bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomarker in Hepatocellular Carcinoma
Authors: Basthi Mohan Pooja , Lochan Rajiv , Shetty Shiran
Published: January 2024

Liver cancer is one of the most prevalent types of cancer and a major contributor to the socioeconomic burden worldwide. The pathogenesis of hepatocellular carcinoma (HCC) is contributed by various etiological factors like virus infection, excessive alcohol consumption, exposure to toxins, or metabolic disorders. Majority of patients are diagnosed with late-stage HCC, which restricts its management to only palliative care. HCC, if diagnosed early, increases the survival and quality of life. Currently available biomarker (alpha-fetoproteins) have several limitations, that impede the early diagnosis and staging of cancer. This warrants the continous search in pursuit of a novel biomarker. Several research works in diverse areas have contributed to the identification of various novel biomarkers that have shown multifaceted application in early disease diagnosis, which further aid in targeted and effective therapy that can prevent cancer progression. This improves the overall health status of the patient along with significant reduction in caretaker’s burden. With the aid of novel technologies, several biomarkers have been investigated and validated in mutliple preliminary research works. Therefore in this review, we have outlined various novel biomarkers that showed promising outcomes in their trials and we have highlighted the developing areas that act as game changers in cancer diagnosis and management.
Disclosing the potential of Cupressus leylandii A.B. Jacks & Dallim, Eucalyptus globulus Labill., Aloysia citrodora Paláu, and Melissa officinalis L. hydrosols as eco-friendly antimicrobial agents
Authors: Almeida Heloísa H. S. , Crugeira Pedro J. L. , Amaral Joana S. , Rodrigues Alírio E. , Barreiro Maria-Filomena
Published: January 2024

Antimicrobial resistance is a major global health concern, threatening the effective prevention and treatment of infections caused by microorganisms. These factors boosted the study of safe and green alternatives, with hydrosols, the by-products of essential oils extraction, emerging as promising natural antimicrobial agents. In this context, four hydrosols obtained from Cupressus leylandii A.B. Jacks & Dallim, Eucalyptus globulus Labill., Aloysia citrodora Paláu and Melissa officinalis L. were studied. Their chemical composition comprises neral, geranial, 1,8-cineole, terpinen-4-ol, and oplopanonyl acetate, compounds with recognised antimicrobial activity. Concerning antimicrobial activity, significant differences were found using different hydrosol concentrations (10–20% v/v) in comparison to a control (without hydrosol), showing the potential of the tested hydrosols to inhibit the microbial growth of Escherichia coli, Staphylococcus aureus, and Candida albicans. A. citrodora hydrosol was the most effective one, inhibiting 90% of E. coli growth and 80% of C. albicans growth, for both hydrosol concentrations (p < 0.0001). With hydrosol concentration increase, it was possible to observe an improved antimicrobial activity with significant reductions (p < 0.0001). The findings of this work indicate the viability of reusing and valuing the hydrosols, encouraging the development of green applications for different fields (e.g., food, agriculture, pharmaceuticals, and cosmetics).

Graphical Abstract
Development of Drug Products for the Treatment of Acute Radiation Syndrome
Authors: Libero Marzella
Published: January 2024

The Food and Drug Administration’s (FDA) approval to market drug products for use as medical countermeasures, to prevent or mitigate injury caused by various threat agents, is commonly based on evidence of efficacy obtained in animals. Animal studies are necessary when human studies are not feasible and challenge studies are not ethical. The successful development of countermeasures to radio-nuclear threats that cause Acute Radiation Syndrome (ARS) provides the opportunity to explore potential areas of overlap in the scientific approaches to studies of injuries caused by radiation and sulfur mustard exposures in animals. The aim is to evaluate the available scientific knowledge for radiation threat agents and sulfur mustard for potential analogies of fundamental mechanisms of organ injury and dysfunction. This evaluation is needed to determine the applicability of regulatory strategies for product development and approval adopted by manufacturers of countermeasures for radiation threat agents. Key elements of an efficient development plan based on animal efficacy studies include characterizing the pathophysiology of organ injury and the mechanism of action (MOA) of the countermeasure; modeling the clinical condition in animals to establish the manifestations of the injury caused by various levels of exposures to the threat agent and the response to various doses of the countermeasure candidate; as well as selecting a maximally effective human dose.
David against Goliath: from riders’ protest to platform cooperativism
Authors: Guichoux Arthur
Published: January 2024

Faced with platforms such as Uber, riders are resisting individually and organising actions such as Riders X Derechos in Spain. Some of these ‘new proletarians’ have even organised themselves into cooperatives. To the global utopia of investor-owned platforms, platform cooperativism opposes the utopia of delivery without exploitation or carbon emissions through local cooperatives owned by riders. Based on the case study of the Mensakas cooperative in Barcelona, this ethnography analyses the link between riders’ protests and cooperative platforms. It questions the concrete effects of ‘counter-platform politics’ and the relationship between politics and labour. It also examines the strategies of intercooperation in the ‘cyclelogistical’ sector to understand the institutional, social, and political conditions that foster the ‘re-embeddedness’ of the bike delivery market.
Platforms in the city and cities at the service of platforms: An urban perspective on the platform economy and workers’ responses
Authors: Dif-Pradalier Maël , Jammet Thomas , Tiberghien Julie , Bignami Filippo , Cuppini Niccolo
Published: January 2024

The social and economic impacts of the emerging platform economy are most obvious in urban settings, where platforms are giving rise to unfamiliar dynamics of inclusion and exclusion, cooperation and division, as well as social and political integration and fragmentation. Platform urbanisation has created a new and unprecedented kind of politics. It has given rise to new political spaces and new subjectivities, resulting in a permanent reorganisation of ‘historical’ assemblages of territory, authority and rights. Drawing on the results of the European-based PLUS Project (Platform Labour in Urban Spaces: Fairness, Welfare, Development), this themed collection offers a fresh perspective on the platform economy by analysing it in terms of the relationship between urban contexts and the ongoing platformisation process, with an emphasis on how this relationship is reshaping (platform) labour and reconfiguring (or even reinvigorating) social action. Along the way, the articles in this issue consider whether platforms are useful for the development of urban environments and labour markets, or whether urban environments and labour markets are useful for the development of platforms. Likewise, they seek to identify the conditions under which relevant actors can mobilise and build alliances to ensure that such forms of development can be made to benefit not only workers but also (urban) citizens and the (urban) environment in general.
Developing The World By Teaching Domestic Consumption: Swiss Supermarkets And The Emergence Of Development Aid Policies In The Early Postwar Period
Authors: Hartmann Heinrich
Published: January 2024

In the early post-Second World War period, Migros of Switzerland was the first European retail business to adopt the American supermarket model. Its success, however, has not only been a matter of technological and logistical innovation. Migros’ founder, Gottlieb Duttweiler, was convinced that consumer education was part and parcel of a new style of selling consumption. This conviction was at the basis of a strategy entering foreign markets and of exporting the Migros model abroad. Similar to post-World War II economic rehabilitation programs, Duttweiler pursued an indigenous modernization agenda, based on a new principle of “rational consumption”—he did not hesitate to label this as a genuine version of entrepreneurial development aid. Against the backdrop of the establishment of Migros’ activities in Turkey, this article discusses the participation of entrepreneurs in the international development policies after the Second World War. The history of Migros Türk sheds light not only on the entrepreneurial approach to modernization policy, which was often different to that adopted in government programs, but also on how this influenced critical consumerism inside and outside Switzerland over the long term.
Naming and Describing Disability in Law and Medicine
Authors: Robinson Heloise , Herring Jonathan
Published: January 2024

This article explores the effects of naming and describing disability in law and medicine. Instead of focusing on substantive issues like medical treatment or legal rights, it will address questions which arise in relation to the use of language itself. When a label which is attached to a disability is associated with a negative meaning, this can have a profound effect on the individual concerned and can create stigma. Overly negative descriptions of disabilities can be misleading, not only for the individual, but also more broadly in society, if there are inaccurate perceptions about disability in the social context. This article will examine some relevant examples of terminology, where these issues arise. It will also suggest that the role of medicine and the law in naming and describing disability is particularly important because in these areas there is, perhaps more than anywhere else, a recognized source of authority for the choice of terminology. Labels and descriptions used in the medical and legal contexts can not only perpetuate existing stigmatization of disabled people, but can also contribute to creating stigma at its source, given that the words used in these contexts can constitute an exercise of power.
Conspicuous leisure, time allocation, and obesity Kuznets curves
Authors: Mathieu-Bolh Nathalie , Wendner Ronald
Published: January 2024

Our growth model explores the complex relationship between income, obesity, and changes in exercise-related behavior. Combining Becker’s theory of time allocation (The Economic Journal 75(299), 493–517, 1965) with Veblen’s theory of conspicuous leisure (The Theory of the Leisure Class, 1st ed. New York: Macmillan, 1899), we determine conditions for dynamic and static obesity Kuznets curves. Considering food consumption and exercise choices, we show that dynamic and static Kuznets curves result from the rising opportunity cost of exercise and peer influence, both increasing with income. Focusing on calorie expenditure, we investigate the rise and slowdown in obesity prevalence in the USA and the correlation between obesity and income per worker. Our numerical simulations indicate that, as the economy grows, exercise choices slow down the rise in obesity prevalence but do not generate a dynamic Kuznets curve in the USA. By contrast, they generate a static Kuznets curve for a population cross section. We discuss policy implications of our findings.
Optimal unemployment insurance with behavioral agents
Authors: Yeung Hon Chung
Published: January 2024

This paper studies how behavioral biases affect the optimal unemployment insurance. I revisit the optimal UI of Landais et al. (2018) and show how the optimal UI formula is modified and leads to novel economic insights. The optimal UI replacement rate is the conventional Baily-Chetty replacement rate, which solves the trade-off between liquidity and job-search incentives, plus a market tightness correction term which shows how welfare is affected by UI through tightness, and plus a behavioral bias correction term, which shows how welfare is affected by UI through job search effort.
Comprehensive evaluation of body composition in a wide age range of Iranian adults using bioelectrical impedance analysis: Tehran Lipid and Glucose Study
Authors: Mohamadzadeh Mahdieh , Valizadeh Majid , Hosseinpanah Farhad , Momenan Amirabbas , Mahdavi Maryam , Barzin Maryam , Azizi Feridoun
Published: January 2024

Objective:

To evaluate sex- and age-stratified body composition (BC) parameters in subjects with wide age range of 20–79 years.

Design:

Cross-sectional.

Setting:

Participants of Tehran Lipid and Glucose Study (TLGS).

Participants:

Two thousand nine hundred seventy participants met our inclusion criteria. They were divided into five age groups, and BC parameters were analysed based on sex and age using a bioelectrical impedance analyser (BIA).

Result:

The mean age of the participants was 42·1 ± 12·5 years, and 54 % of them were males. The mean BMI was 26·7 ± 3·7 kg/m2. Obesity indices were significantly higher in females (P < 0·001); however, skeletal muscle mass (SMM) and fat-free mass (FFM) were significantly higher in males (P < 0·001). Both SMM and FFM decreased significantly after the age of 50 years. Obesity indices significantly increased from the age group of 20–29 to 30–39 years in males and the age groups of 30–39 to 40–49 years and 40–49 to 50–59 years in females. The fat mass ratio (fat mass/SMM) showed two peaks in both sexes (after the ages of 30 and 50 years in males and 40 and 50 years in females). A strong correlation was found between BMI and percentage of body fat (r = 0·823 in females v. r = 0·768 in males).

Conclusion:

This is the first community-based study in the MENA region identifying sex- and age-stratified BC values using BIA. Our findings can be used as a reference for comparison in appropriate settings.
Backwards Causation and Max Black's Abominable Conjunction
Authors: Garrett Brian
Published: January 2024

Philosophers dispute whether an effect can be earlier than its cause (i.e. whether backwards causation can occur). For example, could a trainwreck cause a psychic to have earlier knowledge of it? Max Black tried to show backwards causation to be impossible but he failed to do so, or so I will argue. Nonetheless, his famous article can still teach us something important about certain cases of backwards causation.
Galileo Observation of Electron Spectra Dawn‐Dusk Asymmetry in the Middle Jovian Magnetosphere: Evidence for Convection Electric Field
Authors: Yuan Chongjing , Roussos Elias , Wei Yong , Krupp Norbert , Liu Zhiyang , Wang Jianzhao
Published: January 2024

In Jupiter's middle magnetosphere, debate remains on the controlling physics of electron acceleration to the ultrarelativistic regime. Some local‐time asymmetric processes regulating MeV electrons may have their hold across electron spectra, leaving imprints down to 10–100s keV energies. Spectra at these lower energies can be measured with finite energy resolution, which is hardly achieved for MeV electrons. We investigate 10–100s keV electron spectra using Galileo measurements. We show that at 15–20 RJ, the power‐law exponents exhibit a previously unexpected dawn‐dusk asymmetry. This asymmetry is more prominent for 100s‐keV spectra, persistent but enhanced from 1996 to 2001. These match the theory of transport driven by a dawn‐to‐dusk electric field. Contrary to past expectations of dawn‐to‐dusk electric field at Io plasma torus (IPT) extending outward from 6 RJ, the origin of the field we infer may be completely different, despite its orientation and impacts on electron energization similar with the IPT one.
Stratospheric Temperature and Ozone Impacts of the Hunga Tonga‐Hunga Ha'apai Water Vapor Injection
Authors: Fleming Eric L. , Newman Paul A. , Liang Qing , Oman Luke D.
Published: January 2024

The January 2022 eruption of the Hunga Tonga‐Hunga Ha'apai underwater volcano injected a large amount of water vapor into the mid‐stratosphere. This study uses model simulations to investigate the resulting stratospheric impacts out to 2031. Maximum radiatively‐driven model temperature changes occur in the Southern Hemisphere (SH) subtropics in April–May 2022, with warming of ∼1 K in the lower stratosphere and cooling of 3 K in the mid‐stratosphere. The radiative cooling combined with adiabatic cooling driven by the quasi‐biennial oscillation meridional circulation explains the near‐record cold anomaly observed in the SH subtropical mid‐stratosphere. Projected ozone responses maximize in 2023–2024 as the water vapor plume is transported globally throughout the stratosphere and mesosphere. The excess H2O increases the OH radical, causing a negative global ozone response (2%–10%) in the upper stratosphere and mesosphere due to increased odd hydrogen‐ozone loss, and a small positive ozone response (0.5%–1%) in the mid‐stratosphere due to interference of the NOx catalytic loss cycle by the additional OH. In the lower stratosphere, the excess H2O is projected to increase polar stratospheric clouds and springtime halogen‐ozone loss, enhancing the Antarctic ozone hole by 25–30 DU in 2023. Arctic impact is small, with maximum additional ozone loss of 4–5 DU projected in spring 2024. These responses diminish after 2024 to be quite small by 2031, as the excess H2O is removed from the stratosphere with a 2.5‐year e‐folding time. Given the year‐to‐year variability of the stratosphere, the magnitudes of these ozone responses may be below the threshold of detectability in observations.
MAVEN/IUVS Observations of OH Prompt Emission: Daytime Water Vapor in the Thermosphere of Mars
Authors: Stevens M. H. , Cangi E. M. , Deighan J. , Jain S. K. , Chaffin M. S. , Evans J. S. , Gupta S. , Clarke J. T. , Schneider N. M. , Curry S. M.
Published: January 2024

We report the highest altitude detection of water vapor on Mars to date. The daytime limb observations by the Imaging Ultraviolet Spectrograph (IUVS) on the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft are of hydroxyl (OH) prompt emission near 308 nm, which is excited directly from the photodissociation of water vapor by the solar Lyman‐α flux. Average IUVS daytime water vapor densities near 130 km are 3 × 107 cm−3 around perihelion. The water vapor densities diurnally vary with a peak near midday and no detection at sunrise and sunset. To evaluate the large daytime water vapor densities for self‐consistency, we also report the simultaneous observation of OH solar fluorescence emission near 308 nm in the thermosphere, which enables the retrieval of OH densities. Using a one‐dimensional photochemical model initialized with the daytime IUVS water vapor densities, modeled peak OH densities are in good agreement with the observed IUVS peak OH densities. Because the observed thermospheric temperatures are controlled by solar insolation and cross the water frost point during the day, we suggest that the IUVS observed water vapor is created by the daily sublimation of water ice particles supplied from below. We discuss the implications of the IUVS observations on the present day loss of water vapor from Mars in the form of atomic hydrogen.
Soil Organic Carbon Lateral Movement Processes Integrated Into a Terrestrial Ecosystem Model
Authors: Lu Haibo , Wang Xiaoyuan , Zhang Haicheng , Xie Xianhong , Nakhavali Mahdi , Quine Timothy A. , Xu Wenfang , Xia Jiangzhou , He Bin , Hao Zhixin , Geng Xiu , Yuan Wenping
Published: January 2024

Lateral movement of soil organic carbon (SOC) induced by soil erosion and runoff changes spatial distributions of SOC, and further changes the land‐atmosphere CO2 exchange and terrestrial carbon budget. However, current ecosystem models do not or only poorly integrate the process of SOC lateral movement and cannot simulate the impacts of soil erosion on the carbon cycle. This study integrated SOC erosion and deposition processes into a process‐based ecosystem model (i.e., Integrated BIosphere Simulator (IBIS)), and separately simulated the lateral movements of dissolved organic carbon (DOC) and particulate organic carbon (POC). The model was evaluated in three river basins in Northeast China that are dominated by cropland, forest, and grassland. The results showed that the model reproduced well the production, erosion, and deposition of DOC and POC. The annual SOC lateral movement (1.34–7.22 g C m−2 yr−1) induced by erosion in the three tested basins was 0.27%–1.45% of the annual net primary production. The model developed in this study has great implications for simulating the lateral movements of SOC in terrestrial ecosystems, which can improve model performance in projecting the terrestrial carbon budget.
Twelve Times Faster yet Accurate: A New State‐Of‐The‐Art in Radiation Schemes via Performance and Spectral Optimization
Authors: Ukkonen Peter , Hogan Robin J.
Published: January 2024

Radiation schemes are critical components of Earth system models that need to be both efficient and accurate. Despite the use of approximations such as 1D radiative transfer, radiation can account for a large share of the runtime of expensive climate simulations. Here we seek a new state‐of‐the‐art in speed and accuracy by combining code optimization with improved algorithms. To fully benefit from new spectrally reduced gas optics schemes, we restructure code to avoid short vectorized loops where possible by collapsing the spectral and vertical dimensions. Our main focus is the ecRad radiation scheme, where this requires batching of adjacent cloudy layers, trading some simplicity for improved vectorization and instruction‐level parallelism. When combined with common optimization techniques for serial code and porting widely used two‐stream kernels fully to single precision, we find that ecRad with the TripleClouds solver becomes 12 times faster than the operational radiation scheme in ECMWF's Integrated Forecast System (IFS) cycle 47r3, which uses a less accurate gas optics model (RRMTG) and a more noisy solver (McICA). After applying the spectral reduction and extensive optimizations to the more sophisticated SPARTACUS solver, we find that it’s 2.5 times faster than IFS cy47r3 radiation, making cloud 3D radiative effects affordable to compute in large‐scale models. The code optimization itself gave a threefold speedup for both solvers. While SPARTACUS is still under development, preliminary experiments show slightly improved medium‐range forecasts of 2‐m temperature in the tropics, and in year‐long coupled atmosphere‐ocean simulations the 3D effects warm the surface substantially.
On the use of deep learning for phase recovery
Authors: Wang Kaiqiang , Song Li , Wang Chutian , Ren Zhenbo , Zhao Guangyuan , Dou Jiazhen , Di Jianglei , Barbastathis George , Zhou Renjie , Zhao Jianlin , Lam Edmund Y.
Published: January 2024

Phase recovery (PR) refers to calculating the phase of the light field from its intensity measurements. As exemplified from quantitative phase imaging and coherent diffraction imaging to adaptive optics, PR is essential for reconstructing the refractive index distribution or topography of an object and correcting the aberration of an imaging system. In recent years, deep learning (DL), often implemented through deep neural networks, has provided unprecedented support for computational imaging, leading to more efficient solutions for various PR problems. In this review, we first briefly introduce conventional methods for PR. Then, we review how DL provides support for PR from the following three stages, namely, pre-processing, in-processing, and post-processing. We also review how DL is used in phase image processing. Finally, we summarize the work in DL for PR and provide an outlook on how to better use DL to improve the reliability and efficiency of PR. Furthermore, we present a live-updating resource (https://github.com/kqwang/phase-recovery) for readers to learn more about PR.
Aerosol jet printing of surface acoustic wave microfluidic devices
Authors: Rich Joseph , Cole Brian , Li Teng , Lu Brandon , Fu Hanyu , Smith Brittany N. , Xia Jianping , Yang Shujie , Zhong Ruoyu , Doherty James L. , Kaneko Kanji , Suzuki Hiroaki , Tian Zhenhua , Franklin Aaron D. , Huang Tony Jun
Published: January 2024

The addition of surface acoustic wave (SAW) technologies to microfluidics has greatly advanced lab-on-a-chip applications due to their unique and powerful attributes, including high-precision manipulation, versatility, integrability, biocompatibility, contactless nature, and rapid actuation. However, the development of SAW microfluidic devices is limited by complex and time-consuming micro/nanofabrication techniques and access to cleanroom facilities for multistep photolithography and vacuum-based processing. To simplify the fabrication of SAW microfluidic devices with customizable dimensions and functions, we utilized the additive manufacturing technique of aerosol jet printing. We successfully fabricated customized SAW microfluidic devices of varying materials, including silver nanowires, graphene, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS). To characterize and compare the acoustic actuation performance of these aerosol jet printed SAW microfluidic devices with their cleanroom-fabricated counterparts, the wave displacements and resonant frequencies of the different fabricated devices were directly measured through scanning laser Doppler vibrometry. Finally, to exhibit the capability of the aerosol jet printed devices for lab-on-a-chip applications, we successfully conducted acoustic streaming and particle concentration experiments. Overall, we demonstrated a novel solution-based, direct-write, single-step, cleanroom-free additive manufacturing technique to rapidly develop SAW microfluidic devices that shows viability for applications in the fields of biology, chemistry, engineering, and medicine.
Hydrogels for active photonics
Authors: Ko Byoungsu , Jeon Nara , Kim Jaekyung , Kang Hyunjung , Seong Junhwa , Yun Suhyeon , Badloe Trevon , Rho Junsuk
Published: January 2024

Conventional photonic devices exhibit static optical properties that are design-dependent, including the material’s refractive index and geometrical parameters. However, they still possess attractive optical responses for applications and are already exploited in devices across various fields. Hydrogel photonics has emerged as a promising solution in the field of active photonics by providing primarily deformable geometric parameters in response to external stimuli. Over the past few years, various studies have been undertaken to attain stimuli-responsive photonic devices with tunable optical properties. Herein, we focus on the recent advancements in hydrogel-based photonics and micro/nanofabrication techniques for hydrogels. In particular, fabrication techniques for hydrogel photonic devices are categorized into film growth, photolithography (PL), electron-beam lithography (EBL), and nanoimprint lithography (NIL). Furthermore, we provide insights into future directions and prospects for deformable hydrogel photonics, along with their potential practical applications.
Probing the chemical ‘reactome’ with high-throughput experimentation data
Authors: King-Smith Emma , Berritt Simon , Bernier Louise , Hou Xinjun , Klug-McLeod Jacquelyn L. , Mustakis Jason , Sach Neal W. , Tucker Joseph W. , Yang Qingyi , Howard Roger M. , Lee Alpha A.
Published: January 2024

High-throughput experimentation (HTE) has the potential to improve our understanding of organic chemistry by systematically interrogating reactivity across diverse chemical spaces. Notable bottlenecks include few publicly available large-scale datasets and the need for facile interpretation of these data’s hidden chemical insights. Here we report the development of a high-throughput experimentation analyser, a robust and statistically rigorous framework, which is applicable to any HTE dataset regardless of size, scope or target reaction outcome, which yields interpretable correlations between starting material(s), reagents and outcomes. We improve the HTE data landscape with the disclosure of 39,000+ previously proprietary HTE reactions that cover a breadth of chemistry, including cross-coupling reactions and chiral salt resolutions. The high-throughput experimentation analyser was validated on cross-coupling and hydrogenation datasets, showcasing the elucidation of statistically significant hidden relationships between reaction components and outcomes, as well as highlighting areas of dataset bias and the specific reaction spaces that necessitate further investigation.
High-quality metagenome assembly from long accurate reads with metaMDBG
Authors: Benoit Gaëtan , Raguideau Sébastien , James Robert , Phillippy Adam M. , Chikhi Rayan , Quince Christopher
Published: January 2024

We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.
Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA
Authors: Dai Qing , Ye Chang , Irkliyenko Iryna , Wang Yiding , Sun Hui-Lung , Gao Yun , Liu Yushuai , Beadell Alana , Perea José , Goel Ajay , He Chuan
Published: January 2024

Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level and incomplete C-to-U conversion of certain DNA sequences. We present ultrafast BS-seq (UBS-seq), which uses highly concentrated bisulfite reagents and high reaction temperatures to accelerate the bisulfite reaction by ~13-fold, resulting in reduced DNA damage and lower background noise. UBS-seq allows library construction from small amounts of purified genomic DNA, such as from cell-free DNA or directly from 1 to 100 mouse embryonic stem cells, with less overestimation of 5mC level and higher genome coverage than conventional BS-seq. Additionally, UBS-seq quantitatively maps RNA 5-methylcytosine (m5C) from low inputs of mRNA and allows the detection of m5C stoichiometry in highly structured RNA sequences. Our UBS-seq results identify NSUN2 as the major ‘writer’ protein responsible for the deposition of ~90% of m5C sites in HeLa mRNA and reveal enriched m5C sites in 5′-regions of mammalian mRNA, which may have functional roles in mRNA translation regulation.
Clinical correlates of CT imaging-derived phenotypes among lean and overweight patients with hepatic steatosis
Authors: Song Isabel , Thompson Elizabeth W. , Verma Anurag , MacLean Matthew T. , Duda Jeffrey , Elahi Ameena , Tran Richard , Raghupathy Pavan , Swago Sophia , Hazim Mohamad , Bhattaru Abhijit , Schneider Carolin , Vujkovic Marijana , Torigian Drew A. , Kahn Charles E. , Gee James C. , Borthakur Arijitt , Kripke Colleen M. , Carson Christopher C. , Carr Rotonya , Jehangir Qasim , Ko Yi-An , Litt Harold , Rosen Mark , Mankoff David A. , Schnall Mitchell D. , Shou Haochang , Chirinos Julio , Damrauer Scott M. , Serper Marina , Chen Jinbo , Rader Daniel J. ,   Penn Medicine BioBank, Ritchie Marylyn D. , Weaver JoEllen , Naseer Nawar , Poindexter Afiya , Hu-Sain Khadijah , Livingstone Meghan , Vadivieso Fred , DerOhannessian Stephanie , Tran Teo , Stephanowski Julia , Zielinski Monica , Haubein Ned , Dunn Joseph , Verma Anurag , Kripke Colleen M. , Risman Marjorie , Judy Renae , Verma Shefali S. , Bradford Yuki , Dudek Scott , Drivas Theodore , Witschey Walter R. T. , Sagreiya Hersh
Published: January 2024

The objective of this study is to define CT imaging derived phenotypes for patients with hepatic steatosis, a common metabolic liver condition, and determine its association with patient data from a medical biobank. There is a need to further characterize hepatic steatosis in lean patients, as its epidemiology may differ from that in overweight patients. A deep learning method determined the spleen-hepatic attenuation difference (SHAD) in Hounsfield Units (HU) on abdominal CT scans as a quantitative measure of hepatic steatosis. The patient cohort was stratified by BMI with a threshold of 25 kg/m2 and hepatic steatosis with threshold SHAD ≥  − 1 HU or liver mean attenuation ≤ 40 HU. Patient characteristics, diagnoses, and laboratory results representing metabolism and liver function were investigated. A phenome-wide association study (PheWAS) was performed for the statistical interaction between SHAD and the binary characteristic LEAN. The cohort contained 8914 patients—lean patients with (N = 278, 3.1%) and without (N = 1867, 20.9%) steatosis, and overweight patients with (N = 1863, 20.9%) and without (N = 4906, 55.0%) steatosis. Among all lean patients, those with steatosis had increased rates of cardiovascular disease (41.7 vs 27.8%), hypertension (86.7 vs 49.8%), and type 2 diabetes mellitus (29.1 vs 15.7%) (all p < 0.0001). Ten phenotypes were significant in the PheWAS, including chronic kidney disease, renal failure, and cardiovascular disease. Hepatic steatosis was found to be associated with cardiovascular, kidney, and metabolic conditions, separate from overweight BMI.
Control charts using half-normal and half-exponential power distributions using repetitive sampling
Authors: Naveed Muhammad , Azam Muhammad , Khan Nasrullah , Aslam Muhammad , Saleem Muhammad , Saeed Muhammad
Published: January 2024

This manuscript presents the development of an attribute control chart (ACC) designed to monitor the number of defective items in manufacturing processes. The charts are specifically tailored using time-truncated life test (TTLT) for two lifetime data distributions: the half-normal distribution (HND) and the half-exponential power distribution (HEPD) under a repetitive sampling scheme (RSS). To assess the effectiveness of the proposed control charts, both in-control (IC) and out-of-control (OOC) scenarios are considered by deriving the average run length (ARL). Various factors, including sample sizes, control coefficients, and truncated constants for shifted phases, are taken into account to evaluate the performance of the charts in terms of ARL. The behavior of ARLs is analyzed in the shifted process by introducing shifts in its parameters. The superiority of the HEPD-based chart is highlighted by comparing it with both the HND-based ACC and the ACC based on the Exponential distribution (ED) under TTLT using RSS. The results showcase the superior performance of the proposed HEPD-based chart, indicated by smaller ARL values. Additionally, the benefits of another proposed ACC using HND are compared with the ED-based ACC under RSS, further confirming the effectiveness of the HND-based approach through smaller ARLs Finally, the proposed control charts are evaluated through simulation testing and real-life implementation, emphasizing their practical applicability in real-world manufacturing settings.
Cryogenic fracturing using liquid nitrogen on granite at elevated temperatures: a case study for enhanced geothermal systems in Kazakhstan
Authors: Longinos Sotirios Nik. , Hazlett Randy
Published: January 2024

Cryogenic fracturing using liquid nitrogen (LN2) is a novel stimulation technology that enhances porosity, permeability, and rock-fluid contact area in subsurface formations targetted for geothermal energy extraction. In our experimental study, granite cores collected from the Zhylgyz region in South Kazakhstan were equilibrated at various elevated temperatures before treatments involving LN2 exposure time. Compression, Brazilian, and fracture toughness tests were performed on granite with starting temperatures ranging from 100 to 500 °C to quantify the impact of initial temperature on cryogenic fracturing and to compare with baseline geomechanical tests at 50 °C without LN2 exposure. The results show that LN2 cooling of hot granite induces mechanical rock failure and permeability enhancement. Moreover, the degree of thermo-fracturing augments with initial granite temperature, total freezing time, and number of freezing–thawing cycles. The peak load before failure of granite specimens, both in compression and Brazilian tests, reduces with the increased sample temperature difference and length of LN2 treatment. The fracture toughness of our semi-circular bend (SCB) LN2-treated specimens diminished with increasing temperature difference between granite and boiling point. In both experimental LN2 treatment processes, the specimens with an initial temperature of 500 °C before LN2 treatment formed many new fissures and extensions of pre-existing ones, showing that the plastic behavior is augmented. While cryo-fracturing experimental confirmation is recommended with site-specific samples in planning geothermal operations, these results in our work indicate a threshold downhole temperature, e.g., > 300 °C, for enhanced stimulation outcomes.
Earlier social information has a stronger influence on judgments
Authors: Tump Alan Novaes , Wollny-Huttarsch David , Molleman Lucas , Kurvers Ralf H. J. M.
Published: January 2024

People’s decisions are often informed by the choices of others. Evidence accumulation models provide a mechanistic account of how such social information enters the choice process. Previous research taking this approach has suggested two fundamentally different cognitive mechanisms by which people incorporate social information. On the one hand, individuals may update their evidence level instantaneously when observing social information. On the other hand, they may gradually integrate social information over time. These accounts make different predictions on how the timing of social information impacts its influence. The former predicts that timing has no impact on social information uptake. The latter predicts that social information which arrives earlier has a stronger impact because its impact increases over time. We tested both predictions in two studies in which participants first observed a perceptual stimulus. They then entered a deliberation phase in which social information arrived either early or late before reporting their judgment. In Experiment 1, early social information remained visible until the end and was thus displayed for longer than late social information. In Experiment 2, which was preregistered, early and late social information were displayed for an equal duration. In both studies, early social information had a larger impact on individuals’ judgments. Further, an evidence accumulation analysis found that social information integration was best explained by both an immediate update of evidence and continuous integration over time. Because in social systems, timing plays a key role (e.g., propagation of information in social networks), our findings inform theories explaining the temporal evolution of social impact and the emergent social dynamics.
Cathodoluminescence spectroscopy of monolayer hexagonal boron nitride
Authors: Shima Kohei , Cheng Tin S. , Mellor Christopher J. , Beton Peter H. , Elias Christine , Valvin Pierre , Gil Bernard , Cassabois Guillaume , Novikov Sergei V. , Chichibu Shigefusa F.
Published: January 2024

Cathodoluminescence (CL) spectroscopy is a suitable technique for studying the luminescent properties of optoelectronic materials because CL has no limitation on the excitable bandgap energy and eliminates ambiguous signals due to simple light scattering and resonant Raman scattering potentially involved in the photoluminescence spectra. However, direct CL measurements of atomically thin two-dimensional materials have been difficult due to the small excitation volume that interacts with high-energy electron beams. Herein, distinct CL signals from a monolayer hexagonal BN (hBN), namely mBN, epitaxial film grown on a graphite substrate are shown by using a CL system capable of large-area and surface-sensitive excitation. Spatially resolved CL spectra at 13 K exhibited a predominant 5.5-eV emission band, which has been ascribed to originate from multilayered aggregates of hBN, markedly at thicker areas formed on the step edges of the substrate. Conversely, a faint peak at 6.04 ± 0.01 eV was routinely observed from atomically flat areas, which is assigned as being due to the recombination of phonon-assisted direct excitons of mBN. The CL results support the transition from indirect bandgap in bulk hBN to direct bandgap in mBN. The results also encourage one to elucidate emission properties of other low-dimensional materials by using the present CL configuration.
Global taxonomic and functional patterns in invertebrate assemblages from rocky-intertidal mussel beds
Authors: Cameron Nicole M. , Scrosati Ricardo A. , Valdivia Nelson , Meunier Zechariah D.
Published: January 2024

Mussels form extensive beds in rocky intertidal habitats on temperate seashores worldwide. They are foundation species because their beds host many invertebrates. Mussels and their associated species differ taxonomically among biogeographic regions, but all mussel beds exhibit similar structural and functional properties. Therefore, we investigated if rocky-intertidal mussel beds from around the globe host associated communities that are functionally similar despite their underlying taxonomic differences. We gathered datasets on the abundance of invertebrates found in rocky-intertidal mussel beds from the eastern and western boundaries of the Pacific and Atlantic Oceans from both hemispheres and, then, we compared their taxonomic and functional properties. Taxonomic composition differed markedly among coasts when analyzed at the taxonomic resolution reported by the surveys (often species). However, taxonomic groups with similar ecologies (28 groups including barnacles, decapods, gastropods, polychaetes, etc.) were more universally present in mussel beds. Concomitantly, functional categories of trophic level, body type, and mobility were almost always present on all studied coasts. These taxonomic groups and trait categories, however, showed regional patterns based on their relative abundances. Overall, the ability of mussel beds to host a core community type based on taxonomic groups and functional traits emphasizes their importance for biodiversity and community functioning, making them critical organisms to preserve.
Firefly algorithm based WSN-IoT security enhancement with machine learning for intrusion detection
Authors: Karthikeyan M. , Manimegalai D. , RajaGopal Karthikeyan
Published: January 2024

A Wireless Sensor Network (WSN) aided by the Internet of Things (IoT) is a collaborative system of WSN systems and IoT networks are work to exchange, gather, and handle data. The primary objective of this collaboration is to enhance data analysis and automation to facilitate improved decision-making. Securing IoT with the assistance of WSN necessitates the implementation of protective measures to confirm the safety and reliability of the interconnected WSN and IoT components. This research significantly advances the current state of the art in IoT and WSN security by synergistically harnessing the potential of machine learning and the Firefly Algorithm. The contributions of this work are twofold: firstly, the proposed FA-ML technique exhibits an exceptional capability to enhance intrusion detection accuracy within the WSN-IoT landscape. Secondly, the amalgamation of the Firefly Algorithm and machine learning introduces a novel dimension to the domain of security-oriented optimization techniques. The implications of this research resonate across various sectors, ranging from critical infrastructure protection to industrial automation and beyond, where safeguarding the integrity of interconnected systems are of paramount importance. The amalgamation of cutting-edge machine learning and bio-inspired algorithms marks a pivotal step forward in crafting robust and intelligent security measures for the evolving landscape of IoT-driven technologies. For intrusion detection in the WSN-IoT, the FA-ML method employs a support vector machine (SVM) machine model for classification with parameter tuning accomplished using a Grey Wolf Optimizer (GWO) algorithm. The experimental evaluation is simulated using NSL-KDD Dataset, revealing the remarkable enhancement of the FA-ML technique, achieving a maximum accuracy of 99.34%. In comparison, the KNN-PSO and XGBoost models achieved lower accuracies of 96.42% and 95.36%, respectively. The findings validate the potential of the FA-ML technique as an active security solution for WSN-IoT systems, harnessing the power of machine learning and the Firefly Algorithm to bolster intrusion detection capabilities.
Conditional generative learning for medical image imputation
Authors: Raad Ragheb , Ray Deep , Varghese Bino , Hwang Darryl , Gill Inderbir , Duddalwar Vinay , Oberai Assad A.
Published: January 2024

Image imputation refers to the task of generating a type of medical image given images of another type. This task becomes challenging when the difference between the available images, and the image to be imputed is large. In this manuscript, one such application is considered. It is derived from the dynamic contrast enhanced computed tomography (CECT) imaging of the kidneys: given an incomplete sequence of three CECT images, we are required to impute the missing image. This task is posed as one of probabilistic inference and a generative algorithm to generate samples of the imputed image, conditioned on the available images, is developed, trained, and tested. The output of this algorithm is the “best guess” of the imputed image, and a pixel-wise image of variance in the imputation. It is demonstrated that this best guess is more accurate than those generated by other, deterministic deep-learning based algorithms, including ones which utilize additional information and more complex loss terms. It is also shown that the pixel-wise variance image, which quantifies the confidence in the reconstruction, can be used to determine whether the result of the imputation meets a specified accuracy threshold and is therefore appropriate for a downstream task.
Contribution of uniparental disomy to fetal growth restriction: a whole-exome sequencing series in a prenatal setting
Authors: Li Mengmeng , Hao Na , Jiang Yulin , Xue Huili , Dai Yifang , Wang Mingming , Bai Junjie , Lv Yan , Qi Qingwei , Zhou Xiya
Published: January 2024

Fetal growth restriction (FGR), a leading cause of perinatal morbidity and mortality, is caused by fetal, maternal, and placental factors. Uniparental disomy (UPD) is a rare condition that leads to imprinting effects, low-level mosaic aneuploidies and homozygosity for pathogenic variants. In the present study, UPD events were detected in 5 women with FGR by trio exome sequencing (trio-WES) of a cohort of 150 FGR cases. Furthermore, noninvasive prenatal testing results of the 5 patients revealed a high risk of rare autosomal trisomy. Trio-WES showed no copy-number variations (CNVs) or nondisease-causing mutations associated with FGR. Among the 5 women with FGR, two showed gene imprinting, and two exhibited confined placental mosaicism (CPM) by copy number variant sequencing (CNV-seq). The present study showed that in FGR patients with UPD, the detection of imprinted genes and CPM could enhance the genetic diagnosis of FGR.