bluuebunny/crossref_metadata_2025 huggingface dataset:
Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes
Authors: Thompson Kelsey N. , Bonham Kevin S. , Ilott Nicholas E. , Britton Graham J. , Colmenero Paula , Bullers Samuel J. , McIver Lauren J. , Ma Siyuan , Nguyen Long H. , Filer Andrew , Brough India , Pearson Claire , Moussa Caroline , Kumar Vinod , Lam Lilian H. , Jackson Matthew A. , Pawluk April ,   Inflammatory Arthritis Microbiome Consortium (IAMC) investigators group, Kiriakidis Serafim , Taylor Peter C. , Wedderburn Lucy R. , Marsden Brian , Young Stephen P. , Littman Dan R. , Faith Jeremiah J. , Pratt Arthur G. , Bowness Paul , Raza Karim , Powrie Fiona , Huttenhower Curtis , Ciurtin Coziana , Mauri Claudia
Published: July 2023

Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.
Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse
Authors: DeWolf Susan , Elhanati Yuval , Nichols Katherine , Waters Nicholas R. , Nguyen Chi L. , Slingerland John B. , Rodriguez Natasia , Lyudovyk Olga , Giardina Paul A. , Kousa Anastasia I. , Andrlová Hana , Ceglia Nick , Fei Teng , Kappagantula Rajya , Li Yanyun , Aleynick Nathan , Baez Priscilla , Murali Rajmohan , Hayashi Akimasa , Lee Nicole , Gipson Brianna , Rangesa Madhumitha , Katsamakis Zoe , Dai Anqi , Blouin Amanda G. , Arcila Maria , Masilionis Ignas , Chaligne Ronan , Ponce Doris M. , Landau Heather J. , Politikos Ioannis , Tamari Roni , Hanash Alan M. , Jenq Robert R. , Giralt Sergio A. , Markey Kate A. , Zhang Yanming , Perales Miguel-Angel , Socci Nicholas D. , Greenbaum Benjamin D. , Iacobuzio-Donahue Christine A. , Hollmann Travis J. , van den Brink Marcel R. M. , Peled Jonathan U.
Published: July 2023

T cells are the central drivers of many inflammatory diseases, but the repertoire of tissue-resident T cells at sites of pathology in human organs remains poorly understood. We examined the site-specificity of T cell receptor (TCR) repertoires across tissues (5 to 18 tissues per patient) in prospectively collected autopsies of patients with and without graft-versus-host disease (GVHD), a potentially lethal tissue-targeting complication of allogeneic hematopoietic cell transplantation, and in mouse models of GVHD. Anatomic similarity between tissues was a key determinant of TCR repertoire composition within patients, independent of disease or transplant status. The T cells recovered from peripheral blood and spleens in patients and mice captured a limited portion of the TCR repertoire detected in tissues. Whereas few T cell clones were shared across patients, motif-based clustering revealed shared repertoire signatures across patients in a tissue-specific fashion. T cells at disease sites had a tissue-resident phenotype and were of donor origin based on single-cell chimerism analysis. These data demonstrate the complex composition of T cell populations that persist in human tissues at the end stage of an inflammatory disorder after lymphocyte-directed therapy. These findings also underscore the importance of studying T cell in tissues rather than blood for tissue-based pathologies and suggest the tissue-specific nature of both the endogenous and posttransplant T cell landscape.
ADP-ribosylation-resistant rifabutin analogs show improved bactericidal activity against drug-tolerant
M. abscessus
in caseum surrogate
Authors: Xie Min , Ganapathy Uday S. , Lan Tian , Osiecki Paulina , Sarathy Jansy P. , Dartois Véronique , Aldrich Courtney C. , Dick Thomas
Published: July 2023

Necrotic lesions and cavities filled with caseum are a hallmark of mycobacterial pulmonary disease. Bronchocavitary
Mycobacterium abscessus
disease is associated with poor treatment outcomes. In caseum surrogate,
M. abscessus
entered an extended stationary phase showing tolerance to killing by most current antibiotics, suggesting that caseum persisters contribute to the poor performance of available treatments. Novel ADP-ribosylation-resistant rifabutin analogs exhibited bactericidal activity against these
M. abscessus
persisters at concentrations achievable by rifamycins in caseum.
Evaluation of a Novel Benchtop Tool for Acceleration of Sample Preparation for MALDI-TOF Mass Spectrometry
Authors: Idelevich Evgeny A. , Nedow Betty , Vollmer Marcus , Becker Karsten
Published: July 2023

During the past decade, MALDI-TOF mass spectrometry (MS) has become a standard method for identification of bacteria and yeasts. Nonetheless, further optimization of the identification process is important to streamline workflows and save resources.
Feline herpesvirus 1 (FHV-1) enters the cell by receptor-mediated endocytosis
Authors: Synowiec Aleksandra , Dąbrowska Agnieszka , Pachota Magdalena , Baouche Meriem , Owczarek Katarzyna , Niżański Wojciech , Pyrc Krzysztof
Published: July 2023

Feline herpesvirus type 1 (FHV-1) is an enveloped dsDNA virus belonging to the
Herpesviridae
family and is considered one of the two primary viral etiological factors of feline upper respiratory tract disease. In this study, we investigated the entry of FHV-1 into host cells using two models: the AK-D cell line and primary feline skin fibroblasts (FSFs). We employed confocal microscopy, siRNA silencing, and selective inhibitors of various entry pathways. Our observations revealed that the virus enters cells via pH and dynamin-dependent endocytosis, as the infection was significantly inhibited by NH
4
Cl, bafilomycin A1, dynasore, and mitmab. Additionally, genistein, nystatin, and filipin treatments, siRNA knock-down of caveolin-1, as well as FHV-1 and caveolin-1 colocalization suggest the involvement of caveolin-mediated endocytosis during the entry process. siRNA knock-down of clathrin heavy chain and analysis of virus particle colocalization with clathrin indicated that clathrin-mediated endocytosis also takes part in the primary cells. This is the first study to systematically examine FHV-1 entry into host cells, and for the first time, we describe FHV-1 replication in AK-D and FSFs.

IMPORTANCE

Feline herpesvirus 1 (FHV-1) is one of the most prevalent viruses in cats, causing feline viral rhinotracheitis, which is responsible for over half of viral upper respiratory diseases in cats and can lead to ocular lesions resulting in loss of sight. Although the available vaccine reduces the severity of the disease, it does not prevent infection or limit virus shedding. Despite the clinical relevance, the entry mechanisms of FHV-1 have not been thoroughly studied. Considering the limitations of commonly used models based on immortalized cells, we sought to verify our findings using primary feline skin fibroblasts, the natural target for infection in cats.
Prediction of spectacle refraction uncertainties with discrete IOL power steps and manufacturing tolerances according to ISO using a Monte Carlo model
Authors: Langenbucher Achim , Szentmáry Nóra , Cayless Alan , Bolz Matthias , Hoffmann Peter , Wendelstein Jascha
Published: July 2023

Purpose

The purpose of this study was to develop a concept for predicting the effects of both discrete intraocular lens (IOL) power steps (PS) and power labelling tolerances (LT) on the uncertainty of the refractive outcome (REFU).

Design

Retrospective non-randomised cross-sectional Monte Carlo simulation study.

Methods

We evaluated a dataset containing 16 669 IOLMaster 700 preoperative biometric measurements. The PS and the delivery range of two modern IOLs (Bausch and Lomb enVista and Alcon SA60AT) were considered for this Monte Carlo simulation. The uncertainties from PS or LT were assumed to be normally distributed according to ±½ the IOL PS or the ISO 11979 LT. REFU was recorded and analysed for all simulations.

Results

With both lenses the REFU from discrete PS ranged from 0.11 to 0.12 dpt. Due to the larger PS for low/high power lenses with the enVista/SA60AT, REFU is more dominant in initially myopic/hyperopic eyes. REFU from LT ranged from 0.18 to 0.19 dpt for both lenses. Since LT increases stepwise with IOL power, REFU is more prevalent in initially hyperopic eyes requiring high IOL power values, and for lenses with a wide delivery range towards higher powers.

Conclusions

Since surgeons and patients are typically aware of the effect of discrete PS on REFU, these might be tolerated in cataract surgery. However, REFU resulting from LT is inevitable while the true measured IOL power is not reported on the package, leading to background noise in postoperative achieved refraction.
Implications of rapid population growth on survey design and HIV estimates in the Rakai Community Cohort Study (RCCS), Uganda
Authors: Khalifa Aleya , Ssekubugu Robert , Lessler Justin , Wawer Maria , Santelli John S , Hoffman Susie , Nalugoda Fred , Lutalo Tom , Ndyanabo Anthony , Ssekasanvu Joseph , Kigozi Godfrey , Kagaayi Joseph , Chang Larry W , Grabowski Mary Kathryn
Published: July 2023

Objective

Since rapid population growth challenges longitudinal population-based HIV cohorts in Africa to maintain coverage of their target populations, this study evaluated whether the exclusion of some residents due to growing population size biases key HIV metrics like prevalence and population-level viremia.

Design, setting and participants

Data were obtained from the Rakai Community Cohort Study (RCCS) in south central Uganda, an open population-based cohort which began excluding some residents of newly constructed household structures within its surveillance boundaries in 2008. The study includes adults aged 15–49 years who were censused from 2019 to 2020.

Measures

We fit ensemble machine learning models to RCCS census and survey data to predict HIV seroprevalence and viremia (prevalence of those with viral load >1000 copies/mL) in the excluded population and evaluated whether their inclusion would change overall estimates.

Results

Of the 24 729 census-eligible residents, 2920 (12%) residents were excluded from the RCCS because they were living in new households. The predicted seroprevalence for these excluded residents was 10.8% (95% CI: 9.6% to 11.8%)—somewhat lower than 11.7% (95% CI: 11.2% to 12.3%) in the observed sample. Predicted seroprevalence for younger excluded residents aged 15–24 years was 4.9% (95% CI: 3.6% to 6.1%)—significantly higher than that in the observed sample for the same age group (2.6% (95% CI: 2.2% to 3.1%)), while predicted seroprevalence for older excluded residents aged 25–49 years was 15.0% (95% CI: 13.3% to 16.4%)—significantly lower than their counterparts in the observed sample (17.2% (95% CI: 16.4% to 18.1%)). Over all ages, the predicted prevalence of viremia in excluded residents (3.7% (95% CI: 3.0% to 4.5%)) was significantly higher than that in the observed sample (1.7% (95% CI: 1.5% to 1.9%)), resulting in a higher overall population-level viremia estimate of 2.1% (95% CI: 1.8% to 2.4%).

Conclusions

Exclusion of residents in new households may modestly bias HIV viremia estimates and some age-specific seroprevalence estimates in the RCCS. Overall, HIV seroprevalence estimates were not significantly affected.
How and why educational interventions work to increase knowledge of delirium among healthcare professionals in nursing homes: a protocol for a realist review
Authors: Molitor Vincent , Busse Theresa Sophie , Giehl Chantal , Lauer Romy , Otte Ina Carola , Vollmar Horst Christian , Thürmann Petra , Holle Bernhard , Palm Rebecca
Published: July 2023

Background

Delirium is a neuropathological condition that impairs cognitive performance, attention and consciousness and can be potentially life-threatening. Nursing home residents are particularly vulnerable to developing delirium, but research thus far tends to focus on the acute hospital setting. Healthcare professionals (HCPs) working in nursing homes seem to be little aware of delirium. To improve healthcare for affected or at-risk individuals, increasing knowledge among HCPs is highly relevant. Using the realist review method helps to understand how and why an educational intervention for HCPs on delirium in nursing homes works.

Methods and analysis

In accordance with the Realist And Meta-narrative Evidence Syntheses: Evolving Standards publication standards for realist syntheses, the review process will include the following five steps: (1) search strategy and literature review; (2) study selection and assessment; (3) data extraction; (4) data synthesis and (5) development of an initial programme theory. The literature search will be conducted in the databases Medline (PubMed), CINAHL (Ebsco), Scopus, Web of Science, GeroLit and Carelit. Additional focuses are on snowballing techniques, hand research and grey literature. Studies of any design will be included to develop the initial programme theory. The literature will be selected by two researchers independently. In addition, the experiences of HCPs from nursing homes will be reflected in group discussions. To this end, Context–Mechanism–Outcome configurations (CMOcs) will be established to develop an initial programme theory.

Ethics and dissemination

The results will be disseminated within the scientific community. For this purpose, presentations at scientific conferences as well as publications in peer-reviewed journals are scheduled. In the next step, the CMOcs could serve for the development of a complex educational intervention to increase the knowledge of HCPs on delirium in nursing homes.

Registration details

This protocol has been registered at Open Science Framework (https://doi.org/10.17605/OSF.IO/HTFU4).
Medical AI: is trust really the issue?
Authors: Mainz Jakob Thrane
Published: July 2023

I discuss an influential argument put forward by Hatherley in theJournal of Medical Ethics. Drawing on influential philosophical accounts of interpersonal trust, Hatherley claims that medical artificial intelligence is capable of being reliable, but not trustworthy. Furthermore, Hatherley argues that trust generates moral obligations on behalf of the trustee. For instance, when a patient trusts a clinician, it generates certain moral obligations on behalf of the clinician for her to do what she is entrusted to do. I make three objections to Hatherley’s claims: (1) At least one philosophical account of interagent trust implies that medical AI is capable of being trustworthy. (2) Even if this account should ultimately be rejected, it does not matter much because what we care mostly about is that medical AI is reliable. (3) It is false that trust in itself generates moral obligations on behalf of the trustee.
Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders
Authors: Riquin Kevin , Isidor Bertrand , Mercier Sandra , Nizon Mathilde , Colin Estelle , Bonneau Dominique , Pasquier Laurent , Odent Sylvie , Le Guillou Horn Xavier Maximin , Le Guyader Gwenaël , Toutain Annick , Meyer Vincent , Deleuze Jean-François , Pichon Olivier , Doco-Fenzy Martine , Bézieau Stéphane , Cogné Benjamin
Published: July 2023

Background

Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression.

Methods

We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance.

Results

We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs.

Conclusion

Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.
Changes in exhaled volatile organic compounds following indirect bronchial challenge in suspected asthma
Authors: Peel Adam , Wang Ran , Ahmed Waqar , White Iain , Wilkinson Maxim , Loke Yoon K , Wilson Andrew M , Fowler Stephen J
Published: July 2023

Background

Inhaled mannitol provokes bronchoconstrictionviamediators released during osmotic degranulation of inflammatory cells, and, hence represents a useful diagnostic test for asthma and model for acute attacks. We hypothesised that the mannitol challenge would trigger changes in exhaled volatile organic compounds (VOCs), generating both candidate biomarkers and novel insights into their origin.

Methods

Participants with a clinical diagnosis of asthma, or undergoing investigation for suspected asthma, were recruited. Inhaled mannitol challenges were performed, followed by a sham challenge after 2 weeks in participants with bronchial hyper-responsiveness (BHR). VOCs were collected before and after challenges and analysed using gas chromatography–mass spectrometry.

Results

Forty-six patients (mean (SD) age 52 (16) years) completed a mannitol challenge, of which 16 (35%) were positive, and 15 of these completed a sham challenge. Quantities of 16 of 51 identified VOCs changed following mannitol challenge (p<0.05), of which 11 contributed to a multivariate sparse partial least square discriminative analysis model, with a classification error rate of 13.8%. Five of these 16 VOCs also changed (p<0.05) in quantity following the sham challenge, along with four further VOCs. In patients with BHR to mannitol distinct postchallenge VOC signatures were observed compared with post-sham challenge.

Conclusion

Inhalation of mannitol was associated with changes in breath VOCs, and in people with BHR resulted in a distinct exhaled breath profile when compared with a sham challenge. These differentially expressed VOCs are likely associated with acute airway inflammation and/or bronchoconstriction and merit further investigation as potential biomarkers in asthma.
Fluid evolution and ore genesis of Huaduoshan Cu–Mo prospect, Duobaoshan ore field, northeastern China: evidence from fluid inclusions, H–O–S–Pb isotopes, geochronology, and geochemistry
Authors: Li Hao-ming , Wang Ke-yong , Geng Jian-zhen , Tang Wen-hao , Sun Qing-fei , Wang Xue
Published: July 2023

The Huaduoshan Cu–Mo prospect is in the Duobaoshan orefield, northeast China. The Cu–Mo mineralization occurs in the granodiorites as veinlet-disseminated. The ore-forming process can be divided into four mineralization stages: (I) quartz–pyrite–magnetite; (II) quartz–pyrite–chalcopyrite ± molybdenite; (III) quartz–pyrite–molybdenite–chalcopyrite–sphalerite; and (IV) quartz–calcite–minor pyrite. Liquid-rich two-phase aqueous (L-type), vapour-rich aqueous (V-type) and daughter-minerals three-phase (S-type) fluid inclusions (FIs) were identified at Huaduoshan. The last two types of FIs are absent in stages III and IV. The homogenization temperatures of FIs from stages I to IV are 375–438, 335–378, 283–335, and 223–267 ℃, with corresponding salinities of 2.4–50.4, 2.1–44.9, 2.7–10.1, and 1.7–7.3 wt. % NaCl eqv., respectively. The H–O isotope data of quartz in stages I (δ18OH2O = 6.1–8.0‰, δDH2O = −102.4–−94.6‰) show a magmatic origin of ore-forming fluid; the decreasing δ18OH2O (−6.8–3.2‰) and δDH2O (−117.1–−98.5‰) values of quartz in stage II–IV show the fluid mixing with meteoric water. The S–Pb isotopic values (δ34S = −2.7–0.8; 206Pb/204Pb = 18.236–18.599; 207Pb/204 Pb = 15.504–15.557; 208Pb/204Pb = 37.816–38.629) of pyrites indicate that the ore-forming materials are of magmatic origin. Fluid boiling and mixing may be the major mechanisms of ore precipitation. Zircon U–Pb age (172.1 ± 0.5 Ma) and geochemical data indicate that the ore-related granodiorites are I-type rocks formed in the subduction setting of the Paleo-Pacific Ocean Plate in the Early–Middle Jurassic. In conclusion, we propose that the Huaduoshan Cu–Mo prospect is a porphyry deposit and has potential for further exploration of porphyry Cu–Mo prospecting.
Climate vulnerability for a desert fish: integrating hydrologic exposures, adaptive capacity, and growth potential
Authors: Benjamin Joseph R. , Dunham Jason B. , Anlauf-Dunn Kara J. , Eliason Erika
Published: July 2023

Climate vulnerability can be evaluated by multiple organismal responses. We developed a climate vulnerability framework focused on growth potential of redband trout ( Oncorhynchus mykiss newberri). We employed a bioenergetics model to evaluate spatial variability in growth potential in relation to constraints on body size imposed by stream flow, physiological responses linked to variable thermal regimes, and variation in physiological adaptive capacity inferred from field respirometry. Results indicate that maximum size (g) of redband trout increases with stream discharge. Growth potential is strongly linked to body size, with smaller individuals performing better relative to larger fish in cooler thermal regimes. Annual patterns of growth varied among sites and were related to body size and physiological adaptive capacity. Putatively cold-adapted fish were more likely to exhibit bimodal growth with peaks in spring and autumn, whereas warm-adapted fish exhibit a summer peak in growth potential. These findings offer insights into how climate vulnerability of stream-living fish can be conditioned on both stream flow and thermal regimes, and the potential for physiological adaptive capacity to influence vulnerability.
Erratum: QED-based derivation of the general forms of the relativistic Doppler effect and of the relativistic aberration for uniformly rotating frames and for uniformly accelerated frames
Authors: Sfarti A.
Published: July 2023

The current paper corrects an error that occurred in a previously published paper. The error starts from Sec.  3 , Eq. ( 3.2 ) whereby the scalar value of the wave-vector needs to be corrected. The net result is that the final formulas for the relativistic Doppler effect and for aberration get simplified. The source of the error is an extra multiplication factor by “[Formula: see text]”. We need to replace the incorrect [Formula: see text] in [A. Sfarti, MPLA 37, 2250238 (2022)] with the correct expression [Formula: see text].
Improving the sensitivity of distributed phase estimation under noisy Gaussian environment with noiseless linear amplification
Authors: Tang Jie , Liu Ying , Li JiaHao , Cao YueXiang , Deng Zhifeng , Yu Huicun , Shi Lei , Wei Jiahua
Published: July 2023

The deterioration of precision caused by quantum decoherence in dissipative environments is a longstanding problem in the development of distributed quantum metrology. Therefore, it is significant to effectively overcome the entanglement-distribution loss and channel noise of dissipative environments and improve the measurement-sensitivity. Here, we introduce noiseless linear amplifier (NLA) based on photon catalysis into distributed phase estimation to mitigate the loss and noise. Through utilizing a series of reduction and equivalence relations to simplify the problem of distributed phase estimation to a single-parameter estimation situation, our results show that Photon catalysis (PC)-NLAs can effectively mitigate the loss and noise of dissipative environments, and greatly improve the measurement-sensitivity. More interestingly, we find that adding thermal photons of environment has positive contributions on the measurement-sensitivity under certain circumstances. Our scheme should prove valuable for the global wide-area quantum sensor network.
GAS PERMEABILITY IN POROUS MEDIA WITH ROUGH SURFACES BY FRACTAL-MONTE CARLO SIMULATIONS
Authors: YIN ZUOZHUANG , DUAN SILIANG , GUO XIUYA , WANG HUILI , CHEN RUIJUAN , ZHENG QIAN
Published: July 2023

Gas permeability is an important parameter for gas transport in microporous and nanoporous media. A probability model of gas permeability of fractal porous media with rough surfaces is proposed and numerically simulated by the Monte Carlo technique. This model consists of two gas flow mechanisms: the Poiseuille flow and the Knudsen flow, and can be expressed by structural parameters, such as the pore fractal dimension, the tortuosity fractal dimension, the relative roughness and porosity. The validity of the proposed model is investigated through the available experimental data, and a good agreement is obtained. The predicted results indicate that gas permeability of microporous and nanoporous media with rough surfaces decreases with the increase of the relative roughness and the tortuosity fractal dimension, and increases with the increase of porosity and the pore fractal dimension. Our gas permeability model could reveal the physical mechanisms of gas transport in porous media with rough surfaces.
THE PORE SIZE-DEPENDENT FRACTALITY OF POROUS STRUCTURE IN CEMENT PASTE: ANALYSIS, MODELING AND APPLICATIONS
Authors: XI YANAN , LI WENWEI , LEI DONG , GAO YUN
Published: July 2023

The fractal characteristic of cement paste has been investigated for decades. In this paper, a systematic study referring to analysis, modeling as well as application is presented with respect to the pore size-dependent fractality of the porous structure in cement paste. In particular, the multiscale fractal dimensions other than the traditional single fractal dimension are analyzed for a measure of incomplete fractality. Then, the multiscale solid mass fractal model is introduced and implemented. It is demonstrated that the modeled pore size distribution agrees well with that obtained from the experimental measurement. Moreover, in combination with other analytical (the effective medium theory) and/or numerical (the finite element method) tools, such a pore size-dependent fractality could provide a fast assessment of some basic mechanical and physical properties.
ANALYSIS OF STRESS AND STRUCTURAL CHARACTERISTICS OF SANDSTONE USING CT SCANNING AND FRACTAL THEORY
Authors: LI GANG , MIAO YUAN , WU JINSUI , ZHANG FENGYAN , YIN SHANGXIAN , XU BIN , LI YUANYUAN
Published: July 2023

The pores and fissures in loaded rock masses are the main channels for underground flow, and may cause serious accidents during the development of groundwater resources. This work presents an efficient method for analyzing the microstructure of the loaded rock mass using fractal theory and computed tomography (CT) scanning. A relation between the microstructure features of the sandstone porosity, fractal dimension, and loading stress is developed using an image identification technique. The results demonstrate that the distribution trends of sandstone samples’ slice porosities in the xz- and yz-directions are nearly identical, and the distribution in the xy-direction differs significantly from those in xz- and yz-directions. The total and connected porosities increase with the increase of stress, and the change can be fitted to straight lines. The fractal dimensions of the pores change significantly with stress or loading stress in the xy-direction.
MULTIFRACTAL MODELING OF GAS–WATER RELATIVE PERMEABILITY CONSIDERING MULTISCALE AND MULTIEFFECTS: INVESTIGATION OF UNCONVENTIONAL GAS DEVELOPMENT
Authors: SONG HONGQING , LAO JUNMING , YANG HONGEN , XIE CHIYU , WANG JIULONG
Published: July 2023

Unconventional gas is a momentous energy source due to its considerable reserves and eco-friendly properties, where relative permeability is a key evaluative parameter of unconventional gas extraction. However, the geo-complexity, multiscale and multieffect of the unconventional gas reservoir challenge the relative permeability evaluation and production enhancement. Here, we establish a gas–water flow model by integrating multifractal theory, covering from nanoscale to macroscale and regarding the effects of slip, gas desorption–diffusion and water film separation, to reliably evaluate the relative permeability evolution during unconventional gas development. Based on our model, we describe the permeability of the unconventional reservoir with an 88% less evaluation error compared to the single fractal Darcy with the literature benchmark. Moreover, we characterize the gas–water relative permeability with a no more than 10% evaluation error based on the experimental data. The slip effect plays the most crucial role in the evaluation precision of relative permeability. We reveal that the permeability of the unconventional gas reservoir is decreased by the increase of generalized fractal dimension which enhances the heterogeneity and tortuosity of pores. We uncover that the slip effect facilitates the relative permeability of gas and water. Besides, the gas desorption–diffusion boosts gas relative permeability while limiting water relative permeability, whereas water film separation enhances water relative permeability but hinders gas relative permeability. This work brings insights into the precise description of multiscale and multieffect gas–water porous flow in unconventional gas development.
A HYBRID NUMERICAL/ANALYTICAL MODEL OF TRANSIENT SEEPAGE FOR VERTICAL FRACTURED WELL IN TIGHT GAS RESERVOIR BY USE OF FRACTAL THEORY AND CONFORMAL MAPPING METHOD
Authors: CUI QIANCHEN , ZHAO YULONG , BU CHENGZHONG , ZHENG JIAN , HU HAORAN , ZHANG LIEHUI
Published: July 2023

Insufficient consideration of the complex morphology of hydraulic fractures (HF) and heterogeneous physical properties of fractured reservoirs in seepage models can result in unreliable well testing analyses. The fractal porosity and permeability (FPP) model provides an effective method for characterizing reservoir heterogeneity in the near-wellbore zone. However, its application to scenarios involving irregularly-shaped hydraulic fracture networks and multiple fracture clusters is challenging due to the lack of spatial symmetry. To address this issue, this paper proposes a combined approach of FPP and conformal mapping (FPP-CM) to transform the region of fractured formation into the exterior of the unit disk domain using numerical conformal mapping. The transient seepage flow model of the vertical fracture well (VFW) is then established by coupling it with the FPP model. The typical curve of pressure transient behavior with the division of flow stages was plotted, and the model verification and sensitivity analysis of parameters were conducted. The results indicate that the fractal dimension primarily affects the formation linear flow stage and its subsequent flow stages; with a decrease in fractal dimension resulting in an increase in the position of the typical curve. For VFW with multiple HF wings, a decrease in the included angle of fracture wings causes an increase in the heterogeneity distribution of microfracture physical properties, resulting in an increase in the position of the pseudo-pressure derivative curve during the late flow stage.
A SEEPAGE MODEL FOR SOLID-PHASE PARTICLE INSTABILITY IN POROUS MEDIA-BASED FRACTAL THEORY
Authors: TAN XIAO-HUA , ZHOU XIAO-JUN , LI HAI , PENG XIAN , LI LONG-XIN , LI QIAN , LI QIU , WU TING-TING
Published: July 2023

This paper presents a new fractal seepage model to study the decrease in seepage capacity caused by fluid erosion and pressure changes in porous media. The normalized permeability obtained by our model is in good agreement with the experiments and models in literature and has high accuracy and usability. The results demonstrate that: (1) the larger the instability coefficient, the higher the particle stability, the better the permeability of the porous medium, the later the normalized permeability decreases, and the slower it goes down, and (2) the fractal dimension of the solid skeleton set mainly affects the porosity and permeability of porous media, independent of the stability of solid particles. (3) The fractal dimension of movable particles is one of the main factors affecting the normalized permeability, it does not affect the instability conditions solid-phase particles in the porous media. The proposed model makes full use of the microstructure parameters of porous media, further reveals the mechanism of fluid flow in porous media with particle shedding, and provides a sound theoretical basis for various practical applications in petroleum engineering and other industries.
SMOTE-Based Homogeneous Prediction for Aging-Related Bugs in Cloud-Oriented Software
Authors: Kaur Harguneet , Kaur Arvinder
Published: July 2023

Software aging is the process caused by Aging-Related Bugs (ARBs) which leads to the depletion of resources and degradation of performance in the long run. ARBs are difficult to find and replicate in future studies as they are less in number, thus prediction of ARB is necessary to save cost and time in the testing phase. ARBs are present in low proportion as compared to non-ARBs known as the class Imbalance problem resulting in insufficient training dataset for prediction models. In this study, Synthetic Minority Oversampling Technique (SMOTE) is applied along with homogeneous cross-project ARB prediction to reduce the effect of imbalance problem in software. SMOTE is oversampling of the minority instances synthetically to balance the dataset and improve the capability of defect prediction models. Homogeneous cross-project prediction is implemented where the datasets are different but the distribution of metric sets of both training and testing datasets is similar. The experiment is conducted on five cloud-oriented software such as Cassandra, Hive, Storm, Hadoop HDFS and Hadoop Mapreduce. The novelty of this study is the combination of SMOTE and homogeneous cross-project defect prediction for ARBs in cloud-oriented software. The comparative analysis is also conducted to understand the difference between SMOTE and non-SMOTE results with the help of machine learning classifiers. The result conveys that SMOTE is an efficient method to address class imbalance problem in ARB prediction.
Deep learning-based option pricing for Barndorff–Nielsen and Shephard model
Authors: Arai Takuji
Published: July 2023

This paper aims to develop a deep learning-based numerical method for option prices for the Barndorff–Nielsen and Shephard model, a representative jump-type stochastic volatility model. Using that option prices for the Barndorff–Nielsen and Shephard model satisfy a partial-integro differential equation, we will develop an effective numerical calculation method even in settings where conventional numerical methods are unavailable. In addition, we will implement some numerical experiments.
HACK: Learning a Parametric Head and Neck Model for High-fidelity Animation
Authors: Zhang Longwen , Zhao Zijun , Cong Xinzhou , Zhang Qixuan , Gu Shuqi , Gao Yuchong , Zheng Rui , Yang Wei , Xu Lan , Yu Jingyi
Published: July 2023

Significant advancements have been made in developing parametric models for digital humans, with various approaches concentrating on parts such as the human body, hand, or face. Nevertheless, connectors such as the neck have been overlooked in these models, with rich anatomical priors often unutilized. In this paper, we introduce HACK (Head-And-neCK), a novel parametric model for constructing the head and cervical region of digital humans. Our model seeks to disentangle the full spectrum of neck and larynx motions, facial expressions, and appearance variations, providing personalized and anatomically consistent controls, particularly for the neck regions. To build our HACK model, we acquire a comprehensive multi-modal dataset of the head and neck under various facial expressions. We employ a 3D ultrasound imaging scheme to extract the inner biomechanical structures, namely the precise 3D rotation information of the seven vertebrae of the cervical spine. We then adopt a multi-view photometric approach to capture the geometry and physically-based textures of diverse subjects, who exhibit a diverse range of static expressions as well as sequential head-and-neck movements. Using the multi-modal dataset, we train the parametric HACK model by separating the 3D head and neck depiction into various shape, pose, expression, and larynx blendshapes from the neutral expression and the rest skeletal pose. We adopt an anatomically-consistent skeletal design for the cervical region, and the expression is linked to facial action units for artist-friendly controls. We also propose to optimize the mapping from the identical shape space to the PCA spaces of personalized blendshapes to augment the pose and expression blendshapes, providing personalized properties within the framework of the generic model. Furthermore, we use larynx blendshapes to accurately control the larynx deformation and force the larynx slicing motions along the vertical direction in the UV-space for precise modeling of the larynx beneath the neck skin. HACK addresses the head and neck as a unified entity, offering more accurate and expressive controls, with a new level of realism, particularly for the neck regions. This approach has significant benefits for numerous applications, including geometric fitting and animation, and enables inter-correlation analysis between head and neck for fine-grained motion synthesis and transfer.
Generalizing Shallow Water Simulations with Dispersive Surface Waves
Authors: Jeschke Stefan , Wojtan Chris
Published: July 2023

This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a
bulk flow
(which approximately satisfies the assumptions of the shallow water equations) and
surface waves
(which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an
exact
correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns.
Variational quasi-harmonic maps for computing diffeomorphisms
Authors: Wang Yu , Guo Minghao , Solomon Justin
Published: July 2023

Computation of injective (or inversion-free) maps is a key task in geometry processing, physical simulation, and shape optimization. Despite being a longstanding problem, it remains challenging due to its highly nonconvex and combinatoric nature. We propose computation of
variational quasi-harmonic maps
to obtain smooth inversion-free maps. Our work is built on a key observation about inversion-free maps: A planar map is a diffeomorphism if and only if it is quasi-harmonic and satisfies a special Cauchy boundary condition. We hence equate the inversion-free mapping problem to an optimal control problem derived from our theoretical result, in which we search in the space of parameters that define an elliptic PDE. We show that this problem can be solved by minimizing within a family of functionals. Similarly, our discretized functionals admit exactly injective maps as the minimizers, empirically producing inversion-free discrete maps of triangle meshes. We design efficient numerical procedures for our problem that prioritize robust convergence paths. Experiments show that on challenging examples our methods can achieve up to orders of magnitude improvement over state-of-the-art, in terms of speed or quality. Moreover, we demonstrate how to optimize a generic energy in our framework while restricting to quasi-harmonic maps.
CT2Hair: High-Fidelity 3D Hair Modeling using Computed Tomography
Authors: Shen Yuefan , Saito Shunsuke , Wang Ziyan , Maury Olivier , Wu Chenglei , Hodgins Jessica , Zheng Youyi , Nam Giljoo
Published: July 2023

We introduce CT2Hair, a fully automatic framework for creating high-fidelity 3D hair models that are suitable for use in downstream graphics applications. Our approach utilizes real-world hair wigs as input, and is able to reconstruct hair strands for a wide range of hair styles. Our method leverages computed tomography (CT) to create density volumes of the hair regions, allowing us to see through the hair unlike image-based approaches which are limited to reconstructing the visible surface. To address the noise and limited resolution of the input density volumes, we employ a coarse-to-fine approach. This process first recovers guide strands with estimated 3D orientation fields, and then populates dense strands through a novel neural interpolation of the guide strands. The generated strands are then refined to conform to the input density volumes. We demonstrate the robustness of our approach by presenting results on a wide variety of hair styles and conducting thorough evaluations on both real-world and synthetic datasets. Code and data for this paper are at github.com/facebookresearch/CT2Hair.
Potentially Visible Hidden-Volume Rendering for Multi-View Warping
Authors: Kim Janghun , Lee Sungkil
Published: July 2023

This paper presents the model and rendering algorithm of Potentially Visible Hidden Volumes (PVHVs) for multi-view image warping. PVHVs are 3D volumes that are occluded at a known source view, but potentially visible at novel views. Given a bound of novel views, we define PVHVs using the edges of foreground fragments from the known view and the bound of novel views. PVHVs can be used to batch-test the visibilities of source fragments without iterating individual novel views in multi-fragment rendering, and thereby, cull redundant fragments prior to warping. We realize the model of PVHVs in Depth Peeling (DP). Our Effective Depth Peeling (EDP) can reduce the number of completely hidden fragments, capture important fragments early, and reduce warping cost. We demonstrate the benefit of our PVHVs and EDP in terms of memory, quality, and performance in multi-view warping.
Split-Lohmann Multifocal Displays
Authors: Qin Yingsi , Chen Wei-Yu , O'Toole Matthew , Sankaranarayanan Aswin C.
Published: July 2023

This work provides the design of a multifocal display that can create a dense stack of focal planes in a single shot. We achieve this using a novel computational lens that provides spatial selectivity in its focal length, i.e, the lens appears to have different focal lengths across points on a display behind it. This enables a multifocal display via an appropriate selection of the spatially-varying focal length, thereby avoiding time multiplexing techniques that are associated with traditional focus tunable lenses. The idea central to this design is a modification of a Lohmann lens, a focus tunable lens created with two cubic phase plates that translate relative to each other. Using optical relays and a phase spatial light modulator, we replace the physical translation of the cubic plates with an optical one, while simultaneously allowing for different pixels on the display to undergo different amounts of translations and, consequently, different focal lengths. We refer to this design as a Split-Lohmann multifocal display. Split-Lohmann displays provide a large étendue as well as high spatial and depth resolutions; the absence of time multiplexing and the extremely light computational footprint for content processing makes it suitable for video and interactive experiences. Using a lab prototype, we show results over a wide range of static, dynamic, and interactive 3D scenes, showcasing high visual quality over a large working range.
Language-based Photo Color Adjustment for Graphic Designs
Authors: Wang Zhenwei , Zhao Nanxuan , Hancke Gerhard , Lau Rynson W. H.
Published: July 2023

Adjusting the photo color to associate with some design elements is an essential way for a graphic design to effectively deliver its message and make it aesthetically pleasing. However, existing tools and previous works face a dilemma between the ease of use and level of expressiveness. To this end, we introduce an interactive language-based approach for photo recoloring, which provides an intuitive system that can assist both experts and novices on graphic design. Given a graphic design containing a photo that needs to be recolored, our model can predict the source colors and the target regions, and then recolor the target regions with the source colors based on the given language-based instruction. The multi-granularity of the instruction allows diverse user intentions. The proposed novel task faces several unique challenges, including:
1) color accuracy
for recoloring with exactly the same color from the target design element as specified by the user;
2) multi-granularity instructions
for parsing instructions correctly to generate a specific result or multiple plausible ones; and
3) locality
for recoloring in semantically meaningful local regions to preserve original image semantics. To address these challenges, we propose a model called
LangRecol
with two main components: the language-based source color prediction module and the semantic-palette-based photo recoloring module. We also introduce an approach for generating a synthetic graphic design dataset with instructions to enable model training. We evaluate our model via extensive experiments and user studies. We also discuss several practical applications, showing the effectiveness and practicality of our approach. Please find the code and data at https://zhenwwang.github.io/langrecol.