bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and engineering of artificial biosynthetic pathways—where do we stand and where do we go?
Authors: Sokolova Nika , Peng Bo , Haslinger Kristina
Published: October 2023

The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini‐review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.
The magnified view: from ancient trinkets to single nuclear pore complexes
Authors: Fichtman Boris , Harel Amnon
Published: October 2023

A journey from the earliest known use of lenses and magnifying glasses in ancient times, through the development of microscopes and towards modern electron microscopy techniques. The evolving technology and improved microscopes enabled the discovery of intracellular organelles, the nucleus and nuclear pore complexes (NPCs). Current advances have led to composite three‐dimensional models showing NPC structure in unprecedented detail but relying on the averaging of many images. A complementary approach is field emission scanning electron microscopy providing topographic surface images that are easily and intuitively interpreted by our brain. Recent advances in this technique have made it possible to expose nuclei from human cells and to focus on individual NPCs and their architectural features.
Mechano‐Activated Shape Morphing of Aluminum–Plastic Laminate Composites
Authors: Nguyen Chien , Ramalingam Karthik , Kushnir Zachary , Rouhani Fatemeh , Velankar Sachin S.
Published: October 2023

Many “metallized plastic” packaging films bend if stretched and released. Such behavior can be reproduced in laminate composites prepared by bonding aluminum foil to an adhesive polymer sheet. It is shown that such bending occurs because stretching deforms the aluminum layer permanently (i.e., plastically), whereas the polymer layer deforms elastically. Upon releasing, the aluminum–polymer composite then resolves the strain mismatch by bending, with the aluminum on the convex side of the bend. The curvature is found to increase linearly with the applied strain and to reduce as the aluminum thickness increases. The theory of fully elastic bilayers with strain mismatch is in qualitative agreement with the results, but underpredicts the curvatures. It is shown how such bilayers can be patterned with defects such as holes or slits to realize more complex shape morphing, and also how one may achieve bidirectional bending. Such aluminum–polymer‐layered composites provide an inexpensive platform suitable for rapid prototyping of self‐folding origami structures using robust materials.
2D Materials Beyond Post‐AI Era: Smart Fibers, Soft Robotics, and Single Atom Catalysts
Authors: Lee Gang San , Kim Jin Goo , Kim Jun Tae , Lee Chan Woo , Cha Sujin , Choi Go Bong , Lim Joonwon , Padmajan Sasikala Suchithra , Kim Sang Ouk
Published: October 2023

Recent consecutive discoveries of various 2D materials have triggered significant scientific and technological interests owing to their exceptional material properties, originally stemming from 2D confined geometry. Ever‐expanding library of 2D materials can provide ideal solutions to critical challenges facing in current technological trend of the fourth industrial revolution. Moreover, chemical modification of 2D materials to customize their physical/chemical properties can satisfy the broad spectrum of different specific requirements across diverse application areas. This review focuses on three particular emerging application areas of 2D materials: smart fibers, soft robotics, and single atom catalysts (SACs), which hold immense potentials for academic and technological advancements in the post‐artificial intelligence (AI) era. Smart fibers showcase unconventional functionalities including healthcare/environmental monitoring, energy storage/harvesting, and antipathogenic protection in the forms of wearable fibers and textiles. Soft robotics aligns with future trend to overcome longstanding limitations of hard‐material based mechanics by introducing soft actuators and sensors. SACs are widely useful in energy storage/conversion and environmental management, principally contributing to low carbon footprint for sustainable post‐AI era. Significance and unique values of 2D materials in these emerging applications are highlighted, where the research group has devoted research efforts for more than a decade.
Population Pharmacokinetics and Exposure–Response Analysis for the CTLA‐4 Inhibitor Tremelimumab in Metastatic NSCLC Patients in the Phase III POSEIDON Study
Authors: He Jimmy Zhijian , Duval Vincent , Jauslin Petra , Gonçalves Antonio , Abegesah Aburough , Fan Chunling , Lim KyoungSoo , Song Xuyang , Chen Cecil , Shi Xiaojin , Mann Helen , Krug Lee , Ren Song , Phipps Alex , Gibbs Megan , Zhou Diansong
Published: October 2023

Blockade of CTLA‐4 by tremelimumab combined with anti‐PD‐L1 durvalumab and chemotherapy provided increased antitumor activity and long‐term survival benefits in first‐line metastatic non‐small cell lung cancer (mNSCLC) in the phase III POSEIDON study. We performed population pharmacokinetic modeling for tremelimumab using data from 1,605 patients across 6 studies (including POSEIDON) in multiple tumors (lung cancer, bladder cancer, malignant mesothelioma, and other solid tumors), and identified a 2‐compartment model with linear and time‐varying clearance for tremelimumab. Cox proportional hazard regression models were applied to 326 patients with mNSCLC from POSEIDON to evaluate the association between exposure metrics and efficacy end points, adjusting for baseline prognostic covariates. Improved progression‐free survival (PFS) and overall survival (OS) in the tremelimumab arm (in combination with durvalumab and chemotherapy) was associated with higher tremelimumab exposure (e.g., minimum concentration at 5th dose (Cmin,dose5) and area under the curve at 5th dose (AUCdose5)). However, further case‐matching analyses yielded hazard ratios for the comparison of tremelimumab‐treated patients in the Cmin,dose5 quartile 1 (Q1) subgroup with matched chemotherapy‐treated patients of 1.04 (95% confidence interval (CI): 0.76–1.44) for OS and 0.99 (95% CI: 0.72–1.36) for PFS, suggesting that the observed apparent exposure–response relationship might be confounded. No relationship between tremelimumab exposure and safety (grade ≥3 treatment‐emergent adverse events [AEs], AEs of special interest, or discontinuation due to AEs) was identified. These results support the consistent benefit observed with tremelimumab 75 mg every 3 weeks for up to 5 doses in combination with durvalumab and chemotherapy in POSEIDON as first‐line therapy for mNSCLC.
Model‐Informed Selection of the Recommended Phase III Dose of the Inhibitor of Apoptosis Protein Inhibitor, Xevinapant, in Combination with Cisplatin and Concurrent Radiotherapy in Patients with Locally Advanced Squamous Cell Carcinoma of the Head and Neck
Authors: Vugmeyster Yulia , Ravula Abhigyan , Rouits Elisabeth , Diderichsen Paul Matthias , Kleijn Huub Jan , Koenig Andre , Wang XiaoZhe , Schroeder Andreas , Goteti Kosalaram , Venkatakrishnan Karthik
Published: October 2023

Xevinapant, an oral inhibitor of apoptosis protein (IAP) inhibitor, demonstrated efficacy in combination with chemoradiotherapy in a randomized phase II study (NCT02022098) in patients with locally advanced squamous cell carcinoma of the head and neck at 200 mg/day on days 1–14 of a 3‐week cycle. To confirm 200 mg/day as the recommended phase III dose (RP3D), we integrated preclinical, clinical, pharmacokinetic/pharmacodynamic (PK/PD), and exposure–response modeling results. Population PK/PD modeling of IAP inhibition in peripheral blood mononuclear cells in 21 patients suggested the pharmacologically active dose range was 100–200 mg/day, with a trend for more robust inhibition at the end of the dosing interval at 200 mg/day based on an indirect response model. Additionally, the unbound average plasma concentration at 200 mg/day was similar to that associated with efficacy in preclinical xenograft models. Logistic regression exposure–response analyses of data from 62 patients in the phase II study showed exposure‐related increases in probabilities of locoregional control at 18 months (primary end point), overall response, complete response, and the radiosensitization mechanism‐related composite safety end point “mucositis and/or dysphagia” (P < 0.05). Exposure–response relationships were not discernible for 12 of 13 evaluated safety end points, incidence of dose reductions, and time to first dose reduction. Quantitative integration of all available data, including model‐derived target inhibition profiles, positive exposure‐efficacy relationships, and lack of discernible exposure‐safety relationships for most safety end points, supports selection of xevinapant 200 mg/day on days 1–14 of a 3‐week cycle as the RP3D, allowing for successive dose reductions to 150 and 100 mg/day to manage adverse events.
Deprioritization of Ongoing Clinical Trials
Authors: Bierer Barbara E. , Zarin Deborah A. , Gelinas Luke
Published: October 2023

To be ethical, clinical trials must exhibit a favorable risk‐benefit balance at the time of their initiation. However, in some cases, the expected value of a study decreases while the study is ongoing, due to developments outside of the study itself, such as findings from other studies or an otherwise shifting evidence base. While such situations are acknowledged in the research community, they have not received sufficient attention, given the high costs of uninformative studies, both in material and human capital. In addition, the Covid‐19 pandemic has exposed serious shortcomings with current approaches to monitoring studies for continued relevance and value. In this article, with reference to a case study from the Covid‐19 pandemic, we identify and describe the importance and challenge of ensuring that clinical trials continue to exhibit scientific relevance and value once initiated. We explore the ethical dynamics of these situations and identify unresolved issues. While more empirical work is needed to ensure that proposed solutions to the issues are evidence based, we offer some provisional considerations that amount to a framework for approaching these challenging situations.
A quasi‐solid polymer electrolyte‐based structural battery with high mechanical and electrochemical performance
Authors: Singer Gerald , Hsieh Cheng‐Tien , Jin Tianwei , Lee Seung Hoon , Yang Yuan
Published: October 2023

Structural batteries are attractive for weight reduction in electric transportation. For their practical applications excellent mechanical properties and electrochemical performance are required simultaneously, which remains a grand challenge. In this study, we present a new scalable and low‐cost design, which uses a quasi‐solid polymer electrolyte (QSPE) to achieve both remarkably improved flexural properties and attractive energy density. The QSPE has a high ionic conductivity of 1.2 mS cm−1 and retains 91% capacity over 500 cycles in graphite/NMC532 cells. Moreover, the resulting structural batteries achieved a modulus of 21.7 GPa and a specific energy of 127 Wh kg−1 based on the total cell weight, which to our knowledge is the highest reported value above 15 GPa. We further demonstrate the application of such structural batteries in a model electric car. The presented design concept enables the industrialization of structural batteries in electric transportation and further applications to improve energy efficiency and multifunctionality.

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Similarity in milk microbiota in replicates
Authors: Dahlberg Josef , Pelve Erik , Dicksved Johan
Published: October 2023

Receiving the same results from repeated analysis of the same sample is a basic principle in science. The inability to reproduce previously published results has led to discussions of a reproducibility crisis within science. For studies of microbial communities, the problem of reproducibility is more pronounced and has, in some fields, led to a discussion on the very existence of a constantly present microbiota. In this study, DNA from 44 bovine milk samples were extracted twice and the V3–V4 region of the 16S rRNA gene was sequenced in two separate runs. The FASTQ files from the two data sets were run through the same bioinformatics pipeline using the same settings and results from the two data sets were compared. Milk samples collected maximally 2 h apart were used as replicates and permitted comparisons to be made within the same run. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson's diversity was the same. Multivariate analyses of all samples demonstrate that the sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42%–45% depending on whether binary or abundance‐based similarity indices were used. Within‐run comparisons of milk samples collected maximally 2 h apart showed an average similarity of 39%–47% depending on the similarity index used and that similarity differed significantly between runs. We conclude that repeated DNA extraction and sequencing significantly can affect the results of a low microbial biomass microbiota study.
Lampreys in California (Lampetra spp. and Entosphenus spp.): Mitochondrial phylogenetic analysis reveals previously unrecognized lamprey diversity
Authors: Auringer Grace , Campbell Matthew A. , Goertler Pascale A. L. , Finger Amanda J.
Published: October 2023

Objective

Protecting biodiversity is important for preserving ecosystem functions and services, and understanding the diversity present in a system is necessary for effective conservation. Lampreys display extensive diversity in morphology and life history strategy. The extent of this diversity and the underlying genetic patterns have not yet been fully characterized. Uncertainty about species boundaries and operational taxonomic units hinders lamprey management and conservation. Limited data have been collected on California lampreys (Lampetra spp. and Entosphenus spp.), but evidence suggests widespread population decline across the west coast of North America. Study objectives were to identify which nominal species are present at study sites across northern and central California, determine whether current taxonomic classifications accurately and sufficiently describe lamprey diversity in California, and characterize the biogeographic distribution of genetically distinct lamprey lineages across the study area.

Methods

To achieve these objectives, this study utilized DNA barcoding, phylogenetic analysis, and species delimitation analysis. Lamprey individuals (N = 87) from 19 sites in the Sacramento–San Joaquin River basin, San Francisco Bay, and Klamath River basin were sequenced for the mitochondrial cytochrome b (cyt b) gene, and the data were combined with publicly available lamprey cyt b sequences for analysis.

Result

Results showed relatively deep phylogenetic divergence between Lampetra and Entosphenus. Distinct and genetically divergent lineages were observed within Lampetra, while distinct but genetically similar lineages were observed within Entosphenus. This study revealed novel Lampetra lineages in the Napa River and Alameda Creek, and results suggest that the biogeographic distribution of lamprey diversity may follow patterns observed in other native fishes. Species delimitation results indicated that at least seven separate candidate species of Lampetra can be found in California, suggesting that California holds more species-level diversity than the expected three nominal Lampetra species known to occur in the state.

Conclusion

These results highlight the underestimated diversity of lampreys in California and the need for further assessment of taxonomic classifications and operational taxonomic unit designations of California lampreys.
Hederasaponin C inhibits LPS‐induced acute kidney injury in mice by targeting TLR4 and regulating the PIP2/NF‐κB/NLRP3 signaling pathway
Authors: Han Shan , Li Siyuan , Li Jilang , He Jia , Wang Qin‐Qin , Gao Xiang , Yang Shilin , Li Jingjing , Yuan Renyikun , Zhong Guoyue , Gao Hongwei
Published: October 2023

Acute kidney injury (AKI) is a common clinical condition associated with increased incidence and mortality rates. Hederasaponin C (HSC) is one of the main active components of Pulsatilla chinensis (Bunge) Regel. HSC possesses various pharmacological activities, including anti‐inflammatory activity. However, the protective effect of HSC against lipopolysaccharide (LPS)‐induced AKI in mice remains unclear. Therefore, we investigated the protective effect of HSC against LPS‐induced renal inflammation and the underlying molecular mechanisms. Herein, using MTT and LDH assays to assess both cell viability and LDH activity; using dual staining techniques to identify different cell death patterns; conducting immunoblotting, QRT‐PCR, and immunofluorescence analyses to evaluate levels of protein and mRNA expression; employing immunoblotting, molecular docking, SPR experiments, and CETSA to investigate the interaction between HSC and TLR4; and studying the anti‐inflammatory effects of HSC in the LPS‐induced AKI. The results indicate that HSC inhibits the expression of TLR4 and the activation of NF‐κB and PIP2 signaling pathways, while simultaneously suppressing the activation of the NLRP3 inflammasome. In animal models, HSC ameliorated LPS‐induced AKI and diminished inflammatory response and the level of renal injury markers. These findings suggest that HSC has potential as a therapeutic agent to mitigate sepsis‐related AKI.
The future opportunities and remaining challenges in the application of nanoparticle‐mediated hyperthermia combined with chemo‐radiotherapy in cancer
Authors: Shirvalilou Sakine , Tavangari Zahed , Parsaei Mohammad Hossein , Sargazi Saman , Sheervalilou Roghayeh , Shirvaliloo Milad , Ghaznavi Habib , Khoei Samideh
Published: October 2023

A pivotal cause of death in the modern world, cancer is an insidious pathology that should be diagnosed at an early stage for successful treatment. Development of therapeutic interventions with minimal invasiveness and high efficacy that can discriminate between tumor and normal cells is of particular interest to the clinical science, as they can enhance patient survival. Nanoparticles are an invaluable asset that can be adopted for development of such diagnostic and therapeutic modalities, since they come in very small sizes with modifiable surface, are highly safe and stable, and can be synthesized in a controlled fashion. To date, different nanoparticles have been incorporated into numerous modalities such as tumor‐targeted therapy, thermal therapy, chemotherapy, and radiotherapy. This review article seeks to deliver a brief account of recent advances in research and application of nanoparticles in hyperthermia‐based cancer therapies. The most recent investigations are summarized to highlight the latest advances in the development of combined thermo‐chemo‐radiotherapy, along with the challenges associated with the application of nanoparticles in cancer therapy.

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
Monitoring Hyperproperties with Prefix Transducers
Authors: Chalupa Marek , Henzinger Thomas A.
Published: October 2023

Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism.
Loss of Upk1a and Upk1b expression is linked to stage progression in urothelial carcinoma of the bladder
Authors: Kaczmarek Krystian , Plage Henning , Furlano Kira , Hofbauer Sebastian , Weinberger Sarah , Ralla Bernhard , Franz Antonia , Fendler Annika , de Martino Michela , Roßner Florian , Schallenberg Simon , Elezkurtaj Sefer , Kluth Martina , Lennartz Maximilian , Blessin Niclas C. , Marx Andreas H. , Samtleben Henrik , Fisch Margit , Rink Michael , Slojewski Marcin , Ecke Thorsten , Hallmann Steffen , Koch Stefan , Adamini Nico , Minner Sarah , Simon Ronald , Sauter Guido , Weischenfeldt Joachim , Klatte Tobias , Schlomm Thorsten , Horst David , Zecha Henrik
Published: October 2023

Background

Uroplakin-1a (Upk1a) and uroplakin-1b (Upk1b) have recently been identified as diagnostic markers for the distinction of urothelial carcinomas from other solid tumor entities. Both proteins play an important role in the stabilization and strengthening of epithelial cells that line the bladder.

Methods

To evaluate the prognostic role of uroplakin expression in urothelial carcinomas, more than 2700 urothelial neoplasms were analyzed in a tissue microarray format by immunohistochemistry. To further assess the diagnostic role of uroplakin immunohistochemistry, results were compared with preexisting GATA3 data.

Result

The fraction of Upk1a/Upk1b positive cases decreased slightly from pTaG2 low-grade (88% positive for Upk1a/87% positive for Upk1b) and pTaG2 high-grade (92%/89%) to pTaG3 (83%/88%; p > 0.05) and was lower in muscle-invasive (pT2-4) carcinomas (42%/64%; p < 0.0001/p < 0.0001 for pTa vs. pT2-4). Within pT2-4 carcinomas, high expression of Upk1a and Upk1b was linked to nodal metastasis and lymphatic vessel infiltration (p < 0.05) but unrelated to patient outcome. There were significant associations between Upk1a, Upk1b and GATA3 immunostaining (p < 0.0001 each), but 11% of GATA3 negative cancers were Upk1a/b positive and 8% of Upk1a/b negative cancers were GATA3 positive. Absence of GATA3/Upk1a/b staining was significantly linked to poor patient survival in the subgroup of 126 pT4 carcinomas (p = 0.0004) but not in pT2 and pT3 cancers.

Conclusions

In summary, the results of our study demonstrate that Upk1a and/or Upk1b immunohistochemistry can complement GATA3 for the distinction of urothelial carcinomas. Furthermore, a progressive loss of Upk1a/b expression during stage progression and a prognostic role of the combination GATA3/Upk1a/Upk1b in pT4 carcinomas is evident.
Hydrodynamic regime and cold plasmas hit by short laser pulses
Authors: Fiore Gaetano , De Angelis Monica , Fedele Renato , Guerriero Gabriele , Jovanović Dušan
Published: October 2023

We briefly report and elaborate on some conditions allowing a hydrodynamic description of the impact of a very short and arbitrarily intense laser pulse onto a cold plasma, as well as the localization of the first wave-breaking due to the plasma inhomogeneity. We use a recently developed fully relativistic plane model whereby we reduce the system of the Lorentz–Maxwell and continuity PDEs into a 1-parameter family of decoupled systems of non-autonomous Hamilton equations in dimension 1, with the light-like coordinate $$\xi =ct\!-\!z$$

ξ
=
c
t

-

z

replacing time t as an independent variable. Apriori estimates on the Jacobian $$\hat{J}$$

J
^

of the change from Lagrangian to Eulerian coordinates in terms of the input data (initial density and pulse profile) are obtained applying Liapunov direct method to an associated family of pairs of ODEs; wave-breaking is pinpointed by the inequality $$\hat{J}\le 0$$

J
^

≤
0

. These results may help in drastically simplifying the study of extreme acceleration mechanisms of electrons, which have very important applications.
In-situ gas contents of a multi-section coal seam in Sydney basin for coal and gas outburst management
Authors: Li Zhongbei , Ren Ting , Black Dennis , Qiao Ming , Abedin Itmam , Juric Jessica , Wang Mike
Published: October 2023

The gas content is crucial for evaluating coal and gas outburst potential in underground coal mining. This study focuses on investigating the in-situ coal seam gas content and gas sorption capacity in a representative coal seam with multiple sections (A1, A2, and A3) in the Sydney basin, where the CO2 composition exceeds 90%. The fast direct desorption method and associated devices were described in detail and employed to measure the in-situ gas components (Q1, Q2, and Q3) of the coal seam. The results show that in-situ total gas content (QT) ranges from 9.48 m3/t for the A2 section to 14.80 m3/t for the A3 section, surpassing the Level 2 outburst threshold limit value, thereby necessitating gas drainage measures. Among the gas components, Q2 demonstrates the highest contribution to QT, ranging between 55% and 70%. Furthermore, high-pressure isothermal gas sorption experiments were conducted on coal samples from each seam section to explore their gas sorption capacity. The Langmuir model accurately characterizes CO2 sorption behavior, with fit coefficients (R2) greater than 0.99. Strong positive correlations are observed between in-situ gas content and Langmuir volume, as well as between residual gas content (Q3) and sorption hysteresis. Notably, the A3 seam section is proved to have a higher outburst propensity due to its higher Q1 and Q2 gas contents, lower sorption hysteresis, and reduced coal toughness f value. The insights derived from the study can contribute to the development of effective gas management strategies and enhance the safety and efficiency of coal mining operations.
Online coal dust suppression system for opencast coal mines
Authors: Panicker Senju , Shankar S. S. , Jithin S. , Sandeep S. , Irshad Muhammed , Daniel Jerry , Sajjad Tarique
Published: October 2023

Coal is the major source of power in India and world over. Coal mining is an essential industry which has a major role in the economic development of the country. Most major mining activities contribute directly or indirectly to air pollution. Coal dust is a major air pollutant which affects the personal working in the mines and also people residing in villages near the mines. Air pollution due to coal particulates can affect human health and cause damages to the environment. Hence effective pollution control mechanisms are needed to keep the pollution levels within permissible levels. The easiest and most common method employed for dust suppression worldwide is sprinkling of water. In majority of mines, water sprinklers are operated manually and can lead to wastage of water due to over sprinkling. It can also prove to be ineffective in dust suppression if sprinkling is not done properly. The paper proposes a system which can be deployed to automate the dust suppressions sprinklers. The system will monitor the concentration of PM10 and PM2.5 in the air and initiate sprinkling operation when the particulate matter content exceeds preconfigured limits.
Modeling and petrophysical properties of digital rock models with various pore structure types: An improved workflow
Authors: Li Xiaobin , Wei Wei , Xia Yuxuan , Wang Lei , Cai Jianchao
Published: October 2023

Pore structure is a crucial factor affecting the physical properties of porous materials, and understanding the mechanisms and laws of these effects is of great significance in the fields of geosciences and petroleum engineering. However, it remains a challenge to accurately understand and quantify the relationship between pore structures and effective properties. This paper improves a workflow to focus on investigating the effect of pore structure on physical properties. First, a hybrid modeling approach combining process-based and morphology-based methods is proposed to reconstruct 3D models with diverse pore structure types. Then, the characteristics and differences in pore structure in these models are compared. Finally, the variation laws and pore-scale mechanisms of the influence of pore structure on physical properties (permeability and elasticity) are discussed based on the reconstructed models. The relationship models between pore structure parameters and permeability/elastic parameters in the grain packing model are established. The effect of pore structure evolution on permeability/elasticity and the microscopic mechanism in three types of morphology-based reconstruction models are explored. The influence degree of pore structure on elastic parameters (bulk modulus, shear modulus, P-wave velocity, and S-wave velocity) is quantified, reaching 29.54%, 51.40%, 18.94%, and 23.18%, respectively. This work forms a workflow for exploring the relationship between pore structures and petrophysical properties at the microscopic scale, providing more ideas and references for understanding the complex physical properties in porous media.
A developed dual-site Langmuir model to represent the high-pressure methane adsorption and thermodynamic parameters in shale
Authors: Hu Ke , Zhang Qian , Liu Yufei , Thaika Muhammad Abdurrahman
Published: October 2023

Comprehending the mechanism of methane adsorption in shales is a crucial step towards optimizing the development of deep-buried shale gas. This is because the methane adsorbed in shale represents a significant proportion of the subsurface shale gas resource. To properly characterize the methane adsorption on shale, which exhibits diverse mineral compositions and multi-scale pore sizes, it is crucial to capture the energy heterogeneity of the adsorption sites. In this paper, a dual-site Langmuir model is proposed, which accounts for the temperature and pressure dependence of the density of the adsorbed phase. The model is applied to the isothermals of methane adsorption on shale, at pressures of up to 30 MPa and temperatures ranging from 40 to 100 °C. The results show that the proposed model can describe the adsorption behavior of methane on shale more accurately than conventional models, which assume a constant value for the density of adsorbed phase. Furthermore, the proposed model can be extrapolated to higher temperatures and pressures. Thermodynamic parameters were analyzed using correctly derived equations. The results indicate that the widely used, but incorrect, equation would underestimate the isosteric heat of adsorption. Neglecting the real gas behavior, volume of the adsorbed phase, and energy heterogeneity of the adsorption sites can lead to overestimation of the isosteric heat of adsorption. Furthermore, the isosteric heat evaluated from excess adsorption data can only be used to make a rough estimate of the real isosteric heat at very low pressure.
The Cognitive Neuroscience of Bilingualism
Authors: Schwieter John W. , Festman Julia
Published: October 2023

The Cognitive Neuroscience of Bilingualism presents an introduction to the neural bases and cognitive processes of the bilingual brain. It covers foundational knowledge required for study in the area of bilingualism, including prominent theories and research methodologies, and the state of research in relevant fields of psycholinguistics, cognitive psychology, and neuroscience. Major topics include bilingual development and brain plasticity; aphasia and the bilingual brain; cross-linguistic effects of bilingualism; bilingual lexical and conceptual memory; and cognitive and neurocognitive effects of bilingualism. This book represents the first of its kind to bring together the various psychological and theoretical issues of bilingualism with respect to language processing and representation, while providing insight into the 'reality' of the bilingual brain.
Anterior cerebral falx plane in MR images to estimate the craniofacial midline
Authors: Pei Jun , Liao Xu , Ge Lingling , Liu Jianwei , Jiang Xiling
Published: October 2023

Multiple methods have been proposed for evaluating the symmetry of facial contour by utilizing the median sagittal plane of the skull as a reference and measuring the maxillofacial region. To replace the manual mark point analysis method, we used the anterior cerebral falx plane in MRI images as an indicator of the craniofacial midline. The MRI examination data of 30 individuals were analyzed with a MeVisLab workstation. Two independent examiners performed 15 anthropometric measurements (4 angular, 11 linear) and compared the MRI-based anterior cerebral falx plane with the manual mark point analysis of the craniofacial midline estimation. All measurements were repeated after 3 weeks. Statistical analyses included the repeatability and reproducibility of the 2 methods based on intra-observer and inter-observer correlation coefficients (ICCs), respectively. Precision was estimated by intergroup comparison of the coefficient of variation. The anterior falx plane derived from the MRI data resulted in an intra-observer ICC of 0.869 ± 0.065 (range 0.733–0.936) and inter-observer ICC of 0.876 ± 0.0417 (0.798–0.932) for all measurements, showing significant correlations with the ICC values obtained by the mark point method (p < 0.05). The coefficient of variation showed that the precisions of the 2 methods were statistically comparable. We conclude that, for MRI-based craniofacial midline estimation, measurements made using the anterior cerebral falx plane are as precise, repeatable, and reproducible as those using the manual mark point analysis method. It has a high potential for application in radiation-free 3-dimensional craniofacial analysis.
RETRACTED ARTICLE: Efficacy and safety of arthroscopy in femoroacetabular impingement syndrome: a systematic review and meta-analysis of randomized clinical trials
Authors: Lamo-Espinosa José María , Mariscal Gonzalo , Gómez-Álvarez Jorge , San-Julián Mikel
Published: October 2023

This study aimed to compare the efficacy and safety of arthroscopy with physiotherapy or joint lavage in patients with femoroacetabular impingement (FAI). A meta-analysis using PubMed, Embase, Scopus, and the Cochrane Collaboration Library databases was performed in September 2022. We included studies focusing on patients with FAI who underwent arthroscopic surgery versus those who underwent physiotherapy or arthroscopic lavage. The outcomes were functional scores (iHOT-33 and HOS ADL) and adverse events. Randomized clinical trials were included in the study. The risk of bias in each study was assessed according to Cochrane guidelines for clinical trials. The data were combined using Review Manager version 5.4. (PROSPERO CRD42022375273). Six RCTs were included, from a pool of 839 patients (407 females). The iHOT-33 and HOS ADL scales showed significant differences at 12 months in favor of the arthroscopy group (MD, 10.65; 95% CI 6.54–4.76) and (MD, 8.09; 95% CI 3.11–13.07). MCID was not achieved through arthroscopy in functional variables. The rates of osteoarthritis (OR, 6.18; 95% CI 1.06–36.00) and numbness (OR, 73.73; 95% CI 10.00–43.92) were significantly higher in the arthroscopy group. Arthroscopic surgery showed statistical superiority over the control group without exceeding the MCID in most studies; however, the results might have been influenced by secondary variables. Finally, arthroscopic surgery results in a high rate of conversion to osteoarthritis.
The significance of heterophasic ion exchange in active biomonitoring of heavy metal pollution of surface waters
Authors: Kłos Andrzej , Wierzba Sławomir , Świsłowski Paweł , Cygan Agnieszka , Gruss Łukasz , Wiatkowski Mirosław , Pulikowski Krzysztof , Ziembik Zbigniew , Dołhańczuk-Śródka Agnieszka , Rajfur Małgorzata , Jerz Dominik , Piechaczek-Wereszczyńska Magdalena , Rosik-Dulewska Czesława , Wieczorek Piotr
Published: October 2023

We have carried out studies to examine the possibility of using biosorbents: the epigeic mosses Pleurozium schreberi (Willd. ex Brid.) Mitt., and the epiphytic lichens Hypogymnia physodes (L.) Nyl. in active biomonitoring of heavy metal pollution of surface waters. The dried sea algae Palmaria palmata (L.) Weber & Mohr were used as the third biosorbent. The studies were conducted in the waters of the Turawa Reservoir, a dam reservoir with a significant level of eutrophication in south-western Poland. Incremental concentrations of Mn, Ni, Zn, Cu, Cd, and Pb were determined in the exposed samples. It was shown that a 2-h exposure period increases the concentration of some metals in the exposed samples, even by as much as several hundred percent. High increments of nickel concentrations in the algae Palmaria palmata (mean: 0.0040 mg/g, with the initial concentration of c0 < 0.0016 in the algae) were noted, with negligible increments in concentrations of this metal in mosses and lichens. In contrast, mosses and lichens accumulated relatively high amounts of Cd (mean: 0.0033 mg/g, c0 = 0.00043 mg/g) and Pb (mean: 0.0243 mg/g, c0 = 0.0103 mg/g), respectively.
Whole transcriptome analysis in offspring whose fathers were exposed to a developmental insult: a novel avian model
Authors: Rimawi Issam , Yanai Sunny , Turgeman Gadi , Yanai Joseph
Published: October 2023

Although the effects of paternal exposure to insults on the offspring received limited attention in the past, it is currently gaining interest especially after understanding the mechanisms which may mediate such exposure effects. In the current study, the well-controlled avian model (Fayoumi) was utilized to investigate the effects of paternal exposure to the developmental insult, chlorpyrifos on the offspring’s gene expression via mRNA and small RNA sequencing. Numerous mRNA gene expression changes were detected in the offspring after paternal exposure to the developmental insult, especially in genes related to neurogenesis, learning and memory. qPCR analysis of several genes, that were significantly changed in mRNA sequencing, confirmed the results obtained in mRNA sequencing. On the other hand, small RNA sequencing did not identify significant microRNA genes expression changes in the offspring after paternal exposure to the developmental insult. The effects of the paternal exposure were more pronounced in the female offspring compared to the male offspring. The results identified expression alterations in major genes (some of which were pertinent to the functional changes observed in other forms of early developmental exposure) after paternal insult exposure and provided a direction for future studies involving the most affected genes.
Influence of variant-specific mutations, temperature and pH on conformations of a large set of SARS-CoV-2 spike trimer vaccine antigen candidates
Authors: Stuible Matthew , Schrag Joseph D. , Sheff Joey , Zoubchenok Daria , Lord-Dufour Simon , Cass Brian , L’Abbé Denis , Pelletier Alex , Rossotti Martin A. , Tanha Jamshid , Gervais Christian , Maurice Roger , El Bakkouri Majida , Acchione Mauro , Durocher Yves
Published: October 2023

SARS-CoV-2 subunit vaccines continue to be the focus of intense clinical development worldwide. Protein antigens in these vaccines most commonly consist of the spike ectodomain fused to a heterologous trimerization sequence, designed to mimic the compact, prefusion conformation of the spike on the virus surface. Since 2020, we have produced dozens of such constructs in CHO cells, consisting of spike variants with different mutations fused to different trimerization sequences. This set of constructs displayed notable conformational heterogeneity, with two distinct trimer species consistently detected by analytical size exclusion chromatography. A recent report showed that spike ectodomain fusion constructs can adopt an alternative trimer conformation consisting of loosely associated ectodomain protomers. Here, we applied multiple biophysical and immunological techniques to demonstrate that this alternative conformation is formed to a significant extent by several SARS-CoV-2 variant spike proteins. We have also examined the influence of temperature and pH, which can induce inter-conversion of the two forms. The substantial structural differences between these trimer types may impact their performance as vaccine antigens.
Evaluation of an automated dish preparation system for IVF and embryo culture using a mouse mode
Authors: Zhu Yan , Feng Huai L. , Jiang Man-Xi
Published: October 2023

Manual dish preparation for IVF in human fertility clinics or animal laboratories heavily relies on embryologists' experience, which can lead to occupational illness due to long-term and monotonous operation. Therefore, introducing an automated technique to replace traditional methods is crucial for improving working efficiency and reducing work burden for embryologists. In the current study in the mouse, both manual and automated methods were used to prepare IVF or embryo culture dishes. A one-way analysis of variance was conducted to compare several factors, including preparation time, qualified rates, media osmolality of dishes, fertilization rates, and embryonic development to assess the efficiency and potential of automated preparation. The results showed that automation system significantly reduced the required time and increased the efficiencies and qualified rates of dish preparation, especially for embryo culture dishes, without significantly altering medium osmolalities. There were no significant differences between two preparations in fertilization rates and embryo development in mice. Thus, automated dish preparation can improve working efficiency and qualified rates while maintaining fertilization rates and subsequent embryonic development without compromising osmolality stability of medium. It presents a superior alternative to manual preparation, reducing the workload of embryologists and facilitating the standardization of operational procedures.
Current status of phosphine resistance in Indian field populations of Tribolium castaneum and its influence on antioxidant enzyme activities
Authors: Singh Satyapriya , Nebapure Suresh M. , Taria Sukumar , Sagar Doddachowdappa , Subramanian Sabtharishi
Published: October 2023

Resistance to phosphine is widely reported in several stored product insect pests globally. However, knowledge of its prevalence and the association of antioxidant enzymes with phosphine resistance is limited. Herein, we assessed the levels of phosphine susceptibility and estimated the antioxidant enzyme activities viz., superoxide dismutase (SOD), peroxidase (POX), and catalase (CAT) in selected Indian populations of red flour beetle Tribolium castaneum (Herbst). Dose–response probit assays revealed that the LC50 values ranged from 0.038 to 1.277 mg L−1 showing 2.11 to 70.94-fold resistance to phosphine compared to susceptible check. Activities of antioxidant enzymes varied significantly between the T. castaneum populations following phosphine exposure. The magnitude of SOD activity ranged from 8.77 to18.82 U mg−1 protein, while, the activities of POX and CAT varied between 52.42 and 408.32 and 61.11 to 247.49 µM H2O2 reduced min−1 mg−1 of protein, respectively. The correlation analysis revealed a significant positive association of SOD (r = 0.89) and POX (r = 0.98) with increased resistance ratio, while the CAT (r = − 0.98) is negatively linked with resistance to phosphine. A principal component analysis identified phosphine resistance was closely associated with POX and SOD activities but was unrelated to the CAT activity. Our results throw light on the varied association of antioxidant enzyme activities in response to phosphine fumigation in field populations of T. castaneum. Further studies on the biochemical and molecular basis of phosphine stress in insects may help to devise suitable strategies to safeguard storage commodities and ensure a sustainable environment.
Multicomponent synthesis of pyrimido[4,5-b] quinolines over a carbocationic catalytic system
Authors: Moosavi-Zare Ahmad Reza , Najafi Raha
Published: October 2023

Trityl chloride (TrCl) was efficiently used as a neutral catalyst for the multicomponent cyclization reaction of an aldehyde with dimedone and 6-amino-1,3-dimethyluracil for the preparation of pyrimido[4,5-b] quinolines in chloroform under reflux condition.
Reductive cross-coupling of N-acyl pyrazole and nitroarene using tetrahydroxydiboron: synthesis of secondary amides
Authors: Moon Hayeon , Lee Sunwoo
Published: October 2023

Acyl pyrazoles, in the presence of B2(OH)4, efficiently yield amides when reacted with nitro compounds. The method is versatile, tolerates diverse functional groups, and holds promise for diverse organic molecule synthesis.
Convergence of a second-order scheme for non-local conservation laws
Authors: Gowda G. D. Veerappa , Kenettinkara Sudarshan Kumar , Manoj Nikhil
Published: October 2023

In this article, we present the convergence analysis of a second-order numerical scheme for traffic flow models that incorporate non-local conservation laws. We combine a MUSCL-type spatial reconstruction with strong stability preserving Runge-Kutta time-stepping to devise a fully discrete second-order scheme. The resulting scheme is shown to converge to a weak solution by establishing the maximum principle, bounded variation estimates and L1Lipschitz continuity in time. Further, using a space-step dependent slope limiter, we prove its convergence to the entropy solution. We also propose a MUSCL-Hancock type second-order scheme which requires only one intermediate stage unlike the Runge-Kutta schemes and is easier to implement. The performance of the proposed second-order schemes in comparison to a first-order scheme is demonstrated through several numerical experiments.
The Role of High-Value Agriculture in Capability Expansion: Qualitative Insights into Smallholder Cash Crop Production in Nepal, Laos and Rwanda
Authors: Matthys Marie-Luise , Illien Patrick , Acharya Sushant , Amacker Michèle , Bieri Sabin , Musafili Ildephonse , Sanesathid Outhoumphone
Published: October 2023

High-value agriculture contributes to rural incomes, but does it also contribute to expanding “human capabilities” (Sen, Development as freedom, Knopf, New York, 1999) in a durable way? Through long-term qualitative fieldwork in three landlocked LDCs—Nepal, Rwanda and Laos—resulting in over 150 interviews, we found expansions of the three analysed capabilities: paid work, mobility and social relations. Yet, those improvements were characterised by precariousness: they were mostly not resilient in the face of the economic and environmental risks that high-value agriculture entails. The only example of a durable capability expansion was found in Nepal, where women claimed social spaces through collective organisation. All three study sites showed remarkable consistency in that the considerable risk involved in cash crop production was mainly borne by farmers and rural labourers. Research on mechanisms to guard against these risks at household or individual level is warranted.
An unexplained, long-period radio-transient discovery
Authors: Sieben Jennifer
Published: October 2023

For 30 years the periodic radio emission from the mysterious object was being observed while remaining undiscovered.