julilili42/papers huggingface dataset:
Is There Still a Role for Two-Phase Contrast-Enhanced CT and Virtual Monoenergetic Images in the Era of Photon-Counting Detector CT?
2023-04-18

Background: To compare the diagnostic characteristics between arterial phase imaging versus portal venous phase imaging, applying polychromatic T3D images and low keV virtual monochromatic images using a 1st generation photon-counting CT detector, of CT in patients with hepatocellular carcinoma (HCC). Methods: Consecutive patients with HCC, with a clinical indication for CT imaging, were prospectively enrolled. Virtual monoenergetic images (VMI) were reconstructed at 40 to 70 keV for the PCD-CT. Two independent, blinded radiologists counted all hepatic lesions and quantified their size. The lesion-to-background ratio was quantified for both phases. SNR and CNR were determined for T3D and low VMI images; non-parametric statistics were used. Results: Among 49 oncologic patients (mean age 66.9 ± 11.2 years, eight females), HCC was detected in both arterial and portal venous scans. The signal-to-noise ratio, the CNR liver-to-muscle, the CNR tumor-to-liver, and CNR tumor-to-muscle were 6.58 ± 2.86, 1.40 ± 0.42, 1.13 ± 0.49, and 1.53 ± 0.76 in the arterial phase and 5.93 ± 2.97, 1.73 ± 0.38, 0.79 ± 0.30, and 1.36 ± 0.60 in the portal venous phase with PCD-CT, respectively. There was no significant difference in SNR between the arterial and portal venous phases, including between “T3D” and low keV images (p &gt; 0.05). CNRtumor-to-liver differed significantly between arterial and portal venous contrast phases (p &lt; 0.005) for both “T3D” and all reconstructed keV levels. CNRliver-to-muscle and CNRtumor-to-muscle did not differ in either the arterial or portal venous contrast phases. CNRtumor-to-liver increased in the arterial contrast phase with lower keV in addition to SD. In the portal venous contrast phase, CNRtumor-to-liver decreased with lower keV; whereas, CNRtumor-to-muscle increased with lower keV in both arterial and portal venous contrast phases. CTDI and DLP mean values for the arterial upper abdomen phase were 9.03 ± 3.59 and 275 ± 133, respectively. CTDI and DLP mean values for the abdominal portal venous phase were 8.75 ± 2.99 and 448 ± 157 with PCD-CT, respectively. No statistically significant differences were found concerning the inter-reader agreement for any of the (calculated) keV levels in either the arterial or portal-venous contrast phases. Conclusions: The arterial contrast phase imaging provides higher lesion-to-background ratios of HCC lesions using a PCD-CT; especially, at 40 keV. However, the difference was not subjectively perceived as significant.
Blood transcriptome sequencing identifies biomarkers able to track disease stages in spinocerebellar ataxia type 3
2023-04-18

Abstract Transcriptional dysregulation has been described in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), an autosomal dominant ataxia caused by a polyglutamine expansion in the ataxin-3 protein. As ataxin-3 is ubiquitously expressed, transcriptional alterations in blood may reflect early changes that start before clinical onset and might serve as peripheral biomarkers in clinical and research settings. Our goal was to describe enriched pathways and report dysregulated genes, which can track disease onset, severity or progression in carriers of the ATXN3 mutation (pre-ataxic subjects and patients). Global dysregulation patterns were identified by RNA sequencing of blood samples from 40 carriers of ATXN3 mutation and 20 controls and further compared with transcriptomic data from post-mortem cerebellum samples of MJD patients and controls. Ten genes—ABCA1, CEP72, PTGDS, SAFB2, SFSWAP, CCDC88C, SH2B1, LTBP4, MEG3 and TSPOAP1—whose expression in blood was altered in the pre-ataxic stage and simultaneously, correlated with ataxia severity in the overt disease stage, were analysed by quantitative real-time PCR in blood samples from an independent set of 170 SCA3/MJD subjects and 57 controls. Pathway enrichment analysis indicated the Gαi signalling and the oestrogen receptor signalling to be similarly affected in blood and cerebellum. SAFB2, SFSWAP and LTBP4 were consistently dysregulated in pre-ataxic subjects compared to controls, displaying a combined discriminatory ability of 79%. In patients, ataxia severity was associated with higher levels of MEG3 and TSPOAP1. We propose expression levels of SAFB2, SFSWAP and LTBP4 as well as MEG3 and TSPOAP1 as stratification markers of SCA3/MJD progression, deserving further validation in longitudinal studies and in independent cohorts.
Multi-Horizon Wind Power Forecasting Using Multi-Modal Spatio-Temporal Neural Networks
2023-04-18

Wind energy represents one of the leading renewable energy sectors and is considered instrumental in the ongoing decarbonization process. Accurate forecasts are essential for a reliable large-scale wind power integration, allowing efficient operation and maintenance, planning of unit commitment, and scheduling by system operators. However, due to non-stationarity, randomness, and intermittency, forecasting wind power is challenging. This work investigates a multi-modal approach for wind power forecasting by considering turbine-level time series collected from SCADA systems and high-resolution Numerical Weather Prediction maps. A neural architecture based on stacked Recurrent Neural Networks is proposed to process and combine different data sources containing spatio-temporal patterns. This architecture allows combining the local information from the turbine’s internal operating conditions with future meteorological data from the surrounding area. Specifically, this work focuses on multi-horizon turbine-level hourly forecasts for an entire wind farm with a lead time of 90 h. This work explores the impact of meteorological variables on different spatial scales, from full grids to cardinal point features, on wind power forecasts. Results show that a subset of features associated with all wind directions, even when spatially distant, can produce more accurate forecasts with respect to full grids and reduce computation times. The proposed model outperforms the linear regression baseline and the XGBoost regressor achieving an average skill score of 25%. Finally, the integration of SCADA data in the training process improved the predictions allowing the multi-modal neural network to model not only the meteorological patterns but also the turbine’s internal behavior.
Maltese as a merger of two worlds: A cross-language approach to phonotactic classification
2023-04-18

Maltese is a prime example of a language that emerged through extensive language contact, joining the two linguistic worlds of Semitic and Italo-Romance languages. Previous studies have shown this shared origin on the basis of hands-on comparative methods. However, such approaches may be biased by the researchers perspective and the selected material. To avoid this bias, we employed a naive computational method that classifies words on the basis of their phonotactics. Specifically, we trained a simple two-layer neural network on Tunisian and Italian nouns, i.e. the languages that Maltese emerged from. We used the trained network to classify Maltese nouns based on their phonotactic characteristics as either of Tunisian or of Italian origin. Overall, the network is capable of correctly classifying Maltese nouns as belonging to either of the original languages. Moreover, we find that the classification depends on whether a noun has a sound or broken plural. By manipulating the segment identity in the training input, we found that consonants are more important for the classification of Maltese nouns than vowels. While our results replicate previous comparative studies, they also demonstrate that a more fine grained classification of a language’s origin can be based on individual words and morphological classes.
Trait evolution during a rapid global weed invasion despite little genetic differentiation
2023-04-18

Abstract Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation ( F ST ), and comparing it with phenotypic differentiation ( P ST ), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non‐native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non‐native ranges. The native versus invasive P ST – F ST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C . solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non‐native populations.
The Remarkably Robust, Photoactive Tungsten Iodide Cluster [W6I12(NCC6H5)2]
2023-04-18

Abstract The new heteroleptic tungsten iodide cluster compound [W 6 I 12 (NCC 6 H 5 ) 2 ] is presented. The synthesis is carried‐out from Cs 2 W 6 I 14 and ZnI 2 under solvothermal conditions in benzonitrile solution, yielding red cube‐shaped crystals. [W 6 I 12 (NCC 6 H 5 ) 2 ] represents a heteroleptic [W 6 I 8 ]‐type cluster bearing four apical iodides and two benzonitrile ligands. Molecular [W 6 I 12 (NCC 6 H 5 ) 2 ] clusters form a robust hydrogen bridged crystal structure with high thermal stability and high resistibility against hydrolysis. The electronic structure is analyzed by quantum chemical methods of the calculated electron localization function (ELF) and the band structure. Photoluminescence measurements are performed to verify and describe the photophysical properties of [W 6 I 12 (NCC 6 H 5 ) 2 ]. Finally, the photocatalytic properties of [W 6 I 12 (NCC 6 H 5 ) 2 ] are evaluated as a proof‐of‐concept.
Introduction to the special issue emergence of speech and language from prediction error: error-driven language models
2023-04-18

Last year, 2022, marked the 50th anniversary of the Rescorla-Wagner learning equations – a landmark in the development of learning theory. Originally based on animal learning, the equations and error-driven learning models as a whole were rapidly adopted and applied in several areas of human psychology. While language acquisition research initially took a different path, interest in the role of error-driven learning in language is growing. With the aim of strengthening this emerging research field, sparking discussion and cross-fertilisation of ideas across linguistics, psychology and cognate fields, this Special Issue presents nine papers that address the role of error-driven learning in language. The papers investigate a wide range of subfields of linguistics, and include two review articles, in addition to computational modelling and experimental research. The collection thus serves both as an introduction for those new to the subject and as an overview for those already working in the field.
Why do we trust in online reviews? Integrative literature review and future research directions
2023-04-18

Online reviews are an important information source in decision-making processes. Basing decisions on online reviews, however, requires consumers to trust. Consequently, studying trust has become a major research concern. This article provides an integrative literature review of 70 articles published between 2005 and 2021 that, using both quantitative and qualitative approaches, investigated which factors affect trust in the context of online reviews. Results show that research examined 77 different factors for their effect on trust. For most factors—such as integrity of reviewer, quality of argument, and consistency of review with other reviews—, the findings are relatively distinct. The impact of some other factors—such as homophily, two-sidedness of reviews, and emotionality of reviews—is less clear. To synthesize and systematize the results, I develop a conceptual framework based on a model of the online review process. This framework identifies six groups of factors, namely factors related to reviewers, opinion seekers, platforms, communities, option providers, and external actors. On a more general level, the review finds that research uses many different operationalizations of trust, yet rarely embraces more comprehensive concepts of trust. Based on an assessment of the state of the field, I suggest that future research should corroborate, integrate, and expand upon this body of knowledge.
Recent evolution of flowering time across multiple European plant species correlates with changes in aridity
2023-04-18

Abstract Ongoing global warming and increasing drought frequencies impact plant populations and potentially drive rapid evolutionary adaptations. Historical comparisons, where plants grown from seeds collected in the past are compared to plants grown from freshly collected seeds from populations of the same sites, are a powerful method to investigate recent evolutionary changes across many taxa. We used 21-38 year-old seeds of 13 European plant species, stored in seed banks and originating from Mediterranean and temperate regions, together with recently collected seeds from the same sites for a greenhouse experiment to investigate shifts in flowering phenology as a potential result of adaptive evolution to changes in drought intensities over the last decades. We further used single nucleotide polymorphism (SNP) markers to quantify relatedness and levels of genetic variation. We found that, across species, current populations grew faster and advanced their flowering. These shifts were correlated with changes in aridity at the population origins, suggesting that increased drought induced evolution of earlier flowering, whereas decreased drought lead to weak or inverse shifts in flowering phenology. In five out of the 13 species, however, the SNP markers detected strong differences in genetic variation and relatedness between the past and current populations collected, indicating that other evolutionary processes may have contributed to changes in phenotypes. Our results suggest that changes in aridity may have influenced the evolutionary trajectories of many plant species in different regions of Europe, and that flowering phenology may be one of the key traits that is rapidly evolving. Highlighted student paper We demonstrated that accurately sampled and stored seed collections from conventional seed banks can, with some limitations, be used in a similar way as the increasingly popular resurrection approach sensu stricto. Given the vast availability of seeds stored in seed banks, this opens up a large potential for future research on rapid evolutionary adaptation to changing environmental conditions across a wide variety of taxa suitable for resurrection. Furthermore, this work is unique and novel, as we combine greenhouse experiments with molecular and climatic data to disentangle potential drivers for the observed phenotypic evolution, which, to our knowledge, was never done in resurrection studies.
Accurate long-read sequencing identified GBA variants as a major genetic risk factor in the Luxembourg Parkinson’s study
2023-04-18

<title>Abstract</title> Heterozygous variants in the glucocerebrosidase <italic>GBA</italic>gene are an increasingly recognized risk factor for Parkinson’s disease (PD). Due to the pseudogene <italic>GBAP1</italic> that shares 96% sequence homology with the <italic>GBA</italic>coding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of <italic>GBA</italic>-related PD. We established a novel long-read sequencing technology for assessing the full length of the <italic>GBA</italic> gene. We used subsequent regression models for genotype-phenotype analyses. We sequenced 752 patients with parkinsonism and 806 healthy controls of the Luxembourg Parkinson’s study. All <italic>GBA</italic>variants identified showed a 100% true positive rate by Sanger validation. We found 12% of unrelated PD patients carrying <italic>GBA</italic> variants. Three novel variants of unknown significance (VUS) were identified. Using a structure-based approach, we defined a potential risk prediction method for VUS. This study describes the full landscape of <italic>GBA</italic>-related parkinsonism in Luxembourg, showing a high prevalence of <italic>GBA</italic> variants as the major genetic risk for PD. Our approach provides an important advancement for highly accurate <italic>GBA </italic>variant calling, which is essential for providing access to emerging causative therapies for <italic>GBA</italic> carriers.
Prospects for annihilating dark matter from M31 and M33 observations with the Cherenkov Telescope Array
2023-04-18

M31 and M33 are the closest spiral galaxies and the largest members (together with the Milky Way) of the Local group, which makes them interesting targets for indirect dark matter searches. In this paper, we present studies of the expected sensitivity of the Cherenkov Telescope Array (CTA) to an annihilation signal from weakly interacting massive particles from M31 and M33. We show that a 100 h long observation campaign will allow CTA to probe annihilation cross-sections up to cm s for the annihilation channel (for M31, at a DM mass of 0.3 TeV), improving the current limits derived by HAWC by up to an order of magnitude. We present an estimate of the expected CTA sensitivity, by also taking into account the contributions of the astrophysical background and other possible sources of systematic uncertainty. We also show that CTA might be able to detect the extended emission from the bulge of M31, detected at lower energies by the Fermi/LAT.
Teaching Neuro Images : When alopecia and disk herniations meet vascular leukoencephalopathy
2023-04-18

A 26-year-old Turkish patient presented with progressive spastic gait since age 20 years and premature alopecia. Cerebral and spinal MRI revealed diffuse supra- and infratentorial leukoencephalopathy with recurrent subclinical subcortical infarcts and multiple disk herniations with cervical myelopathy (figure). Targeted panel-sequencing revealed a novel homozygous splice site mutation (c.1005+1G>T; p.?) in HTRA1 , which is known to cause CARASIL (cerebral autosomal-recessive arteriopathy with subcortical infarcts and leukoencephalopathy),1 mostly described in Asians so far.
Classifying the unknown: Insect identification with deep hierarchical Bayesian learning
2023-04-19

Abstract Classifying insect species involves a tedious process of identifying distinctive morphological insect characters by taxonomic experts. Machine learning can harness the power of computers to potentially create an accurate and efficient method for performing this task at scale, given that its analytical processing can be more sensitive to subtle physical differences in insects, which experts may not perceive. However, existing machine learning methods are designed to only classify insect samples into described species, thus failing to identify samples from undescribed species. We propose a novel deep hierarchical Bayesian model for insect classification, given the taxonomic hierarchy inherent in insects. This model can classify samples of both described and undescribed species; described samples are assigned a species while undescribed samples are assigned a genus, which is a pivotal advancement over just identifying them as outliers. We demonstrated this proof of concept on a new database containing paired insect image and DNA barcode data from four insect orders, including 1040 species, which far exceeds the number of species used in existing work. A quarter of the species were excluded from the training set to simulate undescribed species. With the proposed classification framework using combined image and DNA data in the model, species classification accuracy for described species was 96.66% and genus classification accuracy for undescribed species was 81.39%. Including both data sources in the model resulted in significant improvement over including image data only (39.11% accuracy for described species and 35.88% genus accuracy for undescribed species), and modest improvement over including DNA data only (73.39% genus accuracy for undescribed species). Unlike current machine learning methods, the proposed deep hierarchical Bayesian learning approach can simultaneously classify samples of both described and undescribed species, a functionality that could become instrumental in biodiversity monitoring across the globe. This framework can be customized for any taxonomic classification problem for which image and DNA data can be obtained, thus making it relevant for use across all biological kingdoms.
MKK4 Inhibitors—Recent Development Status and Therapeutic Potential
2023-04-19

MKK4 (mitogen-activated protein kinase kinase 4; also referred to as MEK4) is a dual-specificity protein kinase that phosphorylates and regulates both JNK (c-Jun N-terminal kinase) and p38 MAPK (p38 mitogen-activated protein kinase) signaling pathways and therefore has a great impact on cell proliferation, differentiation and apoptosis. Overexpression of MKK4 has been associated with aggressive cancer types, including metastatic prostate and ovarian cancer and triple-negative breast cancer. In addition, MKK4 has been identified as a key regulator in liver regeneration. Therefore, MKK4 is a promising target both for cancer therapeutics and for the treatment of liver-associated diseases, offering an alternative to liver transplantation. The recent reports on new inhibitors, as well as the formation of a startup company investigating an inhibitor in clinical trials, show the importance and interest of MKK4 in drug discovery. In this review, we highlight the significance of MKK4 in cancer development and other diseases, as well as its unique role in liver regeneration. Furthermore, we present the most recent progress in MKK4 drug discovery and future challenges in the development of MKK4-targeting drugs.
Chitin oligomers promote lymphoid innate and adaptive immune cell activation
2023-04-19

Abstract Chitin is a highly abundant N-acetylglucosamine polysaccharide that has been linked to immune responses in the context of fungal infections and allergic asthma, especially to T helper 2 immune responses. Unfortunately, due to the frequent use of crude chitin preparations of unknown purity and degree of polymerization, there is still great uncertainty about how chitin activates different parts of the human immune system. We recently identified chitin oligomers of 6 N-acetylglucosamine units as the smallest immunologically active chitin motif and the innate immune receptor TLR2 as a primary chitin sensor on human and murine myeloid cells, but the response of further immune cells (e.g. lymphoid cells) to oligomeric chitin has not been investigated. Our analysis of primary human immune cells now shows that chitin oligomers activate immune responses of both innate and adaptive lymphocytes: notably, chitin oligomers activated natural killer cells but not B lymphocytes. Moreover, chitin oligomers induced maturation of dendritic cells and enabled potent CD8+ T-cell recall responses. Our results suggest that chitin oligomers not only trigger immediate innate responses in a limited range of myeloid cells but also exert critical activities across the entire human immune system. This highlights chitin oligomer immune activation as an interesting and broadly applicable potential target for both adjuvant development and therapeutic interference in chitin-mediated pathologies.