julilili42/papers huggingface dataset:
Pre-operative lung ablation prediction using deep learning
2024-05-22

Abstract Objective Microwave lung ablation (MWA) is a minimally invasive and inexpensive alternative cancer treatment for patients who are not candidates for surgery/radiotherapy. However, a major challenge for MWA is its relatively high tumor recurrence rates, due to incomplete treatment as a result of inaccurate planning. We introduce a patient-specific, deep-learning model to accurately predict post-treatment ablation zones to aid planning and enable effective treatments. Materials and methods Our IRB-approved retrospective study consisted of ablations with a single applicator/burn/vendor between 01/2015 and 01/2019. The input data included pre-procedure computerized tomography (CT), ablation power/time, and applicator position. The ground truth ablation zone was segmented from follow-up CT post-treatment. Novel deformable image registration optimized for ablation scans and an applicator-centric co-ordinate system for data analysis were applied. Our prediction model was based on the U-net architecture. The registrations were evaluated using target registration error (TRE) and predictions using Bland-Altman plots, Dice co-efficient, precision, and recall, compared against the applicator vendor’s estimates. Results The data included 113 unique ablations from 72 patients (median age 57, interquartile range (IQR) (49–67); 41 women). We obtained a TRE ≤ 2 mm on 52 ablations. Our prediction had no bias from ground truth ablation volumes ( p = 0.169) unlike the vendor’s estimate ( p &lt; 0.001) and had smaller limits of agreement ( p &lt; 0.001). An 11% improvement was achieved in the Dice score. The ability to account for patient-specific in-vivo anatomical effects due to vessels, chest wall, heart, lung boundaries, and fissures was shown. Conclusions We demonstrated a patient-specific deep-learning model to predict the ablation treatment effect prior to the procedure, with the potential for improved planning, achieving complete treatments, and reduce tumor recurrence. Clinical relevance statement Our method addresses the current lack of reliable tools to estimate ablation extents, required for ensuring successful ablation treatments. The potential clinical implications include improved treatment planning, ensuring complete treatments, and reducing tumor recurrence.
Advancing language models through domain knowledge integration: a comprehensive approach to training, evaluation, and optimization of social scientific neural word embeddings
2024-05-22

Abstract This article proposes a comprehensive strategy for training, evaluating, and optimizing domain-specific word2vec-based word embeddings, using social science literature as an example. Our primary objectives are: (1) to train the embeddings utilizing a corpus of social science text, (2) to test their performance against domain-unspecific embeddings using our developed intrinsic and extrinsic evaluation strategy, and (3) to enhance their performance even further by using domain knowledge. As an integral part of this approach, we present SociRel-461 , a domain-knowledge dictionary designed for the intrinsic evaluation and subsequent refinement of social science word embeddings. Using a dataset of 100,000 full-text scientific articles in sociology, we train multiple vector space models, which we then benchmark against a larger, pre-trained general language embedding model as part of our extrinsic evaluation. Furthermore, we developed a transfer learning multi-label classification task for extrinsic evaluation. Our findings reveal that domain-specific embeddings outperform their domain-unspecific counterparts in both intrinsic and extrinsic evaluations. We also investigated the retrofitting post-processing method to enhance domain-unspecific embeddings with the domain knowledge embedded in SociRel-461 . While retrofitting does not enhance our domain-specific vector space models, it significantly improves the performance of the domain-unspecific embeddings. This highlights the potential of retrofitting for the transfer of domain knowledge to domain-unspecific embeddings. Our results emphasize the importance of utilizing domain-specific word embeddings for better performance in domain specific transfer learning tasks, as they outperform conventional embeddings trained on everyday language.
Enamel Caries Lesion Depth Obtained by Optical Coherence Tomography and Transverse Microradiography: A Comparative Study
2024-05-22

Introduction: Visual imaging of subsurface caries lesions is of vital interest in dentistry, which can be obtained by invasive radiography technique as well as by available non-destructive imaging approaches. Thus, as a first step toward the development of a new innovative approach, Spectral-domain optical coherence tomography (SD-OCT) was applied to detect the lesion depth in comparison to the established reference technique (transverse microradiography [TMR]). Methods: Bovine enamel specimens were demineralized for 5 days, following previous studies. For OCT, the resulting artificial lesions were scanned three-dimensionally (SD-OCT) and semi-automated measured (CarLQuant). For TMR, specimens were sectioned and the lesion depth was manually determined (Inspektor Research System). Results: The range of lesion depth detected with OCT was 24.0–174.0 μm (mouth rinse study), 18.0–178.0 μm (toothpastes study) and with TMR 59.2–198.0 μm (mouth rinse study), 33.2–133.4 μm (toothpastes study). We found a strong correlation between both methods in terms of lesion depth (Spearman rank&lt;sub&gt;with outlier&lt;/sub&gt;p &amp;lt; 0.001, Rho = 0.75, Spearman rank&lt;sub&gt;without outlier&lt;/sub&gt;p = 0.001, Rho = 0.79). The two methods produce similar results (Passing-Bablok regression, 1.16). As deeper is the lesion, the smallest is the difference between both methods as indicated by Bland-Altman-plots. Conclusion: Especially in the case of deep lesions, the values obtained by both methods are in agreement, and OCT can potentially substitute TMR to detect and assess lesion depth with the benefit of being non-destructive.
Spatio-Temporal Transferability of Drone-Based Models to Predict Forage Supply in Drier Rangelands
2024-05-22

Unmanned aerial systems offer a cost-effective and reproducible method for monitoring natural resources in expansive areas. But the transferability of developed models, which are often based on single snapshots, is rarely tested. This is particularly relevant in rangelands where forage resources are inherently patchy in space and time, which may limit model transfer. Here, we investigated the accuracy of drone-based models in estimating key proxies of forage provision across two land tenure systems and between two periods of the growing season in semi-arid rangelands. We tested case-specific models and a landscape model, with the expectation that the landscape model performs better than the case-specific models as it captures the highest variability expected in the rangeland system. The landscape model did achieve the lowest error when predicting herbaceous biomass and predicted land cover with better or similar accuracy to the case-specific models. This reinforces the importance of incorporating the widest variation of conditions in predictive models. This study contributes to understanding model transferability in drier rangeland systems characterized by spatial and temporal heterogeneity. By advancing the integration of drone technology for accurate monitoring of such dynamic ecosystems, this research contributes to sustainable rangeland management practices.
Clinical and genetic investigation of 14 families with various forms of short stature syndromes
2024-05-22

Abstract Skeletal dysplasias are a heterogeneous group of disorders presenting mild to lethal defects. Several factors, such as genetic, prenatal, and postnatal environmental may contribute to reduced growth. Fourteen families of Pakistani origin, presenting the syndromic form of short stature either in the autosomal recessive or autosomal dominant manner were clinically and genetically investigated to uncover the underlying genetic etiology. Homozygosity mapping, whole exome sequencing, and Sanger sequencing were used to search for the disease‐causing gene variants. In total, we have identified 13 sequence variants in 10 different genes. The variants in the HSPG2 and XRCC4 genes were not reported previously in the Pakistani population. This study will expand the mutation spectrum of the identified genes and will help in improved diagnosis of the syndromic form of short stature in the local population.
Fossil record misconstrued: Sponge-like fabrics reflect incipient carbonate metamorphism
2024-05-22

<title>Abstract</title> The earliest named stromatolite Cryptozoon Hall, 1884 (Late Cambrian, ca. 490 Ma, eastern New York State), was recently re-interpreted as interlayered microbial mat and non-spiculate (keratosan) sponge deposit. This “classic stromatolite” has come to be central to a fundamental debate concerning the significance or even existence of non-spiculate sponges in carbonate rocks of the Neoproterozoic (Tonian) onward. We determine herein that Cryptozoon has three types of primary carbonate layers: clotted-pelletoidal micrite with microbial filaments, clotted-pelletoidal micrite with vesicular structure, and dense microcrystalline laminae. Using contextual fabric analysis, elemental mapping, cathodoluminescence microscopy, fluid inclusions, electron backscatter diffraction, U–Pb carbonate dating, and regional burial history, the sponge interpretation is rebutted. We conclude that suspect fabric elements are secondary in nature and best explained as products of deep burial alteration. Incipient carbonate metamorphism is early Carboniferous in age (Mississippian, terminal Acadian orogeny). Key petrographic observations include heterogenous recrystallization (aggraded Ostwald ripening) associated with interfingering reaction fronts typical for partially miscible fluids, a granoblastic calcite texture exhibiting preferred crystallographic orientation, and subsequent authigenic white mica (deepest burial; late Carboniferous and Permian Appalachian orogeny). Topotype Cryptozoon is a sub-greenschist metacarbonate stromatolite. The published Tonian to Phanerozoic record of non-spiculate sponges needs to be reassessed.
Clonal evolution and relapse in early‐stage follicular lymphoma – a tree with many branches†
2024-05-22

Abstract Follicular lymphoma (FL) is an indolent B‐cell neoplasm characterised by multistep evolution from premalignant precursor cells carrying the hallmark t(14;18) translocation in the majority of cases. In a new article in The Journal of Pathology , samples of relapsed early‐stage FL – primary manifestation and relapse with or without transformation – initially treated with radiotherapy only, were studied for clonal relationships and evolution. Using somatic mutations and the rearranged immunoglobulin sequences as markers, the majority of paired lymphoma samples showed so‐called branched evolution from a common, possibly premalignant progenitor cell, with both shared and private mutations. In addition, clonally unrelated cases were identified. This and previous studies with similar findings clearly document that relapse or transformation of FL in many instances not necessarily represents a linear progression of disease due to acquisition of additional mutations and therapy resistance, but rather new outgrowths derived from a pool of clonally related, long‐lived, and low proliferating precursor cells, or even unrelated second neoplasms. © 2024 The Authors. The Journal of Pathology published by John Wiley &amp; Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Strong pairwise interactions do not drive interactions in a plant leaf associated microbial community
2024-05-22

Abstract Microbial communities that promote plant growth show promise in reducing the impacts of climate change on plant health and productivity. Understanding microbe-microbe interactions in a community context is paramount for designing effective microbial consortia that enhance plant resilience. In this study, we investigated the dynamics of a synthetic microbial community (SynCom) assembled from Arabidopsis thaliana leaves to elucidate factors shaping community composition and stability. We found notable disparities between in vitro pairwise interactions and those inferred from correlation networks in planta . Our findings suggested that secondary metabolites, particularly antimicrobials, might mediate interactions in vitro , but fade into the background in the community context. Through co-cultivation experiments, we identified the siderophore pseudobactin as a potent antimicrobial agent against several SynCom members, but its impact on community composition in planta was negligible. Notably, dominant SynCom members, such as Pseudomonas koreensis, Flavobacterium pectinovorum , and Sporobolomyces roseus , exhibited only positive correlations, suggesting synergism based on for example exopolysaccharides and biotransformation might drive community dynamics rather than competition. Two correlations between SynCom members in the co-abundance network corresponded with their pairwise in vitro interactions, highlighting the potential for further research, and demonstrating the usefulness of correlation networks in identifying key microbe-microbe interactions. Our findings highlight the importance of considering microbiome-wide interaction studies and synthetic communities in understanding and manipulating plant microbiomes.
Migrating foreign body granulomas after rupture of a breast implant
2024-05-22

Abstract We present the case of an 80‐year‐old female with a history of bluish streaks and painful lumps on her left arm, initially misdiagnosed as a soft tissue infection. Further investigation revealed granulomatous infiltrates in the arm and a ruptured breast implant. Upon presentation, nodular and painful swelling prompted a new biopsy. Histology and electron spectroscopy confirmed silicone deposits within granulomas. The rupture of the breast implant was identified as the likely source of silicone migration to the arm, possibly exacerbated by a past fall. Treatment challenges included the extensive size of the granuloma, leading to a trial of methotrexate therapy with initial improvement but subsequent discontinuation due to poor tolerance. This case underscores the potential for silicone migration from ruptured breast implants to induce distant granulomatous reactions, necessitating individualised treatment approaches.
Crows “count” the number of self-generated vocalizations
2024-05-23

Producing a specific number of vocalizations with purpose requires a sophisticated combination of numerical abilities and vocal control. Whether this capacity exists in animals other than humans is yet unknown. We show that crows can flexibly produce variable numbers of one to four vocalizations in response to arbitrary cues associated with numerical values. The acoustic features of the first vocalization of a sequence were predictive of the total number of vocalizations, indicating a planning process. Moreover, the acoustic features of vocal units predicted their order in the sequence and could be used to read out counting errors during vocal production.
naRNA-LL37 composite DAMPs define sterile NETs as self-propagating drivers of inflammation
2024-05-23

Abstract Neutrophil extracellular traps (NETs) are a key antimicrobial feature of cellular innate immunity mediated by polymorphonuclear neutrophils (PMNs). NETs counteract microbes but are also linked to inflammation in atherosclerosis, arthritis, or psoriasis by unknown mechanisms. Here, we report that NET-associated RNA (naRNA) stimulates further NET formation in naive PMNs via a unique TLR8-NLRP3 inflammasome-dependent pathway. Keratinocytes respond to naRNA with expression of psoriasis-related genes (e.g., IL17, IL36 ) via atypical NOD2-RIPK signaling. In vivo, naRNA drives temporary skin inflammation, which is drastically ameliorated by genetic ablation of RNA sensing. Unexpectedly, the naRNA-LL37 ‘composite damage-associated molecular pattern (DAMP)’ is pre-stored in resting neutrophil granules, defining sterile NETs as inflammatory webs that amplify neutrophil activation. However, the activity of the naRNA-LL37 DAMP is transient and hence supposedly self-limiting under physiological conditions. Collectively, upon dysregulated NET release like in psoriasis, naRNA sensing may represent both a potential cause of disease and a new intervention target.
Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks
2024-05-23

Responses to natural stimuli in area V4—a mid-level area of the visual ventral stream—are well predicted by features from convolutional neural networks (CNNs) trained on image classification. This result has been taken as evidence for the functional role of V4 in object classification. However, we currently do not know if and to what extent V4 plays a role in solving other computational objectives. Here, we investigated normative accounts of V4 (and V1 for comparison) by predicting macaque single-neuron responses to natural images from the representations extracted by 23 CNNs trained on different computer vision tasks including semantic, geometric, 2D, and 3D types of tasks. We found that V4 was best predicted by semantic classification features and exhibited high task selectivity, while the choice of task was less consequential to V1 performance. Consistent with traditional characterizations of V4 function that show its high-dimensional tuning to various 2D and 3D stimulus directions, we found that diverse non-semantic tasks explained aspects of V4 function that are not captured by individual semantic tasks. Nevertheless, jointly considering the features of a pair of semantic classification tasks was sufficient to yield one of our top V4 models, solidifying V4’s main functional role in semantic processing and suggesting that V4’s selectivity to 2D or 3D stimulus properties found by electrophysiologists can result from semantic functional goals.
Validation of Doppler Wind Lidar Measurements with an Uncrewed Aircraft System (UAS) in the Daytime Atmospheric Boundary Layer
2024-05-23

Abstract One of the most widely used systems for wind speed and direction observations at meteorological sites is based on Doppler wind lidar (DWL) technology. The wind vector derivation strategies of these instruments rely on the assumption of stationary and homogeneous horizontal wind, which is often not the case over heterogeneous terrain. This study focuses on the validation of two DWL systems, operated by the German Weather Service [Deutscher Wetterdienst (DWD)] and installed at the boundary layer field site Falkenberg (Lindenberg, Germany), with respect to measurements from a small, fixed-wing uncrewed aircraft system (UAS) of the type Multi-Purpose Airborne Sensor Carrier (MASC-3). A wind vector intercomparison at an altitude range from 100 to 500 m between DWL and UAS is performed, after a quality control of the aircraft’s data accuracy against a cup anemometer and wind vane mounted on a meteorological mast also operating at the location. Both DWL systems exhibit an overall root-mean-square difference in the wind vector retrieval of less than 22% for wind speed and lower than 18° for wind direction. The enhancement or deterioration of these statistics is analyzed with respect to scanning height and atmospheric stability. The limitations of this type of validation approach are highlighted and accounted for in the analysis.
West African Monsoon Dynamics and Its Control on the Stable Oxygen Isotopic Composition of Precipitation in the Late Cenozoic
2024-05-23

Abstract This study presents an overview of the Late Cenozoic evolution of the West African Monsoon (WAM), and the associated changes in atmospheric dynamics and oxygen isotopic composition of precipitation (δ 18 O p ). This evolution is established by using the high‐resolution isotope‐enabled GCM ECHAM5‐wiso to simulate the climatic responses to paleoenvironmental changes during the Mid‐Holocene (MH), Last Glacial Maximum (LGM), and Mid‐Pliocene (MP). The simulated responses are compared to a set of GCM outputs from Paleoclimate Model Intercomparison Project Phase 4 (PMIP4) to assess the added value of a high resolution and model consistency across different time periods. Results show WAM magnitudes and pattern changes that are consistent with PMIP4 models and proxy reconstructions. ECHAM5‐wiso estimates the highest WAM intensification in the MH, with a precipitation increase of up to 150 mm/month reaching 25°N during the monsoon season. The WAM intensification in the MP estimated by ECHAM5‐wiso (up to 80 mm/month) aligns with the mid‐range of the PMIP4 estimates, while the LGM dryness magnitude matches most of the models. Despite an enhanced hydrological cycle in MP, MH simulations indicate a ∼50% precipitation increase and a greater northward extent of WAM than the MP simulations. Strengthened conditions of the WAM in the MH and MP result from a pronounced meridional temperature gradient driving low‐level westerly, Sahel‐Sahara vegetation expansion, and a northward shift of the Africa Easterly Jet. The simulated δ 18 O p values patterns and their relationship with temperature and precipitation are non‐stationarity over time, emphasizing the implications of assuming stationarity in proxy reconstruction transfer functions.
Exploring entertainment utility from football games
2024-05-23

Previous research exploring the role of belief dynamics for consumers in the entertainment industry has largely ignored the fact that emotional reactions are a function of the content and a consumer's disposition towards certain protagonists. By analyzing 19 m tweets in combination with in-play information for 380 football matches played in the English Premier League we contribute to the literature in three ways. First, we present a setting for testing how belief dynamics drive behavior which is characterized by several desirable features for empirical research. Second, we present an approach for detecting fans and haters of a club as well as neutrals via sentiment revealed in Tweets. Third, by looking at behavioral responses to the temporal resolution of uncertainty during a game, we offer a fine-grained empirical test for the popular uncertainty-of-outcome hypothesis in sports.
Temporal and spectral variations of the X-ray pulsar Cen X-3 observed by NuSTAR
2024-05-23

We report a time-resolved analysis of the accreting X-ray pulsar Cen X-3 using observations carried out by NuSTAR , which cover approximately two binary orbits in different intensity states. The pulse profile is relatively stable over the orbital phase and shows energy dependence. It has an obvious double-peaked shape in the energy band below 15 keV –with the second pulse peak decreasing as energy increases– and is gradually dominated by a single peak in higher energy bands. We find that the pulse profile in the energy band of 3–5 keV at high-intensity states shows a subtle triple-peaked shape, with the main peak divided into two subpeaks. We also find a positive correlation between the pulse fraction and both energy and flux. Our spectral analysis reveals that the spectra can be well described by the continuum of Fermi-Dirac cutoff and NPEX models, and the cyclotron line is detected with the centroid energies varying from 26 keV to 29 keV, along with the iron emission line around 6.4 keV. We investigated the dependence between the cyclotron resonant scattering feature (CRSF) centroid energy and luminosity and discuss the theoretical critical luminosity. Although the variation of E cyc − L X is not distinct, there is a possibility that the critical luminosity lies within the range of ∼(0.5 − 4)×10 37 erg s −1 in the band of 4–78 keV. The photon index shows a strong positive correlation with luminosity. Our orbital-phase analysis reveals that the spectral parameters show orbital variability, and the highly variable photoelectric absorption may indicate the existence of clumpy stellar winds.