bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis and Research of Code Revision for Design of Nuclear Safety Related Concrete Structures of Pressurized Water Reactor Nuclear Power Plants in China
Authors: Huang Jun , Zhang Weiguo , Liang Xueyuan , Wu Feifei , Xu Jing , Zhang Shaolin , Yang Wen , Tang Zhiyao
Published: November 2022

NB/T 20012-2010 design requirements for concrete structures related to nuclear safety of PWR nuclear power plants is a standard issued by the National Energy Administration in 2010. It is the top-level standard and important standard for concrete structure design. Due to technological progress and changes in relevant reference standards, some of its contents can not meet the requirements at this stage, On the basis of referring to the latest relevant standards and specifications at home and abroad, the engineering experience in the structural design of nuclear safety related plants of nuclear power plants built and under construction in China was summarized, and the chief editor revised it. This paper mainly analyzes the revised contents, mainly including revising the minimum strength grade of concrete was changed to C30, HRB500, HPB300 steel bars were added, and HPB235, HRB335 steel bars were canceled; improving the safety of the axial compression members that configure the ordinary stirrups, modifying the formula for calculating the bearing capacity of the transverse shear (that is, out-of-plane shear), modifying the formula for calculating the punching bearing capacity (considering the effects of membrane force) ; defining the load effect combination used in the calculation of crack width, and the maximum crack width is calculated according to the relevant specifications of GB 50010; stipulating that short-term stiffness is taken in deflection calculation under normal operation and severe environment, normal operation and extreme environment and abnormal operation conditions; adding contents of structural analysis, basic provisions of mechanism components and beyond the scope of design basis;The Appendix B (informative) “Performance Index of Reinforcement and Concrete at High Temperature” was added;.
Applying Machine Learning to Improve BOA Analysis of CIPS/CILC
Authors: Liao Jun , Mace Alexander , Wang Guoqiang , Fisher Jesse S.
Published: November 2022

CRUD depositions on fuel cladding are generated as a result of coolant chemistry and corrosion of primary system components during the normal operation of a nuclear reactor. These depositions can affect both reactor power peaking and fuel element structural integrity through CRUD Induced Power Shifts (CIPS) and CRUD Induced Local Corrosion (CILC) phenomena, respectively. The CIPS/CILC phenomena are typically assessed using the Boron-induced Offset Anomaly (BOA) computer code, which predicts the characterization of the distribution of CRUD within a reactor and the risk for occurrence of CIPS/CILC within a given cycle.

Machine learning (ML) algorithms have often been applied towards understanding large data sets and acquiring useable information in many industries, including nuclear. In the nuclear engineering field, ML is increasingly being used as a method to improve nuclear power plant efficiency and reduce engineering costs. The application of machine learning to enhance the prediction of CIPS/CILC increases the possibility of reducing the cost associated with CRUD mitigation. In Westinghouse, exploratory analysis was performed to identify ways in which ML could be utilized to improve CIPS risk assessments. There were two paths identified, the first one was ML applications for CIPS with the standalone BOA code, and the second path was ML applications for CIPS calibration with coupled ANC/FUELUDTYDRV/VIPRE-W/BOA code. The exploratory study demonstrated that ML was capable of accurately predicting the boron mass in the cores of selected nuclear power plants as surrogate models of the BOA code.
Assessment of Dynamic Balancing Performance of Synchronized Ice Skaters With Sudden Provocation Test via Principal Component Analysis
Authors: Pálya Zsófia , Petró Bálint , Kiss Rita M.
Published: November 2022

Background: Balancing performance can be affected by regular and high-level athletic training, which has not been fully explored in synchronized ice skaters. This study aimed to analyze the dynamic balancing performance by assessing the principal and compensatory movements performed during the sudden provocation tests and evaluating the parameters that characterize the platform’s motion. Method: Twelve young female synchronized ice skaters and 12 female age-matched controls participated. Sudden provocation tests were completed three times in bipedal stance and in single-leg stances, and sport-specific fatigue session was inserted between the repetitions. Results: Significantly more time was necessary to recover balance for both groups after the fatiguing sessions (p < .05). Interestingly, skaters performed less effectively in the simplest condition (bipedal stance) than the control group (p < .05). The principal component analysis showed that the first principal movement was the same for both groups. The skater group used the upper body and arms more often to compensate, while the control group’s recovery strategy consisted mainly of abduction of the elevated leg. The damping ratio and the relative variance of the first principal movement showed a negative correlation (p < .05), suggesting that those with superior balancing effectiveness recruited more compensatory movements.
Widespread hypertranscription in aggressive human cancers
Authors: Zatzman Matthew , Fuligni Fabio , Ripsman Ryan , Suwal Tannu , Comitani Federico , Edward Lisa-Monique , Denroche Rob , Jang Gun Ho , Notta Faiyaz , Gallinger Steven , Selvanathan Saravana P. , Toretsky Jeffrey A. , Hellmann Matthew D. , Tabori Uri , Huang Annie , Shlien Adam
Published: November 2022

Cancers are often defined by the dysregulation of specific transcriptional programs; however, the importance of global transcriptional changes is less understood. Hypertranscription is the genome-wide increase in RNA output. Hypertranscription’s prevalence, underlying drivers, and prognostic significance are undefined in primary human cancer. This is due, in part, to limitations of expression profiling methods, which assume equal RNA output between samples. Here, we developed a computational method to directly measure hypertranscription in 7494 human tumors, spanning 31 cancer types. Hypertranscription is ubiquitous across cancer, especially in aggressive disease. It defines patient subgroups with worse survival, even within well-established subtypes. Our data suggest that loss of transcriptional suppression underpins the hypertranscriptional phenotype. Single-cell analysis reveals hypertranscriptional clones, which dominate transcript production regardless of their size. Last, patients with hypertranscribed mutations have improved response to immune checkpoint therapy. Our results provide fundamental insights into gene dysregulation across human cancers and may prove useful in identifying patients who would benefit from novel therapies.
Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects
Authors: Chen Qiming , Dai Jiewen , Bian Qian
Published: November 2022

Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human
SOX9
gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates
Sox9
in CNCC-derived Meckel’s cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and
Sox9
, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
Geological, multispectral, and meteorological imaging results from the Mars 2020 Perseverance rover in Jezero crater
Authors: Bell James F. , Maki Justin N. , Alwmark Sanna , Ehlmann Bethany L. , Fagents Sarah A. , Grotzinger John P. , Gupta Sanjeev , Hayes Alexander , Herkenhoff Ken E. , Horgan Briony H. N. , Johnson Jeffrey R. , Kinch Kjartan B. , Lemmon Mark T. , Madsen Morten B. , Núñez Jorge I. , Paar Gerhard , Rice Melissa , Rice James W. , Schmitz Nicole , Sullivan Robert , Vaughan Alicia , Wolff Mike J. , Bechtold Andreas , Bosak Tanja , Duflot Louise E. , Fairén Alberto G. , Garczynski Brad , Jaumann Ralf , Merusi Marco , Million Chase , Ravanis Eleni , Shuster David L. , Simon Justin , St. Clair Michael , Tate Christian , Walter Sebastian , Weiss Benjamin , Bailey Alyssa M. , Bertrand Tanguy , Beyssac Olivier , Brown Adrian J. , Caballo-Perucha Piluca , Caplinger Michael A. , Caudill Christy M. , Cary Francesca , Cisneros Ernest , Cloutis Edward A. , Cluff Nathan , Corlies Paul , Crawford Kelsie , Curtis Sabrina , Deen Robert , Dixon Darian , Donaldson Christopher , Barrington Megan , Ficht Michelle , Fleron Stephanie , Hansen Michael , Harker David , Howson Rachel , Huggett Joshua , Jacob Samantha , Jensen Elsa , Jensen Ole B. , Jodhpurkar Mohini , Joseph Jonathan , Juarez Christian , Kah Linda C. , Kanine Oak , Kristensen Jessica , Kubacki Tex , Lapo Kristiana , Magee Angela , Maimone Michael , Mehall Greg L. , Mehall Laura , Mollerup Jess , Viúdez-Moreiras Daniel , Paris Kristen , Powell Kathryn E. , Preusker Frank , Proton Jon , Rojas Corrine , Sallurday Danny , Saxton Kim , Scheller Eva , Seeger Christina H. , Starr Mason , Stein Nathan , Turenne Nathalie , Van Beek Jason , Winhold Andrew G. , Yingling Rachel
Published: November 2022

Perseverance’s Mastcam-Z instrument provides high-resolution stereo and multispectral images with a unique combination of spatial resolution, spatial coverage, and wavelength coverage along the rover’s traverse in Jezero crater, Mars. Images reveal rocks consistent with an igneous (including volcanic and/or volcaniclastic) and/or impactite origin and limited aqueous alteration, including polygonally fractured rocks with weathered coatings; massive boulder-forming bedrock consisting of mafic silicates, ferric oxides, and/or iron-bearing alteration minerals; and coarsely layered outcrops dominated by olivine. Pyroxene dominates the iron-bearing mineralogy in the fine-grained regolith, while olivine dominates the coarse-grained regolith. Solar and atmospheric imaging observations show significant intra- and intersol variations in dust optical depth and water ice clouds, as well as unique examples of boundary layer vortex action from both natural (dust devil) and Ingenuity helicopter–induced dust lifting. High-resolution stereo imaging also provides geologic context for rover operations, other instrument observations, and sample selection, characterization, and confirmation.
Functional specialization of different PI3K isoforms for the control of neuronal architecture, synaptic plasticity, and cognition
Authors: Sánchez-Castillo Carla , Cuartero María I. , Fernández-Rodrigo Alba , Briz Víctor , López-García Sergio , Jiménez-Sánchez Raquel , López Juan A. , Graupera Mariona , Esteban José A.
Published: November 2022

Neuronal connectivity and activity-dependent synaptic plasticity are fundamental properties that support brain function and cognitive performance. Phosphatidylinositol 3-kinase (PI3K) intracellular signaling controls multiple mechanisms mediating neuronal growth, synaptic structure, and plasticity. However, it is still unclear how these pleiotropic functions are integrated at molecular and cellular levels. To address this issue, we used neuron-specific virally delivered Cre expression to delete either p110α or p110β (the two major catalytic isoforms of type I PI3K) from the hippocampus of adult mice. We found that dendritic and postsynaptic structures are almost exclusively supported by p110α activity, whereas p110β controls neurotransmitter release and metabotropic glutamate receptor–dependent long-term depression at the presynaptic terminal. In addition to these separate functions, p110α and p110β jointly contribute toN-methyl-d-aspartate receptor–dependent postsynaptic long-term potentiation. This molecular and functional specialization is reflected in different proteomes controlled by each isoform and in distinct behavioral alterations for learning/memory and sociability in mice lacking p110α or p110β.
The free fatty acid–binding pocket is a conserved hallmark in pathogenic β-coronavirus spike proteins from SARS-CoV to Omicron
Authors: Toelzer Christine , Gupta Kapil , Yadav Sathish K. N. , Hodgson Lorna , Williamson Maia Kavanagh , Buzas Dora , Borucu Ufuk , Powers Kyle , Stenner Richard , Vasileiou Kate , Garzoni Frederic , Fitzgerald Daniel , Payré Christine , Gautam Gunjan , Lambeau Gérard , Davidson Andrew D. , Verkade Paul , Frank Martin , Berger Imre , Schaffitzel Christiane
Published: November 2022

As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor binding domain (RBD) comprises a free fatty acid (FFA)–binding pocket. FFA binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic β-coronaviruses (β-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2, and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold–causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation, while the open, infectious conformation is devoid of LA. Electron tomography of SARS-CoV-2–infected cells reveals that LA treatment inhibits viral replication, resulting in fewer deformed virions. Our results establish FFA binding as a hallmark of pathogenic β-CoV infection and replication, setting the stage for FFA-based antiviral strategies to overcome COVID-19.
Internal tsunamigenesis and ocean mixing driven by glacier calving in Antarctica
Authors: Meredith Michael P. , Inall Mark E. , Brearley J. Alexander , Ehmen Tobias , Sheen Katy , Munday David , Cook Alison , Retallick Katherine , Van Landeghem Katrien , Gerrish Laura , Annett Amber , Carvalho Filipa , Jones Rhiannon , Naveira Garabato Alberto C. , Bull Christopher Y. S. , Wallis Benjamin J. , Hogg Anna E. , Scourse James
Published: November 2022

Ocean mixing around Antarctica exerts key influences on glacier dynamics and ice shelf retreats, sea ice, and marine productivity, thus affecting global sea level and climate. The conventional paradigm is that this is dominated by winds, tides, and buoyancy forcing. Direct observations from the Antarctic Peninsula demonstrate that glacier calving triggers internal tsunamis, the breaking of which drives vigorous mixing. Being widespread and frequent, these internal tsunamis are at least comparable to winds, and much more important than tides, in driving regional shelf mixing. They are likely relevant everywhere that marine-terminating glaciers calve, including Greenland and across the Arctic. Calving frequency may change with higher ocean temperatures, suggesting possible shifts to internal tsunamigenesis and mixing in a warming climate.
Miniaturizing color-sensitive photodetectors via hybrid nanoantennas toward submicrometer dimensions
Authors: Ho Jinfa , Dong Zhaogang , Leong Hai Sheng , Zhang Jun , Tjiptoharsono Febiana , Daqiqeh Rezaei Soroosh , Goh Ken Choon Hwa , Wu Mengfei , Li Shiqiang , Chee Jingyee , Wong Calvin Pei Yu , Kuznetsov Arseniy I. , Yang Joel K. W.
Published: November 2022

Digital camera sensors use color filters on photodiodes to achieve color selectivity. As the color filters and photosensitive silicon layers are separate elements, these sensors suffer from optical cross-talk, which sets limits to the minimum pixel size. Here, we report hybrid silicon-aluminum nanostructures in the extreme limit of zero distance between color filters and sensors. This design could essentially achieve submicrometer pixel dimensions and minimize the optical cross-talk arising from tilt illuminations. The designed hybrid silicon-aluminum nanostructure has dual functionalities. Crucially, it supports a hybrid Mie-plasmon resonance of magnetic dipole to achieve color-selective light absorption, generating electron hole pairs. Simultaneously, the silicon-aluminum interface forms a Schottky barrier for charge separation and photodetection. This design potentially replaces the traditional dye-based filters for camera sensors at ultrahigh pixel densities with advanced functionalities in sensing polarization and directionality, and UV selectivity via interband plasmons of silicon.
Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning
Authors: Ouyang Wenhao O. , Tan Timothy J.C. , Lei Ruipeng , Song Ge , Kieffer Collin , Andrabi Raiees , Matreyek Kenneth A. , Wu Nicholas C.
Published: November 2022

Increasing the expression level of the SARS-CoV-2 spike (S) protein has been critical for COVID-19 vaccine development. While previous efforts largely focused on engineering the receptor-binding domain (RBD) and the S2 subunit, the amino-terminal domain (NTD) has been long overlooked because of the limited understanding of its biophysical constraints. In this study, the effects of thousands of NTD single mutations on S protein expression were quantified by deep mutational scanning. Our results revealed that in terms of S protein expression, the mutational tolerability of NTD residues was inversely correlated with their proximity to the RBD and S2. We also identified NTD mutations at the interdomain interface that increased S protein expression without altering its antigenicity. Overall, this study not only advances the understanding of the biophysical constraints of the NTD but also provides invaluable insights into S-based immunogen design.
Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions
Authors: Jacquet Stéphanie , Culbertson Michelle , Zhang Chi , El Filali Adil , De La Myre Mory Clément , Pons Jean-Baptiste , Filippi-Codaccioni Ondine , Lauterbur M. Elise , Ngoubangoye Barthélémy , Duhayer Jeanne , Verez Clément , Park Chorong , Dahoui Clara , Carey Clayton M. , Brennan Greg , Enard David , Cimarelli Andrea , Rothenburg Stefan , Elde Nels C. , Pontier Dominique , Etienne Lucie
Published: November 2022

Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the
Myotis
species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.
Rydberg polaritons in ReS
2
crystals
Authors: Coriolano Annalisa , Polimeno Laura , Pugliese Marco , Cannavale Alessandro , Trypogeorgos Dimitrios , Di Renzo Anna , Ardizzone Vincenzo , Rizzo Aurora , Ballarini Dario , Gigli Giuseppe , Maiorano Vincenzo , Rosyadi Adzilah Shahna , Chuang Ching-An , Ho Ching-Hwa , De Marco Luisa , Sanvitto Daniele , De Giorgi Milena
Published: November 2022

Rhenium disulfide belongs to group VII transition metal dichalcogenides (TMDs) with attractive properties such as exceptionally high refractive index and remarkable oscillator strength, large in-plane birefringence, and good chemical stability. Unlike most other TMDs, the peculiar optical properties of rhenium disulfide persist from bulk to the monolayer, making this material potentially suitable for applications in optical devices. In this work, we demonstrate with unprecedented clarity the strong coupling between cavity modes and excited states, which results in a strong polariton interaction, showing the interest of these materials as a solid-state counterpart of Rydberg atomic systems. Moreover, we definitively clarify the nature of important spectral features, shedding light on some controversial aspects or incomplete interpretations and demonstrating that their origin is due to the interesting combination of the very high refractive index and the large oscillator strength expressed by these TMDs.
Protection against SARS-CoV-2 Omicron BA.1 variant challenge in macaques by prime-boost vaccination with Ad26.COV2.S and SpFN
Authors: Yu Jingyou , Thomas Paul V. , McMahan Katherine , Jacob-Dolan Catherine , Liu Jinyan , He Xuan , Hope David , Martinez Elizabeth J. , Chen Wei-Hung , Sciacca Michaela , Hachmann Nicole P. , Lifton Michelle , Miller Jessica , Powers Olivia C. , Hall Kevin , Wu Cindy , Barrett Julia , Swafford Isabella , Currier Jeffrey R. , King Jocelyn , Corbitt Courtney , Chang William C. , Golub Emily , Rees Phyllis A. , Peterson Caroline E. , Hajduczki Agnes , Hussin Elizabeth , Lange Camille , Gong Hua , Matyas Gary R. , Rao Mangala , Paquin-Proulx Dominic , Gromowski Gregory D. , Lewis Mark G. , Andersen Hanne , Davis-Gardner Meredith , Suthar Mehul S. , Michael Nelson L. , Bolton Diane L. , Joyce M. Gordon , Modjarrad Kayvon , Barouch Dan H.
Published: November 2022

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and waning immunity call for next-generation vaccine strategies. Here, we assessed the immunogenicity and protective efficacy of two SARS-CoV-2 vaccines targeting the WA1/2020 spike protein, Ad26.COV2.S (Ad26) and Spike ferritin Nanoparticle (SpFN), in nonhuman primates, delivered as either a homologous (SpFN/SpFN and Ad26/Ad26) or heterologous (Ad26/SpFN) prime-boost regimen. The Ad26/SpFN regimen elicited the highest CD4 T cell and memory B cell responses, the SpFN/SpFN regimen generated the highest binding and neutralizing antibody responses, and the Ad26/Ad26 regimen generated the most robust CD8 T cell responses. Despite these differences, protective efficacy against SARS-CoV-2 Omicron BA.1 challenge was similar for all three regimens. After challenge, all vaccinated monkeys showed significantly reduced peak and day 4 viral loads in both bronchoalveolar lavage and nasal swabs as compared with sham animals. The efficacy conferred by these three immunologically distinct vaccine regimens suggests that both humoral and cellular immunity contribute to protection against SARS-CoV-2 Omicron challenge.
Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection
Authors: Wang Pei , Song Qianqian , Ren Jie , Zhang Weilong , Wang Yuting , Zhou Lin , Wang Dongmei , Chen Kun , Jiang Liping , Zhang Bochao , Chen Wanqing , Qu Chunfeng , Zhao Hong , Jiao Yuchen
Published: November 2022

Cell-free DNA (cfDNA)–based liquid biopsy is a promising approach for the early detection of cancer. A major hurdle is the limited yield of cfDNA from one blood draw, limiting the use of most samples to one test of either mutation or methylation. Here, we develop a technology, Mutation Capsule Plus (MCP), which enables multiplex profiling of one cfDNA sample, including simultaneous detection of genetic and epigenetic alterations and genome-wide discovery of methylation markers. With this technology, we performed de novo screening of methylation markers on cfDNA samples from 30 hepatocellular carcinoma (HCC) cases and 30 non-HCC controls. The methylation markers enriched in HCC cfDNA were further profiled in parallel with a panel of mutations on a training cohort of 60 HCC and 60 non-HCC cases, resulting in an HCC detection model. We validated the model in an independent retrospective cohort with 58 HCC and 198 non-HCC cases and got 90% sensitivity with 94% specificity. Furthermore, we applied the model to a prospective cohort of 311 asymptomatic hepatitis B virus carriers with normal liver ultrasonography and serum AFP concentration. The model detected four of the five HCC cases in the cohort, showing 80% sensitivity and 94% specificity. These findings demonstrate that the MCP technology has potential for the discovery and validation of multiomics biomarkers for the noninvasive detection of cancer. This study also provides a comprehensive database of genetic and epigenetic alterations in the cfDNA of a large cohort of HCC cases and high-risk non-HCC individuals.
Utilizing Alcohol for Alkane Biosynthesis by Introducing a Fatty Alcohol Dehydrogenase
Authors: Sui Yu-An , Kishino Shigenobu , Maruyama Satoshi , Ito Masakazu , Muramatsu Masayoshi , Obata Shusei , Ogawa Jun
Published: November 2022

Alcohol dehydrogenases are a group of enzymes found in many organisms. Unfortunately, studies on these enzymes mainly focus on their activities toward short-chain alcohols.
SMART CUREs: a Professional Development Program for Advancing Teaching Assistant Preparedness To Facilitate Course-Based Undergraduate Research Experiences
Authors: Kern Amie M. , Olimpo Jeffrey T.
Published: November 2022

Course-based undergraduate research experiences (CUREs) have emerged as a viable platform to engage large numbers of students in real-world scientific practices. Historically, CUREs have been offered throughout science, technology, engineering, and mathematics curricula at both the introductory and advanced levels and have been facilitated by a variety of individuals, including faculty members, postdoctoral fellows, and graduate teaching assistants (GTAs).
Expression Ratios of the Antiapoptotic BCL2 Family Members Dictate the Selective Addiction of Kaposi’s Sarcoma-Associated Herpesvirus-Transformed Primary Effusion Lymphoma Cell Lines to MCL1
Authors: Dunham Daniel , Viswanathan Prasanth , Gill Jackson , Manzano Mark
Published: November 2022

Primary effusion lymphoma (PEL) is caused by Kaposi’s sarcoma-associated herpesvirus. We showed previously that PEL cell lines require the antiapoptotic protein MCL1 for survival but not the other BCL2 family proteins.
Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids
Authors: Ares-Arroyo Manuel , Fernández-García Miguel , Wedel Emilia , Montero Natalia , Barbas Coral , Rey-Stolle M. Fernanda , Garcia Antonia , González-Zorn Bruno
Published: November 2022

The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis.
Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions
Authors: Haffner Jacob J. , Katemauswa Mitchelle , Kagone Thérèse S. , Hossain Ekram , Jacobson David , Flores Karina , Parab Adwaita R. , Obregon-Tito Alexandra J. , Tito Raul Y. , Reyes Luis Marin , Troncoso-Corzo Luzmila , Guija-Poma Emilio , Meda Nicolas , Carabin Hélène , Honap Tanvi P. , Sankaranarayanan Krithivasan , Lewis Cecil M. , McCall Laura-Isobel
Published: November 2022

As the world becomes increasingly industrialized, understanding the biological consequences of these lifestyle shifts and what it means for past, present, and future human health is critical. Indeed, industrialization is associated with rises in allergic and autoimmune health conditions and reduced microbial diversity.
Impact on Macrolide Resistance of Genetic Diversity of Mycobacterium abscessus Species
Authors: Jong Bor-En , Wu Ting-Shu , Chen Nan-Yu , Yang Cheng-How , Shu Chin-Chung , Wang Lih-Shinn , Wu Tsu-Lan , Lu Jang-Jhih , Chiu Cheng-Hsun , Lai Hsin-Chih , Chung Wen-Hung
Published: November 2022

Macrolides are the mainstays of the antimycobacterial regimens against
Mycobacterium abscessus
species (formerly
Mycobacterium abscessus
complex).
erm
(41) confers inducible macrolide resistance for
M. abscessus
subsp.
bolletii
strains, and the majority of
M. abscessus
subsp.
abscessus
T28 sequevars. Furthermore, the acquired macrolide resistance of
M. abscessus
species is due to a point mutation in
rrl
.
Transcription Factors BbPacC and Bbmsn2 Jointly Regulate Oosporein Production in Beauveria bassiana
Authors: Chen Xi , Zhang Wenwen , Wang Junyao , Zhu Shengan , Shen Xinchi , Chen Hongjun , Fan Yanhua
Published: November 2022

B. bassiana
produces the red dibenzoquinone pigment oosporein under certain specific conditions, such as alkaline conditions and fungus-killed cadavers. Ooporein possesses antibiotic and insect immune inhibition activities and plays multiple roles during the infection process of
B. bassiana
against insect hosts.
Data science for geoscience: Recent progress and future trends from the perspective of a data life cycle
Authors: Ma* Xiaogang
Published: November 2022

Data science is receiving increased attention in a variety of geoscience disciplines and applications. Many successful data-driven geoscience discoveries have been reported recently, and the number of geoinformatics and data science sessions at many geoscience conferences has begun to increase. Across academia, industry, and government, there is strong interest in knowing more about current progress as well as the potential of data science for geoscience. To address that need, this paper provides a review from the perspective of a data life cycle. The key steps in the data life cycle include concept, collection, preprocessing, analysis, archive, distribution, discovery, and repurpose. Those subjects are intuitive and easy to follow even for geoscientists with very limited experience with cyberinfrastructure, statistics, and machine learning. The review includes two key parts. The first addresses the fundamental concepts and theoretical foundation of data science, and the second summarizes highlights and sharable experience from existing publications centered on each step in the data life cycle. At the end, a vision about the future trends of data science applications in geoscience is provided that includes discussion of open science, smart data, and the science of team science. We hope this review will be useful to data science practitioners in the geoscience community and will lead to more discussions on the best practices and future trends of data science for the geosciences.
Effect of prolonged microcirculation time after thrombectomy on the outcome of acute stroke
Authors: Ji Yachen , Shi Bin , Yuan Quan , Wu Kangfei , Fang Jia , Wang Hao , Miao Zhuang , Sun Yi , Huang Xianjun , Zhou Zhiming
Published: November 2022

Background

Although recanalization can be successful, microcirculatory dysfunction is common in acute large vessel occlusive stroke (LVOS). We assessed the microcirculation time by postprocessing software and analyzed its impact on prognosis in patients treated with mechanical thrombectomy (MT).

Methods

Patients with acute LVOS treated with MT were retrospectively enrolled consecutively. We measured the time to peak (TTP) and cerebral circulation time (CCT) in regions of interest on digital subtraction angiography using syngo iFlow software (Siemens Healthineers, Forchheim, Germany). A modified Rankin score ≤2 at 90 days was defined as a favorable outcome. Logistic regression was used to analyze the effect of each time parameter on prognosis. Then, we included time parameters in the baseline model to construct receiver operating characteristic (ROC) curves to assess the predictive ability for prognosis.

Results

A total of 215 patients were finally included. Of them, 118 (54.9%) had a favourable outcome at 90 days. Multivariate analysis showed that the microvascular cerebral circulation time (mCCT) was significantly associated with poor outcomes (odds ratio (OR) 2.061, 95% confidence interval (CI) 1.414 to 3.005 p<0.001). The area under the ROC curve was significantly enhanced by including mCCT in the baseline model (0.859 vs 0.829, p=0.016, DeLong test).

Conclusions

The mCCT immediately after recanalization is a powerful predictive factor for 90-day functional prognosis.
On generalized distance spectral radius and generalized distance energy of graphs
Authors: Khan Zia Ullah , Zhang Xiao-Dong
Published: November 2022

For a simple connected graph [Formula: see text], let [Formula: see text] and [Formula: see text] be the distance matrix and the diagonal matrix of the vertex transmissions, respectively. The convex linear combination [Formula: see text] of [Formula: see text] and [Formula: see text] is defined as, [Formula: see text], [Formula: see text]. The matrix [Formula: see text], known as generalized distance matrix, is effective in merging the distance spectral and distance signless Laplacian spectral theories. In this paper, we study the spectral radius and energy of the generalized distance matrix [Formula: see text] of a graph [Formula: see text]. We obtain bounds for the generalized distance spectral radius and generalized distance energy of connected graphs in terms of various parameters associated with the structure of graph.
Challenges for seismic velocity modelling of rafts and impacts for pre-salt depth estimations
Authors: Camargo Gisele Nery , González María , Borges Filipe , Maul Alexandre , Mohriak Webster U.
Published: November 2022

Seismic velocity models have significant importance in subsurface studies, notably when applied in structurally challenging areas. In some parts of the Campos Basin, offshore Brazil, the pre-salt reservoir's overburden shows complex structures, mainly due to raft tectonism that positions laterally, resulting in interspersed salt domes, carbonate rafts and siliciclastic sediments. This work used an extensive well database in the Marlim Complex to analyse the raft seismic velocities and their related impacts on pre-salt reservoir models. Based on well data, in combination with detailed seismic interpretation, seven alternative velocity scenarios were proposed for the rafts. The geological motivations for each scenario are discussed with the aim of developing constrained depth models for pre-salt reservoirs. The depth forecast results could be tested by drilled wells, and the resulting models are quantitatively compared in terms of depth predictions and gross-rock volumes. The results show that the topography of the target pre-salt reservoirs can vary considerably, even in scenarios where well and geological constraints are considered. This can impact pre-salt geological characterization and field development.
Conference reports
Authors: Dennis Louise A.
Published: November 2022

This section is compiled from reports of recent events sponsored or run in cooperation with ACM SIGAI. In general these reports were written and submitted by the conference organisers.
EAAI-22 Blue Sky Ideas in Artificial Intelligence Education from the AAAI/ACM SIGAI New and Future AI Educator Program
Authors: Guerzhoy Michael , Neumann Marion , Johnson* Emmanuel , Johnson David , Chai Henry , Garijo Daniel , Lyu Zhuoyue , MacLellan Christopher J.
Published: November 2022

The 12th Symposium on Educational Advances in Artificial Intelligence (EAAI-22, cochaired by Michael Guerzhoy and Marion Neumann) continued the AAAI/ACM SIGAI New and Future AI Educator Program to support the training of early-career university faculty, secondary school faculty, and future educators (PhD candidates or postdocs who intend a career in academia). As part of the program, awardees were asked to address one of the following "blue sky" questions:

•How could/should AI courses incorporate AI Ethics into the curriculum?

•How could we teach AI topics at an early undergraduate or a secondary school level?

•AI has the potential for broad impact to numerous disciplines. How could we make AI education more interdisciplinary, specifically to benefit non-engineering fields?

•How should standard AI courses evolve?

•How could we leverage AI education to promote diversity in the field?

This paper is a collection of their responses, intended to help motivate discussion around these issues in AI education.
AI education matters
Authors: Register Yim , Tan Garcia Joseph William , Kaushal Nayan , Wilder Dev , Xu Xiaobing
Published: November 2022

I always say to my students "you are going to be the future data science leaders of the world". Wherever they end up, I hope they apply critical (Cotter, 2020; Dasgupta & Hill, 2020) and human-centered (Xu, 2019) thinking to the AI decisions they make. As AI algorithms become ever more omnipresent in our lives - from newsfeed organization to product recommendations and beyond - it is our responsibility as educators to equip our students with the necessary tools to interrogate the impacts of AI technology. Luckily, there has been a large push for the integration of ethics into AI curricula. Whether this is in Model AI assignments (Furey & Martin, 2019) or entire conferences (such as FAccT), there is a demand for integrated and critical algorithmic literacies both in the classroom and outside of it.

As a social media researcher and AI educator, my work regularly contends with two pillars: Joy and Justice. In this article I intend to outline ways of integrating both play and critical interrogation into AI education, with examples from AI education scholarship (Druga, Vu, Likhith, & Qiu, 2019; Ko et al., 2020) as well as a light experience report highlighting student work. My students join me on this article as they are the main inspiration for innovative joy and justice practices!
Understanding and mitigating multi-sided exposure bias in recommender systems
Authors: Mansoury Masoud
Published: November 2022

Masoud Mansoury is a postdoctoral researcher at Amsterdam Machine Learning Lab at University of Amsterdam, Netherlands. He is also a member of Discovery Lab collaborating with Data Science team at Elsevier Company in the area of recommender systems. Masoud received his PhD in Computer and Information Science from Eindhoven University of Technology, Netherlands, in 2021. He has published his research works in top conferences such as FAccT, RecSys, and CIKM. His research interests include recommender systems, algorithmic bias, and contextual bandits.

This research conducted by Masoud Mansoury investigated the impact of unfair recommendations on different actors in the system and proposed solutions to tackle the unfairness of recommendations. The solutions were a rating transformation technique that works as a pre-processing step before recommendation generation and a general graph-based solution that works as a post-processing approach after recommendation generation for mitigating the multi-sided exposure bias in the recommendation results. For evaluation, he introduced several metrics for measuring the exposure fairness for items and suppliers, and showed that the proposed metrics better capture the fairness properties in the recommendation results. Extensive experiments on different publicly-available datasets confirmed the superiority of the proposed solutions in improving the exposure fairness for items and suppliers.
A Transformer Based Approach for Abuse Detection in Code Mixed Indic Languages.
Authors: Bansal Vibhuti , Tyagi Mrinal , Sharma Rajesh , Gupta Vedika , Xin Qin
Published: November 2022

The advancement in the number of online social media platforms has entailed active participation from the web users globally. This has also lead to subsequent increase in the cyberbullying cases online. Such incidents diminish an individual’s reputation or defame a community, also posing a threat to the privacy of users in cyberspace. Traditionally, manual checks and handling mechanisms have been used to deal with such textual content. However, an automatic computer-based approach would provide far better solutions to this problem. Existing approaches to automate this task majorly involves classical machine learning models which tend to perform poorly on low resource languages. Owing to the varied background and language of web users, the cyberspace witnesses the presence of multilingual text. An integrated approach to accommodate multilingual text could be the appropriate solution. This paper explores various methods to detect abusive content in 13 Indic code-mixed languages. Firstly, baseline classical machine learning models are compared with Transformer based architecture. Secondly, the paper presents the experimental analysis of four state-of-the-art transformer-based models vis à vis XLM-RoBERTa, indic-BERT, MurilBert and mBERT, out of which XLM Roberta with BiGRU outperforms. Thirdly, the experimental setup of the best performing model XLM-RoBERTa is fed with emoji embeddings that leads to further enhancement of overall performance of the employed model. Finally, the model is trained with the combined dataset of 13 Indic languages, to compare its performance with those of individual language models. The performance of combined model surpassed those of the individual models in terms of F1 score and accuracy, supporting the fact that combined model fits the data better possibly due to its code-mixed nature. This model reports a F1 score of 0.88 on test data while rendering a training loss of 0.28, validation loss of 0.31 and an AUC score of 0.94 for both training and validation.
Coordination-Controlled Electrodeposition of Palladium/Copper Thin Films onto a Pyridine-Terminated Self-Assembled Monolayer
Authors: Yao Zhen , Naden Aaron B. , Baker Richard T. , Buck Manfred
Published: November 2022

A scheme for the electrodeposition of ultrathin bimetallic layers on top of a self-assembled monolayer (SAM) is investigated which combines the deposition of one metal (Pd) coordinated to a functionalized SAM (3-(4-pyridine-4-yl-phenyl)-propane-1-thiol, PyP3) on Au/mica with another metal (Cu) from the bulk electrolyte. The coordination-controlled electrodeposition (CCED) is a four-phase process comprising (i) Pd2+ coordination to the terminal pyridine units of the SAM, (ii) reduction of Pd and nanoparticle formation, (iii) formation of an intermixed shell of Pd and Cu, and (iv) deposition of bulk Cu. Chronoamperometry reveals a fast nucleation phase where Pd nanoparticles form within a few milliseconds and seed the Cu deposition. The Pd-Cu core-shell nature of deposited nanoparticles is confirmed by transmission electron microscopy (TEM). Harnessing the selective coordination of Pd2+ to PyP3, a one-pot procedure is further developed using electrolytes containing both Pd2+ and Cu2+ ions. Thus simplifying complexation and reduction, continuous Pd/Cu films are obtained in a multistep process as verified by scanning tunneling microscopy (STM). With a percolation threshold below 3 nm, CCED, as a SAM-controlled deposition strategy, offers an avenue for generation of ultrathin films.
Inosine, gut microbiota, and cancer immunometabolism
Authors: Samami Elham , Aleebrahim-Dehkordi Elahe , Mohebalizadeh Mehdi , Yaribash Shakila , Saghazadeh Amene , Rezaei Nima
Published: November 2022

This article briefly reviews cancer immunity and the role of gut microbiota in carcinogenesis, followed by an understanding of mechanisms by which inosine is involved in cancer immunometabolism. The immune system plays a paradoxical role in cancer treatment. Antitumor immunity depends on the T-cell priming against tumor antigens, whereas inflammatory mediators trigger the protumor signaling in the tumor microenvironment. Studies link the microbiome with metabolism and immunity—two main factors implicated in carcinogenesis. Gut microbiota has been shown to affect both antitumor immunity and protumor immune signaling. There is mounting evidence that the human microbiome can play a role in the immunotherapeutic effects, both response and resistance. Inosine-5′-monophosphate dehydrogenase (IMPDH) is a highly conservative enzyme widely expressed in mammals. Cell signaling pathways use molecular inosine, a crucial secondary metabolite in purine metabolism and a molecular messenger. Recent research has identified inosine as a critical regulator of immune checkpoint inhibition (ICI) therapeutic response in various tumor types. Some bacterial species were found to produce inosine or its metabolite hypoxanthine and induce T-helper 1 differentiation and effector functions via the inosine-A2AR-cAMP-PKA pathway upon ICI therapy. Also, inosine acts as a substitute carbon source for T-cell metabolism in glucose-restricted environments, i.e., the tumor microenvironment, assisting T-cell proliferation and differentiation while enhancing sensitivity to ICI, reinforcing the notion that inosine metabolism might contribute to antitumor immunity. Also, inosine is a potent agonist of the adenosine receptor, A2AR, and A2AR signaling can affect T-cell responses and antitumor immunity, making the inosine-A2AR pathway blockage a candidate for cancer treatment. Further research is required to investigate inosine as a cancer immunometabolism therapy.
The role of exerkines on brain mitochondria: a mini-review
Authors: Heo Junwon , Noble Emily E. , Call Jarrod A.
Published: November 2022

Exercise benefits many organ systems, including having a panacea-like effect on the brain. For example, aerobic exercise improves cognition and attention and reduces the risk of brain-related diseases, such as dementia, stress, and depression. Recent advances suggest that endocrine signaling from peripheral systems, such as skeletal muscle, mediates the effects of exercise on the brain. Consequently, it has been proposed that factors secreted by all organs in response to physical exercise should be more broadly termed the “exerkines.” Accumulating findings suggest that exerkines derived from skeletal muscle, liver, and adipose tissues directly impact brain mitochondrial function. Mitochondria play a pivotal role in regulating neuronal energy metabolism, neurotransmission, cell repair, and maintenance in the brain, and therefore exerkines may act via impacting brain mitochondria to improve brain function and disease resistance. Therefore, herein we review studies investigating the impact of muscle-, liver-, and adipose tissue-derived exerkines on brain cognitive and metabolic function via modulating mitochondrial bioenergetics, content, and dynamics under healthy and/or disease conditions.
Intraoperative electrical stimulation of the human dorsal spinal cord reveals a map of arm and hand muscle responses
Authors: McIntosh James R. , Joiner Evan F. , Goldberg Jacob L. , Murray Lynda M. , Yasin Bushra , Mendiratta Anil , Karceski Steven C. , Thuet Earl , Modik Oleg , Shelkov Evgeny , Lombardi Joseph M. , Sardar Zeeshan M. , Lehman Ronald A. , Mandigo Christopher , Riew K. Daniel , Harel Noam Y. , Virk Michael S. , Carmel Jason B.
Published: November 2022

A map of muscle responses to cervical epidural stimulation during clinically indicated surgery revealed strongest activation when stimulating laterally compared to midline and revealed differences to be weaker than expected across different segments. In contrast, waveform shapes and latencies were most similar when stimulating midline and laterally, indicating activation of overlapping circuitry. Thus, a map of the cervical spinal cord reveals organization and may help guide stimulation to activate arm and hand muscles strongly and selectively.