bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontology-based feature engineering in machine learning workflows for heterogeneous epilepsy patient records
Authors: Sahoo Satya S. , Kobow Katja , Zhang Jianzhe , Buchhalter Jeffrey , Dayyani Mojtaba , Upadhyaya Dipak P. , Prantzalos Katrina , Bhattacharjee Meenakshi , Blumcke Ingmar , Wiebe Samuel , Lhatoo Samden D. 
Published: November 2022

AbstractBiomedical ontologies are widely used to harmonize heterogeneous data and integrate large volumes of clinical data from multiple sources. This study analyzed the utility of ontologies beyond their traditional roles, that is, in addressing a challenging and currently underserved field of feature engineering in machine learning workflows. Machine learning workflows are being increasingly used to analyze medical records with heterogeneous phenotypic, genotypic, and related medical terms to improve patient care. We performed a retrospective study using neuropathology reports from the German Neuropathology Reference Center for Epilepsy Surgery at Erlangen, Germany. This cohort included 312 patients who underwent epilepsy surgery and were labeled with one or more diagnoses, including dual pathology, hippocampal sclerosis, malformation of cortical dysplasia, tumor, encephalitis, and gliosis. We modeled the diagnosis terms together with their microscopy, immunohistochemistry, anatomy, etiologies, and imaging findings using the description logic-based Web Ontology Language (OWL) in the Epilepsy and Seizure Ontology (EpSO). Three tree-based machine learning models were used to classify the neuropathology reports into one or more diagnosis classes with and without ontology-based feature engineering. We used five-fold cross validation to avoid overfitting with a fixed number of repetitions while leaving out one subset of data for testing, and we used recall, balanced accuracy, and hamming loss as performance metrics for the multi-label classification task. The epilepsy ontology-based feature engineering approach improved the performance of all the three learning models with an improvement of 35.7%, 54.5%, and 33.3% in logistics regression, random forest, and gradient tree boosting models respectively. The run time performance of all three models improved significantly with ontology-based feature engineering with gradient tree boosting model showing a 93.8% reduction in the time required for training and testing of the model. Although, all three models showed an overall improved performance across the three-performance metrics using ontology-based feature engineering, the rate of improvement was not consistent across all input features. To analyze this variation in performance, we computed feature importance scores and found that microscopy had the highest importance score across the three models, followed by imaging, immunohistochemistry, and anatomy in a decreasing order of importance scores. This study showed that ontologies have an important role in feature engineering to make heterogeneous clinical data accessible to machine learning models and also improve the performance of machine learning models in multilabel multiclass classification tasks.
Aging effects in Schelling segregation model
Authors: Abella David , San Miguel Maxi , Ramasco José J. 
Published: November 2022

AbstractThe Schelling model has become a paradigm in social sciences to explain the emergence of residential spatial segregation, even in the presence of high tolerance to mixed neighborhoods by the side of citizens. In particular, we consider a noisy constrained version of the Schelling model, in which agents maximize its satisfaction, related to the composition of the local neighborhood, by infinite-range movements towards satisfying vacancies. We add to it an aging effect by making the probability of agents to move inversely proportional to the time they have been satisfied in their present location. This mechanism simulates the development of an emotional attachment to a location where an agent has been satisfied for a while. The introduction of aging has several major impacts on the model statics and dynamics: the phase transition between a segregated and a mixed phase of the original model disappears, and we observe segregated states with a high level of agent satisfaction even for high values of tolerance. In addition, the new segregated phase is dynamically characterized by a slow power-law coarsening process similar to a glassy-like dynamics.
Design of a multi-epitope protein as a subunit vaccine against lumpy skin disease using an immunoinformatics approach
Authors: Kar Prajna Parimita , Araveti Prasanna Babu , Kuriakose Akshay , Srivastava Anand 
Published: November 2022

AbstractLumpy skin disease (LSD) is a transboundary viral disease of cattle that causes substantial economic loss globally. There is no specific treatment and subunit vaccine for this disease to date. Reports of the global spread of this disease are worrisome. We designed a multi-epitope protein using an immunoinformatics approach in this study. We analyzed the proteome of LSDV and found 32 structural/surface proteins. Four of these 32 proteins were predicted as antigenic and non-homologous to bovine and highly conserved in 26 LSDV isolates. The predicted B-cell epitopes and CTL epitopes were stitched together with the help of an AAY linker leading to the formation of a multi-epitope protein. The in silico study revealed that the modeled subunit vaccine candidate and TLR4 receptor interact with high affinity. This interaction was also found to be stable using a molecular dynamics simulation study. Our study demonstrates a leap towards developing a subunit vaccine against LSD.
An in-depth evaluation of sample and measurement induced influences on static contact angle measurements
Authors: Lößlein Sarah Marie , Merz Rolf , Müller Daniel Wyn , Kopnarski Michael , Mücklich Frank 
Published: November 2022

AbstractStatic contact angle measurements are one of the most popular methods to analyze the wetting behavior of materials of any kind. Although this method is readily applicable without the need of sophisticated machinery, the results obtained for the very same material may vary strongly. The sensitivity of the measurement against environmental conditions, sample preparation and measurement conduction is a main factor for inconsistent results. Since often no detailed measurement protocols exist alongside published data, contact angle values as well as elaborated wetting studies do not allow for any comparison. This paper therefore aims to discuss possible influences on static contact angle measurements and to experimentally demonstrate the extent of these effects. Sample storage conditions, cleaning procedures, droplet volume, water grade and droplet application as well as the influence of evaporation on the static contact angle are investigated in detail. Especially sample storage led to differences in the contact angle up to 60%. Depending on the wetting state, evaporation can reduce the contact angle by 30–50% within 10 min in dry atmospheres. Therefore, this paper reviews an existing approach for a climate chamber and introduces a new measuring setup based on these results. It allows for the observation of the wetting behavior for several minutes by successfully suppressing evaporation without negatively affecting the surface prior to measurement by exposure to high humidity environments.
Neurotoxicity of diesel exhaust extracts in zebrafish and its implications for neurodegenerative disease
Authors: Ha Sung Min , Barnhill Lisa M. , Li Sharon , Bronstein Jeff M. 
Published: November 2022

AbstractLong-term air pollution (AP) exposure, including diesel exhaust exposure, is increasingly being recognized as a major contributor to the development of neurodegenerative diseases such as Parkinson’s and Alzheimer’s disease. How AP increases the risk of neurodegeneration is not well understood but might include direct neurotoxicity and CNS inflammation. We investigated the impact of diesel exhaust particulate extract (DEPe) exposure on the brain and the mechanisms by which microglia and astroglia might mediate neuronal changes. Zebrafish (ZF) were utilized to determine neuronal toxicity of and microglial response to DEPe and single cell RNA sequencing was employed to study cell type-specific transcriptomic responses within the ZF brain. DEPe exposure induced neuronal injury and microglial activation in vivo. However, preventing the development of microglia did not attenuate DEPe-induced neuron loss, leading us to investigate microglial, astroglial, and neuronal response to DEPe exposure at single-cell resolution. Differentially expressed genes and disease-relevant pathways were identified within glial and neuronal clusters after DEPe exposure. Microglia and astroglia existed in multiple states, some of which appear toxic and others protective to neurons. Neuronal transcriptomic analysis revealed that DEPe exposure reduced expression of autophagy-related genes consistent with direct neurotoxicity. In summary, DEPe exposure was neurotoxic in developing ZF larvae and induced neuroinflammation. The microglial inflammatory response did not contribute to neurotoxicity of DEPe and in fact, some glial clusters upregulated transcriptional pathways that are likely protective. Furthermore, DEPe exposure led to reduced expression of autophagy-related genes in neurons that likely contribute to its toxicity.
Coverage maps demonstrate 3D Chopart joint subluxation in weightbearing CT of progressive collapsing foot deformity
Authors: Behrens Andrew , Dibbern Kevin , Lalevée Matthieu , Alencar Mendes de Carvalho Kepler , Lintz Francois , Barbachan Mansur Nacime Salomao , de Cesar Netto Cesar 
Published: November 2022

AbstractA key element of the peritalar subluxation (PTS) seen in progressive collapsing foot deformity (PCFD) occurs through the transverse tarsal joint complex. However, the normal and pathological relations of these joints are not well understood. The objective of this study to compare Chopart articular coverages between PCFD patients and controls using weight-bearing computed tomography (WBCT). In this retrospective case control study, 20 patients with PCFD and 20 matched controls were evaluated. Distance and coverage mapping techniques were used to evaluate the talonavicular and calcaneocuboid interfaces. Principal axes were used to divide the talar head into 6 regions (medial/central/lateral and plantar/dorsal) and the calcaneocuboid interface into 4 regions. Repeated selections were performed to evaluate reliability of joint interface identification. Surface selections had high reliability with an ICC > 0.99. Talar head coverage decreases in plantarmedial and dorsalmedial (− 79%, p = 0.003 and − 77%, p = 0.00004) regions were seen with corresponding increases in plantarlateral and dorsolateral regions (30%, p = 0.0003 and 21%, p = 0.002) in PCFD. Calcaneocuboid coverage decreased in plantar and medial regions (− 12%, p = 0.006 and − 9%, p = 0.037) and increased in the lateral region (13%, p = 0.002). Significant subluxation occurs across the medial regions of the talar head and the plantar medial regions of the calcaneocuboid joint. Coverage and distance mapping provide a baseline for understanding Chopart joint changes in PCFD under full weightbearing conditions.
Dual-channel P-type ternary DNTT–graphene barristor
Authors: Lee Yongsu , Kim Seung-Mo , Kim Kiyung , Kim So-Young , Lee Ho-In , Kwon Heejin , Lee Hae-Won , Kim Chaeeun , Some Surajit , Hwang Hyeon Jun , Lee Byoung Hun 
Published: November 2022

AbstractP-type ternary switch devices are crucial elements for the practical implementation of complementary ternary circuits. This report demonstrates a p-type ternary device showing three distinct electrical output states with controllable threshold voltage values using a dual-channel dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]-thiophene–graphene barristor structure. To obtain transfer characteristics with distinctively separated ternary states, novel structures called contact-resistive and contact-doping layers were developed. The feasibility of a complementary standard ternary inverter design around 1 V was demonstrated using the experimentally calibrated ternary device model.
Synergetic effect of green synthesized reduced graphene oxide and nano-zero valent iron composite for the removal of doxycycline antibiotic from water
Authors: Abdelfatah Ahmed M. , El-Maghrabi Nourhan , Mahmoud Alaa El Din , Fawzy Manal 
Published: November 2022

AbstractIn this work, the synthesis of an rGO/nZVI composite was achieved for the first time using a simple and green procedure via Atriplex halimus leaves extract as a reducing and stabilizing agent to uphold the green chemistry principles such as less hazardous chemical synthesis. Several tools have been used to confirm the successful synthesis of the composite such as SEM, EDX, XPS, XRD, FTIR, and zeta potential which indicated the successful fabrication of the composite. The novel composite was compared with pristine nZVI for the removal aptitude of a doxycycline antibiotic with different initial concentrations to study the synergistic effect between rGO and nZVI. The adsorptive removal of bare nZVI was 90% using the removal conditions of 25 mg L−1, 25 °C, and 0.05 g, whereas the adsorptive removal of doxycycline by the rGO/nZVI composite reached 94.6% confirming the synergistic effect between nZVI and rGO. The adsorption process followed the pseudo-second order and was well-fitted to Freundlich models with a maximum adsorption capacity of 31.61 mg g−1 at 25 °C and pH 7. A plausible mechanism for the removal of DC was suggested. Besides, the reusability of the rGO/nZVI composite was confirmed by having an efficacy of 60% after six successive cycles of regeneration.
Neonatal corticosterone administration increases p27-positive Sertoli cell number and decreases Sertoli cell number in the testes of mice at prepuberty
Authors: Miyaso Hidenobu , Takano Kaiya , Nagahori Kenta , Li Zhong-Lian , Kawata Shinichi , Kuramasu Miyuki , Ogawa Yuki , Yoshioka Hirotaka , Matsuno Yoshiharu , Yokota Satoshi , Itoh Masahiro 
Published: November 2022

AbstractCortisol and corticosterone (CORT) are steroid, antistress hormones and one of the glucocorticoids in humans and animals, respectively. This study evaluated the effects of CORT administration on the male reproductive system in early life stages. CORT was subcutaneously injected at 0.36 (low-), 3.6 (middle-), and 36 (high-dosed) mg/kg body weight from postnatal day (PND) 1 to 10 in ICR mice. We observed a dose-dependent increase in serum CORT levels on PND 10, and serum testosterone levels were significantly increased only in high-dosed-CORT mice. Triiodothyronine levels were significantly higher in the low-dosed mice but lower in the middle- and high-dosed mice. However, testicular weights did not change significantly among the mice. Sertoli cell numbers were significantly reduced in low- and middle-dosed mice, whereas p27-positive Sertoli cell numbers increased in low- and middle-dosed mice. On PND 16, significant increases in testicular and relative testicular weights were observed in all-dosed-CORT mice. On PND 70, a significant decrease in testicular weight, Sertoli cell number, and spermatozoa count was observed. These results revealed that increased serum CORT levels in early life stages could induce p27 expression in Sertoli cells and terminate Sertoli cell proliferation, leading to decreased Sertoli cell number in mouse testes.
A perceptual sound space for auditory displays based on sung-vowel synthesis
Authors: Rocchesso Davide , Andolina Salvatore , Ilardo Giacomo , Palumbo Salvatore Danilo , Galluzzo Ylenia , Randazzo Mario 
Published: November 2022

AbstractWhen designing displays for the human senses, perceptual spaces are of great importance to give intuitive access to physical attributes. Similar to how perceptual spaces based on hue, saturation, and lightness were constructed for visual color, research has explored perceptual spaces for sounds of a given timbral family based on timbre, brightness, and pitch. To promote an embodied approach to the design of auditory displays, we introduce the Vowel–Type–Pitch (VTP) space, a cylindrical sound space based on human sung vowels, whose timbres can be synthesized by the composition of acoustic formants and can be categorically labeled. Vowels are arranged along the circular dimension, while voice type and pitch of the vowel correspond to the remaining two axes of the cylindrical VTP space. The decoupling and perceptual effectiveness of the three dimensions of the VTP space are tested through a vowel labeling experiment, whose results are visualized as maps on circular slices of the VTP cylinder. We discuss implications for the design of auditory and multi-sensory displays that account for human perceptual capabilities.
Mid-infrared hyperspectral sensor based on MEMS Fabry-Pérot interferometer for stand-off sensing applications
Authors: Saleh Abba , Mekhrengin Mikhail , Dönsberg Timo , Kääriäinen Teemu , Genoud Guillaume , Toivonen Juha 
Published: November 2022

AbstractWe report a novel hyperspectral sensor employing a Fabry-Pérot interferometer based on micro-electro-mechnical system and a custom mid-infrared supercontinuum laser. The Fabry-Pérot interferometer allows on-axis filtering, of spectral components of supercontinuum light backscattered from a target, with a spectral resolution of about 25 nm. We demonstrated hyperspectral identification of black polypropylene (PP) and polyethylene (PE500) using the 3–3.5 $$\mu$$
μ
m region of the supercontinuum spectrum and a corresponding measurement rate of 62.5 spectra / s. The resulted spectra show excellent agreement with the reference based on an FTIR spectrometer. Furthermore, we showed that the coloring of the plastics has no effect on their identification at this wavelength range.
Surprising effects of cascading higher order interactions
Authors: Hsieh Hsun-Yi , Vandermeer John , Perfecto Ivette 
Published: November 2022

AbstractMost species are embedded in multi-interaction networks. Consequently, theories focusing on simple pair-wise interactions cannot predict ecological and/or evolutionary outcomes. This study explores how cascading higher-order interactions (HOIs) would affect the population dynamics of a focal species. Employing a system that involves a myrmecophylic beetle, a parasitic wasp that attacks the beetle, an ant, and a parasitic fly that attacks the ant, the study explores how none, one, and two HOIs affect the parasitism and the sex ratio of the beetle. We conducted mesocosm experiments to examine these HOIs on beetle survival and sex ratio and found that the 1st degree HOI does not change the beetle’s survival rate or sex ratio. However, the 2nd degree HOI significantly reduces the beetle’s survival rate and changes its sex ratio from even to strongly female-biased. We applied Bayes’ theorem to analyze the per capita survival probability of female vs. male beetles and suggested that the unexpected results might arise from complex eco-evolutionary dynamics involved with the 1st and 2nd degree HOIs. Field data suggested the HOIs significantly regulate the sex ratio of the beetle. As the same structure of HOIs appears in other systems, we believe the complexity associated with the 2nd degree HOI would be more common than known and deserve more scientific attention.
New finding of Toxorhina (Ceratocheilus) limoniid fly in Eocene Baltic amber and the biogeographical context of the genus
Authors: Kania-Kłosok Iwona , Krzemiński Wiesław , Szwedo Jacek 
Published: November 2022

AbstractBased on new fossil materials, a new species Toxorhina (Ceratocheilus) christelius sp. nov. has been described herein with complete documentation of drawings and photographs. Features such as wide spine on the gonocoxite differentiating the new species of Toxorhina were discussed. Finding new interesting fossil materials also allowed for providing an emended diagnosis and additional description of known Eocene species—Toxorhina (Ceratocheilus) eridanus. Comparison of chosen morphological features of fossil and recent representatives of the genus were given and key for fossil species of subgenus Ceratocheilus was introduced. Distribution of recent Toxorhina and evolutionary history of the genus were discussed. The results of research on fossil materials prove that the stratigraphic range of the subgenus Ceratocheilus and the genus Toxorhina goes back to the Eocene, there is no evidence of their existence on Earth before. Moreover, these insects were probably associated with a warm climate, they were found for example in Baltic amber, the deposits of which were formed mainly in a subtropical climate. The reach diversity of the genus Toxorhina of recent fauna is strictly observed in tropical zones around the world.
Glutathione peroxidase 4 inhibition induces ferroptosis and mTOR pathway suppression in thyroid cancer
Authors: Sekhar Konjeti R. , Hanna David N. , Cyr Sriram , Baechle Jordan J. , Kuravi Sudhakiranmayi , Balusu Ramesh , Rathmell Kimryn , Baregamian Naira 
Published: November 2022

AbstractPapillary thyroid carcinoma (PTC) demonstrates significantly reduced patient survival with metastatic progression. Tumor progression can be influenced by metabolism, including antioxidant glutathione (GSH). Glutathione peroxidase 4 (GPX4) is a selenoenzyme that uses GSH as a co-factor to regulate lipid peroxidation of cell membranes during increased oxidative stress. GPX4 suppression in tumor cells can induce ferroptosis. This study aims to examine ferroptosis as a potentially critical pathway in effective targeting of thyroid cancer (TC) cells. We treated human TC cells (K1, MDA-T68, MDA-T32, TPC1) with (1S,3R)-RSL3 (RSL3), a small-molecule inhibitor of GPX4 and examined the effects on ferroptosis, tumor cell survival and migration, spheroid formation, oxidative stress, DNA damage repair response, and mTOR signaling pathway in vitro. GPX4 inhibition activated ferroptosis, inducing TC cell death, rapid rise in reactive oxygen species and effectively arrested cell migration in vitro. Suppression of mTOR signaling pathway triggered autophagy. GPX4 genetic knockdown mirrored RSL3 effect on mTOR pathway suppression. RSL3 subdued DNA damage repair response by suppressing phosphorylation of nucleophosmin 1 (NPM1). Thus, observed potent induction of ferroptosis, GPX4-dependent novel suppression of mTOR pathway and DNA damage repair response in preclinical in vitro model of TC supports GPX4 targeting for therapeutic benefit in advanced therapy-resistant thyroid cancers.
Surrogacy analysis of intermediate end-points for overall survival in randomized controlled trials of rhabdomyosarcoma
Authors: Kubota Yuta , Tanaka Kazuhiro , Kawano Masanori , Iwasaki Tatsuya , Itonaga Ichiro , Tsumura Hiroshi 
Published: November 2022

AbstractTreatment of malignant tumors, such as rhabdomyosarcoma (RMS), can improve overall survival (OS). It is time-consuming and expensive for patients to obtain benefits from randomized controlled trials (RCTs) with OS as the primary end-point. Therefore, another surrogate end-point is necessary; however, there is no report on the surrogacy analysis of RMS. In this study, we performed a systematic review of RCTs, involving patients with newly diagnosed RMS, and 11 RCTs were identified. We performed a meta-analysis to assess the surrogacy of intermediate end-points for OS. The correlations between surrogate end-points and OS were investigated using Spearman's rank correlation coefficient (ρ). The coefficient of determination (R2) was employed to measure the strength of the association. A total of 5183 patients were randomly allocated to 34 treatment groups. A marginal correlation (R2 = 0.281, ρ = 0.445) between the hazard ratios (HRs) for event-free survival (EFS) and OS was observed. In patients with localized RMS, the EFS HR had a weaker correlation with OS HR in the sensitivity analysis than that in the primary analysis. Overall, the surrogacy of EFS for OS cannot be confirmed.