Miracle-dz/UniFAR-FTUs huggingface dataset:
Edinburgh Research Explorer A systematic approach for the identification of novel, serologically reactive recombinant Varicella-Zoster Virus (VZV) antigens

Background: Varicella-Zoster virus causes chickenpox upon primary infection and shingles after reactivation. Currently available serological tests to detect VZV-specific antibodies are exclusively based on antigens derived from VZV-infected cells. Results: We present a systematic approach for the identification of novel, serologically reactive VZV antigens. Therefore, all VZV open reading frames were cloned into a bacterial expression vector and checked for small scale recombinant protein expression. Serum profiling experiments using purified VZV proteins and clinically defined sera in a microarray revealed 5 putative antigens (ORFs 1, 4, 14, 49, and 68). These were rearranged in line format and validated with pre-characterized sera. Conclusions: The line assay confirmed the seroreactivity of the identified antigens and revealed its suitability for VZV serodiagnostics comparable to commercially available VZV-ELISA. Recombinant ORF68 (gE) proved to be an antigen for high-confidence determination of VZV serostatus. Furthermore, our data suggest that a serological differentiation between chickenpox and herpes zoster may be possible by analysis of the IgM-portfolio against individual viral antigens.
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues

Abstract Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner. Although sc-eQTL mapping is still in its early stage, our database curates the most comprehensive summary statistics of sc-eQTLs published to date. sc-eQTL studies have revolutionized our understanding of gene regulation in specific cellular contexts, and we anticipate that our database will further accelerate the research of functional genomics. Database URL: http://www.sqraolab. com/scqtl
A new sports garment with elastomeric technology optimizes physiological, mechanical, and psychological acute responses to pushing upper-limb resistance exercises

This study aimed to compare the mechanical (lifting velocity and maximum number of repetitions), physiological (muscular activation, lactate, heart rate, and blood pressure), and psychological (rating of perceived exertion) responses to upper-body pushing exercises performed wearing a sports elastomeric garment or a placebo garment. Nineteen physically active young adults randomly completed two training sessions that differed only in the sports garment used (elastomeric technology or placebo). In each session, subjects performed one set of seated shoulder presses and another set of push-ups until muscular failure. The dependent variables were measured immediately after finishing the set of each exercise. Compared to the placebo garment, the elastomeric garment allowed participants to obtain greater muscular activation in the pectoralis major (push-ups: p = 0.04, d = 0.49; seated shoulder press: p < 0.01, d = 0.64), triceps brachialis (push-ups, p < 0.01, d = 0.77; seated shoulder press: p < 0.01, d = 0.65), and anterior deltoid (push-ups: p < 0.01, d = 0.72; seated shoulder press: p < 0.01, d = 0.83) muscles. Similarly, participants performed more repetitions (push-ups: p < 0.01; d = 0.94; seated shoulder press: p = 0.03, d = 0.23), with higher movement velocity (all p ≤ 0.04, all d ≥ 0.47), and lower perceived exertion in the first repetition (push-ups: p < 0.01, d = 0.61; seated shoulder press: p = 0.05; d = 0.76) wearing the elastomeric garment compared to placebo. There were no between-garment differences in most cardiovascular variables (all p ≥ 0.10). Higher diastolic blood pressure was only found after the seated shoulder press wearing the elastomeric garment compared to the placebo (p = 0.04; d = 0.49). Finally, significantly lower blood lactate levels were achieved in the push-ups performed wearing the elastomeric garment (p < 0.01; d = 0.91), but no significant differences were observed in the seated shoulder press (p = 0.08). Overall, the findings of this study suggest that elastomeric technology integrated into a sports garment provides an ergogenic effect on mechanical, physiological, and psychological variables during the execution of pushing upper-limb resistance exercises.
The jelly report: Forecasting jellyfish using email and social media

Ecosystem forecasting has potential societal value, for industry, recreation, and human health applications to name a few. The complexities of ecological systems, the expenses associated with monitoring them, and the suddenness at which forecasts become needed often make forecasts impractical. We tested a novel rapid spin-up daily forecasting system for jellyfish — Cyanea capillata (lion’s mane jellyfish), Aurelia aurita (moon jellyfish), and Staurostoma mertensii (whitecross jellyfish) — in the Gulf of Maine. The system blended satellite data with citizen reports collected via email and social media. The forecasting system took 1–3 weeks of tuning before performance plateaued, after which forecast performance was consistently high. Good model performance did not always correspond with good forecast performance, and predictor variables whose contribution improved model performance in some cases had the opposite effect on forecast performance. An adaptive learning mode provided a very modest improvement in performance. In a test of forecast range, forecast performance decreased significantly at a forecast range of around 1 week. Overall, the approach appeared to be a promising avenue toward rapid spin-up of forecasts for undermonitored systems.
A Combined (U‐Th)/He and Cosmogenic 3He Record of Landscape Armoring by Biogeochemical Iron Cycling

(U‐Th)/He geochronology and cosmogenic 3He in iron oxides reveal mineral precipitation ages as old as 55 Ma and exposure ages greater than 5 Ma for canga‐cemented plateaus in the Quadrilátero Ferrífero, Brazil, showing that lateritic profiles overlying banded iron‐formation (BIF) landscapes in tropical regions have a long history of surface exposure. The long‐term erosion history obtained from cosmogenic 3He on BIF plateaus confirms that relic surfaces persist in the landscape for millions of years. Combined 3He and (U‐Th)/He dating shows that cangas are preferentially goethite cemented by biogeochemical reactions in the subsurface. Importantly, pebbles of hematite‐magnetite in colluvia or shallow creeks draining the canga‐cemented plateaus record a much longer exposure history than in situ canga blocks, showing that even older duricrusts, now eroded, once blanketed these plateaus. Physically stable but biogeochemically dynamic, cangas armor the landscape by pervasive and recurrent iron cycling and cementation, slowing down the delivery of weathered BIF or friable hematite–magnetite ore to erosion.
Short reports : Earliest Evidence for Ground-Edge Axes: 35,400±410 cal BP from Jawoyn Country, Arnhem Land

Evidence for the world's earliest stone tools dates to 3.4 million years ago and pre-dates the earliest known Homo species in eastern Africa. However ground-edged tools did not appear until the dispersal of cognitively fully modern Homo sapiens sapiens out of Africa. We report on the discovery of the earliest securely dated ground-edge implement in the world at Nawarla Gabarnmang (northern Australia). The fragment of ground-edge axe is sandwiched between four statistically indistinguishable AMS radiocarbon dates of 35,400±410 cal BP, indicating technological innovations by fully modern Homo sapiens sapiens at the eastern end of the Out-of-Africa 2 Southern Arc dispersal route.
Fishes Associated with Oil and Gas Platforms in Louisiana's River-Influenced Nearshore Waters

xix CHAPTER I: GENERAL INTRODUCTION . 1 References . 7 CHAPTER II: PHYSICOCHEMICAL FEATURES OF THE LOUISIANA NEARSHORE ZONE (≤ 25 m WATER DEPTH): A HABITAT PERSPECTIVE . 12 Epitome . 12 Introduction . 13 Methods . 17 Coastwide survey . 17 Comprehensive hydrographic analyses . 19 Results . 22 Coastwide survey . 22 Comprehensive hydrographic analyses . 33 Discussion . 40 Conclusions . 45 References . 46 CHAPTER III: COASTWIDE FISH ASSEMBLAGES AROUND SMALL OIL AND GAS PLATFORMS IN LOUISIANA’S NEARSHORE WATERS . 54 Epitome . 54 Introduction . 55 Methods . 59 Field . 59 Video processing . 61 Statistical analyses . 64 Results . 66 Observations . 66 Statistical analyses . 70 Discussion . 85 Conclusions . 92 References . 94
Frequency-specific cortico-subcortical interaction in continuous speaking and listening

Speech production and perception involve complex neural dynamics in the human brain. Using magnetoencephalography (MEG), our study explores the interaction between cortico-cortical and cortico-subcortical connectivities during these processes. Our connectivity findings during speaking revealed a significant connection from the right cerebellum to the left temporal areas in low frequencies, which displayed an opposite trend in high frequencies. Notably, high-frequency connectivity was absent during the listening condition. These findings underscore the vital roles of cortico-cortical and cortico-subcortical connections within the speech production and perception network. The results of our new study enhance our understanding of the complex dynamics of brain connectivity during speech processes, emphasizing the distinct frequency-based interactions between various brain regions.
Identification of ESCRT-III like protein sequences in yeast

Endosomal sorting complex required for transport (ESCRT-III) is a membrane remodeling complex involved in a large number of cellular processes. It appears to perform an essential function in eukaryotes, since to date no eukaryotic organism completely devoid of ESCRT-III has been found. Yet, yeast cells with a deletion of all eight known ESCRT-III genes are viable. We therefore searched for new, previously undiscovered ESCRT-III like proteins in yeast. HHPred uncovered several proteins with similarity to Snf7. The similarity was mostly restricted to the α1-α2 hairpin region of Snf7. A conserved pattern of amino acids was detected in this region. The protein encoded by ORF YPL199c strikingly resembled Snf7 in its secondary structure. Since this protein could be the ninth member of the ESCRT-III family in yeast, we called it Nbr9 (“number nine”). Nbr9 is palmitoylated and localizes to the plasma membrane. In contrast to other palmitoylated proteins, it is not associated with lipid rafts. When NBR9 was deleted in the octuple ESCRT-III deletion background, the yeast cells were still viable. However, despite a number of experiments, we do not have evidence at present that Nbr9 is part of an alternative ESCRT-III complex.
Computational Characterization of 3 9 Splice Variants in the GFAP Isoform Family

Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein specific to central nervous system (CNS) astrocytes. It has been the subject of intense interest due to its association with neurodegenerative diseases, and because of growing evidence that IF proteins not only modulate cellular structure, but also cellular function. Moreover, GFAP has a family of splicing isoforms apparently more complex than that of other CNS IF proteins, consistent with it possessing a range of functional and structural roles. The gene consists of 9 exons, and to date all isoforms associated with 3 9 end splicing have been identified from modifications within intron 7, resulting in the generation of exon 7a (GFAP d / e ) and 7b (GFAP k ). To better understand the nature and functional significance of variation in this region, we used a Bayesian multiple change-point approach to identify conserved regions. This is the first successful application of this method to a single gene – it has previously only been used in whole-genome analyses. We identified several highly or moderately conserved regions throughout the intron 7/7a/7b regions, including untranslated regions and regulatory features, consistent with the biology of GFAP. Several putative unconfirmed features were also identified, including a possible new isoform. We then integrated multiple computational analyses on both the DNA and protein sequences from the mouse, rat and human, showing that the major isoform, GFAP a , has highly conserved structure and features across the three species, whereas the minor isoforms GFAP d / e and GFAP k have low conservation of structure and features at the distal 3 9 end, both relative to each other and relative to GFAP a . The overall picture suggests distinct and tightly regulated functions for the 3 9 end isoforms, consistent with complex astrocyte biology. The results illustrate a computational approach for characterising splicing isoform families, using
KBJNet: Kinematic Bi-Joint Temporal Convolutional Network Attention for Anomaly Detection in Multivariate Time Series Data

Detecting anomalies in multivariate time series data is crucial to ensure the security and stability of industrial processes. Yet, it remains challenging due to the absence of labeled anomaly data, the complexity of time series data, and the large dataset size. We propose KBJNet, an innovative model incorporating Transformer and Dilated Temporal Convolutional Network (TCN) techniques to address these obstacles. Our model employs a Single TCN-Attention Network, utilizing a single layer of Transformer encoder, making it highly efficient for inference. To further enhance its robustness, we introduce a novel adaptive attention mechanism that dynamically weights temporal context, enabling KBJNet to capture long-range dependencies in time series data effectively. The evaluation of KBJNet on eight publicly available datasets revealed that KBJNet considerably outperforms the most recent methods, enhancing F1 scores by as much as 6%. This result represents a significant contribution to
Enabling Non-Experts to Develop Distributed Trust Applications

Distributed trust applications provide strong guarantees of security, in that they require a set of multiple “trust domains” to be compromised in order to compromise an entire application, rather than relying on a central point of attack, which is often the target of attacks and data breaches. Yet, distributed trust has yet to see wide-scale adoption despite its plethora of benefits. The DoTS platform intially proposed and presented by Tan and Kaviani promises to solve many of these issues by addressing the practical needs of distributed trust applications as a software development kit for developers to build applications with distributed trust. In this paper, we present mid-and low-level architectural modifications to the DoTS platform in order to make the platform and API more accessible to developers, while fulfilling its original vision. Wedemonstrate both that our modifications maintain the simplicity of developing new applications on top of DoTS, with our secret key recovery and ( 𝑛,𝑡 ) -threshold ECDSA signing applcia-tions requiring fewer than 500 lines of integration code each, and we demonstrate that it is equally easy to port existing applications to utilize the DoTS platform, replacing over 2,600 lines of code in MP-SPDZ with simple function invocations. We show that, by leveraging the unique conditions of such applications typically executing in distinct trust domains in geographically separated regions, applications utilizing the updated DoTS design suffer as little as 6.4–9.5% overhead compared to ad hoc, complex, application-specific network solutions.
Introducing A Reflective Framework for the Assessment and Recognition of Microcredentials

Assessment and recognition are key aspects of microcredentials, and other courses offered on massive open online course (MOOC) platforms. Microcredentials are designed to address the needs of employers and learners looking for units of study at a higher education level aligned with the requirements of labour markets. This paper reviews current methods for assessment and recognition used in MOOCs and microcredentials, proposing a framework with seven aspects and two checklists for use at planning and design stages. The framework is based on a review of 27 documents and a synthesis process. It provides a tool for microcredential producers to check whether the best ID verification, assessment, recognition, and quality assurance approaches are in place, enabling them to reflect on, and possibly improve, their choices.
Origin and evolution processes of hybrid event beds in the Lower Cretaceous of the Lingshan Island, Eastern China

ABSTRACT On the basis of detailed sedimentological investigation, three types of hybrid event beds (HEBs) together with debrites and turbidites were distinguished in the Lower Cretaceous sedimentary sequence on the Lingshan Island in the Yellow Sea, China. HEB 1, with a total thickness of 63–80 cm and internal bipartite structures, is characterised by a basal massive sandstone sharply overlain by a muddy sandstone interval. It is interpreted to have been formed by particle rearrangement at the base of cohesive debris flows. HEB 2, with a total thickness of 10–71 cm and an internal tripartite structure, is characterised by a normal grading sandstone base, followed by muddy siltstone middle unit and capped with siltstones; the top unit of HEB 2 may in places be partly or completely eroded. The boundary between the lowest unit and the middle unit is gradual, whereas that between the middle unit and the top unit is sharp. HEB 2 may be developed by up-dip muddy substrate erosion. HEB 3, with a total thickness up to 10 cm and an internal bipartite structure, is characterised by a basal massive sandstone sharply overlain by a muddy siltstone interval. The upper unit was probably deposited by cohesive debris flow with some plant fragments and rare mud clasts. HEB 3 may be formed by the deceleration of low-density turbidity currents. The distribution of HEBs together with debrites and turbidites implies a continuous evolution process of sediment gravity flows: debris flow → hybrid flow caused by particle rearrangement → high-density turbidity current → hybrid flow caused by muddy substrate erosion → low-density turbidity current → hybrid flow caused by deceleration.
Brief exposure to enriched environment rapidly shapes the glutamate synapse in the rat brain: a metaplastic �ngerprint

Environmental enrichment (EE) has been shown to produce bene�cial effects in addiction disorders; however, due to its complexity, the underling mechanisms are not yet fully elucidated. Recent evidence suggests that EE, acting as a metaplastic agent, may affect glutamatergic mechanisms underlying appetitive memory and in turn, modulate reward-seeking behaviors. Here, we explore the hypothetical metaplastic effects induced by brief EE exposure on glutamatergic transmission in brain areas involved in rewarding and memory processes. Adult male Sprague-Dawley rats were exposed to EE for 22h and the expression of critical elements of the glutamate synapse were measured 2h after the end of EE in medial prefrontal cortex (mPFC), nucleus accumbens (NAc) and hippocampus (Hipp). We focused our attention on the expression of NMDA and AMPA receptor subunits, their scaffolding proteins SAP102 and SAP97, vesicular and membrane glutamate transporters vGluT1 and GLT-1, and critical structural components such as proteins involved in morphology and function of glutamatergic synapses, PSD95 and Arc/Arg3.1. Our �ndings demonstrate that a brief EE exposure induces metaplastic changes on glutamatergic mPFC-NAc-Hipp brain areas, which are critical for reward and learning processes. Such changes were area-specic and involved a rearrangement of postsynaptic NMDA/AMPA receptor subunit composition, as well as changes in the expression of their main scaffolding proteins thus in�uencing the retention of such receptors at synaptic sites. Our data indicate that brief EE exposure is su�cient to cause metaplastic activity at glutamatergic synapses in mPFC-NAc-Hipp circuits, which may modulate several mental processes such as rewarding, learning and memory processes.
MIT Open Access Articles Learning multimodal graph-to-graph translation for molecular optimization

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines
The “Great White Storm” of 1913

The “Great White Storm” of 1913 was one of the strongest storms to hit the Great Lakes region, and likely one of the most devastating natural disasters in the whole of the United States. The intensity of the storm led to many deaths and important economic damage. The recent development of reanalysis data sets such as version 2c of the “Twentieth Century Reanalysis” (20CRv2c) and the ECMWF reanalyses ERA-20C and CERA-20C provide valuable information to analyse extreme events such as the “Great White Storm” of 1913. It can be used to study the atmospheric mechanisms leading to such intense storms, which might contribute to better assess similar weather events in the future. The “Great White Storm” of 1913 is well reproduced in 20CRv2c. The reanalysis captures the key ingredient responsible for the development of the storm. However, it fails to give a good estimate of smaller scale parameters such as snow depth. Further analyses are required concerning precipitation, as prolonged snowfall was one of the major problems for people during the storm. Although it appears that 20CRv2c better captures the storm than ERA-20C, such conclusions depend critically on the variables studied.
Genetic Improvement of Last Level Cache

With increasing reliance on multi-core parallel computing performance is evermore dominated by interprocessor data communication typically provided by last level cache (LLC) shared between CPUs. In an 8 core 3.6 GHz desktop using multiple local searches, the Magpie parameter tuning genetic improvement (GI) system was able to reduce L3 cache access (load + stores) four fold on an existing open source 7000 line C PARSEC parallel computing VIPS image benchmark.