bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to estimate carbon footprint when training deep learning models? A guide and review
Authors: Bouza Lucía , Bugeau Aurélie , Lannelongue Loïc 
Published: September 2023

Abstract
Machine learning and deep learning models have become essential in the recent fast development of artificial intelligence in many sectors of the society. It is now widely acknowledge that the development of these models has an environmental cost that has been analyzed in many studies. Several online and software tools have been developed to track energy consumption while training machine learning models. In this paper, we propose a comprehensive introduction and comparison of these tools for AI practitioners wishing to start estimating the environmental impact of their work. We review the specific vocabulary, the technical requirements for each tool. We compare the energy consumption estimated by each tool on two deep neural networks for image processing and on different types of servers. From these experiments, we provide some advice for better choosing the right tool and infrastructure.
Interaction phenomena of electrically coupled cells under local reactant starvation in automotive PEMFC stacks
Authors: Nissen Jens , Schrievers Max , Huber Johannes Frieder , Schwämmlein Jan Nicolas , Henkel Florian , Czarnetzki Walter Theodor , Hölzle Markus 
Published: September 2023

Abstract
The local current density distribution of polymer electrolyte membrane fuel cells (PEMFCs) can be distorted by various error states. Differences in current density distributions (CDDs) of adjacent cells in a stack are equilibrized by in-plane currents within the sandwiched bipolar plates. Degradation stressors such as detrimental differences in local cell voltage and current density maxima can thus be generated. A novel method was therefore developed to intentionally manipulate CDD profiles by integrating local artificial starvation into only one fuel cell in an assembly. This technique is applied to automotive-sized PEMFCs single cells as well as in 20 cell short-stack to analyze such voltage and current redistribution phenomena. A drastic distortion of local cell voltage is only observed for stacks, which is explained by a supplementary simulation. The local voltage distribution of an electrically coupled fuel cell is therefore calculated by combining CDD measurements with a spatially resolved polarization curve model. The capabilities and limits of a multipoint cell voltage monitoring measurement device are discussed on this basis. The inspected correlation between these two independent online measurement techniques allows to localize such error states with considerable accuracy during operation of automotive sized PEMFC stacks.
Machine learning of hidden variables in multiscale fluid simulation
Authors: Joglekar Archis S , Thomas Alexander G R 
Published: September 2023

Abstract
Solving fluid dynamics equations often requires the use of closure relations that account for missing microphysics. For example, when solving equations related to fluid dynamics for systems with a large Reynolds number, sub-grid effects become important and a turbulence closure is required, and in systems with a large Knudsen number, kinetic effects become important and a kinetic closure is required. By adding an equation governing the growth and transport of the quantity requiring the closure relation, it becomes possible to capture microphysics through the introduction of ‘hidden variables’ that are non-local in space and time. The behavior of the ‘hidden variables’ in response to the fluid conditions can be learned from a higher fidelity or ab-initio model that contains all the microphysics. In our study, a partial differential equation simulator that is end-to-end differentiable is used to train judiciously placed neural networks against ground-truth simulations. We show that this method enables an Euler equation based approach to reproduce non-linear, large Knudsen number plasma physics that can otherwise only be modeled using Boltzmann-like equation simulators such as Vlasov or particle-in-cell modeling.
A new room temperature viscoelastic inorganic glass
Authors: Wang Weihua 
Published: September 2023

Abstract
Inorganic glass is a non-crystalline material that lacks of a regular, periodic atomic or molecular structure, and are considered as frozen liquids because of the similarity between their static amorphous structures. The atoms and molecules in the glass can gradually rearrange and realign with time, giving rise to deformation or aging in most glass materials. However, viscoelastic behavior could not be readily observable at room temperature (RT) due to its long time scale. The paper introduce and comment a recent work published in Nature Energy, which discover a new class of viscoelastic inorganic glass with Tg well below RT. The VIGLAS is simply synthesized through adding high content of oxygen into tetrachloroaluminates to replace chlorine. The VIGLAS exhibits characteristics similar to both inorganic ceramics and organic polymers, which are particularly relevant in the realm of battery electrolytes where a balance between ionic conductivity and chemo-mechanical compatibility is crucial.
IMM47, a humanized monoclonal antibody that targets CD24, exhibits exceptional anti-tumor efficacy by blocking the CD24/Siglec-10 interaction and can be used as monotherapy or in combination with anti-PD1 antibodies for cancer immunotherapy
Authors: Li Song , Chen Dianze , Guo Huiqin , Yang Yanan , Liu Dandan , Yang Chunmei , Bai Xing , Zhang Wei , Zhang Li , Zhao Gui , Tu Xiaoping , Peng Liang , Liu Sijin , Song Yongping , Jiang Zhongxing , Zhang Ruliang , Yu Jifeng , Tian Wenzhi 
Published: September 2023

Abstract
This study evaluates the anti-tumor mechanism of IMM47, a humanized anti-CD24 mAb. Biolayer interferometry, ELISA and flow cytometry methods were used to measure the IMM47 binding, affinity, ADCC, ADCP, ADCT and CDC activities. In vivo therapeutical efficacy was measured in transplanted mouse models. IMM47 significantly binds granulocytes but not human erythrocytes and blocks CD24’s ability to bind to Siglec-10. IMM47 has strong ADCC, ADCT and ADCP activity against REH cells. IMM47’s in vivo pharmacodynamics showed that IMM47 has strong anti-tumor effects in human siglec-10 transgenic mouse models with a memory immune response. IMM47 also has powerful synergistic therapeutic efficacy when combined with Tislelizumab, Opdivo and Keytruda, by blocking CD24/Siglec-10 interaction through macrophage antigen presentation with strong ADCC, ADCP, ADCT and CDC activities and with a safe profile. IMM47 binding to CD24 is independent of N-glycosylation modification of the extracellular domain.
Survival and critical care use among people with dementia in a large English cohort
Authors: Yorganci Emel , Sleeman Katherine E , Sampson Elizabeth L , Stewart Robert ,   The EMBED-Care Programme, Sampson Elizabeth L , Evans Catherine J , Sleeman Katherine E , Kupeli Nuriye , Moore Kirsten J , Davies Nathan , Ellis-Smith Clare , Ward Jane , Gola Anna , Candy Bridget , Omar Rumana Z , Warren Jason D , Anderson Janet E , Harding Richard , Stewart Robert , Mead Simon 
Published: September 2023

Abstract

Background
Admitting people with dementia to critical care units may not always lead to a clear survival benefit. Critical care admissions of people with dementia vary across countries. Little is known about the use and trends of critical care admissions of people with dementia in England.

Objective
To investigate critical care use and survival among people with dementia in a large London catchment area.

Methods
A retrospective cohort study using data from dementia assessment services in south London, UK (2007–20) linked with national hospitalisation data to ascertain critical care admissions. Outcomes included age–sex-standardised critical care use and 1-year post-critical care admission survival by dementia severity (binary: mild versus moderate/severe). We used logistic regression and Kaplan–Meier survival plots for investigating 1-year survival following a critical care admission and linear regressions for time trends.

Results
Of 19,787 people diagnosed with dementia, 726 (3.7%) had ≥1 critical care admission at any time after receiving their dementia diagnosis. The overall 1-year survival of people with dementia, who had a CCA, was 47.5% (n = 345). Dementia severity was not associated with 1-year survival following a critical care admission (mild dementia versus moderate–severe dementia odds of 1-year mortality OR: 0.90, 95% CI [0.66–1.22]). Over the 12-year period from 2008 to 2019, overall critical care use decreased (β = −0.05; 95% CI = −0.01, −0.0003; P = 0.03), while critical care admissions occurring during the last year of life increased (β = 0.11, 95% CI = 0.01, 0.20, P = 0.03).

Conclusions
In this cohort, while critical care use among people with dementia declined overall, its use increased among those in their last year of life. Survival remains comparable to that observed in general older populations.
Biological evaluation of a phosphate ester prodrug of 10-methyl-aplog-1, a simplified analog of aplysiatoxin, as a possible latency-reversing agent for HIV reactivation
Authors: Maki Jumpei , Hanaki Yusuke , Yanagita Ryo C , Kikumori Masayuki , Kovba Anastasiia , Washizaki Ayaka , Tsukano Chihiro , Akari Hirofumi , Irie Kazuhiro 
Published: September 2023

ABSTRACT
10-Methyl-aplog-1 (10MA-1), a simplified analog of aplysiatoxin, exhibits a high binding affinity for protein kinase C (PKC) isozymes with minimal tumor-promoting and pro-inflammatory activities. A recent study suggests that 10MA-1 could reactivate latent human immunodeficiency virus (HIV) in vitro for HIV eradication strategy. However, further in vivo studies were abandoned by a dose limit caused by the minimal water solubility of 10MA-1. To overcome this problem, we synthesized a phosphate ester of 10MA-1, 18-O-phospho-10-methyl-aplog-1 (phos-10MA-1), to improve water solubility for in vivo studies. The solubility, PKC binding affinity, and biological activity of phos-10MA-1 were examined in vitro, and the biological activity was comparable with 10MA-1. The pharmacokinetic studies in vivo were also examined, which suggest that further optimization for improving metabolic stability is required in the future.
Enantioselective synthesis of the aglycone of burnettramic acid A
Authors: Kuji Kohei , Kawamoto Misaki , Enomoto Masaru , Kuwahara Shigefumi , Meguro Yasuhiro 
Published: September 2023

ABSTRACT
Enantioselective total synthesis of the aglycone of burnettramic acid A, an antifungal pyrrolizidinedione with a terminally mannosylated long acyl chain produced by Aspergillus fungi, has been achieved from a known carboxylic acid by a 14-step sequence. The key steps include 2 types of asymmetric alkylation, coupling of an acetylide intermediate with (S)-epichlorohydrin to provide an acetylenic epoxide in 1 pot, and the Birch reduction to effect desulfonylation, semi-reduction of triple bond, and debenzylation in a concurrent manner. Good agreement of the synthetic aglycone with naturally occurring one in 1H and 13C nuclear magnetic resonance (NMR) spectra, coupled with previously reported unambiguous stereochemical assignment of the sugar moiety, has confirmed the structure of burnettramic acid A.
ePlatypus: an ecosystem for computational analysis of immunogenomics data
Authors: Cotet Tudor-Stefan , Agrafiotis Andreas , Kreiner Victor , Kuhn Raphael , Shlesinger Danielle , Manero-Carranza Marcos , Khodaverdi Keywan , Kladis Evgenios , Desideri Perea Aurora , Maassen-Veeters Dylan , Glänzer Wiona , Massery Solène , Guerci Lorenzo , Hong Kai-Lin , Han Jiami , Stiklioraitis Kostas , D’Arcy Vittoria Martinolli , Dizerens Raphael , Kilchenmann Samuel , Stalder Lucas , Nissen Leon , Vogelsanger Basil , Anzböck Stine , Laslo Daria , Bakker Sophie , Kondorosy Melinda , Venerito Marco , Sanz García Alejandro , Feller Isabelle , Oxenius Annette , Reddy Sai T , Yermanos Alexander 
Published: September 2023

Abstract

Motivation
The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner.

Results
Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.

Availability and implementation
Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.
chem16S: community-level chemical metrics for exploring genomic adaptation to environments
Authors: Dick Jeffrey M , Kang Xun 
Published: September 2023

Abstract

Summary
The chem16S package combines taxonomic classifications of 16S rRNA gene sequences with amino acid compositions of prokaryotic reference proteomes to generate community reference proteomes. Taxonomic classifications from the RDP Classifier or data objects created by the phyloseq R package are supported. Users can calculate and visualize a variety of chemical metrics in order to explore the effects of redox, salinity, and other physicochemical variables on the genomic adaptation of protein sequences at the community level.

Availability and implementation
Development of chem16S is hosted at https://github.com/jedick/chem16S. Version 1.0.0 is freely available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/package=chem16S.
The End of the Age-Crime Curve? A Historical Comparison of Male Arrest Rates in the United States, 1985–2019
Authors: Tuttle James 
Published: September 2023

Abstract
As presented in this article, the overall arrest rate for males in the United States no longer peaks during the late teenage years, contrary to the traditional conceptualization of the age-crime curve. Instead of peaking around age 18 and falling throughout adulthood, the overall arrest rate in 2019 did not peak until age 27. Using a dissimilarity index, the results show that the age-crime curve for overall, violent and property offenses during 2019 differs significantly from that of 1985. However, the age-crime curve is still apparent within the data when examined by birth cohort. It appears that a sudden decline in the proportion of offenses committed by 15-to-19-year-old males is responsible for the shift in the aggregate/cross-sectional age-crime curve.
α5-nAChR/STAT3/CD47 axis contributed to nicotine-related lung adenocarcinoma progression and immune escape
Authors: Kang Guiyu , Jiao Yang , Pan Pan , Fan Huiping , Li Qiang , Li Xiangying , Li Jingtan , Wang Yan , Jia Yanfei , Wang Jingting , Sun Haiji , Ma Xiaoli 
Published: September 2023

Abstract

Objectives
The CHRNΑ5 gene, which encodes the α5-nicotinic acetylcholine receptor (α5-nAChR), is related to lung cancer and nicotine addiction. Smoking is closely related to the immunosuppressive effect of macrophages. CD47, a phagocytosis checkpoint in macrophages, is a therapeutic target in various cancer types. Nevertheless, the relationship between α5-nAChR and CD47 in lung cancer is still unclear.

Methods and Results
The present study showed that α5-nAChR-mediated CD47 expression via STAT3 signaling, consequently leading to tumor progression and immune suppression in lung adenocarcinoma (LUAD). α5-nAChR expression was correlated with STAT3 expression, CD47 expression, smoking status and poor prognosis of LUAD in vivo. In vitro, α5-nAChR expression mediated the phosphorylation of STAT3, and phosphorylated STAT3 bound to the CD47 promoter and mediated CD47 expression. Downregulation of α5-nAChR and/or CD47 significantly reduced cell proliferation, migration, invasion, stemness and IL-10 expression, but increased TNF-α expression and phagocytosis of macrophages in LUAD. Furthermore, α5-nAChR/CD47 signaling contributed to the growth of subcutaneous xenograft tumors and liver metastasis of tumors in mice.

Conclusion
The α5-nAChR/STAT3/CD47 axis contributed to the progression and immune escape of lung cancer and may be a potential target for LUAD immunotherapy.
Electroacupuncture alleviates the relapse of pain-related aversive memory by activating KOR and inhibiting GABAergic neurons in the insular cortex
Authors: Xiao Siqi , Sun Haiju , Zhu Yichen , Shen Zui , Zhu Xixiao , Yao Ping-an , Wang Yifang , Zhang Chi , Yu Wei , Wu Zemin , Sun Jing , Xu Chi , Du Junying , He Xiaofen , Fang Jianqiao , Shao Xiaomei 
Published: September 2023

Abstract
Pain-related aversive memory is common in chronic pain patients. Electroacupuncture has been demonstrated to block pain-related aversive memory. The insular cortex is a key region closely related to aversive behaviors. In our study, a potential mechanism underlying the effect of electroacupuncture treatment on pain-related aversive memory behaviors relative to the insular cortex was investigated. Our study used the chemogenetic method, pharmacological method, electroacupuncture intervention, and behavioral detection. Our study showed that both inhibition of gamma-aminobutyric acidergic neurons and activation of the kappa opioid receptor in the insular cortex blocked the pain-related aversive memory behaviors induced by 2 crossover injections of carrageenan in mice; conversely, both the activation of gamma-aminobutyric acidergic neurons and inhibition of kappa opioid receptor in the insular cortex play similar roles in inducing pain-related aversive memory behaviors following 2 crossover injections of carrageenan. In addition, activation of gamma-aminobutyric acidergic neurons in the insular cortex reversed the effect of kappa opioid receptor activation in the insular cortex. Moreover, electroacupuncture effectively blocked pain-related aversive memory behaviors in model mice, which was reversed by both activation of gamma-aminobutyric acidergic neurons and inhibition of kappa opioid receptor in the insular cortex. The effect of electroacupuncture on blocking pain-related aversive memory behaviors may be related to the activation of the kappa opioid receptor and inhibition of gamma-aminobutyric acidergic neurons in the insular cortex.
Update on Serum Biomarkers in Autoimmune Atrophic Gastritis
Authors: Dottori Ludovica , Pivetta Giulia , Annibale Bruno , Lahner Edith 
Published: September 2023

Abstract

Background
Autoimmune atrophic gastritis (AAG) is a persistent, corpus-restricted immune-mediated destruction of the gastric corpus oxyntic mucosa with reduced gastric acid and intrinsic factor secretion, leading to iron deficiency and pernicious anemia as a consequence of iron and cobalamin malabsorption. Positivity toward parietal cell (PCA) and intrinsic factor (IFA) autoantibodies is very common. AAG may remain asymptomatic for many years, thus making its diagnosis complex and often delayed. Due to the increased risk of gastric neoplasms, a timely diagnosis of AAG is clinically important.

Content
The gold standard for AAG diagnosis is histopathological assessment of gastric biopsies obtained during gastroscopy, but noninvasive, preendoscopic serological screening may be useful in some clinical scenarios. Serum biomarkers for AAG may be divided into 2 groups: gastric autoimmunity-related biomarkers, such as PCA and IFA, and gastric corpus atrophy/reduced gastric acid secretion-related biomarkers, such as serum gastrin and pepsinogens. The present review focuses on the clinical significance and pitfalls of serum biomarkers related to gastric autoimmunity and gastric corpus atrophy, including some discussion of analytical methods.

Summary
Serum assays for PCA, IFA, gastrin, and pepsinogen I show good diagnostic accuracy for noninvasive diagnostic work-up of AAG. Diagnostic performance may increase by combining &gt;1 of these tests, overcoming the problem of seronegative AAG. However, appropriately designed, comparative studies with well-characterized patient cohorts are needed to better define the reliability of these biomarkers in the diagnosis of patients with AAG. Currently, positive serum tests should always be followed by the state-of-art diagnostic test, that is, histopathological assessment of gastric biopsies obtained during gastroscopy to definitively confirm or rule out AAG and eventually neoplastic complications.
Seismic moment tensor inversion with theory errors from 2-D Earth structure: implications for the 2009–2017 DPRK nuclear blasts
Authors: Hu Jinyin , Phạm Thanh-Son , Tkalčić Hrvoje 
Published: September 2023

SUMMARY
Determining the seismic moment tensor (MT) from the observed waveforms with available Earth's structure models is known as seismic waveform MT inversion. It remains challenging for small to moderate-size earthquakes at regional scales. First, because shallow isotropic (ISO) and compensated linear vector dipole (CLVD) components of MT radiate similar long-period waveforms at regional distances, an intrinsic ISO-CVLD ambiguity impedes resolving seismic sources at shallow depths within the Earth's crust. Secondly, regional scales usually bear 3-D structures; thus, inaccurate Earth's structure models can cause unreliable MT solutions but are rarely considered a theory error in the MT inversion. So far, only the error of the 1-D earth model (1-D structural error), apart from data errors, has been explicitly modelled in the source studies because of relatively inexpensive computation. Here, we utilize a hierarchical Bayesian MT inversion to address the above problems. Our approach takes advantage of affine-invariant ensemble samplers to explore the ISO-CLVD trade-off space thoroughly and effectively. Station-specific time-shifts are also searched for as free parameters to treat the structural errors along specific source–station paths (2-D structural errors). Synthetic experiments demonstrate the method's advantage in resolving the dominating ISO components. The explosive events conducted by the Democratic People's Republic of Korea (DPRK) are well-studied, and we use them to demonstrate highly similar source mechanisms, including dominating ISO and significant CLVD components. The recovered station-specific time-shifts from the blasts present a consistent pattern, which provides a better understanding of the azimuthal variation of Earth's 2-D structures surrounding the events’ location.