [0.21, 8.58], p = 0.040, $${eta}_{p}^{2}$$

eta

p

2

= 0.04) by the virtual coach independently increased therapeutic alliance. Affirmative nods increased the treatment credibility (group difference = 1.76 [0.34, 3.11], p = 0.015, $${eta}_{p}^{2}$$

eta

p

2

= 0.05) and expectancy (group difference = 2.28 [0.45, 4.12], p = 0.015, $${eta}_{p}^{2}$$

eta

p

2

= 0.05) but warm facial expressions did not increase treatment credibility (group difference = 0.64 [− 0.75, 2.02], p = 0.363, $${eta}_{p}^{2}$$

eta

p

2

= 0.01) or expectancy (group difference = 0.36 [− 1.48, 2.20], p = 0.700, $${eta}_{p}^{2}$$

eta

p

2

= 0.001). There were no significant interactions between head nods and facial expressions in the occurrence of therapeutic alliance (p = 0.403, $${eta}_{p}^{2}$$

eta

p

2

= 0.01), credibility (p = 0.072, $${eta}_{p}^{2}$$

eta

p

2

= 0.03), or expectancy (p = 0.275, $${eta}_{p}^{2}$$

eta

p

2

= 0.01). Our results demonstrate that in the development of automated VR therapies there is likely to be therapeutic value in detailed consideration of the animations of virtual coaches.
Solid-to-solid polymorphic phase transitions in two isostructural Bi(III) complexes with 1-phenylethyl-N-ethylthiosemicarbazide and halogens
Authors: Grześkiewicz Anita M. , Dutkiewicz Grzegorz , Aygun Ozlem , Ozturk Ibrahim I. , Kubicki Maciej 
Published: July 2023

AbstractTwo isostructural (in room temperature) complexes of Bi(III) with halogens and sulfur ligands have been investigated in terms of the solid-to-solid phase transitions indicated by temperature. Both chloride and bromide (X) complexes of the general formula (µ2-X)-(BiX2L2)2 exhibit some phase transitions between 100 and 333 K, which, apart from the numerous similarities, show significant differences, which have been noted and analyzed in detail in this paper by using different techniques, i.e., powder and single crystal diffraction or DSC. The obtained results have also been collated with those obtained for solid solutions of both complexes.
The accuracy and safety of intraoperative ultrasound-guided external ventricular drainage in intraventricular hemorrhage
Authors: Zhang Lijun , Mu Zhaohui , Shen Guoliang , Yang Ming 
Published: July 2023

AbstractSevere IVH often results in a poor outcome. Currently, EVD is a standard treatment for IVH, but there is little research to show whether using ultrasound to guide the catheter placement improves outcome. Patients with severe IVH who had iUS-guided EVD (the iUS-guided group) were enrolled retrospectively and compared with a group who had EVD performed without ultrasound guidance (the control group) from January 2016 to July 2022. Data were collected on accuracy of the catheter placement, complications and outcome at 3 months assessed by mRS. The accuracy of the EVD placement was classified as optimal placement, sub-optimal placement and misplacement according to the position of the catheter tip. The complications reported are catheter-related hemorrhage, intracranial infection and hydrocephalus. There were 105 cases enrolled, with 72 patients in the iUS-guided group having 131 catheters inserted and 33 patients in the group where ultrasound was not used with a total of 59 catheters. 116 (88.55%) were optimally placed, 12 (9.16%) sub-optimal and 3 (2.29%) misplaced in the iUS-guided group, while 25 (42.37%) were in optimally placed, 30 (50.85%) sub-optimal and 4(6.78%) misplaced in the control group. Accuracy of placement was highly significantly improved using ultrasound (P < 0.001). The operation time and the average catheterized time were longer in the iUS-guided group (P < 0.05), but the complication rates were no different between the groups. The mRS at three months was not significantly different between the two groups. Using iUS to place EVD catheters in patients with severe IVH is a safe technique delivering more accurate catheter placement without increasing the complication rate compared with freehand placement.
Gain-of-function p53R175H blocks apoptosis in a precursor model of ovarian high-grade serous carcinoma
Authors: Haagsma Jacob , Kolendowski Bart , Buensuceso Adrian , Valdes Yudith Ramos , DiMattia Gabriel E. , Shepherd Trevor G. 
Published: July 2023

AbstractOvarian high-grade serous carcinoma (HGSC) is a highly lethal malignancy for which early detection is a challenge and treatment of late-stage disease is ineffective. HGSC initiation involves exfoliation of fallopian tube epithelial (FTE) cells which form multicellular clusters called spheroids that colonize and invade the ovary. HGSC contains universal mutation of the tumour suppressor gene TP53. However, not all TP53 mutations are the same, as specific p53 missense mutants contain gain-of-function (GOF) properties that drive tumour formation. Additionally, the role of GOF p53 in spheroid-mediated spread is poorly understood. In this study, we developed and characterized an in vitro model of HGSC based on mutation of TP53 in mouse oviductal epithelial cells (OVE). We discovered increased bulk spheroid survival and increased anchorage-independent growth in OVE cells expressing the missense mutant p53R175H compared to OVE parental and Trp53ko cells. Transcriptomic analysis on spheroids identified decreased apoptosis signaling due to p53R175H. Further assessment of the apoptosis pathway demonstrated decreased expression of intrinsic and extrinsic apoptosis signaling molecules due to Trp53 deletion and p53R175H, but Caspase-3 activation was only decreased in spheroids with p53R175H. These results highlight this model as a useful tool for discovering early HGSC transformation mechanisms and uncover a potential anti-apoptosis GOF mechanism of p53R175H.
Impact of trap-related non-idealities on the performance of a novel TFET-based biosensor with dual doping-less tunneling junction
Authors: Cherik Iman Chahardah , Mohammadi Saeed 
Published: July 2023

AbstractThis article presents a novel dielectric-modulated biosensor based on a tunneling field-effect transistor. It comprises a dual doping-less tunneling junction that lies above an n+ drain region. By employing the wet-etching technique, two cavities are carved in the gate dielectric, and with the entry of various biomolecules into the cavities, the electrostatic integrity of the gate changes, accordingly. Numerical simulations, carried out by the Silvaco ATLAS device simulator, show that including trap-assisted tunneling significantly modulate the biosensor's main parameters, such as on-state current, subthreshold swing, and transconductance and their corresponding sensitivities. We also evaluate the effect of semi-filled cavities on our proposed biosensor’s performance with various configurations. The FOMs like Ion/Ioff = 2.04 × 106, $${S}_{{I}_{ds}}$$

S

I

ds

=1.48 × 105, and $${S}_{SS}$$

S

SS

=0.61 in the presence of TAT show that our proposed biosensor has a promising performance.
Adaptative response to changes in pyruvate metabolism on the epigenetic landscapes and transcriptomics of bovine embryos
Authors: da Fonseca Junior Aldcejam Martins , Ispada Jessica , dos Santos Erika Cristina , de Lima Camila Bruna , da Silva João Vitor Alcantara , Paulson Erika , Goszczynski Daniel Estanislao , Goissis Marcelo Demarchi , Ross Pablo Juan , Milazzotto Marcella Pecora 
Published: July 2023

AbstractThe epigenetic reprogramming that occurs during the earliest stages of embryonic development has been described as crucial for the initial events of cell specification and differentiation. Recently, the metabolic status of the embryo has gained attention as one of the main factors coordinating epigenetic events. In this work, we investigate the link between pyruvate metabolism and epigenetic regulation by culturing bovine embryos from day 5 in the presence of dichloroacetate (DCA), a pyruvate analog that increases the pyruvate to acetyl-CoA conversion, and iodoacetate (IA), which inhibits the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), leading to glycolysis inhibition. After 8 h of incubation, both DCA and IA-derived embryos presented higher mitochondrial membrane potential. Nevertheless, in both cases, lower levels of acetyl-CoA, ATP-citrate lyase and mitochondrial membrane potential were found in blastocysts, suggesting an adaptative metabolic response, especially in the DCA group. The metabolic alteration found in blastocysts led to changes in the global pattern of H3K9 and H3K27 acetylation and H3K27 trimethylation. Transcriptome analysis revealed that such alterations resulted in molecular differences mainly associated to metabolic processes, establishment of epigenetic marks, control of gene expression and cell cycle. The latter was further confirmed by the alteration of total cell number and cell differentiation in both groups when compared to the control. These results corroborate previous evidence of the relationship between the energy metabolism and the epigenetic reprogramming in preimplantation bovine embryos, reinforcing that the culture system is decisive for precise epigenetic reprogramming, with consequences for the molecular control and differentiation of cells.
Sacubitril/valsartan mitigates cardiac remodeling, systolic dysfunction, and preserves mitochondrial quality in a rat model of mitral regurgitation
Authors: Tantisuwat Lalida , Saengklub Nakkawee , Boonpala Pakit , Kumphune Sarawut , Panyasing Yaowalak , Kalandakanond-Thongsong Sarinee , Kijtawornrat Anusak 
Published: July 2023

AbstractSacubitril/valsartan (SAC/VAL), an angiotensin receptor blocker-neprilysin inhibitor, has been widely used to treat several types of heart failure. Nevertheless, the effects of drugs in mitral regurgitation patients, from the molecular level to therapeutic effects, remain unclear. This study investigates the roles of SAC/VAL on cardiac function, mitochondrial quality, autophagy, mitophagy, and natriuretic peptides in a rat model of chronic mitral regurgitation. Male Sprague–Dawley rats underwent MR induction (n = 16) and sham surgeries (n = 8). Four weeks post-surgery confirmed MR rats were randomly divided into MR (n = 8) and SAC/VAL (n = 8) groups. The SAC/VAL group was administered SAC/VAL, whereas the MR and the sham rats received vehicle via oral gavage daily for 8 weeks. Cardiac geometry, function, and myocardial fibrosis were assessed by echocardiography and histopathology. Spectrophotometry and real-time PCR were performed to assess the pharmacological effects on mitochondrial quality, autophagy, mitophagy, and natriuretic peptides. MR rats demonstrated significant left heart dilation and left ventricular systolic dysfunction compared with the sham group, which could be significantly improved by SAC/VAL. In addition, SAC/VAL significantly reduced myocardial cardiac remodeling and fibrosis in MR rats. SAC/VAL improved the mitochondrial quality by attenuating mitochondrial reactive oxygen species production and mitochondrial depolarization compared with the MR group. Also, the upregulation of autophagy-related, mitophagy-related, and natriuretic peptide system gene expression in MR rats was attenuated by SAC/VAL treatment. In conclusion, this study demonstrated that SAC/VAL treatment could provide numerous beneficial effects in MR conditions, suggesting that this drug may be an effective treatment for MR.
Comparison of various flow maldistribution quantification methods in mini heat exchangers
Authors: Dąbrowski Paweł 
Published: July 2023

AbstractThe aim of study is to compare various flow maldistribution quantification methods, using velocity, mass flow rate, pressure, and temperature. An experimentally validated numerical study has been prepared and a heat exchanger with 34 semi-circular channels with a diameter of 3.1 mm has been tested. The minichannels were heated from the bottom with a heat flux of 50, 60, 70, and 80 kW/m2. The cases for various inlet velocities of 0.1, 0.2, 0.3, and 0.4 m/s have been tested. It results in a total of 16 cases with various heat flux and various inlet velocities of the water. Then, for every 16 cases, the flow maldistribution coefficients, widely used in the literature, have been calculated based on the velocity, pressure, and temperature profiles. The study shows that every method gives other results of the same parameter that should define the flow distribution in the heat exchanger in the same way. Hence, the ambiguities of fluid distribution conclusions in heat exchangers that can be found in the literature may be caused by a different interpretation of the flow maldistribution coefficient. A normalized flow maldistribution coefficient that gives the same results for all thermohydraulic parameters used has been proposed.
Modulation of physicochemical properties and antimicrobial activity of sodium alginate films through the use of chestnut extract and plasticizers
Authors: Janik Weronika , Nowotarski Michał , Ledniowska Kerstin , Shyntum Divine Yufetar , Krukiewicz Katarzyna , Turczyn Roman , Sabura Ewa , Furgoł Simona , Kudła Stanisław , Dudek Gabriela 
Published: July 2023

AbstractDue to the growing demand for robust and environmentally friendly antimicrobial packaging materials, biopolymers have recently become extensively investigated. Although biodegradable biopolymers usually lack mechanical properties, which makes it inevitable to blend them with plasticizers. The purpose of this study was to investigate plasticization efficiency of bio-based plasticizers introduced into sodium alginate compositions containing chestnut extract and their effect on selected film properties, including primarily mechanical and antibacterial properties. The films were prepared by the casting method and sodium alginate was cross-linked with calcium chloride. Six different plasticizers, including three commercially available ones (glycerol, epoxidized soybean oil and palm oil) and three synthesized plasticizers that are mixtures of bio-based plasticizers, were used to compare their influence on the film properties. Interactions between the polymer matrix and the plasticizers were investigated using Fourier transform infrared spectroscopy. The morphological characteristics of the films were characterized by scanning electron microscopy. Thermal properties, tensile strength, elongation at break, hydrophilic, and barrier properties of the obtained films were also determined. To confirm the obtaining of active films through the use of chestnut extract and to study the effect of the proposed plasticizers on the antibacterial activity of the extract, the obtained films were tested against bacteria cultures. The final results showed that all of the obtained films exhibit a hydrophilic character and high barrier effect to oxygen, carbon dioxide and water vapor. In addition, sodium alginate films prepared with chestnut extract and the plasticizer proposed by us, showed better mechanical and antimicrobial properties than the films obtained with chestnut extract and the commercially available plasticizers.
Global response of upper-level aviation turbulence from various sources to climate change
Authors: Kim Soo-Hyun , Kim Jung-Hoon , Chun Hye-Yeong , Sharman Robert D. 
Published: July 2023

AbstractAtmospheric turbulence at commercial aircraft cruising altitudes is a main threat to aviation safety worldwide. As the air transport industry expands and is continuously growing, investigating global response of aviation turbulence under climate change scenarios is required for preparing optimal and safe flying plans for the future. This study examines future frequencies of moderate-or-greater-intensity turbulence generated from various sources, viz., clear-air turbulence and mountain-wave turbulence that are concentrated in midlatitudes, and near-cloud turbulence that is concentrated in tropics and subtropics, using long-term climate model data of high-emissions scenario and historical condition. Here, we show that turbulence generated from all three sources is intensified with higher occurrences globally in changed climate compared to the historical period. Although previous studies have reported intensification of clear-air turbulence in changing climate, implying bumpier flights in the future, we show that intensification of mountain-wave turbulence and near-cloud turbulence can also be expected with changing climate.
Arousal state transitions occlude sensory-evoked neurovascular coupling in neonatal mice
Authors: Gheres Kyle W. , Ünsal Hayreddin S. , Han Xu , Zhang Qingguang , Turner Kevin L. , Zhang Nanyin , Drew Patrick J. 
Published: July 2023

AbstractIn the adult sensory cortex, increases in neural activity elicited by sensory stimulation usually drive vasodilation mediated by neurovascular coupling. However, whether neurovascular coupling is the same in neonatal animals as adults is controversial, as both canonical and inverted responses have been observed. We investigated the nature of neurovascular coupling in unanesthetized neonatal mice using optical imaging, electrophysiology, and BOLD fMRI. We find in neonatal (postnatal day 15, P15) mice, sensory stimulation induces a small increase in blood volume/BOLD signal, often followed by a large decrease in blood volume. An examination of arousal state of the mice revealed that neonatal mice were asleep a substantial fraction of the time, and that stimulation caused the animal to awaken. As cortical blood volume is much higher during REM and NREM sleep than the awake state, awakening occludes any sensory-evoked neurovascular coupling. When neonatal mice are stimulated during an awake period, they showed relatively normal (but slowed) neurovascular coupling, showing that that the typically observed constriction is due to arousal state changes. These result show that sleep-related vascular changes dominate over any sensory-evoked changes, and hemodynamic measures need to be considered in the context of arousal state changes.
Structure and assembly of the NOT10:11 module of the CCR4-NOT complex
Authors: Levdansky Yevgen , Raisch Tobias , Deme Justin C. , Pekovic Filip , Elmlund Hans , Lea Susan M. , Valkov Eugene 
Published: July 2023

AbstractNOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly.
Toxicology knowledge graph for structural birth defects
Authors: Evangelista John Erol , Clarke Daniel J. B. , Xie Zhuorui , Marino Giacomo B. , Utti Vivian , Jenkins Sherry L. , Ahooyi Taha Mohseni , Bologa Cristian G. , Yang Jeremy J. , Binder Jessica L. , Kumar Praveen , Lambert Christophe G. , Grethe Jeffrey S. , Wenger Eric , Taylor Deanne , Oprea Tudor I. , de Bono Bernard , Ma’ayan Avi 
Published: July 2023

Abstract
Background
Birth defects are functional and structural abnormalities that impact about 1 in 33 births in the United States. They have been attributed to genetic and other factors such as drugs, cosmetics, food, and environmental pollutants during pregnancy, but for most birth defects there are no known causes.

Methods
To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes. Specifically, we gathered data from drug/birth-defect associations from co-mentions in published abstracts, gene/birth-defect associations from genetic studies, drug- and preclinical-compound-induced gene expression changes in cell lines, known drug targets, genetic burden scores for human genes, and placental crossing scores for small molecules.

Results
Using ReproTox-KG and semi-supervised learning (SSL), we scored >30,000 preclinical small molecules for their potential to cross the placenta and induce birth defects, and identified >500 birth-defect/gene/drug cliques that can be used to explain molecular mechanisms for drug-induced birth defects. The ReproTox-KG can be accessed via a web-based user interface available at https://maayanlab.cloud/reprotox-kg. This site enables users to explore the associations between birth defects, approved and preclinical drugs, and all human genes.

Conclusions
ReproTox-KG provides a resource for exploring knowledge about the molecular mechanisms of birth defects with the potential of predicting the likelihood of genes and preclinical small molecules to induce birth defects.