Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Ground Glass Opacity Features in Patients With Lung Cancer: Automated Extraction and Longitudinal Analysis via Deep Learning–Based Natural Language Processing

Background: Ground-glass opacities (GGOs) appearing in computed tomography (CT) scans may indicate potential lung malignancy. Proper management of GGOs based on their features can prevent the development of lung cancer. Electronic health records are rich sources of information on GGO nodules and their granular features, but most of the valuable information is embedded in unstructured clinical notes. Objective: We aimed to develop, test, and validate a deep learning–based natural language processing (NLP) tool that automatically extracts GGO features to inform the longitudinal trajectory of GGO status from large-scale radiology notes. Methods: We developed a bidirectional long short-term memory with a conditional random field–based deep-learning NLP pipeline to extract GGO and granular features of GGO retrospectively from radiology notes of 13,216 lung cancer patients. We evaluated the pipeline with quality assessments and analyzed cohort characterization of the distribution of nodule features longitudinally to assess changes in size and solidity over time. Results: Our NLP pipeline built on the GGO ontology we developed achieved between 95% and 100% precision, 89% and 100% recall, and 92% and 100% F 1 -scores on different GGO features. We deployed this GGO NLP model to extract and structure comprehensive characteristics of GGOs from 29,496 radiology notes of 4521 lung cancer patients. Longitudinal analysis revealed that size increased in 16.8% (240/1424) of patients, decreased in 14.6% (208/1424), and remained unchanged in 68.5% (976/1424) in their last note compared to the first note. Among 1127 patients who had longitudinal radiology notes of GGO status, 815 (72.3%) were reported to have stable status, and 259 (23%) had increased/progressed status in the subsequent notes. Conclusions: Our deep learning–based NLP pipeline can automatically extract granular GGO features at scale from electronic health records when this information is documented in radiology notes and help inform the natural history of GGO. This will open the way for a new paradigm in lung cancer prevention and early detection.
Relative effects of static and dynamic abiotic conditions on foraging behaviour in breeding Sandwich terns

: Where and when animals forage depends on the spatio-temporal distribution and catch-ability of their prey. In dynamic environments, animals can repeatedly target areas that provide predictable availability of prey or may search for ephemeral conditions of high prey availability. However, how foraging behaviour is initiated in response to static versus dynamic environmental conditions is difficult to study, since both environmental data sources are often lacking. In this study, central-place foraging Sandwich terns were tracked using GPS loggers during foraging. Hidden Markov models showed that the probability of switching between transit and foraging was most strongly affected by the static variable sediment type. Wave period (a dynamic variable related to weather), salinity (a dynamic variable) and water depth (another static variable) affected the transition probability to a lesser extent. Cloud cover, wind speed and current speed were only included in lower ranked models. Air and water temperature were not included in any model. Consistent with the greater importance of static versus dynamic abiotic conditions, consistency between foraging trips of the same individual varied irrespective of tidal, diurnal or seasonal cycles, although trips made close in time within a season were slightly more similar than trips with a larger time gap. We suggest that Sandwich terns target broad areas with coarser sediments, where sandeels (Ammodytidae) are more common, and that weather variables may be related to prey visibility. Our study suggests that even in highly dynamic environments, static environmental variables may more strongly affect foraging behaviour of coastal seabirds than dynamic variables.
Dynamic CT Study Apnea Syndrome: Cephalometric and Degrees of Severity of Obstructive Sleep Cross-sectional Area Changes in Different Evaluation of the Upper Airway

BACKGROUND AND PURPOSE: The upper airway lumen is narrower in patients with obstructive sleep apnea syndrome (OSAS) than normal subjects. In this study, we examined changes of the upper airway cross-sectional area in each phase of respiration in different degrees of severity of OSAS with dynamic CT and investigated whether these changes have any correlation with sleep apnea severity parameters, including polysomnography (PSG) and cephalometry. MATERIALS AND METHODS: Between May and November 2004, 47 patients who had at least 2 of 3 major symptoms of snoring, daytime somnolence, and apnea with witness were included in this prospective study. As control group, 24 habitual snorers were studied. All patients underwent PSG and upper airway CT. The average number of episodes of apnea and hypopnea per hour of sleep (the apnea-hypopnea index, AHI) was calculated. An AHI of 5 –29 represented mild/moderate OSAS and an AHI > 30 represented severe OSAS. Cross-sectional area of the airway at the level of oropharynx and hypopharynx were obtained in each phase of quiet tidal breathing and at the end of both the forced inspiration and expiration. Six standard cephalometric measurements were made on the lateral scout view. All parameters were compared between controls and mild/moderate and severe OSAS groups. RESULTS: Twenty-seven patients had mild/moderate OSAS, and 20 patients had severe OSAS. Patients with severe OSAS had significantly narrower cross-sectional area at the level of uvula in expiration, more inferiorly positioned hyoid bone, and thicker soft palate compared with patients with mild/moderate OSAS ( P < .05) and the control group ( P < .05). In addition, severe OSAS patients had bigger neck circumference than those in the control group ( P < .05). CONCLUSION: Patients with severe OSAS had
The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational 3 State 4

1 2 The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational 3 State 4 5 6 Authors 7 8 Rachael A. Mansbach,1† Srirupa Chakraborty,1,2† Kien Nguyen,1†, David C. Montefiori,3 Bette 9 Korber,1 S. Gnanakaran1* 10 11 Affiliations 12 1 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 13 87545 14 2 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 15 3 Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710 16 17 * Correspondence and requests for materials should be addressed to S. Gnanakaran 18 gnana@lanl.gov 19 † These authors contributed equally to this work 20 21
Parallel Colorful h-star Core Maintenance in Dynamic Graphs

The higher-order structure cohesive subgraph mining is an important operator in many graph analysis tasks. Recently, the colorful h -star core model has been proposed as an effective alternative to h -clique based cohesive subgraph models, in consideration of both efficiency and utilities in many practical applications. The existing peeling algorithms for colorful h -star core decomposition are to iteratively delete a node with the minimum colorful h -star degree. Hence, these methods are inherently sequential and suffer from two limitations: low parallelism and inefficiency for dynamic graphs. To enable high-performance colorful h -star core decomposition in large-scale graphs, we propose highly parallelizable local algorithms based on a novel concept of colorful h -star n -order H-index and conduct thorough analyses for its properties. Moreover, three optimizations have been developed to further improve the convergence performance. Based on our local algorithm and its optimized variants, we can efficiently maintain colorful h -star cores in dynamic graphs. Furthermore, we design lower and upper bounds for core numbers to facilitate identifying unaffected nodes in presence of graph updates. Extensive experiments conducted on 14 large real-world datasets with billions of edges demonstrate that our proposed algorithms achieve a 10 times faster convergence speed and a three orders of magnitude speedup when handling graph changes.
PrivateFL: Accurate, Differentially Private Federated Learning via Personalized Data Transformation

Federated learning (FL) enables multiple clients to collaboratively train a model with the coordination of a central server. Although FL improves data privacy via keeping each client’s training data locally, an attacker—e.g., an untrusted server— can still compromise the privacy of clients’ local training data via various inference attacks. A de facto approach to preserving FL privacy is Differential Privacy (DP), which adds random noise during training. However, when applied to FL, DP suffers from a key limitation: it sacrifices the model accuracy substantially—which is even more severely than being applied to traditional centralized learning—to achieve a meaningful level of privacy. In this paper, we study the accuracy degradation cause of FL+DP and then design an approach to improve the accuracy. First, we propose that such accuracy degradation is partially because DP introduces additional heterogeneity among FL clients when adding different random noise with clipping bias during local training. To the best of our knowledge, we are the first to associate DP in FL with client heterogeneity. Second, we design P RIVATE FL to learn accurate, differentially private models in FL with reduced heterogeneity. The key idea is to jointly learn a differentially private, personalized data transformation for each client during local training. The personalized data transformation shifts client’s local data distribution to compensate the heterogeneity introduced by DP, thus improving FL model’s accuracy. In the evaluation, we combine and compare P RIVATE FL with eight state-of-the-art differentially private FL methods on seven benchmark datasets, including six image and one non-image datasets. Our results show that P RIVATE FL learns accurate FL models with a small ε , e.g., 93.3% on CIFAR-10 with 100 clients under ( ε = 2, δ = 1 e − 3)-DP. Moreover, P RIVATE FL can be combined with prior works to reduce DP-induced heterogeneity
Construction of Bernstein-based words and their patterns

With inspiration of the deﬁnition of Bernstein basis functions and their recurrence relation, in this paper we give construction of new concept so-called Bernstein-based words. By classifying these Bernstein-based words as ﬁrst and second kind, we investigate their some fundamental properties involving periodicity and symmetricity. Providing schematic algorithms based on tree diagrams, we also illustrate the construction of the Bernstein-based words. Moreover, we give computational implementations of Bernstein-based words in the Wol-fram Language. By executing these implementations, we present some tables of Bernstein-based words and their decimal equivalents. In addition, we present black-white and 4-colored patterns arising from the Bernstein-based words with their potential applications. We also give some ﬁnite sums and generating functions for the lengths of the Bernstein-based words. We show that these functions are of relationships with the Catalan numbers, the centered m-gonal numbers, the Laguerre polynomials, certain ﬁnite sums, and hypergeometric functions. We also raise some open questions and provide some comments on our results. Finally, we investigate relations between the slopes of the Bernstein-based words and the Farey fractions
Dear Editor, We appreciate the prompt reviews and would like to thank the two reviewers for insightful comments and suggestions on our manuscript entitled “Characteristics of fine particle matters at the top of Shanghai Tower” (MS

We appreciate the prompt reviews and would like to thank the two reviewers for insightful comments and suggestions on our manuscript entitled “Characteristics of fine particle matters at the top of Shanghai Tower” (MS No.: egusphere-2022-782). We have carefully considered all comments and suggestions. Listed below are our point-by-point responses to all comments and suggestions of this reviewer (Reviewer’s points in black, our responses in blue).
The manuscript by Zhao et al. aims at estimating future changes in global distributions and the budget of mineral dust aerosol by making use of results from the CMIP6 model

Response: Thank you very much for your constructive suggestions. We have made our best to revise the manuscript following your comments. In this revision, we included all the available model output from CMIP6, validated the model performance with sitelevel AOD, added the uncertainty ranges for the projections, and compared the future changes of dust emissions over vegetation-free grids. We hope our revisions and responses could answer your concerns.
A model for the interaction of phytoplankton aggregates and the environment: approximation and parameter estimation

Abstract We present a model for the dynamics of phytoplankton aggregates and their interaction with the environment in a well-mixed reactor or surface layer of a water column. The biophysical problem yields a nonlinear partial differential equation coupled with a general system of ordinary differential equations. We first develop a finite difference scheme for approximating the solution of this model. Then convergence results are established for the finite difference method and existence-uniqueness of solutions are obtained. A least-squares parameter estimation method is presented to illustrate the performance of the model against a real dataset, and to highlight the effects of aggregate growth on algal bloom dynamics and nutrient consumption rates. The model is well-suited to complement microcosm studies and can accommodate the effects of a wide range of environmental conditions.
The Theory of Turbulent Diffusion in the Atmosphere (III)The Theoretical Distribution of Airborne Pollution from Tall Stacks

The essential features of the turbulent diffusion in the atmosphere exist in that the atmospheric turbulence consists of eddies, whose dimensions are very different from each other, and that the scale of eddies effective for the diffusion is related to the scale of the diffusion phenomenon. In the present paper, the author treated theoretically the turbulent diffusion from a point source by means of the relations between the statistical quantities of the turbulence and the spatial length under analysis. Using this method, it was made possible to take into consideration the circumstances that small eddies are effective-for the diffusion near the point source and large eddies become effective, as the particles depart from the source. By this investigation, the so-called Lagrangian correlation coefficient was derived and the interrelation between the Eulerian and Lagrangian correlation coefficients was obtained.
Derivational and inflectional affixes in @TheGoodQuote’s posts on instagram

This study investigates about two of branches of bound morphemes which focused on derivational and inflectional affixes. The data of the study are on texts of quotes of @TheGoodQuote’s posts on Instagram. Two aims of this study are first is to find out the most frequently found kinds of derivational and inflectional affixes in @TheGoodQuote posts on Instagram and second is to elaborate the processes and to find out intended meanings of derivational and inflectional affixes in @TheGoodQuote posts on Instagram. The descriptive content analysis is the method applied in this study. The researcher uses the classification of derivational affixes by using Fromkin, et al (2014)’s theory about derivation which change grammatical classes which included noun derivation, verb derivation, adjective derivation, and adverb derivation. In addition, the theory from Lieber (2009) about derivation without changing grammatical classes are also involved in this study which consist of negative affixes, quantitative affixes, noun to noun, and prepositional and relation affixes. While, eight inflectional affixes theory used is according to Fromkin, et al (2014). The findings of the study reveal that from 137 words which consist of derivational and inflectional affixes. 62 words indicate derivations which change the grammatical classes which involve 31 for noun derivations which affixes produced are –ation, -ion, -age, -ence, -er, -or, -ment, -th, -ness, -ity, -ty, -dom, 12 for adjective derivations which affixes produced are –ous, -able, -ful, -y, -ish, -ive, -al, -less, 14 for adverb derivations which only found affix produced is –ly, and 5 for verb derivations which affixes produced are en-, em-, -ize. Furthermore, 23 words indicate derivations without changing grammatical classes which involve 10 for negative which affixes produced are un-, dis-, im-. , 6 for noun to noun which affixes produced are -ship and –hood, 3 for preposition and relation which affixes produced are over-, out-, and 4 for quantitative which affixes produced is re-. While, 52 words indicate eight kinds of inflectional affixes by the most frequently found is -s plural (22 words), -s third person singular (6 words), -er comparative (6 words), –ing for present progressive (6 words), 4 for –est superlative (4 words), –en past participle (3 words), –ed past tense (2 words), –‘s possessive (3 words). The intended meanings are about the derivational and inflectional affixes words that related to the quotations that are analyzed.
Jump-based estimation for nonlinear stiffness and damping parameters

To overcome the limitation that only stiffness nonlinearity can be estimated via jump frequencies, this work introduces jump amplitudes as a supplement condition in the estimation of both stiffness and damping nonlinearities. An estimation method is proposed for a single-degree-of-freedom system containing both stiffness and damping nonlinearities. The idea may be applied to other nonlinear systems. The method is based on the measurements of both jump frequencies and jump amplitudes of the system subject to swept-sine excitations respectively in frequency and in amplitude. The experimental data yield frequency response curves at a fixed excitation amplitude and amplitude response curves at a fixed frequency. Based on the measured jump frequencies and jump amplitudes of the displacements, the system parameters can be determined by the method of harmonic balance. A numerical example is presented to demonstrate the application of the proposed approach and to check approximate explicit analytical expressions of the parameter estimation. To validate the effectiveness of the proposed approach, an experiment is performed on a vibration isolator with strongly nonlinear stiffness and damping. The estimation results show that the proposed method can estimate the stiffness and the damping parameters of the system with strong nonlinearities. Hence exploiting the knowledge about nonlinear jump phenomena is a promising approach to parameter estimations.
Application of laser Compton photon beam to nondestructive tests: — A spin-off technology from nuclear physics —@@@― レーザーコンプトン光子ビームの発生と非破壊検査への応用 ―

−89− Synthesiology Vol.8 No.2 pp.89-96(May 2015) 1 はじめに 科学技術には研究機関の基礎研究成果を、企業活動へ 太く強く結びつけることが要求される場合がある。 いわゆ る「橋渡し研究」である。 橋渡し研究とは、自分の拘りや 考え方を整理して社会に受け入れられる姿に徐々に近づけ ていく作業である。 成果を急ぐあまり安易に妥協して周囲 に迎合すると研究レベルが下がってしまうし、自分のやり 方に拘り過ぎると社会から離れてしまう。 繊細で忍耐強い 擦り合わせ作業が必要である。 さらに、タイムリミットもあ る。 研究活動には多くの要因があり、これらのバランスを 取ることで研究は成長し、成果はさまざまな形態で拡散し 人々に利用される。 この論文は、新たなコンセプトの産業用ラジオグラフィ装 置を社会へ提案すること、そして広く公開利用に供すること で産業技術としての価値を見極めることを目的としている。 研究としては装置の性能向上やチャンピオンデータを出すこ とが目的ではなく、ユーザーの声を聴くことでマーケティン グを行い、適切な形で研究成果を社会に橋渡しすることを 目的とした。 さらには、将来の研究につながるスピンオフ 技術の育成や調査も行う。 この研究は以下のシナリオによって構成される。 1要素技術の開発と高度化:要素技術を開発して原理実証 を行う。 2ユーザー利用研究の推進:装置のユーティリティーを高度 化してユーザー利用を推進する。 ユーザーの声を多く聴 き、研究の方向性を微調整する。 3研究成果の検証:得られた成果は当初の予想どおりで あったか、予想外であるなら何を見落としていたか、他に もっと良い方法はないか等を、ユーザーの声を聴きながら 客観的に理解し、当初の研究構想を検証する。 4研究方向性の決定:今後の装置や技術開発の要点を整 理する。 研究を進めるかどうか、費用対効果や所属組織 の諸事情を加味して判断する。 判断結果にしたがって速 やかに行動する。 豊川 弘之
Clinical and genomic diversity of Treponema pallidum subsp. pallidum: A global, multi-center study of early syphilis to inform vaccine research

Background The continuing increase in syphilis rates worldwide necessitates development of a vaccine with global efficacy. We conducted a multi-center, observational study to explore Treponema pallidum subsp. pallidum (TPA) molecular epidemiology essential for vaccine research by analyzing clinical data and specimens from early syphilis patients using whole-genome sequencing (WGS) and publicly available WGS data. Methods We enrolled patients with primary (PS), secondary (SS) or early latent (ELS) syphilis from clinics in China, Colombia, Malawi and the United States between November 2019 - May 2022. Inclusion criteria included age >18 years, and syphilis confirmation by direct detection methods and/or serological testing. TPA detection and WGS were conducted on lesion swabs, skin biopsies/scrapings, whole blood, and/or rabbit-passaged isolates. We compared our WGS data to publicly available genomes, and analysed TPA populations to identify mutations associated with lineage and geography. Findings We screened 2,820 patients and enrolled 233 participants - 77 (33%) with PS, 154 (66%) with SS, and two (1%) with ELS. Median age of participants was 28; 66% were cis-gender male, of which 43% reported identifying as gay, bisexual, or other sexuality. Among all participants, 56 (24%) had HIV co-infection. WGS data from 113 participants demonstrated a predominance of SS14-lineage strains with geographic clustering. Phylogenomic analysis confirmed that Nichols-lineage strains are more genetically diverse than SS14-lineage strains and cluster into more distinct subclades. Differences in single nucleotide variants (SNVs) were evident by TPA lineage and geography. Mapping of highly differentiated SNVs to three-dimensional protein models demonstrated population-specific substitutions, some in outer membrane proteins (OMPs) of interest. Interpretation Our study involving participants from four countries substantiates the global diversity of TPA strains. Additional analyses to explore TPA OMP variability within strains will be vital for vaccine development and improved understanding of syphilis pathogenesis on a population level. Funding National Institutes of Health, Bill and Melinda Gates Foundation
Prebiotic Supplements Correct Oral Probiotic Deficiency for Lasting Allergy Relief

Allergic rhinitis has increased in the last fifty years from affecting less than a percent to more than twenty-six percent of the population[1]. Today, more than one hundred million people in the US suffer from these seasonal or yearlong allergies[2]. The hygiene hypothesis was proposed 30 years ago as a potential explanation for this phenomenon[3], and we built on that with the specific oral hygiene hypothesis[4]. Our longitudinal pilot study suggested that oral probiotic deficiency is the cause of allergic rhinitis[5]. This clinical trial served to verify our theory and evaluate the effectiveness of AllerPops for allergy relief. Through it, we show that AllerPops prebiotic supplements are effective in providing sustained allergy relief (p = 0.002) and can modulate oral beneficial bacteria that produce short-chain fatty acids (SCFA), such as Fusobacteria, Butyrivibrio, and Peptostreptococcus. The clinical improvements correlated with changes in the relative abundance of probiotics significantly: Fusobacteria (R = 0.32, p = 0.009), Butyrivibrio (R = 0.25, p = 0.044), and Peptostreptococcus (R = 0.34, p = 0.005). These results point to the root cause of allergic rhinitis: the lack of oral probiotics that produce SCFA to pacify the immune systems. Future study of AllerPops theory will help society redefine the best oral hygiene practice to protect oral probiotics so that we may prevent both allergies and dental/gum diseases. The trial was retrospectively registered at clinicaltrials.com, with registration number NCT05956691, on July 20,2023.